Standards, dissemination, and best practices in systems biology.
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[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.