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Contributed/BNGPlayground_Examples/biology/jnkmapksignaling/metadata.yaml rename to Examples/biology/jnkmapksignaling/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/kirchannelregulation/README.md b/Examples/biology/kirchannelregulation/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/kirchannelregulation/README.md rename to Examples/biology/kirchannelregulation/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/kirchannelregulation/kir-channel-regulation.bngl b/Examples/biology/kirchannelregulation/kir-channel-regulation.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/kirchannelregulation/kir-channel-regulation.bngl rename to Examples/biology/kirchannelregulation/kir-channel-regulation.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/kirchannelregulation/metadata.yaml b/Examples/biology/kirchannelregulation/metadata.yaml similarity index 100% rename from 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Contributed/BNGPlayground_Examples/biology/lacoperonregulation/metadata.yaml rename to Examples/biology/lacoperonregulation/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/lipidmediatedpip3signaling/README.md b/Examples/biology/lipidmediatedpip3signaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/lipidmediatedpip3signaling/README.md rename to Examples/biology/lipidmediatedpip3signaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/lipidmediatedpip3signaling/lipid-mediated-pip3-signaling.bngl b/Examples/biology/lipidmediatedpip3signaling/lipid-mediated-pip3-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/lipidmediatedpip3signaling/lipid-mediated-pip3-signaling.bngl rename to Examples/biology/lipidmediatedpip3signaling/lipid-mediated-pip3-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/lipidmediatedpip3signaling/metadata.yaml 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Contributed/BNGPlayground_Examples/biology/negativefeedbackloop/metadata.yaml rename to Examples/biology/negativefeedbackloop/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/negativefeedbackloop/negative-feedback-loop.bngl b/Examples/biology/negativefeedbackloop/negative-feedback-loop.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/negativefeedbackloop/negative-feedback-loop.bngl rename to Examples/biology/negativefeedbackloop/negative-feedback-loop.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/neurotransmitterrelease/README.md b/Examples/biology/neurotransmitterrelease/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/neurotransmitterrelease/README.md rename to Examples/biology/neurotransmitterrelease/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/neurotransmitterrelease/metadata.yaml b/Examples/biology/neurotransmitterrelease/metadata.yaml similarity index 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Contributed/BNGPlayground_Examples/biology/oxidativestressresponse/metadata.yaml rename to Examples/biology/oxidativestressresponse/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/oxidativestressresponse/oxidative-stress-response.bngl b/Examples/biology/oxidativestressresponse/oxidative-stress-response.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/oxidativestressresponse/oxidative-stress-response.bngl rename to Examples/biology/oxidativestressresponse/oxidative-stress-response.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/p38mapksignaling/README.md b/Examples/biology/p38mapksignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/p38mapksignaling/README.md rename to Examples/biology/p38mapksignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/p38mapksignaling/metadata.yaml b/Examples/biology/p38mapksignaling/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/p38mapksignaling/metadata.yaml rename to Examples/biology/p38mapksignaling/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/p38mapksignaling/p38-mapk-signaling.bngl b/Examples/biology/p38mapksignaling/p38-mapk-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/p38mapksignaling/p38-mapk-signaling.bngl rename to Examples/biology/p38mapksignaling/p38-mapk-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/p53mdm2oscillator/README.md b/Examples/biology/p53mdm2oscillator/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/p53mdm2oscillator/README.md rename to Examples/biology/p53mdm2oscillator/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/p53mdm2oscillator/metadata.yaml b/Examples/biology/p53mdm2oscillator/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/p53mdm2oscillator/metadata.yaml rename to Examples/biology/p53mdm2oscillator/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/p53mdm2oscillator/p53-mdm2-oscillator.bngl b/Examples/biology/p53mdm2oscillator/p53-mdm2-oscillator.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/p53mdm2oscillator/p53-mdm2-oscillator.bngl rename to Examples/biology/p53mdm2oscillator/p53-mdm2-oscillator.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/parp1mediateddnarepair/README.md b/Examples/biology/parp1mediateddnarepair/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/parp1mediateddnarepair/README.md rename to Examples/biology/parp1mediateddnarepair/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/parp1mediateddnarepair/metadata.yaml b/Examples/biology/parp1mediateddnarepair/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/parp1mediateddnarepair/metadata.yaml rename to Examples/biology/parp1mediateddnarepair/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/parp1mediateddnarepair/parp1-mediated-dna-repair.bngl b/Examples/biology/parp1mediateddnarepair/parp1-mediated-dna-repair.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/parp1mediateddnarepair/parp1-mediated-dna-repair.bngl rename to Examples/biology/parp1mediateddnarepair/parp1-mediated-dna-repair.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/phosphorelaychain/README.md b/Examples/biology/phosphorelaychain/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/phosphorelaychain/README.md rename to Examples/biology/phosphorelaychain/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/phosphorelaychain/metadata.yaml b/Examples/biology/phosphorelaychain/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/phosphorelaychain/metadata.yaml rename to Examples/biology/phosphorelaychain/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/phosphorelaychain/phosphorelay-chain.bngl b/Examples/biology/phosphorelaychain/phosphorelay-chain.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/phosphorelaychain/phosphorelay-chain.bngl rename to Examples/biology/phosphorelaychain/phosphorelay-chain.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/plateletactivation/README.md b/Examples/biology/plateletactivation/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/plateletactivation/README.md rename to Examples/biology/plateletactivation/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/plateletactivation/metadata.yaml b/Examples/biology/plateletactivation/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/plateletactivation/metadata.yaml rename to Examples/biology/plateletactivation/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/plateletactivation/platelet-activation.bngl b/Examples/biology/plateletactivation/platelet-activation.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/plateletactivation/platelet-activation.bngl rename to Examples/biology/plateletactivation/platelet-activation.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/predatorpreydynamics/README.md b/Examples/biology/predatorpreydynamics/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/predatorpreydynamics/README.md rename to Examples/biology/predatorpreydynamics/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/predatorpreydynamics/metadata.yaml b/Examples/biology/predatorpreydynamics/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/predatorpreydynamics/metadata.yaml rename to Examples/biology/predatorpreydynamics/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/predatorpreydynamics/predator-prey-dynamics.bngl b/Examples/biology/predatorpreydynamics/predator-prey-dynamics.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/predatorpreydynamics/predator-prey-dynamics.bngl rename to Examples/biology/predatorpreydynamics/predator-prey-dynamics.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/quorumsensingcircuit/README.md b/Examples/biology/quorumsensingcircuit/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/quorumsensingcircuit/README.md rename to Examples/biology/quorumsensingcircuit/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/quorumsensingcircuit/metadata.yaml b/Examples/biology/quorumsensingcircuit/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/quorumsensingcircuit/metadata.yaml rename to Examples/biology/quorumsensingcircuit/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/quorumsensingcircuit/quorum-sensing-circuit.bngl b/Examples/biology/quorumsensingcircuit/quorum-sensing-circuit.bngl similarity index 95% rename from Contributed/BNGPlayground_Examples/biology/quorumsensingcircuit/quorum-sensing-circuit.bngl rename to Examples/biology/quorumsensingcircuit/quorum-sensing-circuit.bngl index a2edc7e..143fd45 100644 --- a/Contributed/BNGPlayground_Examples/biology/quorumsensingcircuit/quorum-sensing-circuit.bngl +++ b/Examples/biology/quorumsensingcircuit/quorum-sensing-circuit.bngl @@ -33,7 +33,6 @@ begin reaction rules Autoinducer() + Gene(state~off) -> Gene(state~on) + Autoinducer() k_activate Gene(state~on) -> Gene(state~on) + Protein() k_export Protein() -> 0 k_import - # FIX: Add Autoinducer dynamics (was conserved) Protein() -> Protein() + Autoinducer() 0.1 # Protein produces AI Autoinducer() -> 0 0.05 # AI degradation Autoinducer_env() -> 0 0.02 # Environmental AI clearance diff --git a/Contributed/BNGPlayground_Examples/biology/rabgtpasecycle/README.md b/Examples/biology/rabgtpasecycle/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/rabgtpasecycle/README.md rename to Examples/biology/rabgtpasecycle/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/rabgtpasecycle/metadata.yaml b/Examples/biology/rabgtpasecycle/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/rabgtpasecycle/metadata.yaml rename to Examples/biology/rabgtpasecycle/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/rabgtpasecycle/rab-gtpase-cycle.bngl b/Examples/biology/rabgtpasecycle/rab-gtpase-cycle.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/rabgtpasecycle/rab-gtpase-cycle.bngl rename to Examples/biology/rabgtpasecycle/rab-gtpase-cycle.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/ranklranksignaling/README.md b/Examples/biology/ranklranksignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/ranklranksignaling/README.md rename to Examples/biology/ranklranksignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/ranklranksignaling/metadata.yaml b/Examples/biology/ranklranksignaling/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/ranklranksignaling/metadata.yaml rename to Examples/biology/ranklranksignaling/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/ranklranksignaling/rankl-rank-signaling.bngl b/Examples/biology/ranklranksignaling/rankl-rank-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/ranklranksignaling/rankl-rank-signaling.bngl rename to Examples/biology/ranklranksignaling/rankl-rank-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/rasgefgapcycle/README.md b/Examples/biology/rasgefgapcycle/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/rasgefgapcycle/README.md rename to Examples/biology/rasgefgapcycle/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/rasgefgapcycle/metadata.yaml b/Examples/biology/rasgefgapcycle/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/rasgefgapcycle/metadata.yaml rename to Examples/biology/rasgefgapcycle/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/rasgefgapcycle/ras-gef-gap-cycle.bngl b/Examples/biology/rasgefgapcycle/ras-gef-gap-cycle.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/rasgefgapcycle/ras-gef-gap-cycle.bngl rename to Examples/biology/rasgefgapcycle/ras-gef-gap-cycle.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/repressilatoroscillator/README.md b/Examples/biology/repressilatoroscillator/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/repressilatoroscillator/README.md rename to Examples/biology/repressilatoroscillator/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/repressilatoroscillator/metadata.yaml b/Examples/biology/repressilatoroscillator/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/repressilatoroscillator/metadata.yaml rename to Examples/biology/repressilatoroscillator/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/repressilatoroscillator/repressilator-oscillator.bngl b/Examples/biology/repressilatoroscillator/repressilator-oscillator.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/repressilatoroscillator/repressilator-oscillator.bngl rename to Examples/biology/repressilatoroscillator/repressilator-oscillator.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/retinoicacidsignaling/README.md b/Examples/biology/retinoicacidsignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/retinoicacidsignaling/README.md rename to Examples/biology/retinoicacidsignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/retinoicacidsignaling/metadata.yaml b/Examples/biology/retinoicacidsignaling/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/retinoicacidsignaling/metadata.yaml rename to Examples/biology/retinoicacidsignaling/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/retinoicacidsignaling/retinoic-acid-signaling.bngl b/Examples/biology/retinoicacidsignaling/retinoic-acid-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/retinoicacidsignaling/retinoic-acid-signaling.bngl rename to Examples/biology/retinoicacidsignaling/retinoic-acid-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/rhogtpaseactincytoskeleton/README.md b/Examples/biology/rhogtpaseactincytoskeleton/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/rhogtpaseactincytoskeleton/README.md rename to Examples/biology/rhogtpaseactincytoskeleton/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/rhogtpaseactincytoskeleton/metadata.yaml b/Examples/biology/rhogtpaseactincytoskeleton/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/rhogtpaseactincytoskeleton/metadata.yaml rename to Examples/biology/rhogtpaseactincytoskeleton/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/rhogtpaseactincytoskeleton/rho-gtpase-actin-cytoskeleton.bngl b/Examples/biology/rhogtpaseactincytoskeleton/rho-gtpase-actin-cytoskeleton.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/rhogtpaseactincytoskeleton/rho-gtpase-actin-cytoskeleton.bngl rename to Examples/biology/rhogtpaseactincytoskeleton/rho-gtpase-actin-cytoskeleton.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/shp2phosphataseregulation/README.md b/Examples/biology/shp2phosphataseregulation/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/shp2phosphataseregulation/README.md rename to Examples/biology/shp2phosphataseregulation/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/shp2phosphataseregulation/metadata.yaml b/Examples/biology/shp2phosphataseregulation/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/shp2phosphataseregulation/metadata.yaml rename to Examples/biology/shp2phosphataseregulation/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/shp2phosphataseregulation/shp2-phosphatase-regulation.bngl b/Examples/biology/shp2phosphataseregulation/shp2-phosphatase-regulation.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/shp2phosphataseregulation/shp2-phosphatase-regulation.bngl rename to Examples/biology/shp2phosphataseregulation/shp2-phosphatase-regulation.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/signalamplificationcascade/README.md b/Examples/biology/signalamplificationcascade/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/signalamplificationcascade/README.md rename to Examples/biology/signalamplificationcascade/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/signalamplificationcascade/metadata.yaml b/Examples/biology/signalamplificationcascade/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/signalamplificationcascade/metadata.yaml rename to Examples/biology/signalamplificationcascade/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/signalamplificationcascade/signal-amplification-cascade.bngl b/Examples/biology/signalamplificationcascade/signal-amplification-cascade.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/signalamplificationcascade/signal-amplification-cascade.bngl rename to Examples/biology/signalamplificationcascade/signal-amplification-cascade.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/simpledimerization/README.md b/Examples/biology/simpledimerization/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/simpledimerization/README.md rename to Examples/biology/simpledimerization/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/simpledimerization/metadata.yaml b/Examples/biology/simpledimerization/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/simpledimerization/metadata.yaml rename to Examples/biology/simpledimerization/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/simpledimerization/simple-dimerization.bngl b/Examples/biology/simpledimerization/simple-dimerization.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/simpledimerization/simple-dimerization.bngl rename to Examples/biology/simpledimerization/simple-dimerization.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/sirepidemicmodel/README.md b/Examples/biology/sirepidemicmodel/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/sirepidemicmodel/README.md rename to Examples/biology/sirepidemicmodel/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/sirepidemicmodel/metadata.yaml b/Examples/biology/sirepidemicmodel/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/sirepidemicmodel/metadata.yaml rename to Examples/biology/sirepidemicmodel/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/sirepidemicmodel/sir-epidemic-model.bngl b/Examples/biology/sirepidemicmodel/sir-epidemic-model.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/sirepidemicmodel/sir-epidemic-model.bngl rename to Examples/biology/sirepidemicmodel/sir-epidemic-model.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/smadtgfbetasignaling/README.md b/Examples/biology/smadtgfbetasignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/smadtgfbetasignaling/README.md rename to Examples/biology/smadtgfbetasignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/smadtgfbetasignaling/metadata.yaml b/Examples/biology/smadtgfbetasignaling/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/smadtgfbetasignaling/metadata.yaml rename to Examples/biology/smadtgfbetasignaling/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/smadtgfbetasignaling/smad-tgf-beta-signaling.bngl b/Examples/biology/smadtgfbetasignaling/smad-tgf-beta-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/smadtgfbetasignaling/smad-tgf-beta-signaling.bngl rename to Examples/biology/smadtgfbetasignaling/smad-tgf-beta-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/sonichedgehoggradient/README.md b/Examples/biology/sonichedgehoggradient/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/sonichedgehoggradient/README.md rename to Examples/biology/sonichedgehoggradient/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/sonichedgehoggradient/metadata.yaml b/Examples/biology/sonichedgehoggradient/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/sonichedgehoggradient/metadata.yaml rename to Examples/biology/sonichedgehoggradient/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/sonichedgehoggradient/sonic-hedgehog-gradient.bngl b/Examples/biology/sonichedgehoggradient/sonic-hedgehog-gradient.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/sonichedgehoggradient/sonic-hedgehog-gradient.bngl rename to Examples/biology/sonichedgehoggradient/sonic-hedgehog-gradient.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/stat3mediatedtranscription/README.md b/Examples/biology/stat3mediatedtranscription/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/stat3mediatedtranscription/README.md rename to Examples/biology/stat3mediatedtranscription/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/stat3mediatedtranscription/metadata.yaml b/Examples/biology/stat3mediatedtranscription/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/stat3mediatedtranscription/metadata.yaml rename to Examples/biology/stat3mediatedtranscription/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/stat3mediatedtranscription/stat3-mediated-transcription.bngl b/Examples/biology/stat3mediatedtranscription/stat3-mediated-transcription.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/stat3mediatedtranscription/stat3-mediated-transcription.bngl rename to Examples/biology/stat3mediatedtranscription/stat3-mediated-transcription.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/stressresponseadaptation/README.md b/Examples/biology/stressresponseadaptation/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/stressresponseadaptation/README.md rename to Examples/biology/stressresponseadaptation/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/stressresponseadaptation/metadata.yaml b/Examples/biology/stressresponseadaptation/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/stressresponseadaptation/metadata.yaml rename to Examples/biology/stressresponseadaptation/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/stressresponseadaptation/stress-response-adaptation.bngl b/Examples/biology/stressresponseadaptation/stress-response-adaptation.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/stressresponseadaptation/stress-response-adaptation.bngl rename to Examples/biology/stressresponseadaptation/stress-response-adaptation.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/synapticplasticityltp/README.md b/Examples/biology/synapticplasticityltp/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/synapticplasticityltp/README.md rename to Examples/biology/synapticplasticityltp/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/synapticplasticityltp/metadata.yaml b/Examples/biology/synapticplasticityltp/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/synapticplasticityltp/metadata.yaml rename to Examples/biology/synapticplasticityltp/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/synapticplasticityltp/synaptic-plasticity-ltp.bngl b/Examples/biology/synapticplasticityltp/synaptic-plasticity-ltp.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/synapticplasticityltp/synaptic-plasticity-ltp.bngl rename to Examples/biology/synapticplasticityltp/synaptic-plasticity-ltp.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/tcellactivation/README.md b/Examples/biology/tcellactivation/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/tcellactivation/README.md rename to Examples/biology/tcellactivation/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/tcellactivation/metadata.yaml b/Examples/biology/tcellactivation/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/tcellactivation/metadata.yaml rename to Examples/biology/tcellactivation/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/tcellactivation/t-cell-activation.bngl b/Examples/biology/tcellactivation/t-cell-activation.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/tcellactivation/t-cell-activation.bngl rename to Examples/biology/tcellactivation/t-cell-activation.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/tlr3dsrnasensing/README.md b/Examples/biology/tlr3dsrnasensing/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/tlr3dsrnasensing/README.md rename to Examples/biology/tlr3dsrnasensing/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/tlr3dsrnasensing/metadata.yaml b/Examples/biology/tlr3dsrnasensing/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/tlr3dsrnasensing/metadata.yaml rename to Examples/biology/tlr3dsrnasensing/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/tlr3dsrnasensing/tlr3-dsrna-sensing.bngl b/Examples/biology/tlr3dsrnasensing/tlr3-dsrna-sensing.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/tlr3dsrnasensing/tlr3-dsrna-sensing.bngl rename to Examples/biology/tlr3dsrnasensing/tlr3-dsrna-sensing.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/tnfinducedapoptosis/README.md b/Examples/biology/tnfinducedapoptosis/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/tnfinducedapoptosis/README.md rename to Examples/biology/tnfinducedapoptosis/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/tnfinducedapoptosis/metadata.yaml b/Examples/biology/tnfinducedapoptosis/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/tnfinducedapoptosis/metadata.yaml rename to Examples/biology/tnfinducedapoptosis/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/tnfinducedapoptosis/tnf-induced-apoptosis.bngl b/Examples/biology/tnfinducedapoptosis/tnf-induced-apoptosis.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/tnfinducedapoptosis/tnf-induced-apoptosis.bngl rename to Examples/biology/tnfinducedapoptosis/tnf-induced-apoptosis.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/twocomponentsystem/README.md b/Examples/biology/twocomponentsystem/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/twocomponentsystem/README.md rename to Examples/biology/twocomponentsystem/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/twocomponentsystem/metadata.yaml b/Examples/biology/twocomponentsystem/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/twocomponentsystem/metadata.yaml rename to Examples/biology/twocomponentsystem/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/twocomponentsystem/two-component-system.bngl b/Examples/biology/twocomponentsystem/two-component-system.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/twocomponentsystem/two-component-system.bngl rename to Examples/biology/twocomponentsystem/two-component-system.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/vegfangiogenesis/README.md b/Examples/biology/vegfangiogenesis/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/vegfangiogenesis/README.md rename to Examples/biology/vegfangiogenesis/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/vegfangiogenesis/metadata.yaml b/Examples/biology/vegfangiogenesis/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/vegfangiogenesis/metadata.yaml rename to Examples/biology/vegfangiogenesis/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/vegfangiogenesis/vegf-angiogenesis.bngl b/Examples/biology/vegfangiogenesis/vegf-angiogenesis.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/vegfangiogenesis/vegf-angiogenesis.bngl rename to Examples/biology/vegfangiogenesis/vegf-angiogenesis.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/viralsensinginnateimmunity/README.md b/Examples/biology/viralsensinginnateimmunity/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/viralsensinginnateimmunity/README.md rename to Examples/biology/viralsensinginnateimmunity/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/viralsensinginnateimmunity/metadata.yaml b/Examples/biology/viralsensinginnateimmunity/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/viralsensinginnateimmunity/metadata.yaml rename to Examples/biology/viralsensinginnateimmunity/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/viralsensinginnateimmunity/viral-sensing-innate-immunity.bngl b/Examples/biology/viralsensinginnateimmunity/viral-sensing-innate-immunity.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/viralsensinginnateimmunity/viral-sensing-innate-immunity.bngl rename to Examples/biology/viralsensinginnateimmunity/viral-sensing-innate-immunity.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/wntbetacateninsignaling/README.md b/Examples/biology/wntbetacateninsignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/wntbetacateninsignaling/README.md rename to Examples/biology/wntbetacateninsignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/wntbetacateninsignaling/metadata.yaml b/Examples/biology/wntbetacateninsignaling/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/wntbetacateninsignaling/metadata.yaml rename to Examples/biology/wntbetacateninsignaling/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/wntbetacateninsignaling/wnt-beta-catenin-signaling.bngl b/Examples/biology/wntbetacateninsignaling/wnt-beta-catenin-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/wntbetacateninsignaling/wnt-beta-catenin-signaling.bngl rename to Examples/biology/wntbetacateninsignaling/wnt-beta-catenin-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/woundhealingpdgfsignaling/README.md b/Examples/biology/woundhealingpdgfsignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/woundhealingpdgfsignaling/README.md rename to Examples/biology/woundhealingpdgfsignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/woundhealingpdgfsignaling/metadata.yaml b/Examples/biology/woundhealingpdgfsignaling/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/woundhealingpdgfsignaling/metadata.yaml rename to Examples/biology/woundhealingpdgfsignaling/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/biology/woundhealingpdgfsignaling/wound-healing-pdgf-signaling.bngl b/Examples/biology/woundhealingpdgfsignaling/wound-healing-pdgf-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/woundhealingpdgfsignaling/wound-healing-pdgf-signaling.bngl rename to Examples/biology/woundhealingpdgfsignaling/wound-healing-pdgf-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentendocytosis/README.md b/Examples/compartments/compartmentendocytosis/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/compartments/compartmentendocytosis/README.md rename to Examples/compartments/compartmentendocytosis/README.md diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentendocytosis/compartment_endocytosis.bngl b/Examples/compartments/compartmentendocytosis/compartment_endocytosis.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/compartments/compartmentendocytosis/compartment_endocytosis.bngl rename to Examples/compartments/compartmentendocytosis/compartment_endocytosis.bngl diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentendocytosis/metadata.yaml b/Examples/compartments/compartmentendocytosis/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/compartments/compartmentendocytosis/metadata.yaml rename to Examples/compartments/compartmentendocytosis/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentmembranebound/README.md b/Examples/compartments/compartmentmembranebound/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/compartments/compartmentmembranebound/README.md rename to Examples/compartments/compartmentmembranebound/README.md diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentmembranebound/compartment_membrane_bound.bngl b/Examples/compartments/compartmentmembranebound/compartment_membrane_bound.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/compartments/compartmentmembranebound/compartment_membrane_bound.bngl rename to Examples/compartments/compartmentmembranebound/compartment_membrane_bound.bngl diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentmembranebound/metadata.yaml b/Examples/compartments/compartmentmembranebound/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/compartments/compartmentmembranebound/metadata.yaml rename to Examples/compartments/compartmentmembranebound/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentnestedtransport/README.md b/Examples/compartments/compartmentnestedtransport/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/compartments/compartmentnestedtransport/README.md rename to Examples/compartments/compartmentnestedtransport/README.md diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentnestedtransport/compartment_nested_transport.bngl b/Examples/compartments/compartmentnestedtransport/compartment_nested_transport.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/compartments/compartmentnestedtransport/compartment_nested_transport.bngl rename to Examples/compartments/compartmentnestedtransport/compartment_nested_transport.bngl diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentnestedtransport/metadata.yaml b/Examples/compartments/compartmentnestedtransport/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/compartments/compartmentnestedtransport/metadata.yaml rename to Examples/compartments/compartmentnestedtransport/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentnucleartransport/README.md b/Examples/compartments/compartmentnucleartransport/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/compartments/compartmentnucleartransport/README.md rename to Examples/compartments/compartmentnucleartransport/README.md diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentnucleartransport/compartment_nuclear_transport.bngl b/Examples/compartments/compartmentnucleartransport/compartment_nuclear_transport.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/compartments/compartmentnucleartransport/compartment_nuclear_transport.bngl rename to Examples/compartments/compartmentnucleartransport/compartment_nuclear_transport.bngl diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentnucleartransport/metadata.yaml b/Examples/compartments/compartmentnucleartransport/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/compartments/compartmentnucleartransport/metadata.yaml rename to Examples/compartments/compartmentnucleartransport/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentorganelleexchange/README.md b/Examples/compartments/compartmentorganelleexchange/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/compartments/compartmentorganelleexchange/README.md rename to Examples/compartments/compartmentorganelleexchange/README.md diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentorganelleexchange/compartment_organelle_exchange.bngl b/Examples/compartments/compartmentorganelleexchange/compartment_organelle_exchange.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/compartments/compartmentorganelleexchange/compartment_organelle_exchange.bngl rename to Examples/compartments/compartmentorganelleexchange/compartment_organelle_exchange.bngl diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentorganelleexchange/metadata.yaml b/Examples/compartments/compartmentorganelleexchange/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/compartments/compartmentorganelleexchange/metadata.yaml rename to Examples/compartments/compartmentorganelleexchange/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/cs/csdiffiehellman/README.md b/Examples/cs/csdiffiehellman/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/csdiffiehellman/README.md rename to Examples/cs/csdiffiehellman/README.md diff --git a/Contributed/BNGPlayground_Examples/cs/csdiffiehellman/cs_diffie_hellman.bngl b/Examples/cs/csdiffiehellman/cs_diffie_hellman.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/csdiffiehellman/cs_diffie_hellman.bngl rename to Examples/cs/csdiffiehellman/cs_diffie_hellman.bngl diff --git a/Contributed/BNGPlayground_Examples/cs/csdiffiehellman/metadata.yaml b/Examples/cs/csdiffiehellman/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/csdiffiehellman/metadata.yaml rename to Examples/cs/csdiffiehellman/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/cs/cshashfunction/README.md b/Examples/cs/cshashfunction/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/cshashfunction/README.md rename to Examples/cs/cshashfunction/README.md diff --git a/Contributed/BNGPlayground_Examples/cs/cshashfunction/cs_hash_function.bngl b/Examples/cs/cshashfunction/cs_hash_function.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/cshashfunction/cs_hash_function.bngl rename to Examples/cs/cshashfunction/cs_hash_function.bngl diff --git a/Contributed/BNGPlayground_Examples/cs/cshashfunction/metadata.yaml b/Examples/cs/cshashfunction/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/cshashfunction/metadata.yaml rename to Examples/cs/cshashfunction/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/cs/cshuffman/README.md b/Examples/cs/cshuffman/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/cshuffman/README.md rename to Examples/cs/cshuffman/README.md diff --git a/Contributed/BNGPlayground_Examples/cs/cshuffman/cs_huffman.bngl b/Examples/cs/cshuffman/cs_huffman.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/cshuffman/cs_huffman.bngl rename to Examples/cs/cshuffman/cs_huffman.bngl diff --git a/Contributed/BNGPlayground_Examples/cs/cshuffman/metadata.yaml b/Examples/cs/cshuffman/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/cshuffman/metadata.yaml rename to Examples/cs/cshuffman/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/cs/csmontecarlopi/README.md b/Examples/cs/csmontecarlopi/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/csmontecarlopi/README.md rename to Examples/cs/csmontecarlopi/README.md diff --git a/Contributed/BNGPlayground_Examples/cs/csmontecarlopi/cs_monte_carlo_pi.bngl b/Examples/cs/csmontecarlopi/cs_monte_carlo_pi.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/csmontecarlopi/cs_monte_carlo_pi.bngl rename to Examples/cs/csmontecarlopi/cs_monte_carlo_pi.bngl diff --git a/Contributed/BNGPlayground_Examples/cs/csmontecarlopi/metadata.yaml b/Examples/cs/csmontecarlopi/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/csmontecarlopi/metadata.yaml rename to Examples/cs/csmontecarlopi/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/cs/cspagerank/README.md b/Examples/cs/cspagerank/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/cspagerank/README.md rename to Examples/cs/cspagerank/README.md diff --git a/Contributed/BNGPlayground_Examples/cs/cspagerank/cs_pagerank.bngl b/Examples/cs/cspagerank/cs_pagerank.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/cspagerank/cs_pagerank.bngl rename to Examples/cs/cspagerank/cs_pagerank.bngl diff --git a/Contributed/BNGPlayground_Examples/cs/cspagerank/metadata.yaml b/Examples/cs/cspagerank/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/cspagerank/metadata.yaml rename to Examples/cs/cspagerank/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/cs/cspidcontroller/README.md b/Examples/cs/cspidcontroller/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/cspidcontroller/README.md rename to Examples/cs/cspidcontroller/README.md diff --git a/Contributed/BNGPlayground_Examples/cs/cspidcontroller/cs_pid_controller.bngl b/Examples/cs/cspidcontroller/cs_pid_controller.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/cspidcontroller/cs_pid_controller.bngl rename to Examples/cs/cspidcontroller/cs_pid_controller.bngl diff --git a/Contributed/BNGPlayground_Examples/cs/cspidcontroller/metadata.yaml b/Examples/cs/cspidcontroller/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/cspidcontroller/metadata.yaml rename to Examples/cs/cspidcontroller/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/cs/csregexnfa/README.md b/Examples/cs/csregexnfa/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/csregexnfa/README.md rename to Examples/cs/csregexnfa/README.md diff --git a/Contributed/BNGPlayground_Examples/cs/csregexnfa/cs_regex_nfa.bngl b/Examples/cs/csregexnfa/cs_regex_nfa.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/csregexnfa/cs_regex_nfa.bngl rename to Examples/cs/csregexnfa/cs_regex_nfa.bngl diff --git a/Contributed/BNGPlayground_Examples/cs/csregexnfa/metadata.yaml b/Examples/cs/csregexnfa/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/csregexnfa/metadata.yaml rename to Examples/cs/csregexnfa/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/ecology/ecocoevolutionhostparasite/README.md b/Examples/ecology/ecocoevolutionhostparasite/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/ecology/ecocoevolutionhostparasite/README.md rename to Examples/ecology/ecocoevolutionhostparasite/README.md diff --git a/Contributed/BNGPlayground_Examples/ecology/ecocoevolutionhostparasite/eco_coevolution_host_parasite.bngl b/Examples/ecology/ecocoevolutionhostparasite/eco_coevolution_host_parasite.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/ecology/ecocoevolutionhostparasite/eco_coevolution_host_parasite.bngl rename to Examples/ecology/ecocoevolutionhostparasite/eco_coevolution_host_parasite.bngl diff --git a/Contributed/BNGPlayground_Examples/ecology/ecocoevolutionhostparasite/metadata.yaml b/Examples/ecology/ecocoevolutionhostparasite/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/ecology/ecocoevolutionhostparasite/metadata.yaml rename to Examples/ecology/ecocoevolutionhostparasite/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/ecology/ecofoodwebchaos3sp/README.md b/Examples/ecology/ecofoodwebchaos3sp/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/ecology/ecofoodwebchaos3sp/README.md rename to Examples/ecology/ecofoodwebchaos3sp/README.md diff --git a/Contributed/BNGPlayground_Examples/ecology/ecofoodwebchaos3sp/eco_food_web_chaos_3sp.bngl b/Examples/ecology/ecofoodwebchaos3sp/eco_food_web_chaos_3sp.bngl similarity index 96% rename from Contributed/BNGPlayground_Examples/ecology/ecofoodwebchaos3sp/eco_food_web_chaos_3sp.bngl rename to Examples/ecology/ecofoodwebchaos3sp/eco_food_web_chaos_3sp.bngl index 3f63d01..acd4c93 100644 --- a/Contributed/BNGPlayground_Examples/ecology/ecofoodwebchaos3sp/eco_food_web_chaos_3sp.bngl +++ b/Examples/ecology/ecofoodwebchaos3sp/eco_food_web_chaos_3sp.bngl @@ -65,7 +65,7 @@ begin reaction rules # 4. Death C() -> 0 d1 P() -> 0 d2 - # FIX: Add resource dynamics (total R was conserved) + 0 -> R() 1.0 # Resource regeneration R() -> 0 0.01 # Resource natural decay end reaction rules diff --git a/Contributed/BNGPlayground_Examples/ecology/ecofoodwebchaos3sp/metadata.yaml b/Examples/ecology/ecofoodwebchaos3sp/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/ecology/ecofoodwebchaos3sp/metadata.yaml rename to Examples/ecology/ecofoodwebchaos3sp/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/ecology/ecolotkavolterragrid/README.md b/Examples/ecology/ecolotkavolterragrid/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/ecology/ecolotkavolterragrid/README.md rename to Examples/ecology/ecolotkavolterragrid/README.md diff --git a/Contributed/BNGPlayground_Examples/ecology/ecolotkavolterragrid/eco_lotka_volterra_grid.bngl b/Examples/ecology/ecolotkavolterragrid/eco_lotka_volterra_grid.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/ecology/ecolotkavolterragrid/eco_lotka_volterra_grid.bngl rename to Examples/ecology/ecolotkavolterragrid/eco_lotka_volterra_grid.bngl diff --git a/Contributed/BNGPlayground_Examples/ecology/ecolotkavolterragrid/metadata.yaml b/Examples/ecology/ecolotkavolterragrid/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/ecology/ecolotkavolterragrid/metadata.yaml rename to Examples/ecology/ecolotkavolterragrid/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/ecology/ecomutualismobligate/README.md b/Examples/ecology/ecomutualismobligate/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/ecology/ecomutualismobligate/README.md rename to Examples/ecology/ecomutualismobligate/README.md diff --git a/Contributed/BNGPlayground_Examples/ecology/ecomutualismobligate/eco_mutualism_obligate.bngl b/Examples/ecology/ecomutualismobligate/eco_mutualism_obligate.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/ecology/ecomutualismobligate/eco_mutualism_obligate.bngl rename to Examples/ecology/ecomutualismobligate/eco_mutualism_obligate.bngl diff --git a/Contributed/BNGPlayground_Examples/ecology/ecomutualismobligate/metadata.yaml b/Examples/ecology/ecomutualismobligate/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/ecology/ecomutualismobligate/metadata.yaml rename to Examples/ecology/ecomutualismobligate/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/ecology/ecorockpaperscissorsspatial/README.md b/Examples/ecology/ecorockpaperscissorsspatial/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/ecology/ecorockpaperscissorsspatial/README.md rename to Examples/ecology/ecorockpaperscissorsspatial/README.md diff --git a/Contributed/BNGPlayground_Examples/ecology/ecorockpaperscissorsspatial/eco_rock_paper_scissors_spatial.bngl b/Examples/ecology/ecorockpaperscissorsspatial/eco_rock_paper_scissors_spatial.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/ecology/ecorockpaperscissorsspatial/eco_rock_paper_scissors_spatial.bngl rename to Examples/ecology/ecorockpaperscissorsspatial/eco_rock_paper_scissors_spatial.bngl diff --git a/Contributed/BNGPlayground_Examples/ecology/ecorockpaperscissorsspatial/metadata.yaml b/Examples/ecology/ecorockpaperscissorsspatial/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/ecology/ecorockpaperscissorsspatial/metadata.yaml rename to Examples/ecology/ecorockpaperscissorsspatial/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/energy/energyallosterymwc/README.md b/Examples/energy/energyallosterymwc/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/energy/energyallosterymwc/README.md rename to Examples/energy/energyallosterymwc/README.md diff --git a/Contributed/BNGPlayground_Examples/energy/energyallosterymwc/energy_allostery_mwc.bngl b/Examples/energy/energyallosterymwc/energy_allostery_mwc.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/energy/energyallosterymwc/energy_allostery_mwc.bngl rename to Examples/energy/energyallosterymwc/energy_allostery_mwc.bngl diff --git a/Contributed/BNGPlayground_Examples/energy/energyallosterymwc/metadata.yaml b/Examples/energy/energyallosterymwc/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/energy/energyallosterymwc/metadata.yaml rename to Examples/energy/energyallosterymwc/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/energy/energycatalysismm/README.md b/Examples/energy/energycatalysismm/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/energy/energycatalysismm/README.md rename to Examples/energy/energycatalysismm/README.md diff --git a/Contributed/BNGPlayground_Examples/energy/energycatalysismm/energy_catalysis_mm.bngl b/Examples/energy/energycatalysismm/energy_catalysis_mm.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/energy/energycatalysismm/energy_catalysis_mm.bngl rename to Examples/energy/energycatalysismm/energy_catalysis_mm.bngl diff --git a/Contributed/BNGPlayground_Examples/energy/energycatalysismm/metadata.yaml b/Examples/energy/energycatalysismm/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/energy/energycatalysismm/metadata.yaml rename to Examples/energy/energycatalysismm/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/energy/energycooperativityadh/README.md b/Examples/energy/energycooperativityadh/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/energy/energycooperativityadh/README.md rename to Examples/energy/energycooperativityadh/README.md diff --git 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a/Contributed/BNGPlayground_Examples/energy/energylinearchain/energy_linear_chain.bngl b/Examples/energy/energylinearchain/energy_linear_chain.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/energy/energylinearchain/energy_linear_chain.bngl rename to Examples/energy/energylinearchain/energy_linear_chain.bngl diff --git a/Contributed/BNGPlayground_Examples/energy/energylinearchain/metadata.yaml b/Examples/energy/energylinearchain/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/energy/energylinearchain/metadata.yaml rename to Examples/energy/energylinearchain/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/energy/energytransportpump/README.md b/Examples/energy/energytransportpump/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/energy/energytransportpump/README.md rename to Examples/energy/energytransportpump/README.md diff --git a/Contributed/BNGPlayground_Examples/energy/energytransportpump/energy_transport_pump.bngl b/Examples/energy/energytransportpump/energy_transport_pump.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/energy/energytransportpump/energy_transport_pump.bngl rename to Examples/energy/energytransportpump/energy_transport_pump.bngl diff --git a/Contributed/BNGPlayground_Examples/energy/energytransportpump/metadata.yaml b/Examples/energy/energytransportpump/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/energy/energytransportpump/metadata.yaml rename to Examples/energy/energytransportpump/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/feature-demos/featurefunctionalratesvolume/README.md b/Examples/feature-demos/featurefunctionalratesvolume/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/feature-demos/featurefunctionalratesvolume/README.md rename to 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a/Contributed/BNGPlayground_Examples/feature-demos/featureglobalfunctionsscan/README.md b/Examples/feature-demos/featureglobalfunctionsscan/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/feature-demos/featureglobalfunctionsscan/README.md rename to Examples/feature-demos/featureglobalfunctionsscan/README.md diff --git a/Contributed/BNGPlayground_Examples/feature-demos/featureglobalfunctionsscan/feature_global_functions_scan.bngl b/Examples/feature-demos/featureglobalfunctionsscan/feature_global_functions_scan.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/feature-demos/featureglobalfunctionsscan/feature_global_functions_scan.bngl rename to Examples/feature-demos/featureglobalfunctionsscan/feature_global_functions_scan.bngl diff --git a/Contributed/BNGPlayground_Examples/feature-demos/featureglobalfunctionsscan/metadata.yaml b/Examples/feature-demos/featureglobalfunctionsscan/metadata.yaml similarity index 100% rename from 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Contributed/BNGPlayground_Examples/nfsim/nfsimringclosurepolymer/README.md rename to Examples/nfsim/nfsimringclosurepolymer/README.md diff --git a/Contributed/BNGPlayground_Examples/nfsim/nfsimringclosurepolymer/metadata.yaml b/Examples/nfsim/nfsimringclosurepolymer/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/nfsim/nfsimringclosurepolymer/metadata.yaml rename to Examples/nfsim/nfsimringclosurepolymer/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/nfsim/nfsimringclosurepolymer/nfsim_ring_closure_polymer.bngl b/Examples/nfsim/nfsimringclosurepolymer/nfsim_ring_closure_polymer.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/nfsim/nfsimringclosurepolymer/nfsim_ring_closure_polymer.bngl rename to Examples/nfsim/nfsimringclosurepolymer/nfsim_ring_closure_polymer.bngl diff --git a/Contributed/BNGPlayground_Examples/physics/phlorenzattractor/README.md b/Examples/physics/phlorenzattractor/README.md similarity index 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Contributed/BNGPlayground_Examples/physics/phnbodygravity/README.md rename to Examples/physics/phnbodygravity/README.md diff --git a/Contributed/BNGPlayground_Examples/physics/phnbodygravity/metadata.yaml b/Examples/physics/phnbodygravity/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/physics/phnbodygravity/metadata.yaml rename to Examples/physics/phnbodygravity/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/physics/phnbodygravity/ph_nbody_gravity.bngl b/Examples/physics/phnbodygravity/ph_nbody_gravity.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/physics/phnbodygravity/ph_nbody_gravity.bngl rename to Examples/physics/phnbodygravity/ph_nbody_gravity.bngl diff --git a/Contributed/BNGPlayground_Examples/physics/phschrodinger/README.md b/Examples/physics/phschrodinger/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/physics/phschrodinger/README.md rename to Examples/physics/phschrodinger/README.md diff --git a/Contributed/BNGPlayground_Examples/physics/phschrodinger/metadata.yaml b/Examples/physics/phschrodinger/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/physics/phschrodinger/metadata.yaml rename to Examples/physics/phschrodinger/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/physics/phschrodinger/ph_schrodinger.bngl b/Examples/physics/phschrodinger/ph_schrodinger.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/physics/phschrodinger/ph_schrodinger.bngl rename to Examples/physics/phschrodinger/ph_schrodinger.bngl diff --git a/Contributed/BNGPlayground_Examples/physics/phwaveequation/README.md b/Examples/physics/phwaveequation/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/physics/phwaveequation/README.md rename to Examples/physics/phwaveequation/README.md diff --git a/Contributed/BNGPlayground_Examples/physics/phwaveequation/metadata.yaml b/Examples/physics/phwaveequation/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/physics/phwaveequation/metadata.yaml rename to Examples/physics/phwaveequation/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/physics/phwaveequation/ph_wave_equation.bngl b/Examples/physics/phwaveequation/ph_wave_equation.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/physics/phwaveequation/ph_wave_equation.bngl rename to Examples/physics/phwaveequation/ph_wave_equation.bngl diff --git a/Contributed/BNGPlayground_Examples/processes/processactintreadmilling/README.md b/Examples/processes/processactintreadmilling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/processes/processactintreadmilling/README.md rename to Examples/processes/processactintreadmilling/README.md diff --git a/Contributed/BNGPlayground_Examples/processes/processactintreadmilling/metadata.yaml b/Examples/processes/processactintreadmilling/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/processes/processactintreadmilling/metadata.yaml rename to Examples/processes/processactintreadmilling/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/processes/processactintreadmilling/process_actin_treadmilling.bngl b/Examples/processes/processactintreadmilling/process_actin_treadmilling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/processes/processactintreadmilling/process_actin_treadmilling.bngl rename to Examples/processes/processactintreadmilling/process_actin_treadmilling.bngl diff --git a/Contributed/BNGPlayground_Examples/processes/processautophagyflux/README.md b/Examples/processes/processautophagyflux/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/processes/processautophagyflux/README.md rename to Examples/processes/processautophagyflux/README.md diff --git a/Contributed/BNGPlayground_Examples/processes/processautophagyflux/metadata.yaml b/Examples/processes/processautophagyflux/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/processes/processautophagyflux/metadata.yaml rename to Examples/processes/processautophagyflux/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/processes/processautophagyflux/process_autophagy_flux.bngl b/Examples/processes/processautophagyflux/process_autophagy_flux.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/processes/processautophagyflux/process_autophagy_flux.bngl rename to Examples/processes/processautophagyflux/process_autophagy_flux.bngl diff --git a/Contributed/BNGPlayground_Examples/processes/processcelladhesionstrength/README.md b/Examples/processes/processcelladhesionstrength/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/processes/processcelladhesionstrength/README.md rename to Examples/processes/processcelladhesionstrength/README.md diff --git a/Contributed/BNGPlayground_Examples/processes/processcelladhesionstrength/metadata.yaml b/Examples/processes/processcelladhesionstrength/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/processes/processcelladhesionstrength/metadata.yaml rename to Examples/processes/processcelladhesionstrength/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/processes/processcelladhesionstrength/process_cell_adhesion_strength.bngl b/Examples/processes/processcelladhesionstrength/process_cell_adhesion_strength.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/processes/processcelladhesionstrength/process_cell_adhesion_strength.bngl rename to Examples/processes/processcelladhesionstrength/process_cell_adhesion_strength.bngl diff --git a/Contributed/BNGPlayground_Examples/processes/processkineticproofreadingtcr/README.md b/Examples/processes/processkineticproofreadingtcr/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/processes/processkineticproofreadingtcr/README.md rename to Examples/processes/processkineticproofreadingtcr/README.md diff --git a/Contributed/BNGPlayground_Examples/processes/processkineticproofreadingtcr/metadata.yaml b/Examples/processes/processkineticproofreadingtcr/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/processes/processkineticproofreadingtcr/metadata.yaml rename to Examples/processes/processkineticproofreadingtcr/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/processes/processkineticproofreadingtcr/process_kinetic_proofreading_tcr.bngl b/Examples/processes/processkineticproofreadingtcr/process_kinetic_proofreading_tcr.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/processes/processkineticproofreadingtcr/process_kinetic_proofreading_tcr.bngl rename to Examples/processes/processkineticproofreadingtcr/process_kinetic_proofreading_tcr.bngl diff --git a/Contributed/BNGPlayground_Examples/processes/processquorumsensingswitch/README.md b/Examples/processes/processquorumsensingswitch/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/processes/processquorumsensingswitch/README.md rename to Examples/processes/processquorumsensingswitch/README.md diff --git a/Contributed/BNGPlayground_Examples/processes/processquorumsensingswitch/metadata.yaml b/Examples/processes/processquorumsensingswitch/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/processes/processquorumsensingswitch/metadata.yaml rename to Examples/processes/processquorumsensingswitch/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/processes/processquorumsensingswitch/process_quorum_sensing_switch.bngl b/Examples/processes/processquorumsensingswitch/process_quorum_sensing_switch.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/processes/processquorumsensingswitch/process_quorum_sensing_switch.bngl rename to Examples/processes/processquorumsensingswitch/process_quorum_sensing_switch.bngl diff --git a/Contributed/BNGPlayground_Examples/signal-processing/spfouriersynthesizer/README.md b/Examples/signal-processing/spfouriersynthesizer/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/signal-processing/spfouriersynthesizer/README.md rename to Examples/signal-processing/spfouriersynthesizer/README.md diff --git a/Contributed/BNGPlayground_Examples/signal-processing/spfouriersynthesizer/metadata.yaml b/Examples/signal-processing/spfouriersynthesizer/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/signal-processing/spfouriersynthesizer/metadata.yaml rename to Examples/signal-processing/spfouriersynthesizer/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/signal-processing/spfouriersynthesizer/sp_fourier_synthesizer.bngl b/Examples/signal-processing/spfouriersynthesizer/sp_fourier_synthesizer.bngl similarity index 95% rename from Contributed/BNGPlayground_Examples/signal-processing/spfouriersynthesizer/sp_fourier_synthesizer.bngl rename to Examples/signal-processing/spfouriersynthesizer/sp_fourier_synthesizer.bngl index d63aca1..b3289bf 100644 --- a/Contributed/BNGPlayground_Examples/signal-processing/spfouriersynthesizer/sp_fourier_synthesizer.bngl +++ b/Examples/signal-processing/spfouriersynthesizer/sp_fourier_synthesizer.bngl @@ -87,7 +87,7 @@ begin functions ds1() = 1*omega * c1() dc1() = -1*omega * s1() - ds3() = 3*omega * (Cos1 - amp_offset) # Using Cos1 as approx + ds3() = 3*ds1() - 12*s1()*s1()*ds1() ds5() = 5*omega * (Cos1 - amp_offset) ds7() = 7*omega * (Cos1 - amp_offset) ds9() = 9*omega * (Cos1 - amp_offset) @@ -111,8 +111,7 @@ begin reaction rules C1() -> 0 if(dc1() < 0,-dc1()/max(Cos1,0.001),0) # 3rd harmonic: d(S3)/dt = 3*omega*cos(3*omega*t) - # Hack: use sin(3x) = 3*sin(x) - 4*sin^3(x) identity - # Actually,just couple each harmonic independently + # Uses sin(3x) = 3*sin(x) - 4*sin^3(x) identity 0 -> S3() if(ds3() > 0,ds3(),0) S3() -> 0 if(ds3() < 0,-ds3()/max(Sin3,0.001),0) diff --git a/Contributed/BNGPlayground_Examples/signal-processing/spimageconvolution/README.md b/Examples/signal-processing/spimageconvolution/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/signal-processing/spimageconvolution/README.md rename to Examples/signal-processing/spimageconvolution/README.md diff --git a/Contributed/BNGPlayground_Examples/signal-processing/spimageconvolution/metadata.yaml b/Examples/signal-processing/spimageconvolution/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/signal-processing/spimageconvolution/metadata.yaml rename to Examples/signal-processing/spimageconvolution/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/signal-processing/spimageconvolution/sp_image_convolution.bngl b/Examples/signal-processing/spimageconvolution/sp_image_convolution.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/signal-processing/spimageconvolution/sp_image_convolution.bngl rename to Examples/signal-processing/spimageconvolution/sp_image_convolution.bngl diff --git a/Contributed/BNGPlayground_Examples/signal-processing/spkalmanfilter/README.md b/Examples/signal-processing/spkalmanfilter/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/signal-processing/spkalmanfilter/README.md rename to Examples/signal-processing/spkalmanfilter/README.md diff --git a/Contributed/BNGPlayground_Examples/signal-processing/spkalmanfilter/metadata.yaml b/Examples/signal-processing/spkalmanfilter/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/signal-processing/spkalmanfilter/metadata.yaml rename to Examples/signal-processing/spkalmanfilter/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/signal-processing/spkalmanfilter/sp_kalman_filter.bngl b/Examples/signal-processing/spkalmanfilter/sp_kalman_filter.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/signal-processing/spkalmanfilter/sp_kalman_filter.bngl rename to Examples/signal-processing/spkalmanfilter/sp_kalman_filter.bngl diff --git a/Contributed/BNGPlayground_Examples/synbio/synbiobandpassfilter/README.md b/Examples/synbio/synbiobandpassfilter/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/synbio/synbiobandpassfilter/README.md rename to Examples/synbio/synbiobandpassfilter/README.md diff --git a/Contributed/BNGPlayground_Examples/synbio/synbiobandpassfilter/metadata.yaml b/Examples/synbio/synbiobandpassfilter/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/synbio/synbiobandpassfilter/metadata.yaml rename to Examples/synbio/synbiobandpassfilter/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/synbio/synbiobandpassfilter/synbio_band_pass_filter.bngl b/Examples/synbio/synbiobandpassfilter/synbio_band_pass_filter.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/synbio/synbiobandpassfilter/synbio_band_pass_filter.bngl rename to Examples/synbio/synbiobandpassfilter/synbio_band_pass_filter.bngl diff --git a/Contributed/BNGPlayground_Examples/synbio/synbiocountermolecular/README.md b/Examples/synbio/synbiocountermolecular/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/synbio/synbiocountermolecular/README.md rename to Examples/synbio/synbiocountermolecular/README.md diff --git a/Contributed/BNGPlayground_Examples/synbio/synbiocountermolecular/metadata.yaml b/Examples/synbio/synbiocountermolecular/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/synbio/synbiocountermolecular/metadata.yaml rename to Examples/synbio/synbiocountermolecular/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/synbio/synbiocountermolecular/synbio_counter_molecular.bngl b/Examples/synbio/synbiocountermolecular/synbio_counter_molecular.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/synbio/synbiocountermolecular/synbio_counter_molecular.bngl rename to Examples/synbio/synbiocountermolecular/synbio_counter_molecular.bngl diff --git a/Contributed/BNGPlayground_Examples/synbio/synbioedgedetector/README.md b/Examples/synbio/synbioedgedetector/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/synbio/synbioedgedetector/README.md rename to Examples/synbio/synbioedgedetector/README.md diff --git a/Contributed/BNGPlayground_Examples/synbio/synbioedgedetector/metadata.yaml b/Examples/synbio/synbioedgedetector/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/synbio/synbioedgedetector/metadata.yaml rename to Examples/synbio/synbioedgedetector/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/synbio/synbioedgedetector/synbio_edge_detector.bngl b/Examples/synbio/synbioedgedetector/synbio_edge_detector.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/synbio/synbioedgedetector/synbio_edge_detector.bngl rename to Examples/synbio/synbioedgedetector/synbio_edge_detector.bngl diff --git a/Contributed/BNGPlayground_Examples/synbio/synbiologicgatesenzymatic/README.md b/Examples/synbio/synbiologicgatesenzymatic/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/synbio/synbiologicgatesenzymatic/README.md rename to Examples/synbio/synbiologicgatesenzymatic/README.md diff --git a/Contributed/BNGPlayground_Examples/synbio/synbiologicgatesenzymatic/metadata.yaml b/Examples/synbio/synbiologicgatesenzymatic/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/synbio/synbiologicgatesenzymatic/metadata.yaml rename to Examples/synbio/synbiologicgatesenzymatic/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/synbio/synbiologicgatesenzymatic/synbio_logic_gates_enzymatic.bngl b/Examples/synbio/synbiologicgatesenzymatic/synbio_logic_gates_enzymatic.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/synbio/synbiologicgatesenzymatic/synbio_logic_gates_enzymatic.bngl rename to Examples/synbio/synbiologicgatesenzymatic/synbio_logic_gates_enzymatic.bngl diff --git a/Contributed/BNGPlayground_Examples/synbio/synbiooscillatorsynchronization/README.md b/Examples/synbio/synbiooscillatorsynchronization/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/synbio/synbiooscillatorsynchronization/README.md rename to Examples/synbio/synbiooscillatorsynchronization/README.md diff --git a/Contributed/BNGPlayground_Examples/synbio/synbiooscillatorsynchronization/metadata.yaml b/Examples/synbio/synbiooscillatorsynchronization/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Examples/synbio/synbiooscillatorsynchronization/metadata.yaml rename to Examples/synbio/synbiooscillatorsynchronization/metadata.yaml diff --git a/Contributed/BNGPlayground_Examples/synbio/synbiooscillatorsynchronization/synbio_oscillator_synchronization.bngl b/Examples/synbio/synbiooscillatorsynchronization/synbio_oscillator_synchronization.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/synbio/synbiooscillatorsynchronization/synbio_oscillator_synchronization.bngl rename to Examples/synbio/synbiooscillatorsynchronization/synbio_oscillator_synchronization.bngl diff --git a/Contributed/BNGPlayground_Examples/wacky/wackyalchemystone/README.md b/Examples/wacky/wackyalchemystone/README.md similarity index 100% rename from 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Contributed/BNGPlayground_Validation/nfkbillustratingprotocols/nfkb_illustrating_protocols.bngl rename to Tutorials/nfkbillustratingprotocols/nfkb_illustrating_protocols.bngl diff --git a/Contributed/BNGPlayground_PublicRuntime/polymerfixed/README.md b/Tutorials/polymerfixed/README.md similarity index 100% rename from Contributed/BNGPlayground_PublicRuntime/polymerfixed/README.md rename to Tutorials/polymerfixed/README.md diff --git a/Contributed/BNGPlayground_PublicRuntime/polymerfixed/metadata.yaml b/Tutorials/polymerfixed/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_PublicRuntime/polymerfixed/metadata.yaml rename to Tutorials/polymerfixed/metadata.yaml diff --git a/Contributed/BNGPlayground_PublicRuntime/polymerfixed/polymer_fixed.bngl b/Tutorials/polymerfixed/polymer_fixed.bngl similarity index 100% rename from Contributed/BNGPlayground_PublicRuntime/polymerfixed/polymer_fixed.bngl rename to Tutorials/polymerfixed/polymer_fixed.bngl diff --git 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a/Contributed/BNGPlayground_Validation/testANGsynthesissimple/README.md b/Tutorials/testANGsynthesissimple/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/testANGsynthesissimple/README.md rename to Tutorials/testANGsynthesissimple/README.md diff --git a/Contributed/BNGPlayground_Validation/testANGsynthesissimple/metadata.yaml b/Tutorials/testANGsynthesissimple/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/testANGsynthesissimple/metadata.yaml rename to Tutorials/testANGsynthesissimple/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/testANGsynthesissimple/test_ANG_synthesis_simple.bngl b/Tutorials/testANGsynthesissimple/test_ANG_synthesis_simple.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/testANGsynthesissimple/test_ANG_synthesis_simple.bngl rename to Tutorials/testANGsynthesissimple/test_ANG_synthesis_simple.bngl diff --git 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Tutorials/testnetworkgen/test_network_gen.bngl diff --git a/Contributed/BNGPlayground_Validation/testsat/README.md b/Tutorials/testsat/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/testsat/README.md rename to Tutorials/testsat/README.md diff --git a/Contributed/BNGPlayground_Validation/testsat/metadata.yaml b/Tutorials/testsat/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/testsat/metadata.yaml rename to Tutorials/testsat/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/testsat/test_sat.bngl b/Tutorials/testsat/test_sat.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/testsat/test_sat.bngl rename to Tutorials/testsat/test_sat.bngl diff --git a/Contributed/BNGPlayground_Validation/testsynthesiscBNGLsimple/README.md b/Tutorials/testsynthesiscBNGLsimple/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesiscBNGLsimple/README.md rename to Tutorials/testsynthesiscBNGLsimple/README.md diff --git a/Contributed/BNGPlayground_Validation/testsynthesiscBNGLsimple/metadata.yaml b/Tutorials/testsynthesiscBNGLsimple/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesiscBNGLsimple/metadata.yaml rename to Tutorials/testsynthesiscBNGLsimple/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/testsynthesiscBNGLsimple/test_synthesis_cBNGL_simple.bngl b/Tutorials/testsynthesiscBNGLsimple/test_synthesis_cBNGL_simple.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesiscBNGLsimple/test_synthesis_cBNGL_simple.bngl rename to Tutorials/testsynthesiscBNGLsimple/test_synthesis_cBNGL_simple.bngl diff --git a/Contributed/BNGPlayground_Validation/testsynthesiscomplex/README.md b/Tutorials/testsynthesiscomplex/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesiscomplex/README.md rename to 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a/Contributed/BNGPlayground_Validation/testsynthesiscomplex0cBNGL/metadata.yaml b/Tutorials/testsynthesiscomplex0cBNGL/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesiscomplex0cBNGL/metadata.yaml rename to Tutorials/testsynthesiscomplex0cBNGL/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/testsynthesiscomplex0cBNGL/test_synthesis_complex_0_cBNGL.bngl b/Tutorials/testsynthesiscomplex0cBNGL/test_synthesis_complex_0_cBNGL.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesiscomplex0cBNGL/test_synthesis_complex_0_cBNGL.bngl rename to Tutorials/testsynthesiscomplex0cBNGL/test_synthesis_complex_0_cBNGL.bngl diff --git a/Contributed/BNGPlayground_Validation/testsynthesiscomplexsourcecBNGL/README.md b/Tutorials/testsynthesiscomplexsourcecBNGL/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesiscomplexsourcecBNGL/README.md rename to Tutorials/testsynthesiscomplexsourcecBNGL/README.md diff --git a/Contributed/BNGPlayground_Validation/testsynthesiscomplexsourcecBNGL/metadata.yaml b/Tutorials/testsynthesiscomplexsourcecBNGL/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesiscomplexsourcecBNGL/metadata.yaml rename to Tutorials/testsynthesiscomplexsourcecBNGL/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/testsynthesiscomplexsourcecBNGL/test_synthesis_complex_source_cBNGL.bngl b/Tutorials/testsynthesiscomplexsourcecBNGL/test_synthesis_complex_source_cBNGL.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesiscomplexsourcecBNGL/test_synthesis_complex_source_cBNGL.bngl rename to Tutorials/testsynthesiscomplexsourcecBNGL/test_synthesis_complex_source_cBNGL.bngl diff --git a/Contributed/BNGPlayground_Validation/testsynthesissimple/README.md b/Tutorials/testsynthesissimple/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesissimple/README.md rename to Tutorials/testsynthesissimple/README.md diff --git a/Contributed/BNGPlayground_Validation/testsynthesissimple/metadata.yaml b/Tutorials/testsynthesissimple/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesissimple/metadata.yaml rename to Tutorials/testsynthesissimple/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/testsynthesissimple/test_synthesis_simple.bngl b/Tutorials/testsynthesissimple/test_synthesis_simple.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesissimple/test_synthesis_simple.bngl rename to Tutorials/testsynthesissimple/test_synthesis_simple.bngl diff --git a/Contributed/BNGPlayground_Validation/tlmr/README.md b/Tutorials/tlmr/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/tlmr/README.md rename to Tutorials/tlmr/README.md diff --git a/Contributed/BNGPlayground_Validation/tlmr/metadata.yaml b/Tutorials/tlmr/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/tlmr/metadata.yaml rename to Tutorials/tlmr/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/tlmr/tlmr.bngl b/Tutorials/tlmr/tlmr.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/tlmr/tlmr.bngl rename to Tutorials/tlmr/tlmr.bngl diff --git a/Contributed/BNGPlayground_Validation/toyjim/README.md b/Tutorials/toyjim/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/toyjim/README.md rename to Tutorials/toyjim/README.md diff --git a/Contributed/BNGPlayground_Validation/toyjim/metadata.yaml b/Tutorials/toyjim/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/toyjim/metadata.yaml rename to Tutorials/toyjim/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/toyjim/toy-jim.bngl b/Tutorials/toyjim/toy-jim.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/toyjim/toy-jim.bngl rename to Tutorials/toyjim/toy-jim.bngl diff --git a/Contributed/BNGPlayground_Validation/univsynth/README.md b/Tutorials/univsynth/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/univsynth/README.md rename to Tutorials/univsynth/README.md diff --git a/Contributed/BNGPlayground_Validation/univsynth/metadata.yaml b/Tutorials/univsynth/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/univsynth/metadata.yaml rename to Tutorials/univsynth/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/univsynth/univ_synth.bngl b/Tutorials/univsynth/univ_synth.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/univsynth/univ_synth.bngl rename to Tutorials/univsynth/univ_synth.bngl diff --git a/manifest.json b/manifest.json index da96b57..e067230 100644 --- a/manifest.json +++ b/manifest.json @@ -131,7 +131,7 @@ "id": "actions_syntax", "name": "actions syntax", "description": "Original values used to generate parabola.exp", - "path": "PyBioNetGen/tests/actionssyntax/actions_syntax.bngl", + "path": "Published/PyBioNetGen/tests/actionssyntax/actions_syntax.bngl", "file": "actions_syntax.bngl", "tags": [ "actions", @@ -169,7 +169,7 @@ "id": "akt-signaling", "name": "akt signaling", "description": "Signaling rates", - "path": "Contributed/BNGPlayground_Examples/biology/aktsignaling/akt-signaling.bngl", + "path": "Examples/biology/aktsignaling/akt-signaling.bngl", "file": "akt-signaling.bngl", "tags": [ "akt", @@ -304,7 +304,7 @@ "id": "allosteric-activation", "name": "allosteric activation", "description": "Binding constants", - "path": "Contributed/BNGPlayground_Examples/biology/allostericactivation/allosteric-activation.bngl", + "path": "Examples/biology/allostericactivation/allosteric-activation.bngl", "file": "allosteric-activation.bngl", "tags": [ "allosteric", @@ -342,7 +342,7 @@ "id": "ampk-signaling", "name": "ampk signaling", "description": "AMPK signaling: The cellular energy sensor.", - "path": "Contributed/BNGPlayground_Examples/biology/ampksignaling/ampk-signaling.bngl", + "path": "Examples/biology/ampksignaling/ampk-signaling.bngl", "file": "ampk-signaling.bngl", "tags": [ "ampk", @@ -425,7 +425,7 @@ "id": "apoptosis-cascade", "name": "apoptosis cascade", "description": "Apoptosis cascade: Integrated extrinsic and intrinsic death signaling.", - "path": "Contributed/BNGPlayground_Examples/biology/apoptosiscascade/apoptosis-cascade.bngl", + "path": "Examples/biology/apoptosiscascade/apoptosis-cascade.bngl", "file": "apoptosis-cascade.bngl", "tags": [ "apoptosis", @@ -593,7 +593,7 @@ "id": "auto-activation-loop", "name": "auto activation loop", "description": "Auto-activation loop: A positive feedback circuit.", - "path": "Contributed/BNGPlayground_Examples/biology/autoactivationloop/auto-activation-loop.bngl", + "path": "Examples/biology/autoactivationloop/auto-activation-loop.bngl", "file": "auto-activation-loop.bngl", "tags": [ "auto", @@ -614,7 +614,7 @@ "id": "autophagy-regulation", "name": "autophagy regulation", "description": "Autophagy regulation: mTOR and AMPK competition on the ULK1 switch.", - "path": "Contributed/BNGPlayground_Examples/biology/autophagyregulation/autophagy-regulation.bngl", + "path": "Examples/biology/autophagyregulation/autophagy-regulation.bngl", "file": "autophagy-regulation.bngl", "tags": [ "autophagy", @@ -911,7 +911,7 @@ "id": "bcr-signaling", "name": "bcr signaling", "description": "BCR signaling: The B-cell antigen receptor cascade.", - "path": "Contributed/BNGPlayground_Examples/biology/bcrsignaling/bcr-signaling.bngl", + "path": "Examples/biology/bcrsignaling/bcr-signaling.bngl", "file": "bcr-signaling.bngl", "tags": [ "bcr", @@ -987,7 +987,7 @@ "id": "beta-adrenergic-response", "name": "beta adrenergic response", "description": "Beta-adrenergic signaling: GPCR pathway and desensitization.", - "path": "Contributed/BNGPlayground_Examples/biology/betaadrenergicresponse/beta-adrenergic-response.bngl", + "path": "Examples/biology/betaadrenergicresponse/beta-adrenergic-response.bngl", "file": "beta-adrenergic-response.bngl", "tags": [ "beta", @@ -1105,7 +1105,7 @@ "id": "bistable-toggle-switch", "name": "bistable toggle switch", "description": "Genetic Toggle Switch: Mutual repression circuit.", - "path": "Contributed/BNGPlayground_Examples/biology/bistabletoggleswitch/bistable-toggle-switch.bngl", + "path": "Examples/biology/bistabletoggleswitch/bistable-toggle-switch.bngl", "file": "bistable-toggle-switch.bngl", "tags": [ "bistable", @@ -1212,7 +1212,7 @@ "id": "blood-coagulation-thrombin", "name": "blood coagulation thrombin", "description": "Blood coagulation: Thrombin burst and feedback propagation.", - "path": "Contributed/BNGPlayground_Examples/biology/bloodcoagulationthrombin/blood-coagulation-thrombin.bngl", + "path": "Examples/biology/bloodcoagulationthrombin/blood-coagulation-thrombin.bngl", "file": "blood-coagulation-thrombin.bngl", "tags": [ "blood", @@ -1271,7 +1271,7 @@ "id": "bmp-signaling", "name": "bmp signaling", "description": "BMP-Smad signaling: Developmental gradient relay.", - "path": "Contributed/BNGPlayground_Examples/biology/bmpsignaling/bmp-signaling.bngl", + "path": "Examples/biology/bmpsignaling/bmp-signaling.bngl", "file": "bmp-signaling.bngl", "tags": [ "bmp", @@ -1293,7 +1293,7 @@ "id": "bng_error", "name": "bng error", "description": "Original values used to generate parabola.exp", - "path": "PyBioNetGen/tests/bngerror/bng_error.bngl", + "path": "Published/PyBioNetGen/tests/bngerror/bng_error.bngl", "file": "bng_error.bngl", "tags": [ "bng", @@ -1439,7 +1439,7 @@ "id": "brusselator-oscillator", "name": "brusselator oscillator", "description": "The Brusselator: Auto-catalytic chemical oscillator.", - "path": "Contributed/BNGPlayground_Examples/biology/brusselatoroscillator/brusselator-oscillator.bngl", + "path": "Examples/biology/brusselatoroscillator/brusselator-oscillator.bngl", "file": "brusselator-oscillator.bngl", "tags": [ "brusselator", @@ -1513,7 +1513,7 @@ "id": "calcineurin-nfat-pathway", "name": "calcineurin nfat pathway", "description": "NFAT Signaling: Calcium-dependent nuclear translocation.", - "path": "Contributed/BNGPlayground_Examples/biology/calcineurinnfatpathway/calcineurin-nfat-pathway.bngl", + "path": "Examples/biology/calcineurinnfatpathway/calcineurin-nfat-pathway.bngl", "file": "calcineurin-nfat-pathway.bngl", "tags": [ "calcineurin", @@ -1534,7 +1534,7 @@ "id": "calcium-spike-signaling", "name": "calcium spike signaling", "description": "Calcium spikes: Oscillations driven by IP3R and CICR feedback.", - "path": "Contributed/BNGPlayground_Examples/biology/calciumspikesignaling/calcium-spike-signaling.bngl", + "path": "Examples/biology/calciumspikesignaling/calcium-spike-signaling.bngl", "file": "calcium-spike-signaling.bngl", "tags": [ "calcium", @@ -1614,7 +1614,7 @@ "id": "CaOscillate_Func", "name": "CaOscillate_Func", "description": "Calcium oscillations (func)", - "path": "Contributed/BNGPlayground_Validation/CaOscillateFunc/CaOscillate_Func.bngl", + "path": "Tutorials/CaOscillateFunc/CaOscillate_Func.bngl", "file": "CaOscillate_Func.bngl", "tags": [ "validation", @@ -1635,7 +1635,7 @@ "id": "CaOscillate_Sat", "name": "CaOscillate_Sat", "description": "Calcium oscillations (sat)", - "path": "Contributed/BNGPlayground_Validation/CaOscillateSat/CaOscillate_Sat.bngl", + "path": "Tutorials/CaOscillateSat/CaOscillate_Sat.bngl", "file": "CaOscillate_Sat.bngl", "tags": [ "validation", @@ -1692,7 +1692,7 @@ "id": "caspase-activation-loop", "name": "caspase activation loop", "description": "Caspase activation loop: The executioner feedback system.", - "path": "Contributed/BNGPlayground_Examples/biology/caspaseactivationloop/caspase-activation-loop.bngl", + "path": "Examples/biology/caspaseactivationloop/caspase-activation-loop.bngl", "file": "caspase-activation-loop.bngl", "tags": [ "caspase", @@ -1714,7 +1714,7 @@ "id": "catalysis", "name": "catalysis", "description": "Catalysis in energy BNG", - "path": "Contributed/BNGPlayground_Validation/catalysis/catalysis.bngl", + "path": "Tutorials/catalysis/catalysis.bngl", "file": "catalysis.bngl", "tags": [ "validation", @@ -1759,7 +1759,7 @@ "id": "cd40-signaling", "name": "cd40 signaling", "description": "CD40 Signaling: B-cell activation and TRAF-mediated relay.", - "path": "Contributed/BNGPlayground_Examples/biology/cd40signaling/cd40-signaling.bngl", + "path": "Examples/biology/cd40signaling/cd40-signaling.bngl", "file": "cd40-signaling.bngl", "tags": [ "cd40", @@ -1799,7 +1799,7 @@ "id": "cell-cycle-checkpoint", "name": "cell cycle checkpoint", "description": "Cell cycle checkpoint: Mitotic entry switch (CDK1).", - "path": "Contributed/BNGPlayground_Examples/biology/cellcyclecheckpoint/cell-cycle-checkpoint.bngl", + "path": "Examples/biology/cellcyclecheckpoint/cell-cycle-checkpoint.bngl", "file": "cell-cycle-checkpoint.bngl", "tags": [ "cell", @@ -1969,7 +1969,7 @@ "id": "checkpoint-kinase-signaling", "name": "checkpoint kinase signaling", "description": "DNA Checkpoint: ATM/ATR mediated damage sensing.", - "path": "Contributed/BNGPlayground_Examples/biology/checkpointkinasesignaling/checkpoint-kinase-signaling.bngl", + "path": "Examples/biology/checkpointkinasesignaling/checkpoint-kinase-signaling.bngl", "file": "checkpoint-kinase-signaling.bngl", "tags": [ "checkpoint", @@ -2043,7 +2043,7 @@ "id": "chemotaxis-signal-transduction", "name": "chemotaxis signal transduction", "description": "Bacterial Chemotaxis: Adaptation through methylation.", - "path": "Contributed/BNGPlayground_Examples/biology/chemotaxissignaltransduction/chemotaxis-signal-transduction.bngl", + "path": "Examples/biology/chemotaxissignaltransduction/chemotaxis-signal-transduction.bngl", "file": "chemotaxis-signal-transduction.bngl", "tags": [ "chemotaxis", @@ -2178,7 +2178,7 @@ "id": "circadian-oscillator", "name": "circadian oscillator", "description": "title: Vilar Circadian Oscillator Model", - "path": "Contributed/BNGPlayground_Examples/biology/circadianoscillator/circadian-oscillator.bngl", + "path": "Examples/biology/circadianoscillator/circadian-oscillator.bngl", "file": "circadian-oscillator.bngl", "tags": [ "circadian", @@ -2260,7 +2260,7 @@ "id": "clock-bmal1-gene-circuit", "name": "clock bmal1 gene circuit", "description": "BMAL1-CLOCK: The master activator of the circadian circuit.", - "path": "Contributed/BNGPlayground_Examples/biology/clockbmal1genecircuit/clock-bmal1-gene-circuit.bngl", + "path": "Examples/biology/clockbmal1genecircuit/clock-bmal1-gene-circuit.bngl", "file": "clock-bmal1-gene-circuit.bngl", "tags": [ "clock", @@ -2389,7 +2389,7 @@ "id": "compartment_endocytosis", "name": "compartment endocytosis", "description": "Model: compartment_endocytosis.bngl", - "path": "Contributed/BNGPlayground_Examples/compartments/compartmentendocytosis/compartment_endocytosis.bngl", + "path": "Examples/compartments/compartmentendocytosis/compartment_endocytosis.bngl", "file": "compartment_endocytosis.bngl", "tags": [ "compartment", @@ -2408,7 +2408,7 @@ "id": "compartment_membrane_bound", "name": "compartment membrane bound", "description": "Model: compartment_membrane_bound.bngl", - "path": "Contributed/BNGPlayground_Examples/compartments/compartmentmembranebound/compartment_membrane_bound.bngl", + "path": "Examples/compartments/compartmentmembranebound/compartment_membrane_bound.bngl", "file": "compartment_membrane_bound.bngl", "tags": [ "compartment", @@ -2429,7 +2429,7 @@ "id": "compartment_nested_transport", "name": "compartment nested transport", "description": "Model: compartment_nested_transport.bngl", - "path": "Contributed/BNGPlayground_Examples/compartments/compartmentnestedtransport/compartment_nested_transport.bngl", + "path": "Examples/compartments/compartmentnestedtransport/compartment_nested_transport.bngl", "file": "compartment_nested_transport.bngl", "tags": [ "compartment", @@ -2449,7 +2449,7 @@ "id": "compartment_nuclear_transport", "name": "compartment nuclear transport", "description": "Model: compartment_nuclear_transport.bngl", - "path": "Contributed/BNGPlayground_Examples/compartments/compartmentnucleartransport/compartment_nuclear_transport.bngl", + "path": "Examples/compartments/compartmentnucleartransport/compartment_nuclear_transport.bngl", "file": "compartment_nuclear_transport.bngl", "tags": [ "compartment", @@ -2469,7 +2469,7 @@ "id": "compartment_organelle_exchange", "name": "compartment organelle exchange", "description": "Model: compartment_organelle_exchange.bngl", - "path": "Contributed/BNGPlayground_Examples/compartments/compartmentorganelleexchange/compartment_organelle_exchange.bngl", + "path": "Examples/compartments/compartmentorganelleexchange/compartment_organelle_exchange.bngl", "file": "compartment_organelle_exchange.bngl", "tags": [ "compartment", @@ -2489,7 +2489,7 @@ "id": "competitive-enzyme-inhibition", "name": "competitive enzyme inhibition", "description": "Competitive inhibition: Inhibitor (I) and Substrate (S) compete for the same", - "path": "Contributed/BNGPlayground_Examples/biology/competitiveenzymeinhibition/competitive-enzyme-inhibition.bngl", + "path": "Examples/biology/competitiveenzymeinhibition/competitive-enzyme-inhibition.bngl", "file": "competitive-enzyme-inhibition.bngl", "tags": [ "competitive", @@ -2510,7 +2510,7 @@ "id": "complement-activation-cascade", "name": "complement activation cascade", "description": "Complement System: Pathogen opsonization and the Alternative Pathway.", - "path": "Contributed/BNGPlayground_Examples/biology/complementactivationcascade/complement-activation-cascade.bngl", + "path": "Examples/biology/complementactivationcascade/complement-activation-cascade.bngl", "file": "complement-activation-cascade.bngl", "tags": [ "complement", @@ -2554,7 +2554,7 @@ "id": "contact-inhibition-hippo-yap", "name": "contact inhibition hippo yap", "description": "Hippo Pathway: Contact inhibition and YAP regulation.", - "path": "Contributed/BNGPlayground_Examples/biology/contactinhibitionhippoyap/contact-inhibition-hippo-yap.bngl", + "path": "Examples/biology/contactinhibitionhippoyap/contact-inhibition-hippo-yap.bngl", "file": "contact-inhibition-hippo-yap.bngl", "tags": [ "contact", @@ -2575,7 +2575,7 @@ "id": "continue", "name": "continue", "description": "Test trajectory continuation", - "path": "Contributed/BNGPlayground_Validation/continue/continue.bngl", + "path": "Tutorials/continue/continue.bngl", "file": "continue.bngl", "tags": [ "validation", @@ -2595,7 +2595,7 @@ "id": "cooperative-binding", "name": "cooperative binding", "description": "Cooperative binding: The binding of the first ligand molecule increases", - "path": "Contributed/BNGPlayground_Examples/biology/cooperativebinding/cooperative-binding.bngl", + "path": "Examples/biology/cooperativebinding/cooperative-binding.bngl", "file": "cooperative-binding.bngl", "tags": [ "cooperative", @@ -2674,7 +2674,7 @@ "id": "cs_diffie_hellman", "name": "cs diffie hellman", "description": "Model: cs_diffie_hellman.bngl", - "path": "Contributed/BNGPlayground_Examples/cs/csdiffiehellman/cs_diffie_hellman.bngl", + "path": "Examples/cs/csdiffiehellman/cs_diffie_hellman.bngl", "file": "cs_diffie_hellman.bngl", "tags": [ "cs", @@ -2695,7 +2695,7 @@ "id": "cs_hash_function", "name": "cs hash function", "description": "Cryptographic Hash Function in BNGL", - "path": "Contributed/BNGPlayground_Examples/cs/cshashfunction/cs_hash_function.bngl", + "path": "Examples/cs/cshashfunction/cs_hash_function.bngl", "file": "cs_hash_function.bngl", "tags": [ "cs", @@ -2720,7 +2720,7 @@ "id": "cs_huffman", "name": "cs huffman", "description": "Model: cs_huffman.bngl", - "path": "Contributed/BNGPlayground_Examples/cs/cshuffman/cs_huffman.bngl", + "path": "Examples/cs/cshuffman/cs_huffman.bngl", "file": "cs_huffman.bngl", "tags": [ "cs", @@ -2740,7 +2740,7 @@ "id": "cs_monte_carlo_pi", "name": "cs monte carlo pi", "description": "Model: cs_monte_carlo_pi.bngl", - "path": "Contributed/BNGPlayground_Examples/cs/csmontecarlopi/cs_monte_carlo_pi.bngl", + "path": "Examples/cs/csmontecarlopi/cs_monte_carlo_pi.bngl", "file": "cs_monte_carlo_pi.bngl", "tags": [ "cs", @@ -2762,7 +2762,7 @@ "id": "cs_pagerank", "name": "cs pagerank", "description": "Model: cs_pagerank.bngl", - "path": "Contributed/BNGPlayground_Examples/cs/cspagerank/cs_pagerank.bngl", + "path": "Examples/cs/cspagerank/cs_pagerank.bngl", "file": "cs_pagerank.bngl", "tags": [ "cs", @@ -2780,7 +2780,7 @@ "id": "cs_pid_controller", "name": "cs pid controller", "description": "PID Controller in BNGL", - "path": "Contributed/BNGPlayground_Examples/cs/cspidcontroller/cs_pid_controller.bngl", + "path": "Examples/cs/cspidcontroller/cs_pid_controller.bngl", "file": "cs_pid_controller.bngl", "tags": [ "cs", @@ -2802,7 +2802,7 @@ "id": "cs_regex_nfa", "name": "cs regex nfa", "description": "Model: cs_regex_nfa.bngl", - "path": "Contributed/BNGPlayground_Examples/cs/csregexnfa/cs_regex_nfa.bngl", + "path": "Examples/cs/csregexnfa/cs_regex_nfa.bngl", "file": "cs_regex_nfa.bngl", "tags": [ "cs", @@ -2973,7 +2973,7 @@ "id": "degranulation_model", "name": "PyBNG: Degranulation model", "description": "Degranulation model", - "path": "PyBioNetGen/core/degranulationmodel/degranulation_model.bngl", + "path": "Published/PyBioNetGen/core/degranulationmodel/degranulation_model.bngl", "file": "degranulation_model.bngl", "tags": [ "published", @@ -3106,7 +3106,7 @@ "id": "dna-damage-repair", "name": "dna damage repair", "description": "DNA damage sensing and repair pathway (ATM-CHK2-p53 axis)", - "path": "Contributed/BNGPlayground_Examples/biology/dnadamagerepair/dna-damage-repair.bngl", + "path": "Examples/biology/dnadamagerepair/dna-damage-repair.bngl", "file": "dna-damage-repair.bngl", "tags": [ "dna", @@ -3127,7 +3127,7 @@ "id": "dna-methylation-dynamics", "name": "dna methylation dynamics", "description": "DNA Methylation: Maintenance and de novo dynamics.", - "path": "Contributed/BNGPlayground_Examples/biology/dnamethylationdynamics/dna-methylation-dynamics.bngl", + "path": "Examples/biology/dnamethylationdynamics/dna-methylation-dynamics.bngl", "file": "dna-methylation-dynamics.bngl", "tags": [ "dna", @@ -3239,7 +3239,7 @@ "id": "dr5-apoptosis-signaling", "name": "dr5 apoptosis signaling", "description": "DR5 (TRAIL) Signaling: Extrinsic apoptosis and DISC formation.", - "path": "Contributed/BNGPlayground_Examples/biology/dr5apoptosissignaling/dr5-apoptosis-signaling.bngl", + "path": "Examples/biology/dr5apoptosissignaling/dr5-apoptosis-signaling.bngl", "file": "dr5-apoptosis-signaling.bngl", "tags": [ "dr5", @@ -3279,7 +3279,7 @@ "id": "dual-site-phosphorylation", "name": "dual site phosphorylation", "description": "Dual-site phosphorylation: Requires two sequential modifications for activity.", - "path": "Contributed/BNGPlayground_Examples/biology/dualsitephosphorylation/dual-site-phosphorylation.bngl", + "path": "Examples/biology/dualsitephosphorylation/dual-site-phosphorylation.bngl", "file": "dual-site-phosphorylation.bngl", "tags": [ "dual", @@ -3373,7 +3373,7 @@ "id": "e2f-rb-cell-cycle-switch", "name": "e2f rb cell cycle switch", "description": "E2F/Rb Switch: The G1/S transition gate.", - "path": "Contributed/BNGPlayground_Examples/biology/e2frbcellcycleswitch/e2f-rb-cell-cycle-switch.bngl", + "path": "Examples/biology/e2frbcellcycleswitch/e2f-rb-cell-cycle-switch.bngl", "file": "e2f-rb-cell-cycle-switch.bngl", "tags": [ "e2f", @@ -3414,7 +3414,7 @@ "id": "eco_coevolution_host_parasite", "name": "eco coevolution host parasite", "description": "Model: eco_coevolution_host_parasite.bngl", - "path": "Contributed/BNGPlayground_Examples/ecology/ecocoevolutionhostparasite/eco_coevolution_host_parasite.bngl", + "path": "Examples/ecology/ecocoevolutionhostparasite/eco_coevolution_host_parasite.bngl", "file": "eco_coevolution_host_parasite.bngl", "tags": [ "eco", @@ -3432,7 +3432,7 @@ "id": "eco_food_web_chaos_3sp", "name": "eco food web chaos 3sp", "description": "Model: eco_food_web_chaos_3sp.bngl", - "path": "Contributed/BNGPlayground_Examples/ecology/ecofoodwebchaos3sp/eco_food_web_chaos_3sp.bngl", + "path": "Examples/ecology/ecofoodwebchaos3sp/eco_food_web_chaos_3sp.bngl", "file": "eco_food_web_chaos_3sp.bngl", "tags": [ "eco", @@ -3456,7 +3456,7 @@ "id": "eco_lotka_volterra_grid", "name": "eco lotka volterra grid", "description": "Model: eco_lotka_volterra_grid.bngl", - "path": "Contributed/BNGPlayground_Examples/ecology/ecolotkavolterragrid/eco_lotka_volterra_grid.bngl", + "path": "Examples/ecology/ecolotkavolterragrid/eco_lotka_volterra_grid.bngl", "file": "eco_lotka_volterra_grid.bngl", "tags": [ "eco", @@ -3476,7 +3476,7 @@ "id": "eco_mutualism_obligate", "name": "eco mutualism obligate", "description": "Model: eco_mutualism_obligate.bngl", - "path": "Contributed/BNGPlayground_Examples/ecology/ecomutualismobligate/eco_mutualism_obligate.bngl", + "path": "Examples/ecology/ecomutualismobligate/eco_mutualism_obligate.bngl", "file": "eco_mutualism_obligate.bngl", "tags": [ "eco", @@ -3495,7 +3495,7 @@ "id": "eco_rock_paper_scissors_spatial", "name": "eco rock paper scissors spatial", "description": "Model: eco_rock_paper_scissors_spatial.bngl", - "path": "Contributed/BNGPlayground_Examples/ecology/ecorockpaperscissorsspatial/eco_rock_paper_scissors_spatial.bngl", + "path": "Examples/ecology/ecorockpaperscissorsspatial/eco_rock_paper_scissors_spatial.bngl", "file": "eco_rock_paper_scissors_spatial.bngl", "tags": [ "eco", @@ -3516,7 +3516,7 @@ "id": "egfr", "name": "egfr", "description": "Blinov et al. 2006. Biosystems, 83:136", - "path": "PyBioNetGen/core/egfr/egfr.bngl", + "path": "Published/PyBioNetGen/core/egfr/egfr.bngl", "file": "egfr.bngl", "tags": [ "egfr", @@ -3535,7 +3535,7 @@ "id": "egfr_ground", "name": "egfr ground", "description": "Blinov et al. 2006. Biosystems, 83:136", - "path": "PyBioNetGen/core/egfrground/egfr_ground.bngl", + "path": "Published/PyBioNetGen/core/egfrground/egfr_ground.bngl", "file": "egfr_ground.bngl", "tags": [ "egfr", @@ -3555,7 +3555,7 @@ "id": "egfr_net", "name": "egfr_net", "description": "check detailed balanced", - "path": "Contributed/BNGPlayground_Validation/egfrnet/egfr_net.bngl", + "path": "Tutorials/egfrnet/egfr_net.bngl", "file": "egfr_net.bngl", "tags": [ "validation", @@ -3576,7 +3576,7 @@ "id": "egfr_net_red", "name": "egfr_net_red", "description": "Reduced state-space version of EGFR_NET.BNGL with equivalent ODE dynamics", - "path": "Contributed/BNGPlayground_Validation/egfrnetred/egfr_net_red.bngl", + "path": "Tutorials/egfrnetred/egfr_net_red.bngl", "file": "egfr_net_red.bngl", "tags": [ "validation", @@ -3601,7 +3601,7 @@ "id": "egfr_nf", "name": "egfr nf", "description": "Filename: example2_starting_point.bngl", - "path": "PyBioNetGen/core/egfrnf/egfr_nf.bngl", + "path": "Published/PyBioNetGen/core/egfrnf/egfr_nf.bngl", "file": "egfr_nf.bngl", "tags": [ "egfr", @@ -3621,7 +3621,7 @@ "id": "egfr_ode", "name": "egfr ode", "description": "Filename: example1.bngl", - "path": "PyBioNetGen/core/egfrode/egfr_ode.bngl", + "path": "Published/PyBioNetGen/core/egfrode/egfr_ode.bngl", "file": "egfr_ode.bngl", "tags": [ "egfr", @@ -3641,7 +3641,7 @@ "id": "egfr_ode", "name": "PyBNG: EGFR ODE", "description": "EGFR ODE", - "path": "PyBioNetGen/core/egfrode_published-models_PyBNG/egfr_ode.bngl", + "path": "Published/PyBioNetGen/core/egfrode_published-models_PyBNG/egfr_ode.bngl", "file": "egfr_ode.bngl", "tags": [ "published", @@ -3663,7 +3663,7 @@ "id": "egfr_path", "name": "egfr_path", "description": "The primary focus of the model developed by Kholodenko", - "path": "Contributed/BNGPlayground_Validation/egfrpath/egfr_path.bngl", + "path": "Tutorials/egfrpath/egfr_path.bngl", "file": "egfr_path.bngl", "tags": [ "validation", @@ -3702,7 +3702,7 @@ "id": "egfr-signaling-pathway", "name": "egfr signaling pathway", "description": "Enhanced EGFR Signaling: Combinatorial complexity with multiple phosphorylation sites.", - "path": "Contributed/BNGPlayground_Examples/biology/egfrsignalingpathway/egfr-signaling-pathway.bngl", + "path": "Examples/biology/egfrsignalingpathway/egfr-signaling-pathway.bngl", "file": "egfr-signaling-pathway.bngl", "tags": [ "egfr", @@ -3722,7 +3722,7 @@ "id": "egg", "name": "egg", "description": "BioNetGen model: egg", - "path": "PyBioNetGen/tests/egg/egg.bngl", + "path": "Published/PyBioNetGen/tests/egg/egg.bngl", "file": "egg.bngl", "tags": [ "egg", @@ -3741,7 +3741,7 @@ "id": "eif2a-stress-response", "name": "eif2a stress response", "description": "Integrated Stress Response: eIF2alpha and the translational gate.", - "path": "Contributed/BNGPlayground_Examples/biology/eif2astressresponse/eif2a-stress-response.bngl", + "path": "Examples/biology/eif2astressresponse/eif2a-stress-response.bngl", "file": "eif2a-stress-response.bngl", "tags": [ "eif2a", @@ -3833,7 +3833,7 @@ "id": "endosomal-sorting-rab", "name": "endosomal sorting rab", "description": "Endosomal Sorting: Rab GTPase conversion and effector recruitment.", - "path": "Contributed/BNGPlayground_Examples/biology/endosomalsortingrab/endosomal-sorting-rab.bngl", + "path": "Examples/biology/endosomalsortingrab/endosomal-sorting-rab.bngl", "file": "endosomal-sorting-rab.bngl", "tags": [ "endosomal", @@ -3855,7 +3855,7 @@ "id": "energy_allostery_mwc", "name": "energy allostery mwc", "description": "Model: energy_allostery_mwc.bngl", - "path": "Contributed/BNGPlayground_Examples/energy/energyallosterymwc/energy_allostery_mwc.bngl", + "path": "Examples/energy/energyallosterymwc/energy_allostery_mwc.bngl", "file": "energy_allostery_mwc.bngl", "tags": [ "energy", @@ -3874,7 +3874,7 @@ "id": "energy_catalysis_mm", "name": "energy catalysis mm", "description": "Model: energy_catalysis_mm.bngl", - "path": "Contributed/BNGPlayground_Examples/energy/energycatalysismm/energy_catalysis_mm.bngl", + "path": "Examples/energy/energycatalysismm/energy_catalysis_mm.bngl", "file": "energy_catalysis_mm.bngl", "tags": [ "energy", @@ -3894,7 +3894,7 @@ "id": "energy_cooperativity_adh", "name": "energy cooperativity adh", "description": "Model: energy_cooperativity_adh.bngl", - "path": "Contributed/BNGPlayground_Examples/energy/energycooperativityadh/energy_cooperativity_adh.bngl", + "path": "Examples/energy/energycooperativityadh/energy_cooperativity_adh.bngl", "file": "energy_cooperativity_adh.bngl", "tags": [ "energy", @@ -3913,7 +3913,7 @@ "id": "energy_example1", "name": "energy_example1", "description": "Illustration of energy modeling approach w/ a simple protein scaffold model", - "path": "Contributed/BNGPlayground_Validation/energyexample1/energy_example1.bngl", + "path": "Tutorials/energyexample1/energy_example1.bngl", "file": "energy_example1.bngl", "tags": [ "validation", @@ -3936,7 +3936,7 @@ "id": "energy_linear_chain", "name": "energy linear chain", "description": "Model: energy_linear_chain.bngl", - "path": "Contributed/BNGPlayground_Examples/energy/energylinearchain/energy_linear_chain.bngl", + "path": "Examples/energy/energylinearchain/energy_linear_chain.bngl", "file": "energy_linear_chain.bngl", "tags": [ "energy", @@ -3955,7 +3955,7 @@ "id": "energy_transport_pump", "name": "energy transport pump", "description": "Model: energy_transport_pump.bngl", - "path": "Contributed/BNGPlayground_Examples/energy/energytransportpump/energy_transport_pump.bngl", + "path": "Examples/energy/energytransportpump/energy_transport_pump.bngl", "file": "energy_transport_pump.bngl", "tags": [ "energy", @@ -3977,7 +3977,7 @@ "id": "er-stress-response", "name": "er stress response", "description": "Rate Constants", - "path": "Contributed/BNGPlayground_Examples/biology/erstressresponse/er-stress-response.bngl", + "path": "Examples/biology/erstressresponse/er-stress-response.bngl", "file": "er-stress-response.bngl", "tags": [ "er", @@ -4023,7 +4023,7 @@ "id": "erk-nuclear-translocation", "name": "erk nuclear translocation", "description": "ERK Translocation: Spatial signaling and transcriptional assembly.", - "path": "Contributed/BNGPlayground_Examples/biology/erknucleartranslocation/erk-nuclear-translocation.bngl", + "path": "Examples/biology/erknucleartranslocation/erk-nuclear-translocation.bngl", "file": "erk-nuclear-translocation.bngl", "tags": [ "erk", @@ -4044,7 +4044,7 @@ "id": "ErrNoFrees", "name": "ErrNoFrees", "description": "An example from a real application", - "path": "PyBioNetGen/tests/ErrNoFrees/ErrNoFrees.bngl", + "path": "Published/PyBioNetGen/tests/ErrNoFrees/ErrNoFrees.bngl", "file": "ErrNoFrees.bngl", "tags": [ "errnofrees", @@ -4076,30 +4076,11 @@ "visible": false, "collectionId": "Mallela2022_MSAs" }, - { - "id": "example1", - "name": "example1", - "description": "Example file for BNG2 tutorial.", - "path": "Contributed/BNGPlayground_Validation/example1/example1.bngl", - "file": "example1.bngl", - "tags": [ - "validation", - "example1", - "version", - "generate_network", - "simulate_ode" - ], - "category": "validation", - "bng2_compatible": false, - "origin": "test-case", - "visible": true, - "collectionId": null - }, { "id": "example1", "name": "example1", "description": "Filename: example1.bngl", - "path": "PyBioNetGen/core/example1/example1.bngl", + "path": "Published/PyBioNetGen/core/example1/example1.bngl", "file": "example1.bngl", "tags": [ "example1", @@ -4115,11 +4096,30 @@ "visible": false, "collectionId": null }, + { + "id": "example1", + "name": "example1", + "description": "Example file for BNG2 tutorial.", + "path": "Tutorials/example1/example1.bngl", + "file": "example1.bngl", + "tags": [ + "validation", + "example1", + "version", + "generate_network", + "simulate_ode" + ], + "category": "validation", + "bng2_compatible": false, + "origin": "test-case", + "visible": true, + "collectionId": null + }, { "id": "example2_starting_point", "name": "example2 starting point", "description": "Filename: example2_starting_point.bngl", - "path": "PyBioNetGen/core/example2startingpoint/example2_starting_point.bngl", + "path": "Published/PyBioNetGen/core/example2startingpoint/example2_starting_point.bngl", "file": "example2_starting_point.bngl", "tags": [ "example2", @@ -4284,7 +4284,7 @@ "id": "fceri_gamma2", "name": "fceri gamma2", "description": "BioNetGen model: fceri gamma2", - "path": "PyBioNetGen/core/fcerigamma2/fceri_gamma2.bngl", + "path": "Published/PyBioNetGen/core/fcerigamma2/fceri_gamma2.bngl", "file": "fceri_gamma2.bngl", "tags": [ "fceri", @@ -4304,7 +4304,7 @@ "id": "fceri_gamma2_ground_truth", "name": "fceri gamma2 ground truth", "description": "BioNetGen model: fceri gamma2 ground truth", - "path": "PyBioNetGen/core/fcerigamma2groundtruth/fceri_gamma2_ground_truth.bngl", + "path": "Published/PyBioNetGen/core/fcerigamma2groundtruth/fceri_gamma2_ground_truth.bngl", "file": "fceri_gamma2_ground_truth.bngl", "tags": [ "fceri", @@ -4368,7 +4368,7 @@ "id": "fceri_ji_comp", "name": "fceri_ji_comp", "description": "Ligand-receptor binding", - "path": "Contributed/BNGPlayground_Validation/fcerijicomp/fceri_ji_comp.bngl", + "path": "Tutorials/fcerijicomp/fceri_ji_comp.bngl", "file": "fceri_ji_comp.bngl", "tags": [ "validation", @@ -4417,7 +4417,7 @@ "id": "feature_functional_rates_volume", "name": "feature functional rates volume", "description": "Model: feature_functional_rates_volume.bngl", - "path": "Contributed/BNGPlayground_Examples/feature-demos/featurefunctionalratesvolume/feature_functional_rates_volume.bngl", + "path": "Examples/feature-demos/featurefunctionalratesvolume/feature_functional_rates_volume.bngl", "file": "feature_functional_rates_volume.bngl", "tags": [ "feature", @@ -4438,7 +4438,7 @@ "id": "feature_global_functions_scan", "name": "feature global functions scan", "description": "Model: feature_global_functions_scan.bngl", - "path": "Contributed/BNGPlayground_Examples/feature-demos/featureglobalfunctionsscan/feature_global_functions_scan.bngl", + "path": "Examples/feature-demos/featureglobalfunctionsscan/feature_global_functions_scan.bngl", "file": "feature_global_functions_scan.bngl", "tags": [ "feature", @@ -4459,7 +4459,7 @@ "id": "feature_local_functions_explicit", "name": "feature local functions explicit", "description": "Model: feature_local_functions_explicit.bngl", - "path": "Contributed/BNGPlayground_Examples/feature-demos/featurelocalfunctionsexplicit/feature_local_functions_explicit.bngl", + "path": "Examples/feature-demos/featurelocalfunctionsexplicit/feature_local_functions_explicit.bngl", "file": "feature_local_functions_explicit.bngl", "tags": [ "feature", @@ -4482,7 +4482,7 @@ "id": "feature_symmetry_factors_cyclic", "name": "feature symmetry factors cyclic", "description": "Model: feature_symmetry_factors_cyclic.bngl", - "path": "Contributed/BNGPlayground_Examples/feature-demos/featuresymmetryfactorscyclic/feature_symmetry_factors_cyclic.bngl", + "path": "Examples/feature-demos/featuresymmetryfactorscyclic/feature_symmetry_factors_cyclic.bngl", "file": "feature_symmetry_factors_cyclic.bngl", "tags": [ "feature", @@ -4503,7 +4503,7 @@ "id": "feature_synthesis_degradation_ss", "name": "feature synthesis degradation ss", "description": "Model: feature_synthesis_degradation_ss.bngl", - "path": "Contributed/BNGPlayground_Examples/feature-demos/featuresynthesisdegradationss/feature_synthesis_degradation_ss.bngl", + "path": "Examples/feature-demos/featuresynthesisdegradationss/feature_synthesis_degradation_ss.bngl", "file": "feature_synthesis_degradation_ss.bngl", "tags": [ "feature", @@ -4524,7 +4524,7 @@ "id": "fgf-signaling-pathway", "name": "fgf signaling pathway", "description": "FGF Signaling: FGFR dimerization and FRS2-Ras/PI3K relay.", - "path": "Contributed/BNGPlayground_Examples/biology/fgfsignalingpathway/fgf-signaling-pathway.bngl", + "path": "Examples/biology/fgfsignalingpathway/fgf-signaling-pathway.bngl", "file": "fgf-signaling-pathway.bngl", "tags": [ "fgf", @@ -4654,7 +4654,7 @@ "id": "free_missing", "name": "free missing", "description": "Original values used to generate parabola.exp", - "path": "PyBioNetGen/tests/freemissing/free_missing.bngl", + "path": "Published/PyBioNetGen/tests/freemissing/free_missing.bngl", "file": "free_missing.bngl", "tags": [ "free", @@ -4782,7 +4782,7 @@ "id": "gas6-axl-signaling", "name": "gas6 axl signaling", "description": "GAS6/AXL Signaling: AKT activation and SOCS feedback.", - "path": "Contributed/BNGPlayground_Examples/biology/gas6axlsignaling/gas6-axl-signaling.bngl", + "path": "Examples/biology/gas6axlsignaling/gas6-axl-signaling.bngl", "file": "gas6-axl-signaling.bngl", "tags": [ "gas6", @@ -4803,7 +4803,7 @@ "id": "gene-expression-toggle", "name": "gene expression toggle", "description": "Kinetic Parameters", - "path": "Contributed/BNGPlayground_Examples/biology/geneexpressiontoggle/gene-expression-toggle.bngl", + "path": "Examples/biology/geneexpressiontoggle/gene-expression-toggle.bngl", "file": "gene-expression-toggle.bngl", "tags": [ "gene", @@ -4822,7 +4822,7 @@ "id": "genetic_bistability_energy", "name": "genetic bistability energy", "description": "Model: genetic_bistability_energy.bngl", - "path": "Contributed/BNGPlayground_Examples/genetics/geneticbistabilityenergy/genetic_bistability_energy.bngl", + "path": "Examples/genetics/geneticbistabilityenergy/genetic_bistability_energy.bngl", "file": "genetic_bistability_energy.bngl", "tags": [ "genetic", @@ -4843,7 +4843,7 @@ "id": "genetic_dna_replication_stochastic", "name": "genetic dna replication stochastic", "description": "Model: genetic_dna_replication_stochastic.bngl", - "path": "Contributed/BNGPlayground_Examples/genetics/geneticdnareplicationstochastic/genetic_dna_replication_stochastic.bngl", + "path": "Examples/genetics/geneticdnareplicationstochastic/genetic_dna_replication_stochastic.bngl", "file": "genetic_dna_replication_stochastic.bngl", "tags": [ "genetic", @@ -4864,7 +4864,7 @@ "id": "genetic_goodwin_oscillator", "name": "genetic goodwin oscillator", "description": "Model: genetic_goodwin_oscillator.bngl", - "path": "Contributed/BNGPlayground_Examples/genetics/geneticgoodwinoscillator/genetic_goodwin_oscillator.bngl", + "path": "Examples/genetics/geneticgoodwinoscillator/genetic_goodwin_oscillator.bngl", "file": "genetic_goodwin_oscillator.bngl", "tags": [ "genetic", @@ -4885,7 +4885,7 @@ "id": "genetic_translation_kinetics", "name": "genetic translation kinetics", "description": "Model: genetic_translation_kinetics.bngl", - "path": "Contributed/BNGPlayground_Examples/genetics/genetictranslationkinetics/genetic_translation_kinetics.bngl", + "path": "Examples/genetics/genetictranslationkinetics/genetic_translation_kinetics.bngl", "file": "genetic_translation_kinetics.bngl", "tags": [ "genetic", @@ -4905,7 +4905,7 @@ "id": "genetic_turing_pattern_1d", "name": "genetic turing pattern 1d", "description": "Model: genetic_turing_pattern_1d.bngl", - "path": "Contributed/BNGPlayground_Examples/genetics/geneticturingpattern1d/genetic_turing_pattern_1d.bngl", + "path": "Examples/genetics/geneticturingpattern1d/genetic_turing_pattern_1d.bngl", "file": "genetic_turing_pattern_1d.bngl", "tags": [ "genetic", @@ -4960,7 +4960,7 @@ "id": "glioblastoma-egfrviii-signaling", "name": "glioblastoma egfrviii signaling", "description": "EGFRvIII in Glioblastoma: Constitutive AKT drive and escape from decay.", - "path": "Contributed/BNGPlayground_Examples/biology/glioblastomaegfrviiisignaling/glioblastoma-egfrviii-signaling.bngl", + "path": "Examples/biology/glioblastomaegfrviiisignaling/glioblastoma-egfrviii-signaling.bngl", "file": "glioblastoma-egfrviii-signaling.bngl", "tags": [ "glioblastoma", @@ -4981,7 +4981,7 @@ "id": "glycolysis-branch-point", "name": "glycolysis branch point", "description": "BioNetGen model: glycolysis branch point", - "path": "Contributed/BNGPlayground_Examples/biology/glycolysisbranchpoint/glycolysis-branch-point.bngl", + "path": "Examples/biology/glycolysisbranchpoint/glycolysis-branch-point.bngl", "file": "glycolysis-branch-point.bngl", "tags": [ "glycolysis", @@ -5001,7 +5001,7 @@ "id": "gm_game_of_life", "name": "gm game of life", "description": "Model: gm_game_of_life.bngl", - "path": "Contributed/BNGPlayground_Examples/generative/gmgameoflife/gm_game_of_life.bngl", + "path": "Examples/generative/gmgameoflife/gm_game_of_life.bngl", "file": "gm_game_of_life.bngl", "tags": [ "gm", @@ -5020,7 +5020,7 @@ "id": "gm_ray_marcher", "name": "gm ray marcher", "description": "Ray Marching Renderer in BNGL", - "path": "Contributed/BNGPlayground_Examples/generative/gmraymarcher/gm_ray_marcher.bngl", + "path": "Examples/generative/gmraymarcher/gm_ray_marcher.bngl", "file": "gm_ray_marcher.bngl", "tags": [ "gm", @@ -5081,7 +5081,7 @@ "id": "gpcr-desensitization-arrestin", "name": "gpcr desensitization arrestin", "description": "GPCR Desensitization: Arrestin-mediated spatial sequestration.", - "path": "Contributed/BNGPlayground_Examples/biology/gpcrdesensitizationarrestin/gpcr-desensitization-arrestin.bngl", + "path": "Examples/biology/gpcrdesensitizationarrestin/gpcr-desensitization-arrestin.bngl", "file": "gpcr-desensitization-arrestin.bngl", "tags": [ "gpcr", @@ -5431,7 +5431,7 @@ "id": "Haugh2b", "name": "Haugh2b", "description": "R(KD,Y1~U,Y2~U) 1.00", - "path": "Contributed/BNGPlayground_Validation/Haugh2b/Haugh2b.bngl", + "path": "Tutorials/Haugh2b/Haugh2b.bngl", "file": "Haugh2b.bngl", "tags": [ "validation", @@ -5452,7 +5452,7 @@ "id": "hedgehog-signaling-pathway", "name": "hedgehog signaling pathway", "description": "Hedgehog (Hh) Signaling: Ciliary translocation and Gli processing.", - "path": "Contributed/BNGPlayground_Examples/biology/hedgehogsignalingpathway/hedgehog-signaling-pathway.bngl", + "path": "Examples/biology/hedgehogsignalingpathway/hedgehog-signaling-pathway.bngl", "file": "hedgehog-signaling-pathway.bngl", "tags": [ "hedgehog", @@ -5474,7 +5474,7 @@ "id": "heise", "name": "heise", "description": "Validate state inheritance in a symmetric context", - "path": "Contributed/BNGPlayground_Validation/heise/heise.bngl", + "path": "Tutorials/heise/heise.bngl", "file": "heise.bngl", "tags": [ "validation", @@ -5495,7 +5495,7 @@ "id": "hematopoietic-growth-factor", "name": "hematopoietic growth factor", "description": "Kinetic Parameters", - "path": "Contributed/BNGPlayground_Examples/biology/hematopoieticgrowthfactor/hematopoietic-growth-factor.bngl", + "path": "Examples/biology/hematopoieticgrowthfactor/hematopoietic-growth-factor.bngl", "file": "hematopoietic-growth-factor.bngl", "tags": [ "hematopoietic", @@ -5534,7 +5534,7 @@ "id": "hif1a_degradation_loop", "name": "hif1a degradation loop", "description": "HIF-1alpha Oxygen Sensing: Hydroxylation and VHL-mediated decay.", - "path": "Contributed/BNGPlayground_Examples/biology/hif1adegradationloop/hif1a_degradation_loop.bngl", + "path": "Examples/biology/hif1adegradationloop/hif1a_degradation_loop.bngl", "file": "hif1a_degradation_loop.bngl", "tags": [ "hif1a", @@ -5739,7 +5739,7 @@ "id": "hypoxia-response-signaling", "name": "hypoxia response signaling", "description": "Rate Constants", - "path": "Contributed/BNGPlayground_Examples/biology/hypoxiaresponsesignaling/hypoxia-response-signaling.bngl", + "path": "Examples/biology/hypoxiaresponsesignaling/hypoxia-response-signaling.bngl", "file": "hypoxia-response-signaling.bngl", "tags": [ "hypoxia", @@ -5759,7 +5759,7 @@ "id": "IGF1R_Model_receptor_activation_bnf", "name": "IGF1R Model receptor activation bnf", "description": "Author: William S. Hlavacek", - "path": "PyBioNetGen/core/IGF1RModelreceptoractivationbnf/IGF1R_Model_receptor_activation_bnf.bngl", + "path": "Published/PyBioNetGen/core/IGF1RModelreceptoractivationbnf/IGF1R_Model_receptor_activation_bnf.bngl", "file": "IGF1R_Model_receptor_activation_bnf.bngl", "tags": [ "igf1r", @@ -5779,7 +5779,7 @@ "id": "il1b-signaling", "name": "il1b signaling", "description": "IL-1beta Signaling: MyD88/IRAK assembly and NF-kB translocation.", - "path": "Contributed/BNGPlayground_Examples/biology/il1bsignaling/il1b-signaling.bngl", + "path": "Examples/biology/il1bsignaling/il1b-signaling.bngl", "file": "il1b-signaling.bngl", "tags": [ "il1b", @@ -5799,7 +5799,7 @@ "id": "il6-jak-stat-pathway", "name": "il6 jak stat pathway", "description": "IL-6 Signaling: gp130 hexamerization and pSTAT3 import.", - "path": "Contributed/BNGPlayground_Examples/biology/il6jakstatpathway/il6-jak-stat-pathway.bngl", + "path": "Examples/biology/il6jakstatpathway/il6-jak-stat-pathway.bngl", "file": "il6-jak-stat-pathway.bngl", "tags": [ "il6", @@ -5820,7 +5820,7 @@ "id": "immune-synapse-formation", "name": "immune synapse formation", "description": "Kinetic Parameters", - "path": "Contributed/BNGPlayground_Examples/biology/immunesynapseformation/immune-synapse-formation.bngl", + "path": "Examples/biology/immunesynapseformation/immune-synapse-formation.bngl", "file": "immune-synapse-formation.bngl", "tags": [ "immune", @@ -5859,7 +5859,7 @@ "id": "inflammasome-activation", "name": "inflammasome activation", "description": "Rate Constants", - "path": "Contributed/BNGPlayground_Examples/biology/inflammasomeactivation/inflammasome-activation.bngl", + "path": "Examples/biology/inflammasomeactivation/inflammasome-activation.bngl", "file": "inflammasome-activation.bngl", "tags": [ "inflammasome", @@ -5923,7 +5923,7 @@ "id": "inositol-phosphate-metabolism", "name": "inositol phosphate metabolism", "description": "Inositol Phosphate (IP) Metabolism: PLC signaling and branch points.", - "path": "Contributed/BNGPlayground_Examples/biology/inositolphosphatemetabolism/inositol-phosphate-metabolism.bngl", + "path": "Examples/biology/inositolphosphatemetabolism/inositol-phosphate-metabolism.bngl", "file": "inositol-phosphate-metabolism.bngl", "tags": [ "inositol", @@ -5945,7 +5945,7 @@ "id": "insulin-glucose-homeostasis", "name": "insulin glucose homeostasis", "description": "Insulin-Glucose: Compartmentalized transport.", - "path": "Contributed/BNGPlayground_Examples/biology/insulinglucosehomeostasis/insulin-glucose-homeostasis.bngl", + "path": "Examples/biology/insulinglucosehomeostasis/insulin-glucose-homeostasis.bngl", "file": "insulin-glucose-homeostasis.bngl", "tags": [ "insulin", @@ -5965,7 +5965,7 @@ "id": "interferon-signaling", "name": "interferon signaling", "description": "Rate Constants", - "path": "Contributed/BNGPlayground_Examples/biology/interferonsignaling/interferon-signaling.bngl", + "path": "Examples/biology/interferonsignaling/interferon-signaling.bngl", "file": "interferon-signaling.bngl", "tags": [ "interferon", @@ -6003,7 +6003,7 @@ "id": "ire1a-xbp1-er-stress", "name": "ire1a xbp1 er stress", "description": "IRE1a/XBP1 ER Stress: Chaperone buffering and mRNA decay (RIDD).", - "path": "Contributed/BNGPlayground_Examples/biology/ire1axbp1erstress/ire1a-xbp1-er-stress.bngl", + "path": "Examples/biology/ire1axbp1erstress/ire1a-xbp1-er-stress.bngl", "file": "ire1a-xbp1-er-stress.bngl", "tags": [ "ire1a", @@ -6025,7 +6025,7 @@ "id": "issue_198_short", "name": "issue_198_short", "description": "No description available", - "path": "Contributed/BNGPlayground_Validation/issue198short/issue_198_short.bngl", + "path": "Tutorials/issue198short/issue_198_short.bngl", "file": "issue_198_short.bngl", "tags": [ "validation", @@ -6102,7 +6102,7 @@ "id": "jak-stat-cytokine-signaling", "name": "jak stat cytokine signaling", "description": "Rate Constants", - "path": "Contributed/BNGPlayground_Examples/biology/jakstatcytokinesignaling/jak-stat-cytokine-signaling.bngl", + "path": "Examples/biology/jakstatcytokinesignaling/jak-stat-cytokine-signaling.bngl", "file": "jak-stat-cytokine-signaling.bngl", "tags": [ "jak", @@ -6163,7 +6163,7 @@ "id": "jnk-mapk-signaling", "name": "jnk mapk signaling", "description": "JNK MAPK Signaling: Scaffold-mediated activation and feedback.", - "path": "Contributed/BNGPlayground_Examples/biology/jnkmapksignaling/jnk-mapk-signaling.bngl", + "path": "Examples/biology/jnkmapksignaling/jnk-mapk-signaling.bngl", "file": "jnk-mapk-signaling.bngl", "tags": [ "jnk", @@ -6305,7 +6305,7 @@ "id": "Kiefhaber_emodel", "name": "Kiefhaber_emodel", "description": "Allow molar units to be used for bimolecular rate constants", - "path": "Contributed/BNGPlayground_Validation/Kiefhaberemodel/Kiefhaber_emodel.bngl", + "path": "Tutorials/Kiefhaberemodel/Kiefhaber_emodel.bngl", "file": "Kiefhaber_emodel.bngl", "tags": [ "validation", @@ -6363,7 +6363,7 @@ "id": "kir-channel-regulation", "name": "kir channel regulation", "description": "Kir Channel Regulation: PIP2 modulation and G-protein potentiation.", - "path": "Contributed/BNGPlayground_Examples/biology/kirchannelregulation/kir-channel-regulation.bngl", + "path": "Examples/biology/kirchannelregulation/kir-channel-regulation.bngl", "file": "kir-channel-regulation.bngl", "tags": [ "kir", @@ -6441,7 +6441,7 @@ "id": "Korwek_2023", "name": "Korwek_2023", "description": "This BioNetGen file features the article:", - "path": "Contributed/BNGPlayground_Validation/Korwek2023/Korwek_2023.bngl", + "path": "Published/Korwek2023/Korwek_2023.bngl", "file": "Korwek_2023.bngl", "tags": [ "validation", @@ -6505,7 +6505,7 @@ "id": "l-type-calcium-channel-dynamics", "name": "l type calcium channel dynamics", "description": "L-type Calcium Channel: Voltage gating and CDI (Calcium-dependent inactivation).", - "path": "Contributed/BNGPlayground_Examples/biology/ltypecalciumchanneldynamics/l-type-calcium-channel-dynamics.bngl", + "path": "Examples/biology/ltypecalciumchanneldynamics/l-type-calcium-channel-dynamics.bngl", "file": "l-type-calcium-channel-dynamics.bngl", "tags": [ "l", @@ -6528,7 +6528,7 @@ "id": "lac-operon-regulation", "name": "lac operon regulation", "description": "Kinetic Parameters", - "path": "Contributed/BNGPlayground_Examples/biology/lacoperonregulation/lac-operon-regulation.bngl", + "path": "Examples/biology/lacoperonregulation/lac-operon-regulation.bngl", "file": "lac-operon-regulation.bngl", "tags": [ "lac", @@ -6849,7 +6849,7 @@ "id": "LilyIgE", "name": "LilyIgE", "description": "An example from a real application", - "path": "PyBioNetGen/tests/LilyIgE/LilyIgE.bngl", + "path": "Published/PyBioNetGen/tests/LilyIgE/LilyIgE.bngl", "file": "LilyIgE.bngl", "tags": [ "lilyige", @@ -6966,7 +6966,7 @@ "id": "lipid-mediated-pip3-signaling", "name": "lipid mediated pip3 signaling", "description": "Kinetic Parameters", - "path": "Contributed/BNGPlayground_Examples/biology/lipidmediatedpip3signaling/lipid-mediated-pip3-signaling.bngl", + "path": "Examples/biology/lipidmediatedpip3signaling/lipid-mediated-pip3-signaling.bngl", "file": "lipid-mediated-pip3-signaling.bngl", "tags": [ "lipid", @@ -7045,7 +7045,7 @@ "id": "localfunc", "name": "localfunc", "description": "Test local function expansion", - "path": "Contributed/BNGPlayground_Validation/localfunc/localfunc.bngl", + "path": "Tutorials/localfunc/localfunc.bngl", "file": "localfunc.bngl", "tags": [ "validation", @@ -7382,7 +7382,7 @@ "id": "mapk-signaling-cascade", "name": "mapk signaling cascade", "description": "Rate Constants", - "path": "Contributed/BNGPlayground_Examples/biology/mapksignalingcascade/mapk-signaling-cascade.bngl", + "path": "Examples/biology/mapksignalingcascade/mapk-signaling-cascade.bngl", "file": "mapk-signaling-cascade.bngl", "tags": [ "mapk", @@ -7727,7 +7727,7 @@ "id": "meta_formal_game_theory", "name": "meta formal game theory", "description": "Model: meta_formal_game_theory.bngl", - "path": "Contributed/BNGPlayground_Examples/meta/metaformalgametheory/meta_formal_game_theory.bngl", + "path": "Examples/meta/metaformalgametheory/meta_formal_game_theory.bngl", "file": "meta_formal_game_theory.bngl", "tags": [ "meta", @@ -7750,7 +7750,7 @@ "id": "meta_formal_molecular_clock", "name": "meta formal molecular clock", "description": "Model: meta_formal_molecular_clock.bngl", - "path": "Contributed/BNGPlayground_Examples/meta/metaformalmolecularclock/meta_formal_molecular_clock.bngl", + "path": "Examples/meta/metaformalmolecularclock/meta_formal_molecular_clock.bngl", "file": "meta_formal_molecular_clock.bngl", "tags": [ "meta", @@ -7772,7 +7772,7 @@ "id": "meta_formal_petri_net", "name": "meta formal petri net", "description": "Model: meta_formal_petri_net.bngl", - "path": "Contributed/BNGPlayground_Examples/meta/metaformalpetrinet/meta_formal_petri_net.bngl", + "path": "Examples/meta/metaformalpetrinet/meta_formal_petri_net.bngl", "file": "meta_formal_petri_net.bngl", "tags": [ "meta", @@ -7812,7 +7812,7 @@ "id": "michaelis-menten-kinetics", "name": "michaelis menten kinetics", "description": "Kinetic Constants", - "path": "Contributed/BNGPlayground_Examples/biology/michaelismentenkinetics/michaelis-menten-kinetics.bngl", + "path": "Examples/biology/michaelismentenkinetics/michaelis-menten-kinetics.bngl", "file": "michaelis-menten-kinetics.bngl", "tags": [ "michaelis", @@ -7853,7 +7853,7 @@ "id": "michment", "name": "michment", "description": "Michaelis Menten", - "path": "Contributed/BNGPlayground_Validation/michment/michment.bngl", + "path": "Tutorials/michment/michment.bngl", "file": "michment.bngl", "tags": [ "validation", @@ -7872,7 +7872,7 @@ "id": "michment_cont", "name": "michment_cont", "description": "Michaelis Menten Continue", - "path": "Contributed/BNGPlayground_Validation/michmentcont/michment_cont.bngl", + "path": "Tutorials/michmentcont/michment_cont.bngl", "file": "michment_cont.bngl", "tags": [ "validation", @@ -7929,7 +7929,7 @@ "id": "ml_gradient_descent", "name": "ml gradient descent", "description": "Gradient Descent Optimizer in BNGL", - "path": "Contributed/BNGPlayground_Examples/ml/mlgradientdescent/ml_gradient_descent.bngl", + "path": "Examples/ml/mlgradientdescent/ml_gradient_descent.bngl", "file": "ml_gradient_descent.bngl", "tags": [ "ml", @@ -7951,7 +7951,7 @@ "id": "ml_hopfield", "name": "ml hopfield", "description": "Model: ml_hopfield.bngl", - "path": "Contributed/BNGPlayground_Examples/ml/mlhopfield/ml_hopfield.bngl", + "path": "Examples/ml/mlhopfield/ml_hopfield.bngl", "file": "ml_hopfield.bngl", "tags": [ "ml", @@ -7972,7 +7972,7 @@ "id": "ml_kmeans", "name": "ml kmeans", "description": "Model: ml_kmeans.bngl", - "path": "Contributed/BNGPlayground_Examples/ml/mlkmeans/ml_kmeans.bngl", + "path": "Examples/ml/mlkmeans/ml_kmeans.bngl", "file": "ml_kmeans.bngl", "tags": [ "ml", @@ -7992,7 +7992,7 @@ "id": "ml_q_learning", "name": "ml q learning", "description": "Q-Learning Agent in BNGL", - "path": "Contributed/BNGPlayground_Examples/ml/mlqlearning/ml_q_learning.bngl", + "path": "Examples/ml/mlqlearning/ml_q_learning.bngl", "file": "ml_q_learning.bngl", "tags": [ "ml", @@ -8014,7 +8014,7 @@ "id": "ml_svm", "name": "ml svm", "description": "Model: ml_svm.bngl", - "path": "Contributed/BNGPlayground_Examples/ml/mlsvm/ml_svm.bngl", + "path": "Examples/ml/mlsvm/ml_svm.bngl", "file": "ml_svm.bngl", "tags": [ "ml", @@ -8053,7 +8053,7 @@ "id": "model", "name": "model", "description": "filename: model.bngl", - "path": "PyBioNetGen/core/model/model.bngl", + "path": "Published/PyBioNetGen/core/model/model.bngl", "file": "model.bngl", "tags": [ "model", @@ -8075,7 +8075,7 @@ "id": "model", "name": "model", "description": "A model of IgE receptor signaling", - "path": "PyBioNetGen/core/model_Degranulation_aMCMC/model.bngl", + "path": "Published/PyBioNetGen/core/model_Degranulation_aMCMC/model.bngl", "file": "model.bngl", "tags": [ "model", @@ -8097,7 +8097,7 @@ "id": "model_tofit", "name": "model tofit", "description": "A model of IgE receptor signaling", - "path": "PyBioNetGen/core/modeltofit/model_tofit.bngl", + "path": "Published/PyBioNetGen/core/modeltofit/model_tofit.bngl", "file": "model_tofit.bngl", "tags": [ "model", @@ -8219,7 +8219,7 @@ "id": "Motivating_example", "name": "Motivating_example", "description": "Signal Transduction with receptor internalization", - "path": "Contributed/BNGPlayground_Validation/Motivatingexample/Motivating_example.bngl", + "path": "Tutorials/Motivatingexample/Motivating_example.bngl", "file": "Motivating_example.bngl", "tags": [ "validation", @@ -8244,7 +8244,7 @@ "id": "Motivating_example_cBNGL", "name": "Motivating_example_cBNGL", "description": "Signal transduction with receptor internalization", - "path": "Contributed/BNGPlayground_Validation/MotivatingexamplecBNGL/Motivating_example_cBNGL.bngl", + "path": "Tutorials/MotivatingexamplecBNGL/Motivating_example_cBNGL.bngl", "file": "Motivating_example_cBNGL.bngl", "tags": [ "validation", @@ -8270,7 +8270,7 @@ "id": "motor", "name": "motor", "description": "Motor protein", - "path": "Contributed/BNGPlayground_Validation/motor/motor.bngl", + "path": "Tutorials/motor/motor.bngl", "file": "motor.bngl", "tags": [ "validation", @@ -8325,7 +8325,7 @@ "id": "mt_arithmetic_compiler", "name": "mt arithmetic compiler", "description": "Model: mt_arithmetic_compiler.bngl", - "path": "Contributed/BNGPlayground_Examples/meta/mtarithmeticcompiler/mt_arithmetic_compiler.bngl", + "path": "Examples/meta/mtarithmeticcompiler/mt_arithmetic_compiler.bngl", "file": "mt_arithmetic_compiler.bngl", "tags": [ "mt", @@ -8345,7 +8345,7 @@ "id": "mt_bngl_interpreter", "name": "mt bngl interpreter", "description": "Model: mt_bngl_interpreter.bngl", - "path": "Contributed/BNGPlayground_Examples/meta/mtbnglinterpreter/mt_bngl_interpreter.bngl", + "path": "Examples/meta/mtbnglinterpreter/mt_bngl_interpreter.bngl", "file": "mt_bngl_interpreter.bngl", "tags": [ "mt", @@ -8367,7 +8367,7 @@ "id": "mt_music_sequencer", "name": "mt music sequencer", "description": "Music Sequencer / Chord Synthesizer in BNGL", - "path": "Contributed/BNGPlayground_Examples/meta/mtmusicsequencer/mt_music_sequencer.bngl", + "path": "Examples/meta/mtmusicsequencer/mt_music_sequencer.bngl", "file": "mt_music_sequencer.bngl", "tags": [ "mt", @@ -8392,7 +8392,7 @@ "id": "mt_pascal_triangle", "name": "mt pascal triangle", "description": "Model: mt_pascal_triangle.bngl", - "path": "Contributed/BNGPlayground_Examples/meta/mtpascaltriangle/mt_pascal_triangle.bngl", + "path": "Examples/meta/mtpascaltriangle/mt_pascal_triangle.bngl", "file": "mt_pascal_triangle.bngl", "tags": [ "mt", @@ -8410,7 +8410,7 @@ "id": "mt_quine", "name": "mt quine", "description": "Model: mt_quine.bngl", - "path": "Contributed/BNGPlayground_Examples/meta/mtquine/mt_quine.bngl", + "path": "Examples/meta/mtquine/mt_quine.bngl", "file": "mt_quine.bngl", "tags": [ "mt", @@ -8428,7 +8428,7 @@ "id": "mtor-signaling", "name": "mtor signaling", "description": "mTOR Signaling Pathway", - "path": "Contributed/BNGPlayground_Examples/biology/mtorsignaling/mtor-signaling.bngl", + "path": "Examples/biology/mtorsignaling/mtor-signaling.bngl", "file": "mtor-signaling.bngl", "tags": [ "mtor", @@ -8448,7 +8448,7 @@ "id": "mtorc2-signaling", "name": "mtorc2 signaling", "description": "mTORC2 signaling regulates cell survival and growth via AKT and SGK1.", - "path": "Contributed/BNGPlayground_Examples/biology/mtorc2signaling/mtorc2-signaling.bngl", + "path": "Examples/biology/mtorc2signaling/mtorc2-signaling.bngl", "file": "mtorc2-signaling.bngl", "tags": [ "mtorc2", @@ -8528,7 +8528,7 @@ "id": "mwc", "name": "mwc", "description": "Monod-Wyman-Changeux model", - "path": "Contributed/BNGPlayground_Validation/mwc/mwc.bngl", + "path": "Tutorials/mwc/mwc.bngl", "file": "mwc.bngl", "tags": [ "validation", @@ -8548,7 +8548,7 @@ "id": "myogenic-differentiation", "name": "myogenic differentiation", "description": "Myogenic Differentiation", - "path": "Contributed/BNGPlayground_Examples/biology/myogenicdifferentiation/myogenic-differentiation.bngl", + "path": "Examples/biology/myogenicdifferentiation/myogenic-differentiation.bngl", "file": "myogenic-differentiation.bngl", "tags": [ "myogenic", @@ -8567,7 +8567,7 @@ "id": "Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC", "name": "Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC", "description": "Runtime-only BNGL model migrated from public/models: Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC", - "path": "Contributed/BNGPlayground_PublicRuntime/MyrtleBeachConwayNorthMyrtleBeachSCNC/Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC.bngl", + "path": "Published/MyrtleBeachConwayNorthMyrtleBeachSCNC/Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC.bngl", "file": "Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC.bngl", "tags": [ "myrtle", @@ -8647,7 +8647,7 @@ "id": "negative-feedback-loop", "name": "negative feedback loop", "description": "Negative Feedback Loop", - "path": "Contributed/BNGPlayground_Examples/biology/negativefeedbackloop/negative-feedback-loop.bngl", + "path": "Examples/biology/negativefeedbackloop/negative-feedback-loop.bngl", "file": "negative-feedback-loop.bngl", "tags": [ "negative", @@ -8667,7 +8667,7 @@ "id": "neurotransmitter-release", "name": "neurotransmitter release", "description": "Neurotransmitter Release", - "path": "Contributed/BNGPlayground_Examples/biology/neurotransmitterrelease/neurotransmitter-release.bngl", + "path": "Examples/biology/neurotransmitterrelease/neurotransmitter-release.bngl", "file": "neurotransmitter-release.bngl", "tags": [ "neurotransmitter", @@ -8741,7 +8741,7 @@ "id": "nfkb", "name": "nfkb", "description": "NF-kB signaling pathway", - "path": "Contributed/BNGPlayground_Validation/nfkb/nfkb.bngl", + "path": "Tutorials/nfkb/nfkb.bngl", "file": "nfkb.bngl", "tags": [ "validation", @@ -8764,7 +8764,7 @@ "id": "nfkb_illustrating_protocols", "name": "nfkb_illustrating_protocols", "description": "NF-kB signaling pathway", - "path": "Contributed/BNGPlayground_Validation/nfkbillustratingprotocols/nfkb_illustrating_protocols.bngl", + "path": "Tutorials/nfkbillustratingprotocols/nfkb_illustrating_protocols.bngl", "file": "nfkb_illustrating_protocols.bngl", "tags": [ "validation", @@ -8789,7 +8789,7 @@ "id": "nfkb-feedback", "name": "nfkb feedback", "description": "TNFalpha-induced NF-kB signaling with IkappaB-alpha feedback.", - "path": "Contributed/BNGPlayground_Examples/biology/nfkbfeedback/nfkb-feedback.bngl", + "path": "Examples/biology/nfkbfeedback/nfkb-feedback.bngl", "file": "nfkb-feedback.bngl", "tags": [ "nfkb", @@ -8808,7 +8808,7 @@ "id": "NFmodel", "name": "NFmodel", "description": "BioNetGen model: NFmodel", - "path": "PyBioNetGen/tests/NFmodel/NFmodel.bngl", + "path": "Published/PyBioNetGen/tests/NFmodel/NFmodel.bngl", "file": "NFmodel.bngl", "tags": [ "nfmodel", @@ -8826,7 +8826,7 @@ "id": "nfsim_aggregation_gelation", "name": "nfsim aggregation gelation", "description": "Model: nfsim_aggregation_gelation.bngl", - "path": "Contributed/BNGPlayground_Examples/nfsim/nfsimaggregationgelation/nfsim_aggregation_gelation.bngl", + "path": "Examples/nfsim/nfsimaggregationgelation/nfsim_aggregation_gelation.bngl", "file": "nfsim_aggregation_gelation.bngl", "tags": [ "nfsim", @@ -8844,7 +8844,7 @@ "id": "nfsim_coarse_graining", "name": "nfsim coarse graining", "description": "Model: nfsim_coarse_graining.bngl", - "path": "Contributed/BNGPlayground_Examples/nfsim/nfsimcoarsegraining/nfsim_coarse_graining.bngl", + "path": "Examples/nfsim/nfsimcoarsegraining/nfsim_coarse_graining.bngl", "file": "nfsim_coarse_graining.bngl", "tags": [ "nfsim", @@ -8862,7 +8862,7 @@ "id": "nfsim_dynamic_compartments", "name": "nfsim dynamic compartments", "description": "Model: nfsim_dynamic_compartments.bngl", - "path": "Contributed/BNGPlayground_Examples/nfsim/nfsimdynamiccompartments/nfsim_dynamic_compartments.bngl", + "path": "Examples/nfsim/nfsimdynamiccompartments/nfsim_dynamic_compartments.bngl", "file": "nfsim_dynamic_compartments.bngl", "tags": [ "nfsim", @@ -8882,7 +8882,7 @@ "id": "nfsim_hybrid_particle_field", "name": "nfsim hybrid particle field", "description": "Model: nfsim_hybrid_particle_field.bngl", - "path": "Contributed/BNGPlayground_Examples/nfsim/nfsimhybridparticlefield/nfsim_hybrid_particle_field.bngl", + "path": "Examples/nfsim/nfsimhybridparticlefield/nfsim_hybrid_particle_field.bngl", "file": "nfsim_hybrid_particle_field.bngl", "tags": [ "nfsim", @@ -8900,7 +8900,7 @@ "id": "nfsim_ring_closure_polymer", "name": "nfsim ring closure polymer", "description": "Model: nfsim_ring_closure_polymer.bngl", - "path": "Contributed/BNGPlayground_Examples/nfsim/nfsimringclosurepolymer/nfsim_ring_closure_polymer.bngl", + "path": "Examples/nfsim/nfsimringclosurepolymer/nfsim_ring_closure_polymer.bngl", "file": "nfsim_ring_closure_polymer.bngl", "tags": [ "nfsim", @@ -8939,7 +8939,7 @@ "id": "nn_xor", "name": "nn xor", "description": "Model: nn_xor.bngl", - "path": "Contributed/BNGPlayground_Examples/ml/nnxor/nn_xor.bngl", + "path": "Examples/ml/nnxor/nn_xor.bngl", "file": "nn_xor.bngl", "tags": [ "nn", @@ -8962,7 +8962,7 @@ "id": "no_frees", "name": "no frees", "description": "Original values used to generate parabola.exp", - "path": "PyBioNetGen/tests/nofrees/no_frees.bngl", + "path": "Published/PyBioNetGen/tests/nofrees/no_frees.bngl", "file": "no_frees.bngl", "tags": [ "no", @@ -8982,7 +8982,7 @@ "id": "no_generate_network", "name": "no generate network", "description": "Original values used to generate parabola.exp", - "path": "PyBioNetGen/tests/nogeneratenetwork/no_generate_network.bngl", + "path": "Published/PyBioNetGen/tests/nogeneratenetwork/no_generate_network.bngl", "file": "no_generate_network.bngl", "tags": [ "no", @@ -9002,7 +9002,7 @@ "id": "no_suffix", "name": "no suffix", "description": "Original values used to generate parabola.exp", - "path": "PyBioNetGen/tests/nosuffix/no_suffix.bngl", + "path": "Published/PyBioNetGen/tests/nosuffix/no_suffix.bngl", "file": "no_suffix.bngl", "tags": [ "no", @@ -9022,7 +9022,7 @@ "id": "no-cgmp-signaling", "name": "no cgmp signaling", "description": "Nitric Oxide (NO) / cGMP signaling pathway.", - "path": "Contributed/BNGPlayground_Examples/biology/nocgmpsignaling/no-cgmp-signaling.bngl", + "path": "Examples/biology/nocgmpsignaling/no-cgmp-signaling.bngl", "file": "no-cgmp-signaling.bngl", "tags": [ "no", @@ -9120,7 +9120,7 @@ "id": "notch-delta-lateral-inhibition", "name": "notch delta lateral inhibition", "description": "Notch-Delta Lateral Inhibition", - "path": "Contributed/BNGPlayground_Examples/biology/notchdeltalateralinhibition/notch-delta-lateral-inhibition.bngl", + "path": "Examples/biology/notchdeltalateralinhibition/notch-delta-lateral-inhibition.bngl", "file": "notch-delta-lateral-inhibition.bngl", "tags": [ "notch", @@ -9334,7 +9334,7 @@ "id": "oxidative-stress-response", "name": "oxidative stress response", "description": "Oxidative Stress Response (Keap1-Nrf2 Pathway)", - "path": "Contributed/BNGPlayground_Examples/biology/oxidativestressresponse/oxidative-stress-response.bngl", + "path": "Examples/biology/oxidativestressresponse/oxidative-stress-response.bngl", "file": "oxidative-stress-response.bngl", "tags": [ "oxidative", @@ -9373,7 +9373,7 @@ "id": "p38-mapk-signaling", "name": "p38 mapk signaling", "description": "p38 MAPK stress signaling cascade.", - "path": "Contributed/BNGPlayground_Examples/biology/p38mapksignaling/p38-mapk-signaling.bngl", + "path": "Examples/biology/p38mapksignaling/p38-mapk-signaling.bngl", "file": "p38-mapk-signaling.bngl", "tags": [ "p38", @@ -9393,7 +9393,7 @@ "id": "p53-mdm2-oscillator", "name": "p53 mdm2 oscillator", "description": "BioNetGen model: p53 mdm2 oscillator", - "path": "Contributed/BNGPlayground_Examples/biology/p53mdm2oscillator/p53-mdm2-oscillator.bngl", + "path": "Examples/biology/p53mdm2oscillator/p53-mdm2-oscillator.bngl", "file": "p53-mdm2-oscillator.bngl", "tags": [ "p53", @@ -9429,7 +9429,7 @@ "id": "parabola", "name": "parabola", "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", - "path": "PyBioNetGen/core/parabola/parabola.bngl", + "path": "Published/PyBioNetGen/core/parabola/parabola.bngl", "file": "parabola.bngl", "tags": [ "parabola", @@ -9449,7 +9449,7 @@ "id": "parabola", "name": "parabola", "description": "Original values used to generate parabola.exp", - "path": "PyBioNetGen/core/parabola_demo/parabola.bngl", + "path": "Published/PyBioNetGen/core/parabola_demo/parabola.bngl", "file": "parabola.bngl", "tags": [ "parabola", @@ -9468,7 +9468,7 @@ "id": "parabola", "name": "parabola", "description": "Original values used to generate parabola.exp", - "path": "PyBioNetGen/tests/parabola/parabola.bngl", + "path": "Published/PyBioNetGen/tests/parabola/parabola.bngl", "file": "parabola.bngl", "tags": [ "parabola", @@ -9488,7 +9488,7 @@ "id": "parabola", "name": "parabola", "description": "Original values used to generate parabola.exp", - "path": "PyBioNetGen/tests/parabola_bngl_files/parabola.bngl", + "path": "Published/PyBioNetGen/tests/parabola_bngl_files/parabola.bngl", "file": "parabola.bngl", "tags": [ "parabola", @@ -9507,7 +9507,7 @@ "id": "parabola", "name": "parabola", "description": "Original values used to generate parabola.exp", - "path": "PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/parabola.bngl", + "path": "Published/PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/parabola.bngl", "file": "parabola.bngl", "tags": [ "parabola", @@ -9526,7 +9526,7 @@ "id": "parabola_ground", "name": "parabola ground", "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", - "path": "PyBioNetGen/core/parabolaground/parabola_ground.bngl", + "path": "Published/PyBioNetGen/core/parabolaground/parabola_ground.bngl", "file": "parabola_ground.bngl", "tags": [ "parabola", @@ -9547,7 +9547,7 @@ "id": "parabola2", "name": "parabola2", "description": "A file for testing behavior with duplicate file names", - "path": "PyBioNetGen/tests/parabola2/parabola2.bngl", + "path": "Published/PyBioNetGen/tests/parabola2/parabola2.bngl", "file": "parabola2.bngl", "tags": [ "parabola2", @@ -9567,7 +9567,7 @@ "id": "ParamsEverywhere", "name": "ParamsEverywhere", "description": "An example from a real application", - "path": "PyBioNetGen/tests/ParamsEverywhere/ParamsEverywhere.bngl", + "path": "Published/PyBioNetGen/tests/ParamsEverywhere/ParamsEverywhere.bngl", "file": "ParamsEverywhere.bngl", "tags": [ "paramseverywhere", @@ -9585,7 +9585,7 @@ "id": "parp1-mediated-dna-repair", "name": "parp1 mediated dna repair", "description": "PARP1-mediated DNA damage sensing and repair.", - "path": "Contributed/BNGPlayground_Examples/biology/parp1mediateddnarepair/parp1-mediated-dna-repair.bngl", + "path": "Examples/biology/parp1mediateddnarepair/parp1-mediated-dna-repair.bngl", "file": "parp1-mediated-dna-repair.bngl", "tags": [ "parp1", @@ -9667,7 +9667,7 @@ "id": "ph_lorenz_attractor", "name": "ph lorenz attractor", "description": "Lorenz Attractor in BNGL", - "path": "Contributed/BNGPlayground_Examples/physics/phlorenzattractor/ph_lorenz_attractor.bngl", + "path": "Examples/physics/phlorenzattractor/ph_lorenz_attractor.bngl", "file": "ph_lorenz_attractor.bngl", "tags": [ "ph", @@ -9689,7 +9689,7 @@ "id": "ph_nbody_gravity", "name": "ph nbody gravity", "description": "Model: ph_nbody_gravity.bngl", - "path": "Contributed/BNGPlayground_Examples/physics/phnbodygravity/ph_nbody_gravity.bngl", + "path": "Examples/physics/phnbodygravity/ph_nbody_gravity.bngl", "file": "ph_nbody_gravity.bngl", "tags": [ "ph", @@ -9708,7 +9708,7 @@ "id": "ph_schrodinger", "name": "ph schrodinger", "description": "Model: ph_schrodinger.bngl", - "path": "Contributed/BNGPlayground_Examples/physics/phschrodinger/ph_schrodinger.bngl", + "path": "Examples/physics/phschrodinger/ph_schrodinger.bngl", "file": "ph_schrodinger.bngl", "tags": [ "ph", @@ -9725,7 +9725,7 @@ "id": "ph_wave_equation", "name": "ph wave equation", "description": "Model: ph_wave_equation.bngl", - "path": "Contributed/BNGPlayground_Examples/physics/phwaveequation/ph_wave_equation.bngl", + "path": "Examples/physics/phwaveequation/ph_wave_equation.bngl", "file": "ph_wave_equation.bngl", "tags": [ "ph", @@ -9802,7 +9802,7 @@ "id": "phosphorelay-chain", "name": "phosphorelay chain", "description": "BioNetGen model: phosphorelay chain", - "path": "Contributed/BNGPlayground_Examples/biology/phosphorelaychain/phosphorelay-chain.bngl", + "path": "Examples/biology/phosphorelaychain/phosphorelay-chain.bngl", "file": "phosphorelay-chain.bngl", "tags": [ "phosphorelay", @@ -9875,7 +9875,7 @@ "id": "platelet-activation", "name": "platelet activation", "description": "BioNetGen model: platelet activation", - "path": "Contributed/BNGPlayground_Examples/biology/plateletactivation/platelet-activation.bngl", + "path": "Examples/biology/plateletactivation/platelet-activation.bngl", "file": "platelet-activation.bngl", "tags": [ "platelet", @@ -9940,7 +9940,7 @@ "id": "polymer_fixed", "name": "polymer_fixed", "description": "Runtime-only BNGL model migrated from public/models: polymer_fixed", - "path": "Contributed/BNGPlayground_PublicRuntime/polymerfixed/polymer_fixed.bngl", + "path": "Tutorials/polymerfixed/polymer_fixed.bngl", "file": "polymer_fixed.bngl", "tags": [ "polymer", @@ -9956,7 +9956,7 @@ "id": "polynomial", "name": "polynomial", "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", - "path": "PyBioNetGen/core/polynomial/polynomial.bngl", + "path": "Published/PyBioNetGen/core/polynomial/polynomial.bngl", "file": "polynomial.bngl", "tags": [ "polynomial", @@ -9978,7 +9978,7 @@ "id": "polynomial", "name": "polynomial", "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", - "path": "PyBioNetGen/tests/polynomial/polynomial.bngl", + "path": "Published/PyBioNetGen/tests/polynomial/polynomial.bngl", "file": "polynomial.bngl", "tags": [ "polynomial", @@ -10000,7 +10000,7 @@ "id": "polynomial", "name": "polynomial", "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", - "path": "PyBioNetGen/tests/polynomial_full_tests_T6-check/polynomial.bngl", + "path": "Published/PyBioNetGen/tests/polynomial_full_tests_T6-check/polynomial.bngl", "file": "polynomial.bngl", "tags": [ "polynomial", @@ -10022,7 +10022,7 @@ "id": "polynomial_ground", "name": "polynomial ground", "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", - "path": "PyBioNetGen/core/polynomialground/polynomial_ground.bngl", + "path": "Published/PyBioNetGen/core/polynomialground/polynomial_ground.bngl", "file": "polynomial_ground.bngl", "tags": [ "polynomial", @@ -10153,7 +10153,7 @@ "id": "predator-prey-dynamics", "name": "predator prey dynamics", "description": "BioNetGen model: predator prey dynamics", - "path": "Contributed/BNGPlayground_Examples/biology/predatorpreydynamics/predator-prey-dynamics.bngl", + "path": "Examples/biology/predatorpreydynamics/predator-prey-dynamics.bngl", "file": "predator-prey-dynamics.bngl", "tags": [ "predator", @@ -10188,7 +10188,7 @@ "id": "process_actin_treadmilling", "name": "process actin treadmilling", "description": "Model: process_actin_treadmilling.bngl", - "path": "Contributed/BNGPlayground_Examples/processes/processactintreadmilling/process_actin_treadmilling.bngl", + "path": "Examples/processes/processactintreadmilling/process_actin_treadmilling.bngl", "file": "process_actin_treadmilling.bngl", "tags": [ "process", @@ -10207,7 +10207,7 @@ "id": "process_autophagy_flux", "name": "process autophagy flux", "description": "Model: process_autophagy_flux.bngl", - "path": "Contributed/BNGPlayground_Examples/processes/processautophagyflux/process_autophagy_flux.bngl", + "path": "Examples/processes/processautophagyflux/process_autophagy_flux.bngl", "file": "process_autophagy_flux.bngl", "tags": [ "process", @@ -10229,7 +10229,7 @@ "id": "process_cell_adhesion_strength", "name": "process cell adhesion strength", "description": "Model: process_cell_adhesion_strength.bngl", - "path": "Contributed/BNGPlayground_Examples/processes/processcelladhesionstrength/process_cell_adhesion_strength.bngl", + "path": "Examples/processes/processcelladhesionstrength/process_cell_adhesion_strength.bngl", "file": "process_cell_adhesion_strength.bngl", "tags": [ "process", @@ -10251,7 +10251,7 @@ "id": "process_kinetic_proofreading_tcr", "name": "process kinetic proofreading tcr", "description": "Model: process_kinetic_proofreading_tcr.bngl", - "path": "Contributed/BNGPlayground_Examples/processes/processkineticproofreadingtcr/process_kinetic_proofreading_tcr.bngl", + "path": "Examples/processes/processkineticproofreadingtcr/process_kinetic_proofreading_tcr.bngl", "file": "process_kinetic_proofreading_tcr.bngl", "tags": [ "process", @@ -10270,7 +10270,7 @@ "id": "process_quorum_sensing_switch", "name": "process quorum sensing switch", "description": "Model: process_quorum_sensing_switch.bngl", - "path": "Contributed/BNGPlayground_Examples/processes/processquorumsensingswitch/process_quorum_sensing_switch.bngl", + "path": "Examples/processes/processquorumsensingswitch/process_quorum_sensing_switch.bngl", "file": "process_quorum_sensing_switch.bngl", "tags": [ "process", @@ -10328,7 +10328,7 @@ "id": "pt303", "name": "pt303", "description": "c = 0.20 /d t_1/2 = 3.5 d (inferred)", - "path": "PyBioNetGen/HIVdynamics/pt303/pt303.bngl", + "path": "Published/PyBioNetGen/HIVdynamics/pt303/pt303.bngl", "file": "pt303.bngl", "tags": [ "pt303", @@ -10350,7 +10350,7 @@ "id": "pt403", "name": "pt403", "description": "c = 0.23 /d t_1/2 = 3.0 d (inferred)", - "path": "PyBioNetGen/HIVdynamics/pt403/pt403.bngl", + "path": "Published/PyBioNetGen/HIVdynamics/pt403/pt403.bngl", "file": "pt403.bngl", "tags": [ "pt403", @@ -10372,7 +10372,7 @@ "id": "pt409", "name": "pt409", "description": "c = 0.39 /d t_1/2 = 1.8 d (inferred)", - "path": "PyBioNetGen/HIVdynamics/pt409/pt409.bngl", + "path": "Published/PyBioNetGen/HIVdynamics/pt409/pt409.bngl", "file": "pt409.bngl", "tags": [ "pt409", @@ -10451,7 +10451,7 @@ "id": "quorum-sensing-circuit", "name": "quorum sensing circuit", "description": "BioNetGen model: quorum sensing circuit", - "path": "Contributed/BNGPlayground_Examples/biology/quorumsensingcircuit/quorum-sensing-circuit.bngl", + "path": "Examples/biology/quorumsensingcircuit/quorum-sensing-circuit.bngl", "file": "quorum-sensing-circuit.bngl", "tags": [ "quorum", @@ -10472,7 +10472,7 @@ "id": "rab-gtpase-cycle", "name": "rab gtpase cycle", "description": "BioNetGen model: rab gtpase cycle", - "path": "Contributed/BNGPlayground_Examples/biology/rabgtpasecycle/rab-gtpase-cycle.bngl", + "path": "Examples/biology/rabgtpasecycle/rab-gtpase-cycle.bngl", "file": "rab-gtpase-cycle.bngl", "tags": [ "rab", @@ -10510,7 +10510,7 @@ "id": "RAFi", "name": "RAFi", "description": "BioNetGen model: RAFi", - "path": "PyBioNetGen/core/RAFi/RAFi.bngl", + "path": "Published/PyBioNetGen/core/RAFi/RAFi.bngl", "file": "RAFi.bngl", "tags": [ "rafi", @@ -10529,7 +10529,7 @@ "id": "RAFi_ground", "name": "RAFi ground", "description": "BioNetGen model: RAFi ground", - "path": "PyBioNetGen/core/RAFiground/RAFi_ground.bngl", + "path": "Published/PyBioNetGen/core/RAFiground/RAFi_ground.bngl", "file": "RAFi_ground.bngl", "tags": [ "rafi", @@ -10567,7 +10567,7 @@ "id": "rankl-rank-signaling", "name": "rankl rank signaling", "description": "RANKL-RANK-OPG signaling in bone remodeling.", - "path": "Contributed/BNGPlayground_Examples/biology/ranklranksignaling/rankl-rank-signaling.bngl", + "path": "Examples/biology/ranklranksignaling/rankl-rank-signaling.bngl", "file": "rankl-rank-signaling.bngl", "tags": [ "rankl", @@ -10587,7 +10587,7 @@ "id": "ras-gef-gap-cycle", "name": "ras gef gap cycle", "description": "Ras-GEF-GAP cycle with explicit nucleotide exchange.", - "path": "Contributed/BNGPlayground_Examples/biology/rasgefgapcycle/ras-gef-gap-cycle.bngl", + "path": "Examples/biology/rasgefgapcycle/ras-gef-gap-cycle.bngl", "file": "ras-gef-gap-cycle.bngl", "tags": [ "ras", @@ -10627,7 +10627,7 @@ "id": "rec_dim", "name": "rec_dim", "description": "Ligand-receptor binding", - "path": "Contributed/BNGPlayground_Validation/recdim/rec_dim.bngl", + "path": "Tutorials/recdim/rec_dim.bngl", "file": "rec_dim.bngl", "tags": [ "validation", @@ -10648,7 +10648,7 @@ "id": "rec_dim_comp", "name": "rec_dim_comp", "description": "name dimension volume contained_by", - "path": "Contributed/BNGPlayground_Validation/recdimcomp/rec_dim_comp.bngl", + "path": "Tutorials/recdimcomp/rec_dim_comp.bngl", "file": "rec_dim_comp.bngl", "tags": [ "validation", @@ -10672,7 +10672,7 @@ "id": "receptor", "name": "receptor", "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", - "path": "PyBioNetGen/core/receptor/receptor.bngl", + "path": "Published/PyBioNetGen/core/receptor/receptor.bngl", "file": "receptor.bngl", "tags": [ "receptor", @@ -10690,7 +10690,7 @@ "id": "receptor_nf", "name": "receptor nf", "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", - "path": "PyBioNetGen/core/receptornf/receptor_nf.bngl", + "path": "Published/PyBioNetGen/core/receptornf/receptor_nf.bngl", "file": "receptor_nf.bngl", "tags": [ "receptor", @@ -10708,7 +10708,7 @@ "id": "receptor_nf", "name": "receptor nf", "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", - "path": "PyBioNetGen/tests/receptornf/receptor_nf.bngl", + "path": "Published/PyBioNetGen/tests/receptornf/receptor_nf.bngl", "file": "receptor_nf.bngl", "tags": [ "receptor", @@ -10770,7 +10770,7 @@ "id": "repressilator-oscillator", "name": "repressilator oscillator", "description": "BioNetGen model: repressilator oscillator", - "path": "Contributed/BNGPlayground_Examples/biology/repressilatoroscillator/repressilator-oscillator.bngl", + "path": "Examples/biology/repressilatoroscillator/repressilator-oscillator.bngl", "file": "repressilator-oscillator.bngl", "tags": [ "repressilator", @@ -10794,7 +10794,7 @@ "id": "retinoic-acid-signaling", "name": "retinoic acid signaling", "description": "BioNetGen model: retinoic acid signaling", - "path": "Contributed/BNGPlayground_Examples/biology/retinoicacidsignaling/retinoic-acid-signaling.bngl", + "path": "Examples/biology/retinoicacidsignaling/retinoic-acid-signaling.bngl", "file": "retinoic-acid-signaling.bngl", "tags": [ "retinoic", @@ -10815,7 +10815,7 @@ "id": "rho-gtpase-actin-cytoskeleton", "name": "rho gtpase actin cytoskeleton", "description": "RhoA-GTPase regulation of the actin cytoskeleton.", - "path": "Contributed/BNGPlayground_Examples/biology/rhogtpaseactincytoskeleton/rho-gtpase-actin-cytoskeleton.bngl", + "path": "Examples/biology/rhogtpaseactincytoskeleton/rho-gtpase-actin-cytoskeleton.bngl", "file": "rho-gtpase-actin-cytoskeleton.bngl", "tags": [ "rho", @@ -11378,7 +11378,7 @@ "id": "SHP2_base_model", "name": "SHP2_base_model", "description": "Base model of Shp2 regulation", - "path": "Contributed/BNGPlayground_Validation/SHP2basemodel/SHP2_base_model.bngl", + "path": "Tutorials/SHP2basemodel/SHP2_base_model.bngl", "file": "SHP2_base_model.bngl", "tags": [ "validation", @@ -11399,7 +11399,7 @@ "id": "shp2-phosphatase-regulation", "name": "shp2 phosphatase regulation", "description": "SHP2 phosphatase regulation via autoinhibition and SH2 binding.", - "path": "Contributed/BNGPlayground_Examples/biology/shp2phosphataseregulation/shp2-phosphatase-regulation.bngl", + "path": "Examples/biology/shp2phosphataseregulation/shp2-phosphatase-regulation.bngl", "file": "shp2-phosphatase-regulation.bngl", "tags": [ "shp2", @@ -12337,7 +12337,7 @@ "id": "signal-amplification-cascade", "name": "signal amplification cascade", "description": "BioNetGen model: signal amplification cascade", - "path": "Contributed/BNGPlayground_Examples/biology/signalamplificationcascade/signal-amplification-cascade.bngl", + "path": "Examples/biology/signalamplificationcascade/signal-amplification-cascade.bngl", "file": "signal-amplification-cascade.bngl", "tags": [ "signal", @@ -12379,7 +12379,7 @@ "id": "Simple", "name": "Simple", "description": "An example from a real application", - "path": "PyBioNetGen/tests/Simple/Simple.bngl", + "path": "Published/PyBioNetGen/tests/Simple/Simple.bngl", "file": "Simple.bngl", "tags": [ "simple", @@ -12398,7 +12398,7 @@ "id": "Simple_AddActions", "name": "Simple AddActions", "description": "An example from a real application", - "path": "PyBioNetGen/tests/SimpleAddActions/Simple_AddActions.bngl", + "path": "Published/PyBioNetGen/tests/SimpleAddActions/Simple_AddActions.bngl", "file": "Simple_AddActions.bngl", "tags": [ "simple", @@ -12418,7 +12418,7 @@ "id": "Simple_Answer", "name": "Simple Answer", "description": "An example from a real application", - "path": "PyBioNetGen/tests/SimpleAnswer/Simple_Answer.bngl", + "path": "Published/PyBioNetGen/tests/SimpleAnswer/Simple_Answer.bngl", "file": "Simple_Answer.bngl", "tags": [ "simple", @@ -12438,7 +12438,7 @@ "id": "Simple_GenOnly", "name": "Simple GenOnly", "description": "An example from a real application", - "path": "PyBioNetGen/tests/SimpleGenOnly/Simple_GenOnly.bngl", + "path": "Published/PyBioNetGen/tests/SimpleGenOnly/Simple_GenOnly.bngl", "file": "Simple_GenOnly.bngl", "tags": [ "simple", @@ -12458,7 +12458,7 @@ "id": "simple_nf_seed", "name": "simple nf seed", "description": "BioNetGen model: simple nf seed", - "path": "PyBioNetGen/tests/simplenfseed/simple_nf_seed.bngl", + "path": "Published/PyBioNetGen/tests/simplenfseed/simple_nf_seed.bngl", "file": "simple_nf_seed.bngl", "tags": [ "simple", @@ -12479,7 +12479,7 @@ "id": "simple_nfsim_test", "name": "simple_nfsim_test", "description": "Runtime-only BNGL model migrated from public/models: simple_nfsim_test", - "path": "Contributed/BNGPlayground_PublicRuntime/simplenfsimtest/simple_nfsim_test.bngl", + "path": "Tutorials/simplenfsimtest/simple_nfsim_test.bngl", "file": "simple_nfsim_test.bngl", "tags": [ "simple", @@ -12496,7 +12496,7 @@ "id": "Simple_nogen", "name": "Simple nogen", "description": "An example from a real application", - "path": "PyBioNetGen/tests/Simplenogen/Simple_nogen.bngl", + "path": "Published/PyBioNetGen/tests/Simplenogen/Simple_nogen.bngl", "file": "Simple_nogen.bngl", "tags": [ "simple", @@ -12515,7 +12515,7 @@ "id": "simple_sbml_import", "name": "simple_sbml_import", "description": "SBML import test", - "path": "Contributed/BNGPlayground_Validation/simplesbmlimport/simple_sbml_import.bngl", + "path": "Tutorials/simplesbmlimport/simple_sbml_import.bngl", "file": "simple_sbml_import.bngl", "tags": [ "validation", @@ -12536,7 +12536,7 @@ "id": "simple_system", "name": "simple_system", "description": "Simple binding system", - "path": "Contributed/BNGPlayground_Validation/simplesystem/simple_system.bngl", + "path": "Tutorials/simplesystem/simple_system.bngl", "file": "simple_system.bngl", "tags": [ "validation", @@ -12555,7 +12555,7 @@ "id": "simple-dimerization", "name": "simple dimerization", "description": "BioNetGen model: simple dimerization", - "path": "Contributed/BNGPlayground_Examples/biology/simpledimerization/simple-dimerization.bngl", + "path": "Examples/biology/simpledimerization/simple-dimerization.bngl", "file": "simple-dimerization.bngl", "tags": [ "simple", @@ -12628,7 +12628,7 @@ "id": "sir-epidemic-model", "name": "sir epidemic model", "description": "BioNetGen model: sir epidemic model", - "path": "Contributed/BNGPlayground_Examples/biology/sirepidemicmodel/sir-epidemic-model.bngl", + "path": "Examples/biology/sirepidemicmodel/sir-epidemic-model.bngl", "file": "sir-epidemic-model.bngl", "tags": [ "sir", @@ -12648,7 +12648,7 @@ "id": "smad-tgf-beta-signaling", "name": "smad tgf beta signaling", "description": "BioNetGen model: smad tgf beta signaling", - "path": "Contributed/BNGPlayground_Examples/biology/smadtgfbetasignaling/smad-tgf-beta-signaling.bngl", + "path": "Examples/biology/smadtgfbetasignaling/smad-tgf-beta-signaling.bngl", "file": "smad-tgf-beta-signaling.bngl", "tags": [ "smad", @@ -12670,7 +12670,7 @@ "id": "sonic-hedgehog-gradient", "name": "sonic hedgehog gradient", "description": "Sonic Hedgehog (Shh) morphogen gradient formation.", - "path": "Contributed/BNGPlayground_Examples/biology/sonichedgehoggradient/sonic-hedgehog-gradient.bngl", + "path": "Examples/biology/sonichedgehoggradient/sonic-hedgehog-gradient.bngl", "file": "sonic-hedgehog-gradient.bngl", "tags": [ "sonic", @@ -12708,7 +12708,7 @@ "id": "sp_fourier_synthesizer", "name": "sp fourier synthesizer", "description": "Fourier Series Synthesizer in BNGL", - "path": "Contributed/BNGPlayground_Examples/signal-processing/spfouriersynthesizer/sp_fourier_synthesizer.bngl", + "path": "Examples/signal-processing/spfouriersynthesizer/sp_fourier_synthesizer.bngl", "file": "sp_fourier_synthesizer.bngl", "tags": [ "sp", @@ -12732,7 +12732,7 @@ "id": "sp_image_convolution", "name": "sp image convolution", "description": "Image Convolution Filter in BNGL", - "path": "Contributed/BNGPlayground_Examples/signal-processing/spimageconvolution/sp_image_convolution.bngl", + "path": "Examples/signal-processing/spimageconvolution/sp_image_convolution.bngl", "file": "sp_image_convolution.bngl", "tags": [ "sp", @@ -12752,7 +12752,7 @@ "id": "sp_kalman_filter", "name": "sp kalman filter", "description": "Kalman Filter in BNGL", - "path": "Contributed/BNGPlayground_Examples/signal-processing/spkalmanfilter/sp_kalman_filter.bngl", + "path": "Examples/signal-processing/spkalmanfilter/sp_kalman_filter.bngl", "file": "sp_kalman_filter.bngl", "tags": [ "sp", @@ -12919,7 +12919,7 @@ "id": "stat3-mediated-transcription", "name": "stat3 mediated transcription", "description": "STAT3-mediated transcription and feedback.", - "path": "Contributed/BNGPlayground_Examples/biology/stat3mediatedtranscription/stat3-mediated-transcription.bngl", + "path": "Examples/biology/stat3mediatedtranscription/stat3-mediated-transcription.bngl", "file": "stat3-mediated-transcription.bngl", "tags": [ "stat3", @@ -12957,7 +12957,7 @@ "id": "stress-response-adaptation", "name": "stress response adaptation", "description": "BioNetGen model: stress response adaptation", - "path": "Contributed/BNGPlayground_Examples/biology/stressresponseadaptation/stress-response-adaptation.bngl", + "path": "Examples/biology/stressresponseadaptation/stress-response-adaptation.bngl", "file": "stress-response-adaptation.bngl", "tags": [ "stress", @@ -13104,7 +13104,7 @@ "id": "synaptic-plasticity-ltp", "name": "synaptic plasticity ltp", "description": "Initial Concentrations", - "path": "Contributed/BNGPlayground_Examples/biology/synapticplasticityltp/synaptic-plasticity-ltp.bngl", + "path": "Examples/biology/synapticplasticityltp/synaptic-plasticity-ltp.bngl", "file": "synaptic-plasticity-ltp.bngl", "tags": [ "synaptic", @@ -13127,7 +13127,7 @@ "id": "synbio_band_pass_filter", "name": "synbio band pass filter", "description": "Model: synbio_band_pass_filter.bngl", - "path": "Contributed/BNGPlayground_Examples/synbio/synbiobandpassfilter/synbio_band_pass_filter.bngl", + "path": "Examples/synbio/synbiobandpassfilter/synbio_band_pass_filter.bngl", "file": "synbio_band_pass_filter.bngl", "tags": [ "synbio", @@ -13149,7 +13149,7 @@ "id": "synbio_counter_molecular", "name": "synbio counter molecular", "description": "Model: synbio_counter_molecular.bngl", - "path": "Contributed/BNGPlayground_Examples/synbio/synbiocountermolecular/synbio_counter_molecular.bngl", + "path": "Examples/synbio/synbiocountermolecular/synbio_counter_molecular.bngl", "file": "synbio_counter_molecular.bngl", "tags": [ "synbio", @@ -13168,7 +13168,7 @@ "id": "synbio_edge_detector", "name": "synbio edge detector", "description": "Model: synbio_edge_detector.bngl", - "path": "Contributed/BNGPlayground_Examples/synbio/synbioedgedetector/synbio_edge_detector.bngl", + "path": "Examples/synbio/synbioedgedetector/synbio_edge_detector.bngl", "file": "synbio_edge_detector.bngl", "tags": [ "synbio", @@ -13188,7 +13188,7 @@ "id": "synbio_logic_gates_enzymatic", "name": "synbio logic gates enzymatic", "description": "Model: synbio_logic_gates_enzymatic.bngl", - "path": "Contributed/BNGPlayground_Examples/synbio/synbiologicgatesenzymatic/synbio_logic_gates_enzymatic.bngl", + "path": "Examples/synbio/synbiologicgatesenzymatic/synbio_logic_gates_enzymatic.bngl", "file": "synbio_logic_gates_enzymatic.bngl", "tags": [ "synbio", @@ -13212,7 +13212,7 @@ "id": "synbio_oscillator_synchronization", "name": "synbio oscillator synchronization", "description": "Model: synbio_oscillator_synchronization.bngl", - "path": "Contributed/BNGPlayground_Examples/synbio/synbiooscillatorsynchronization/synbio_oscillator_synchronization.bngl", + "path": "Examples/synbio/synbiooscillatorsynchronization/synbio_oscillator_synchronization.bngl", "file": "synbio_oscillator_synchronization.bngl", "tags": [ "synbio", @@ -13250,7 +13250,7 @@ "id": "t-cell-activation", "name": "t cell activation", "description": "BioNetGen model: t cell activation", - "path": "Contributed/BNGPlayground_Examples/biology/tcellactivation/t-cell-activation.bngl", + "path": "Examples/biology/tcellactivation/t-cell-activation.bngl", "file": "t-cell-activation.bngl", "tags": [ "t", @@ -13306,7 +13306,7 @@ "id": "tcr", "name": "tcr", "description": "A model of T cell receptor signaling", - "path": "PyBioNetGen/core/tcr/tcr.bngl", + "path": "Published/PyBioNetGen/core/tcr/tcr.bngl", "file": "tcr.bngl", "tags": [ "tcr", @@ -13328,7 +13328,7 @@ "id": "test_ANG_synthesis_simple", "name": "test_ANG_synthesis_simple", "description": "Synthesis network test", - "path": "Contributed/BNGPlayground_Validation/testANGsynthesissimple/test_ANG_synthesis_simple.bngl", + "path": "Tutorials/testANGsynthesissimple/test_ANG_synthesis_simple.bngl", "file": "test_ANG_synthesis_simple.bngl", "tags": [ "validation", @@ -13353,7 +13353,7 @@ "id": "test_fixed", "name": "test_fixed", "description": "# actions ##", - "path": "Contributed/BNGPlayground_Validation/testfixed/test_fixed.bngl", + "path": "Tutorials/testfixed/test_fixed.bngl", "file": "test_fixed.bngl", "tags": [ "validation", @@ -13374,7 +13374,7 @@ "id": "test_MM", "name": "test_MM", "description": "Kinetic constants", - "path": "Contributed/BNGPlayground_Validation/testMM/test_MM.bngl", + "path": "Tutorials/testMM/test_MM.bngl", "file": "test_MM.bngl", "tags": [ "validation", @@ -13395,7 +13395,7 @@ "id": "test_mratio", "name": "test_mratio", "description": "Reaction ratio test", - "path": "Contributed/BNGPlayground_Validation/testmratio/test_mratio.bngl", + "path": "Tutorials/testmratio/test_mratio.bngl", "file": "test_mratio.bngl", "tags": [ "validation", @@ -13417,7 +13417,7 @@ "id": "test_network_gen", "name": "test_network_gen", "description": "fceri model with network generation", - "path": "Contributed/BNGPlayground_Validation/testnetworkgen/test_network_gen.bngl", + "path": "Tutorials/testnetworkgen/test_network_gen.bngl", "file": "test_network_gen.bngl", "tags": [ "validation", @@ -13439,7 +13439,7 @@ "id": "test_sat", "name": "test_sat", "description": "Kinetic constants", - "path": "Contributed/BNGPlayground_Validation/testsat/test_sat.bngl", + "path": "Tutorials/testsat/test_sat.bngl", "file": "test_sat.bngl", "tags": [ "validation", @@ -13460,7 +13460,7 @@ "id": "test_synthesis_cBNGL_simple", "name": "test_synthesis_cBNGL_simple", "description": "Compartmental synthesis", - "path": "Contributed/BNGPlayground_Validation/testsynthesiscBNGLsimple/test_synthesis_cBNGL_simple.bngl", + "path": "Tutorials/testsynthesiscBNGLsimple/test_synthesis_cBNGL_simple.bngl", "file": "test_synthesis_cBNGL_simple.bngl", "tags": [ "validation", @@ -13485,7 +13485,7 @@ "id": "test_synthesis_complex", "name": "test_synthesis_complex", "description": "Complex synthesis test", - "path": "Contributed/BNGPlayground_Validation/testsynthesiscomplex/test_synthesis_complex.bngl", + "path": "Tutorials/testsynthesiscomplex/test_synthesis_complex.bngl", "file": "test_synthesis_complex.bngl", "tags": [ "validation", @@ -13509,7 +13509,7 @@ "id": "test_synthesis_complex_0_cBNGL", "name": "test_synthesis_complex_0_cBNGL", "description": "volume-surface", - "path": "Contributed/BNGPlayground_Validation/testsynthesiscomplex0cBNGL/test_synthesis_complex_0_cBNGL.bngl", + "path": "Tutorials/testsynthesiscomplex0cBNGL/test_synthesis_complex_0_cBNGL.bngl", "file": "test_synthesis_complex_0_cBNGL.bngl", "tags": [ "validation", @@ -13537,7 +13537,7 @@ "id": "test_synthesis_complex_source_cBNGL", "name": "test_synthesis_complex_source_cBNGL", "description": "volume-surface", - "path": "Contributed/BNGPlayground_Validation/testsynthesiscomplexsourcecBNGL/test_synthesis_complex_source_cBNGL.bngl", + "path": "Tutorials/testsynthesiscomplexsourcecBNGL/test_synthesis_complex_source_cBNGL.bngl", "file": "test_synthesis_complex_source_cBNGL.bngl", "tags": [ "validation", @@ -13565,7 +13565,7 @@ "id": "test_synthesis_simple", "name": "test_synthesis_simple", "description": "Simple synthesis test", - "path": "Contributed/BNGPlayground_Validation/testsynthesissimple/test_synthesis_simple.bngl", + "path": "Tutorials/testsynthesissimple/test_synthesis_simple.bngl", "file": "test_synthesis_simple.bngl", "tags": [ "validation", @@ -13623,39 +13623,39 @@ }, { "id": "tlbr", - "name": "TLBR Tutorial", - "description": "Ligand binding", - "path": "Published/tlbr/tlbr.bngl", + "name": "tlbr", + "description": "A model of trivalent ligand, bivalent receptor", + "path": "Published/PyBioNetGen/core/tlbr/tlbr.bngl", "file": "tlbr.bngl", "tags": [ - "published", - "immunology", "tlbr", "l", "r", - "simulate_rm" + "lambda", + "fl" ], - "category": "immunology", - "bng2_compatible": false, + "category": "other", + "bng2_compatible": true, "origin": "published", "visible": false, "collectionId": null }, { "id": "tlbr", - "name": "tlbr", - "description": "A model of trivalent ligand, bivalent receptor", - "path": "PyBioNetGen/core/tlbr/tlbr.bngl", + "name": "TLBR Tutorial", + "description": "Ligand binding", + "path": "Published/tlbr/tlbr.bngl", "file": "tlbr.bngl", "tags": [ + "published", + "immunology", "tlbr", "l", "r", - "lambda", - "fl" + "simulate_rm" ], - "category": "other", - "bng2_compatible": true, + "category": "immunology", + "bng2_compatible": false, "origin": "published", "visible": false, "collectionId": null @@ -13664,7 +13664,7 @@ "id": "tlmr", "name": "tlmr", "description": "Trivalent ligand monovalent receptor", - "path": "Contributed/BNGPlayground_Validation/tlmr/tlmr.bngl", + "path": "Tutorials/tlmr/tlmr.bngl", "file": "tlmr.bngl", "tags": [ "validation", @@ -13684,7 +13684,7 @@ "id": "tlr3-dsrna-sensing", "name": "tlr3 dsrna sensing", "description": "TLR3-mediated dsRNA sensing and TRIF pathway activation.", - "path": "Contributed/BNGPlayground_Examples/biology/tlr3dsrnasensing/tlr3-dsrna-sensing.bngl", + "path": "Examples/biology/tlr3dsrnasensing/tlr3-dsrna-sensing.bngl", "file": "tlr3-dsrna-sensing.bngl", "tags": [ "tlr3", @@ -13704,7 +13704,7 @@ "id": "tnf-induced-apoptosis", "name": "tnf induced apoptosis", "description": "BioNetGen model: tnf induced apoptosis", - "path": "Contributed/BNGPlayground_Examples/biology/tnfinducedapoptosis/tnf-induced-apoptosis.bngl", + "path": "Examples/biology/tnfinducedapoptosis/tnf-induced-apoptosis.bngl", "file": "tnf-induced-apoptosis.bngl", "tags": [ "tnf", @@ -13784,7 +13784,7 @@ "id": "toy-jim", "name": "toy-jim", "description": "The model consists of a monovalent extracellular ligand,", - "path": "Contributed/BNGPlayground_Validation/toyjim/toy-jim.bngl", + "path": "Tutorials/toyjim/toy-jim.bngl", "file": "toy-jim.bngl", "tags": [ "validation", @@ -13885,7 +13885,7 @@ "id": "Tricky", "name": "Tricky", "description": "An example from a real application", - "path": "PyBioNetGen/tests/Tricky/Tricky.bngl", + "path": "Published/PyBioNetGen/tests/Tricky/Tricky.bngl", "file": "Tricky.bngl", "tags": [ "tricky", @@ -13903,7 +13903,7 @@ "id": "TrickyUS", "name": "TrickyUS", "description": "An example from a real application", - "path": "PyBioNetGen/tests/TrickyUS/TrickyUS.bngl", + "path": "Published/PyBioNetGen/tests/TrickyUS/TrickyUS.bngl", "file": "TrickyUS.bngl", "tags": [ "trickyus", @@ -13921,7 +13921,7 @@ "id": "trivial", "name": "trivial", "description": "A trivial model file for testing MCMC distributions.", - "path": "PyBioNetGen/tests/trivial/trivial.bngl", + "path": "Published/PyBioNetGen/tests/trivial/trivial.bngl", "file": "trivial.bngl", "tags": [ "trivial", @@ -14013,7 +14013,7 @@ "id": "two-component-system", "name": "two component system", "description": "BioNetGen model: two component system", - "path": "Contributed/BNGPlayground_Examples/biology/twocomponentsystem/two-component-system.bngl", + "path": "Examples/biology/twocomponentsystem/two-component-system.bngl", "file": "two-component-system.bngl", "tags": [ "two", @@ -14033,7 +14033,7 @@ "id": "univ_synth", "name": "univ_synth", "description": "example of universal synthesis", - "path": "Contributed/BNGPlayground_Validation/univsynth/univ_synth.bngl", + "path": "Tutorials/univsynth/univ_synth.bngl", "file": "univ_synth.bngl", "tags": [ "validation", @@ -14145,7 +14145,7 @@ "id": "vegf-angiogenesis", "name": "vegf angiogenesis", "description": "VEGF-mediated signaling in angiogenesis.", - "path": "Contributed/BNGPlayground_Examples/biology/vegfangiogenesis/vegf-angiogenesis.bngl", + "path": "Examples/biology/vegfangiogenesis/vegf-angiogenesis.bngl", "file": "vegf-angiogenesis.bngl", "tags": [ "vegf", @@ -14261,7 +14261,7 @@ "id": "viral-sensing-innate-immunity", "name": "viral sensing innate immunity", "description": "BioNetGen model: viral sensing innate immunity", - "path": "Contributed/BNGPlayground_Examples/biology/viralsensinginnateimmunity/viral-sensing-innate-immunity.bngl", + "path": "Examples/biology/viralsensinginnateimmunity/viral-sensing-innate-immunity.bngl", "file": "viral-sensing-innate-immunity.bngl", "tags": [ "viral", @@ -14342,7 +14342,7 @@ "id": "wacky_alchemy_stone", "name": "wacky alchemy stone", "description": "Model: wacky_alchemy_stone.bngl", - "path": "Contributed/BNGPlayground_Examples/wacky/wackyalchemystone/wacky_alchemy_stone.bngl", + "path": "Examples/wacky/wackyalchemystone/wacky_alchemy_stone.bngl", "file": "wacky_alchemy_stone.bngl", "tags": [ "wacky", @@ -14361,7 +14361,7 @@ "id": "wacky_black_hole", "name": "wacky black hole", "description": "Model: wacky_black_hole.bngl", - "path": "Contributed/BNGPlayground_Examples/wacky/wackyblackhole/wacky_black_hole.bngl", + "path": "Examples/wacky/wackyblackhole/wacky_black_hole.bngl", "file": "wacky_black_hole.bngl", "tags": [ "wacky", @@ -14382,7 +14382,7 @@ "id": "wacky_bouncing_ball", "name": "wacky bouncing ball", "description": "Model: wacky_bouncing_ball.bngl", - "path": "Contributed/BNGPlayground_Examples/wacky/wackybouncingball/wacky_bouncing_ball.bngl", + "path": "Examples/wacky/wackybouncingball/wacky_bouncing_ball.bngl", "file": "wacky_bouncing_ball.bngl", "tags": [ "wacky", @@ -14401,7 +14401,7 @@ "id": "wacky_traffic_jam_asep", "name": "wacky traffic jam asep", "description": "Model: wacky_traffic_jam_asep.bngl", - "path": "Contributed/BNGPlayground_Examples/wacky/wackytrafficjamasep/wacky_traffic_jam_asep.bngl", + "path": "Examples/wacky/wackytrafficjamasep/wacky_traffic_jam_asep.bngl", "file": "wacky_traffic_jam_asep.bngl", "tags": [ "wacky", @@ -14423,7 +14423,7 @@ "id": "wacky_zombie_infection", "name": "wacky zombie infection", "description": "Model: wacky_zombie_infection.bngl", - "path": "Contributed/BNGPlayground_Examples/wacky/wackyzombieinfection/wacky_zombie_infection.bngl", + "path": "Examples/wacky/wackyzombieinfection/wacky_zombie_infection.bngl", "file": "wacky_zombie_infection.bngl", "tags": [ "wacky", @@ -14624,7 +14624,7 @@ "id": "wnt-beta-catenin-signaling", "name": "wnt beta catenin signaling", "description": "Wnt/Beta-Catenin signaling (Canonical pathway).", - "path": "Contributed/BNGPlayground_Examples/biology/wntbetacateninsignaling/wnt-beta-catenin-signaling.bngl", + "path": "Examples/biology/wntbetacateninsignaling/wnt-beta-catenin-signaling.bngl", "file": "wnt-beta-catenin-signaling.bngl", "tags": [ "wnt", @@ -14665,7 +14665,7 @@ "id": "wound-healing-pdgf-signaling", "name": "wound healing pdgf signaling", "description": "BioNetGen model: wound healing pdgf signaling", - "path": "Contributed/BNGPlayground_Examples/biology/woundhealingpdgfsignaling/wound-healing-pdgf-signaling.bngl", + "path": "Examples/biology/woundhealingpdgfsignaling/wound-healing-pdgf-signaling.bngl", "file": "wound-healing-pdgf-signaling.bngl", "tags": [ "wound", diff --git a/metadata-schema.yaml b/metadata-schema.yaml index 1e9d945..fcd08c9 100644 --- a/metadata-schema.yaml +++ b/metadata-schema.yaml @@ -22,7 +22,7 @@ date: published: YYYY-MM-DD tags: string[] -category: enum(signaling, regulation, metabolism, gene-expression, epidemiology, immunology, tutorial, validation, showcase, synthetic-biology, ecology, physics, computer-science, other) +category: enum(signaling, regulation, metabolism, gene-expression, epidemiology, immunology, tutorial, validation, showcase, synthetic-biology, ecology, physics, computer-science, other, compartments, energy, feature-demos, nfsim, processes, wacky, cs, biology, genetics, ml, signal-processing, mechanistic-modeling, biophysics) compatibility: bng2_compatible: boolean diff --git a/scripts/generate-manifest.js b/scripts/generate-manifest.js index bce3f82..a9f81c6 100644 --- a/scripts/generate-manifest.js +++ b/scripts/generate-manifest.js @@ -1,7 +1,8 @@ const fs = require('fs'); const path = require('path'); +const { listModelFiles } = require('./utils'); -const SEARCH_ROOTS = ['Published', 'Contributed', 'Tutorials', 'PyBioNetGen']; +const SEARCH_ROOTS = ['Published', 'Examples', 'Tutorials']; function parseArgs(argv) { let root = path.resolve(__dirname, '..'); @@ -43,8 +44,10 @@ function parseScalar(rawValue) { return value; } -function setNested(target, dottedPath, value) { - const parts = dottedPath.split('.'); +function setNested(target, parts, value) { + const blockedKeys = new Set(['__proto__', 'constructor', 'prototype']); + if (parts.some((part) => blockedKeys.has(part))) return; + let cursor = target; for (let index = 0; index < parts.length - 1; index += 1) { const part = parts[index]; @@ -97,7 +100,7 @@ function parseMetadataYaml(content) { continue; } - setNested(result, dottedPath, parseScalar(rawValue)); + setNested(result, pathParts, parseScalar(rawValue)); } return result; @@ -120,13 +123,6 @@ function listMetadataFiles(dir, results = []) { return results; } -function listModelFiles(dir) { - return fs.readdirSync(dir, { withFileTypes: true }) - .filter(entry => entry.isFile() && entry.name.endsWith('.bngl')) - .map(entry => entry.name) - .sort(); -} - function buildEntry(root, metadata, metadataFile, modelFile, isCollection) { const modelDir = path.dirname(metadataFile); const relativeModelPath = path.relative(root, path.join(modelDir, modelFile)).replace(/\\/g, '/'); @@ -168,4 +164,10 @@ function main() { console.log(`Generated ${manifestEntries.length} manifest entries at ${output}`); } -main(); \ No newline at end of file +if (require.main === module) { + main(); +} + +module.exports = { + buildEntry, +}; \ No newline at end of file diff --git a/scripts/generate-manifest.test.js b/scripts/generate-manifest.test.js new file mode 100644 index 0000000..eeef552 --- /dev/null +++ b/scripts/generate-manifest.test.js @@ -0,0 +1,96 @@ +const test = require('node:test'); +const assert = require('node:assert'); +const path = require('path'); +const { buildEntry } = require('./generate-manifest.js'); + +test('buildEntry', async (t) => { + await t.test('handles a single model with full metadata', () => { + const root = '/path/to/root'; + const metadataFile = '/path/to/root/Published/ModelA/metadata.yaml'; + const modelFile = 'model_a.bngl'; + const isCollection = false; + + const metadata = { + id: 'model_a', + name: 'Model A', + description: 'A test model', + tags: ['test', 'model'], + category: 'validation', + compatibility: { bng2_compatible: true }, + source: { origin: 'published' }, + playground: { visible: true }, + }; + + const entry = buildEntry(root, metadata, metadataFile, modelFile, isCollection); + + assert.strictEqual(entry.id, 'model_a'); + assert.strictEqual(entry.name, 'Model A'); + assert.strictEqual(entry.description, 'A test model'); + // Using string replacement because path.relative varies by platform in tests + assert.strictEqual(entry.path, 'Published/ModelA/model_a.bngl'); + assert.strictEqual(entry.file, 'model_a.bngl'); + assert.deepStrictEqual(entry.tags, ['test', 'model']); + assert.strictEqual(entry.category, 'validation'); + assert.strictEqual(entry.bng2_compatible, true); + assert.strictEqual(entry.origin, 'published'); + assert.strictEqual(entry.visible, true); + assert.strictEqual(entry.collectionId, null); + }); + + await t.test('handles a collection entry', () => { + const root = '/path/to/root'; + const metadataFile = '/path/to/root/Contributed/CollectionB/metadata.yaml'; + const modelFile = 'variant_1.bngl'; + const isCollection = true; + + const metadata = { + id: 'collection_b', + name: 'Collection B', + collection: { type: 'parameter-fit-variants' } + }; + + const entry = buildEntry(root, metadata, metadataFile, modelFile, isCollection); + + assert.strictEqual(entry.id, 'variant_1'); + assert.strictEqual(entry.name, 'Collection B - variant_1'); + assert.strictEqual(entry.collectionId, 'collection_b'); + }); + + await t.test('handles missing metadata with appropriate fallbacks', () => { + const root = '/path/to/root'; + const metadataFile = '/path/to/root/Tutorials/ModelC/metadata.yaml'; + const modelFile = 'model_c.bngl'; + const isCollection = false; + + const metadata = {}; + + const entry = buildEntry(root, metadata, metadataFile, modelFile, isCollection); + + assert.strictEqual(entry.id, 'model_c'); + assert.strictEqual(entry.name, 'model_c'); + assert.strictEqual(entry.description, ''); + assert.deepStrictEqual(entry.tags, []); + assert.strictEqual(entry.category, 'other'); + assert.strictEqual(entry.bng2_compatible, false); + assert.strictEqual(entry.origin, 'other'); + assert.strictEqual(entry.visible, false); + assert.strictEqual(entry.collectionId, null); + }); + + await t.test('handles partial compatibility and playground metadata', () => { + const root = '/path/to/root'; + const metadataFile = '/path/to/root/Tutorials/ModelD/metadata.yaml'; + const modelFile = 'model_d.bngl'; + const isCollection = false; + + const metadata = { + compatibility: {}, + playground: {} + }; + + const entry = buildEntry(root, metadata, metadataFile, modelFile, isCollection); + + assert.strictEqual(entry.bng2_compatible, false); + assert.strictEqual(entry.visible, false); + }); +}); diff --git a/scripts/tests/validate-metadata.test.js b/scripts/tests/validate-metadata.test.js new file mode 100644 index 0000000..3f6db8b --- /dev/null +++ b/scripts/tests/validate-metadata.test.js @@ -0,0 +1,41 @@ +const { test } = require('node:test'); +const assert = require('node:assert'); +const { parseScalar } = require('../validate-metadata.js'); + +test('parseScalar', async (t) => { + await t.test('parses boolean strings', () => { + assert.strictEqual(parseScalar('true'), true); + assert.strictEqual(parseScalar('false'), false); + assert.strictEqual(parseScalar(' true '), true); + }); + + await t.test('parses null string', () => { + assert.strictEqual(parseScalar('null'), null); + assert.strictEqual(parseScalar(' null '), null); + }); + + await t.test('parses numeric strings', () => { + assert.strictEqual(parseScalar('42'), 42); + assert.strictEqual(parseScalar('-10'), -10); + assert.strictEqual(parseScalar('0'), 0); + assert.strictEqual(parseScalar(' 123 '), 123); + }); + + await t.test('parses array representations', () => { + assert.deepStrictEqual(parseScalar('[]'), []); + assert.deepStrictEqual(parseScalar('[a, b]'), ['a', 'b']); + assert.deepStrictEqual(parseScalar('["a", "b"]'), ['a', 'b']); + assert.deepStrictEqual(parseScalar(' [ 1 , 2 ] '), ['1', '2']); + }); + + await t.test('parses double-quoted strings', () => { + assert.strictEqual(parseScalar('"hello"'), 'hello'); + assert.strictEqual(parseScalar(' "world" '), 'world'); + }); + + await t.test('falls back to plain strings', () => { + assert.strictEqual(parseScalar('hello'), 'hello'); + assert.strictEqual(parseScalar('12.34'), '12.34'); // doesn't parse as int + assert.strictEqual(parseScalar(''), ''); + }); +}); diff --git a/scripts/utils.js b/scripts/utils.js new file mode 100644 index 0000000..d0f4c2c --- /dev/null +++ b/scripts/utils.js @@ -0,0 +1,12 @@ +const fs = require('fs'); + +function listModelFiles(dir) { + return fs.readdirSync(dir, { withFileTypes: true }) + .filter((entry) => entry.isFile() && entry.name.endsWith('.bngl')) + .map((entry) => entry.name) + .sort(); +} + +module.exports = { + listModelFiles +}; diff --git a/scripts/validate-metadata.js b/scripts/validate-metadata.js index 834f1ab..6cb8645 100644 --- a/scripts/validate-metadata.js +++ b/scripts/validate-metadata.js @@ -1,7 +1,8 @@ const fs = require('fs'); const path = require('path'); +const { listModelFiles } = require('./utils'); -const SEARCH_ROOTS = ['Published', 'Contributed', 'Tutorials', 'PyBioNetGen']; +const SEARCH_ROOTS = ['Published', 'Examples', 'Tutorials']; const CATEGORY_VALUES = new Set([ 'signaling', 'regulation', @@ -17,6 +18,19 @@ const CATEGORY_VALUES = new Set([ 'physics', 'computer-science', 'other', + 'compartments', + 'energy', + 'feature-demos', + 'nfsim', + 'processes', + 'wacky', + 'cs', + 'biology', + 'genetics', + 'ml', + 'signal-processing', + 'mechanistic-modeling', + 'biophysics', ]); const ORIGIN_VALUES = new Set([ 'published', @@ -54,6 +68,9 @@ function parseScalar(rawValue) { function setNested(target, dottedPath, value) { const parts = dottedPath.split('.'); + const blockedKeys = new Set(['__proto__', 'constructor', 'prototype']); + if (parts.some((part) => blockedKeys.has(part))) return; + let cursor = target; for (let index = 0; index < parts.length - 1; index += 1) { const part = parts[index]; @@ -123,13 +140,6 @@ function listMetadataFiles(dir, results = []) { return results; } -function listModelFiles(dir) { - return fs.readdirSync(dir, { withFileTypes: true }) - .filter((entry) => entry.isFile() && entry.name.endsWith('.bngl')) - .map((entry) => entry.name) - .sort(); -} - function normalizeModelKey(value) { return String(value || '') .replace(/\.bngl$/i, '') @@ -257,4 +267,12 @@ function main() { console.log(`Validated ${metadataFiles.length} metadata files.`); } -main(); \ No newline at end of file +if (require.main === module) { + main(); +} + +module.exports = { + parseScalar, + validateMetadataFile, + parseMetadataYaml, +}; \ No newline at end of file diff --git a/scripts/validate-metadata.test.js b/scripts/validate-metadata.test.js new file mode 100644 index 0000000..f161308 --- /dev/null +++ b/scripts/validate-metadata.test.js @@ -0,0 +1,109 @@ +const test = require('node:test'); +const assert = require('node:assert'); +const { parseMetadataYaml } = require('./validate-metadata.js'); + +test('parseMetadataYaml', async (t) => { + await t.test('parses basic key-value pairs', () => { + const yaml = ` +id: my-model +name: "My Model" +description: A test model +featured: true +count: 42 + `; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { + id: 'my-model', + name: 'My Model', + description: 'A test model', + featured: true, + count: 42 + }); + }); + + await t.test('ignores empty lines and comments', () => { + const yaml = ` +# This is a comment +id: model-1 + +# Another comment + +name: test + `; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { + id: 'model-1', + name: 'test' + }); + }); + + await t.test('parses list arrays (tags)', () => { + const yaml = ` +id: model-tags +tags: + - biology + - physics + - chemistry + `; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { + id: 'model-tags', + tags: ['biology', 'physics', 'chemistry'] + }); + }); + + await t.test('parses nested objects', () => { + const yaml = ` +id: nested-model +compatibility: + bng2_compatible: true + simulation_methods: [ode, ssa] +source: + origin: published + original_repository: "http://example.com" + `; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { + id: 'nested-model', + compatibility: { + bng2_compatible: true, + simulation_methods: ['ode', 'ssa'] + }, + source: { + origin: 'published', + original_repository: 'http://example.com' + } + }); + }); + + await t.test('parses deeply nested objects', () => { + const yaml = ` +a: + b: + c: + d: value + `; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { + a: { + b: { + c: { + d: 'value' + } + } + } + }); + }); + + await t.test('handles empty tags array', () => { + const yaml = ` +id: empty-tags +tags: + `; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { + id: 'empty-tags', + tags: [] + }); + }); +}); diff --git a/tests/validate-metadata.test.js b/tests/validate-metadata.test.js new file mode 100644 index 0000000..748d276 --- /dev/null +++ b/tests/validate-metadata.test.js @@ -0,0 +1,151 @@ +const test = require('node:test'); +const assert = require('node:assert'); +const fs = require('fs'); +const path = require('path'); +const os = require('os'); +const { validateMetadataFile } = require('../scripts/validate-metadata'); + +function withTempDir(testFn) { + const tempDir = fs.mkdtempSync(path.join(os.tmpdir(), 'validate-metadata-test-')); + try { + testFn(tempDir); + } finally { + fs.rmSync(tempDir, { recursive: true, force: true }); + } +} + +test('validateMetadataFile is imported correctly', () => { + assert.strictEqual(typeof validateMetadataFile, 'function'); +}); + +const VALID_METADATA_YAML = ` +id: "test-model" +name: "Test Model" +description: "A test model" +tags: + - test + - mock +category: "other" +compatibility: + bng2_compatible: true + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false + simulation_methods: [ode, ssa] +source: + origin: "published" + original_repository: "https://github.com/example/repo" +playground: + visible: true + gallery_category: "Test" + featured: false + difficulty: "beginner" +`; + +test('valid metadata file passes validation without errors', () => { + withTempDir((tempDir) => { + const metadataFile = path.join(tempDir, 'metadata.yaml'); + fs.writeFileSync(metadataFile, VALID_METADATA_YAML); + fs.writeFileSync(path.join(tempDir, 'README.md'), '# Test Model'); + fs.writeFileSync(path.join(tempDir, 'testmodel.bngl'), 'begin model\nend model'); + + const errors = []; + validateMetadataFile(metadataFile, errors); + + assert.deepStrictEqual(errors, []); + }); +}); + +test('missing README.md adds error', () => { + withTempDir((tempDir) => { + const metadataFile = path.join(tempDir, 'metadata.yaml'); + fs.writeFileSync(metadataFile, VALID_METADATA_YAML); + fs.writeFileSync(path.join(tempDir, 'testmodel.bngl'), 'begin model\nend model'); + + const errors = []; + validateMetadataFile(metadataFile, errors); + + assert.strictEqual(errors.length, 1); + assert.match(errors[0], /missing README\.md/); + }); +}); + +test('missing .bngl file adds error', () => { + withTempDir((tempDir) => { + const metadataFile = path.join(tempDir, 'metadata.yaml'); + fs.writeFileSync(metadataFile, VALID_METADATA_YAML); + fs.writeFileSync(path.join(tempDir, 'README.md'), '# Test Model'); + + const errors = []; + validateMetadataFile(metadataFile, errors); + + assert.strictEqual(errors.length, 1); + assert.match(errors[0], /no \.bngl files found alongside metadata\.yaml/); + }); +}); + +test('invalid metadata structure adds errors', () => { + withTempDir((tempDir) => { + const metadataFile = path.join(tempDir, 'metadata.yaml'); + const invalidYaml = ` +id: "test-model" +# missing name and description +category: "invalid-category" +# missing source, playground, and compatibility +`; + fs.writeFileSync(metadataFile, invalidYaml); + fs.writeFileSync(path.join(tempDir, 'README.md'), '# Test Model'); + fs.writeFileSync(path.join(tempDir, 'testmodel.bngl'), 'begin model\nend model'); + + const errors = []; + validateMetadataFile(metadataFile, errors); + + assert.ok(errors.length > 0); + assert.ok(errors.some(e => e.includes('missing or invalid name'))); + assert.ok(errors.some(e => e.includes('missing or invalid description'))); + assert.ok(errors.some(e => e.includes('invalid category ("invalid-category")'))); + assert.ok(errors.some(e => e.includes('missing compatibility section'))); + assert.ok(errors.some(e => e.includes('missing source section'))); + assert.ok(errors.some(e => e.includes('missing playground section'))); + }); +}); + +test('multiple models without collection adds error if no primary model', () => { + withTempDir((tempDir) => { + const metadataFile = path.join(tempDir, 'metadata.yaml'); + fs.writeFileSync(metadataFile, VALID_METADATA_YAML); // id: "test-model" + fs.writeFileSync(path.join(tempDir, 'README.md'), '# Test Model'); + // none of these match "test-model" + fs.writeFileSync(path.join(tempDir, 'othermodel1.bngl'), 'begin model\nend model'); + fs.writeFileSync(path.join(tempDir, 'othermodel2.bngl'), 'begin model\nend model'); + + const errors = []; + validateMetadataFile(metadataFile, errors); + + assert.strictEqual(errors.length, 1); + assert.match(errors[0], /multiple \.bngl files require either a collection section or a primary model file/); + }); +}); + +test('multiple models with collection valid count', () => { + withTempDir((tempDir) => { + const metadataFile = path.join(tempDir, 'metadata.yaml'); + const collectionYaml = VALID_METADATA_YAML + ` +collection: + type: "parameter-fit-variants" + parent_model: "test-model" + variant_key: "test" + count: 2 +`; + fs.writeFileSync(metadataFile, collectionYaml); + fs.writeFileSync(path.join(tempDir, 'README.md'), '# Test Model'); + fs.writeFileSync(path.join(tempDir, 'model1.bngl'), ''); + fs.writeFileSync(path.join(tempDir, 'model2.bngl'), ''); + + const errors = []; + validateMetadataFile(metadataFile, errors); + + assert.deepStrictEqual(errors, []); + }); +});