Standards, dissemination, and best practices in systems biology.

[1]  Chris J. Myers,et al.  Dynamic Flux Balance Analysis Models in SBML , 2018, bioRxiv.

[2]  Su-In Lee,et al.  Reproducibility standards for machine learning in the life sciences , 2021, Nature Methods.

[3]  P. Nithiarasu,et al.  Biomechanics of cells and subcellular components: A comprehensive review of computational models and applications , 2021, International journal for numerical methods in biomedical engineering.

[4]  H. Sauro The Practice of Ensuring Repeatable and Reproducible Computational Models , 2021, 2107.05386.

[5]  David P. Nickerson,et al.  libOmexMeta: enabling semantic annotation of models to support FAIR principles , 2021, Bioinform..

[6]  A. Dobson,et al.  Towards an ecosystem model of infectious disease , 2021, Nature Ecology & Evolution.

[7]  Herbert M Sauro,et al.  Publishing reproducible dynamic kinetic models , 2020, Briefings Bioinform..

[8]  Philipp Noll,et al.  History and Evolution of Modeling in Biotechnology: Modeling & Simulation, Application and Hardware Performance , 2020, Computational and structural biotechnology journal.

[9]  Hiroaki Kitano,et al.  SBML Level 3: an extensible format for the exchange and reuse of biological models , 2020, Molecular systems biology.

[10]  Jonathan R. Karr,et al.  Best Practices for Making Reproducible Biochemical Models. , 2020, Cell systems.

[11]  Alfonso Valencia,et al.  Towards FAIR principles for research software , 2020, Data Sci..

[12]  Matthias König,et al.  Executable Simulation Model of the Liver , 2020, bioRxiv.

[13]  Egon L. Willighagen,et al.  FAIR Principles: Interpretations and Implementation Considerations , 2020, Data Intelligence.

[14]  Bernhard O. Palsson,et al.  BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree , 2019, Nucleic Acids Res..

[15]  Jonathan R. Karr,et al.  BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks , 2019, Genome Biology.

[16]  Philip G Williams,et al.  Characterization of Leptazolines A-D, Polar Oxazolines from the Cyanobacterium Leptolyngbya sp., Reveals a Glitch with the "Willoughby-Hoye" Scripts for Calculating NMR Chemical Shifts. , 2019, Organic letters.

[17]  Jason A. Papin,et al.  Community standards to facilitate development and address challenges in metabolic modeling , 2019, bioRxiv.

[18]  Joseph L. Hellerstein,et al.  Recent advances in biomedical simulations: a manifesto for model engineering , 2019, F1000Research.

[19]  Edoardo Saccenti,et al.  Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling , 2018, bioRxiv.

[20]  Chris J. Myers,et al.  The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2 , 2018, J. Integr. Bioinform..

[21]  Erwin B. Montgomery,et al.  Case Studies in Computational Biomedical Research , 2019, Reproducibility in Biomedical Research.

[22]  Jason G. Bragg,et al.  A quantitative model of nitrogen fixation in the presence of ammonium , 2018, PloS one.

[23]  Jonathan Strutz,et al.  Bayesian inference of metabolic kinetics from genome-scale multiomics data , 2018, bioRxiv.

[24]  Orkun S. Soyer,et al.  Integrated human-virus metabolic stoichiometric modelling predicts host-based antiviral targets against Chikungunya, Dengue and Zika viruses , 2018, Journal of The Royal Society Interface.

[25]  The war over supercooled water , 2018, Physics Today.

[26]  Rajanikanth Vadigepalli,et al.  Credibility, Replicability, and Reproducibility in Simulation for Biomedicine and Clinical Applications in Neuroscience , 2018, Front. Neuroinform..

[27]  Wolfgang Müller,et al.  SABIO-RK: an updated resource for manually curated biochemical reaction kinetics , 2017, Nucleic Acids Res..

[28]  Jonathan R. Karr,et al.  Emerging whole-cell modeling principles and methods. , 2017, Current opinion in biotechnology.

[29]  Perry L. Miller,et al.  Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience , 2016, Journal of Computational Neuroscience.

[30]  John P. A. Ioannidis,et al.  What does research reproducibility mean? , 2016, Science Translational Medicine.

[31]  Richard C. Gerkin,et al.  Unit testing, model validation, and biological simulation , 2015, F1000Research.

[32]  Ronan M. T. Fleming,et al.  Do genome-scale models need exact solvers or clearer standards? , 2015, Molecular systems biology.

[33]  Carole A. Goble,et al.  SEEK: a systems biology data and model management platform , 2015, BMC Systems Biology.

[34]  Nan Xu,et al.  Reconstruction and analysis of the genome-scale metabolic model of Lactobacillus casei LC2W. , 2015, Gene.

[35]  Frank T. Bergmann,et al.  COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project , 2014, BMC Bioinformatics.

[36]  Fangfang Xia,et al.  Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model , 2012, Nucleic acids research.

[37]  Pedro Mendes,et al.  Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network , 2012, BMC Systems Biology.

[38]  H. Lennernäs,et al.  The pharmacokinetics and hepatic disposition of repaglinide in pigs: mechanistic modeling of metabolism and transport. , 2012, Molecular pharmaceutics.

[39]  James D. Herbsleb,et al.  Social coding in GitHub: transparency and collaboration in an open software repository , 2012, CSCW.

[40]  Jacky L. Snoep,et al.  Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language , 2011, BMC Systems Biology.

[41]  Jatinder Singh,et al.  FigShare , 2011, Journal of pharmacology & pharmacotherapeutics.

[42]  Peter J. Hunter,et al.  Bioinformatics Applications Note Databases and Ontologies the Physiome Model Repository 2 , 2022 .

[43]  Neil Swainston,et al.  Further developments towards a genome-scale metabolic model of yeast , 2010, BMC Systems Biology.

[44]  Herbert M. Sauro,et al.  Antimony: a modular model definition language , 2009, Bioinform..

[45]  Sarala M. Wimalaratne,et al.  The Systems Biology Graphical Notation , 2009, Nature Biotechnology.

[46]  Markus J. Herrgård,et al.  A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology , 2008, Nature Biotechnology.

[47]  William Rand,et al.  Making Models Match: Replicating an Agent-Based Model , 2007, J. Artif. Soc. Soc. Simul..

[48]  John Gould,et al.  Toward the automated generation of genome-scale metabolic networks in the SEED , 2007, BMC Bioinformatics.

[49]  Xin-Guang Zhu,et al.  Chlorophyll a fluorescence induction kinetics in leaves predicted from a model describing each discrete step of excitation energy and electron transfer associated with Photosystem II , 2005, Planta.

[50]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[51]  A. Hodgkin,et al.  A quantitative description of membrane current and its application to conduction and excitation in nerve , 1990, Bulletin of mathematical biology.