BioModelsapplication/xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1303010000?filename=MODEL1303010000.pdfhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1303010000?filename=MODEL1303010000-biopax3.owlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1303010000?filename=MODEL1303010000-biopax2.owlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1303010000?filename=MODEL1303010000_url.xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1303010000?filename=MODEL1303010000_urn.xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1303010000?filename=MODEL1303010000.scihttps://www.ebi.ac.uk/biomodels/model/download/MODEL1303010000?filename=MODEL1303010000.pnghttps://www.ebi.ac.uk/biomodels/model/download/MODEL1303010000?filename=MODEL1303010000.xpphttps://www.ebi.ac.uk/biomodels/model/download/MODEL1303010000?filename=MODEL1303010000.vcmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1303010000?filename=MODEL1303010000.mprimaryOK200Jeremy MuhlichNon-curatedordinary differential equation modelL2V1https://www.ebi.ac.uk/biomodels/MODEL130301000023423320falseBioModelsSBMLModelsLopez2013 extrinsic apoptosis M1a embedded2013MODEL1303010000Carlos F Lopez, Jeremy L Muhlich, John A Bachman, Peter K SorgerCarlos F Lopez23423320, Mathematical equations are fundamental to modeling biological networks, but as networks get large and revisions frequent, it becomes difficult to manage equations directly or to combine previously developed models. Multiple simultaneous efforts to create graphical standards, rule-based languages, and integrated software workbenches aim to simplify biological modeling but none fully meets the need for transparent, extensible, and reusable models. In this paper we describe PySB, an approach in which models are not only created using programs, they are programs. PySB draws on programmatic modeling concepts from little b and ProMot, the rule-based languages BioNetGen and Kappa and the growing library of Python numerical tools. Central to PySB is a library of macros encoding familiar biochemical actions such as binding, catalysis, and polymerization, making it possible to use a high-level, action-oriented vocabulary to construct detailed models. As Python programs, PySB models leverage tools and practices from the open-source software community, substantially advancing our ability to distribute and manage the work of testing biochemical hypotheses. We illustrate these ideas using new and previously published models of apoptosis.. null, 9. Department of Cancer Biology, Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN, USA.jeremy_muhlich@hms.harvard.eduHarvard Medical SchoolMathematical equations are fundamental to modeling biological networks, but as networks get large and revisions frequent, it becomes difficult to manage equations directly or to combine previously developed models. Multiple simultaneous efforts to create graphical standards, rule-based languages, and integrated software workbenches aim to simplify biological modeling but none fully meets the need for transparent, extensible, and reusable models. In this paper we describe PySB, an approach in which models are not only created using programs, they are programs. PySB draws on programmatic modeling concepts from little b and ProMot, the rule-based languages BioNetGen and Kappa and the growing library of Python numerical tools. Central to PySB is a library of macros encoding familiar biochemical actions such as binding, catalysis, and polymerization, making it possible to use a high-level, action-oriented vocabulary to construct detailed models. As Python programs, PySB models leverage tools and practices from the open-source software community, substantially advancing our ability to distribute and manage the work of testing biochemical hypotheses. We illustrate these ideas using new and previously published models of apoptosis.Programming biological models in Python using PySB.Lopez Carlos F CF, Muhlich Jeremy L JL, Bachman John A JA, Sorger Peter K PKextrinsic apoptotic signaling pathway in presence of ligand, death receptor-mediated apoptosis, extrinsic apoptosis.Boas, Dnmlp1, python, Dlp1, Anaconda, Drp1, Boa, Anacondas, Pythons, AI450666., 6330417M19Rik, Boinae, PythonDesc, DESCR., Description, Descriptive, Descriptor, description, Product Description/AppearanceDnmlp1, big, Ghrfr, criteria, Polymerizations, Languages, HSN1E, Anaconda, caspase-dependent programmed cell death, Mbp1, Caspase Dependent Apoptosis, Anacondas, Catalyses, Computer, guidelines, type I programmed cell death, apoptotic programmed cell death, Boinae, activation of apoptosis, froggy, Gyltl1a, python, large, Aim, AIM, Generic Action, Extrinsic Pathway Apoptoses, Programmed, Software Engineering, Type I, myd, Computer Program, Application, Boas, Open Source Softwares, DNMT1, programmed cell death by apoptosis., Dlp1, DNMT1_HUMAN, Vocabularies, MDDGB6, Software Application, ligand, Open, Open Source Software, Computer Programs and Programming, Mbp-1, LARGE, apoptosis activator activity, Computer Software Application, BPFD#36, API6, Intrinsic Pathway Apoptosis, high frequency, Reference, Tools, Classic, Classic Apoptosis, great, execution phase of apoptotic process, Classical Apoptosis, Preparation, Reference Standard, CXXC finger protein 9, DNA MTase HsaI, Apoptosis, Applications Software, DNA (cytosine-5)-methyltransferase 1, cellular suicide, Standard Preparation, Open Source, Standard Preparations, Standardization, cell suicide, Computer Software, Papers, Caspase-Dependent Apoptosis, gyltl1b-b, apoptotic cell death, DNMT, Boa, lit, MCMT, Source Softwares, Software Tools, Tool, Python, Programs, Program, Computer Applications, Software Tool, signaling (initiator) caspase activity, induction of apoptosis, Intrinsic Pathway, MDDGA6, mKIAA0609, DNA methyltransferase HsaI, Programmed Cell Death, Extrinsic Pathway Apoptosis, Computer Applications Software, Computer Applications Softwares, Softwares, Caspase-Dependent, KIAA0609, Software, Library, little, CXXC9, fg, apoptosis signaling, Action, ADCADN, Software Applications, gyltl1b, frequent, Dialects, UNQ203/PRO229, CT-2, apoptosis, Standard, Source Software, DNA (cytosine-5-)-methyltransferase 1, Drp1, mdc1d, Engineering, expanded, Cell Death, Dialect, 6330417M19Rik, CXXC-type zinc finger protein 9, Classic Apoptoses, Intrinsic Pathway Apoptoses, Computer Programs, MDC1D, Preparations, Applications, Applications Softwares, enr, clear, hyaline, induction of apoptosis by p53, enlarged, apoptotic program, Standards, Extrinsic Pathway, commitment to apoptosis, Pythons, Classical, Apoptoses, CLEC2C, m.HsaI, Computer Software Applications, AI450666falseLopez2013 - extrinsic apoptosis M1a embeddedNo description2013-03-262005-01-012013-03-01MODEL130301000023423320MODEL1303010000GO:0097190GO:0031264GO:00432939606P50591O14763O15519Q14790Q9NZS9O14727P42574P55212P55211P09874P98170P55957Q92934Q07812Q16611P10415Q07817Q07820Q13794P99999Q9NR28