. (2009). Credit where credit is overdue. Nature biotechnology. 27 [PubMed]

Altman DG, Simera I, Hoey J, Moher D, Schulz K. (2008). EQUATOR: reporting guidelines for health research. Open medicine : a peer-reviewed, independent, open-access journal. 2 [PubMed]

Arrowsmith J. (2011). Trial watch: Phase II failures: 2008-2010. Nature reviews. Drug discovery. 10 [PubMed]

Asai Y et al. (2008). Specifications of insilicoML 1.0: a multilevel biophysical model description language. The journal of physiological sciences : JPS. 58 [PubMed]

Bechhofer S. (2013). Why linked data is not enough for scientists Future Generation Comput. Syst. 29(2)

Begley CG, Ellis LM. (2012). Drug development: Raise standards for preclinical cancer research. Nature. 483 [PubMed]

Begley CG, Ioannidis JP. (2015). Reproducibility in science: improving the standard for basic and preclinical research. Circulation research. 116 [PubMed]

Bell AW et al. (2009). A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. Nature methods. 6 [PubMed]

Bergmann FT et al. (2014). COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC bioinformatics. 15 [PubMed]

Bergmann FT, Cooper J, Le Novère N, Nickerson D, Waltemath D. (2015). Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2. Journal of integrative bioinformatics. 12 [PubMed]

Boettiger . (2015). An introduction to Docker for reproducible research ACM SIGOPS Oper. Syst. Rev.. 49(1)

Collins FS, Tabak LA. (2014). Policy: NIH plans to enhance reproducibility. Nature. 505 [PubMed]

Cooper J, Scharm M, Mirams GR. (2016). The Cardiac Electrophysiology Web Lab. Biophysical journal. 110 [PubMed]

Courtot M et al. (2011). Controlled vocabularies and semantics in systems biology. Molecular systems biology. 7 [PubMed]

Demir E et al. (2010). The BioPAX community standard for pathway data sharing. Nature biotechnology. 28 [PubMed]

Donoho DL, Buckheit JB. (1995). Wavelab and reproducible research Wavelets and Statistics.

ENCODE Project Consortium. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature. 489 [PubMed]

Errington TM et al. (2014). An open investigation of the reproducibility of cancer biology research. eLife. 3 [PubMed]

Et AL, Bechhofer S. (). Research objects: Towards exchange and reuse of digital knowledge Future Web Collaborative Sci.

Et AL, Hetherington J. (2007). Addressing the challenges of multiscale model management in systems biology Comput. Chemi. Eng.. 31(8)

Et AL, Hucka M. (2011). A profile of today’s SBML–Compatible software Proc. IEEE e-Science Workshops.

Et AL, Lord P. (2006). Large-scale data sharing in the life sciences: Data standards, incentives, barriers and funding models, the joint data standards study http://www. mrc. ac.uk/pdfjdss_final_report.pdf.

Et AL, Piccolo SR. (2015). Tools and techniques for computational reproducibility, bioRxiv.

Galdzicki M et al. (2014). The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nature biotechnology. 32 [PubMed]

García-Berthou E, Alcaraz C. (2004). Incongruence between test statistics and P values in medical papers. BMC medical research methodology. 4 [PubMed]

Garijo D et al. (2013). Quantifying reproducibility in computational biology: the case of the tuberculosis drugome. PloS one. 8 [PubMed]

Gleeson P et al. (2010). NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PLoS computational biology. 6 [PubMed]

Goecks J, Nekrutenko A, Taylor J, Galaxy Team. (2010). Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome biology. 11 [PubMed]

Henkel R. (2015). Combining computational models, semantic annotations and simulation experiments in a graph database Database. 2015

Henkel R, Endler L, Peters A, Le Novère N, Waltemath D. (2010). Ranked retrieval of Computational Biology models. BMC bioinformatics. 11 [PubMed]

Hines ML, Morse T, Migliore M, Carnevale NT, Shepherd GM. (2004). ModelDB: A Database to Support Computational Neuroscience. Journal of computational neuroscience. 17 [PubMed]

Hoops S et al. (2006). COPASI--a COmplex PAthway SImulator. Bioinformatics (Oxford, England). 22 [PubMed]

Hucka M et al. (2003). The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics (Oxford, England). 19 [PubMed]

Hucka M et al. (2015). Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative. Frontiers in bioengineering and biotechnology. 3 [PubMed]

Ioannidis JP. (2005). Why most published research findings are false. PLoS medicine. 2 [PubMed]

Ioannidis JP. (2014). How to make more published research true. PLoS medicine. 11 [PubMed]

Ioannidis JP et al. (2009). Repeatability of published microarray gene expression analyses. Nature genetics. 41 [PubMed]

Ioannidis JP et al. (2014). Increasing value and reducing waste in research design, conduct, and analysis. Lancet (London, England). 383 [PubMed]

Jaeger D et al. (2012). The Open Source Brain Initiative: enabling collaborative modelling in computational neuroscience Twenty First Annual Computational Neuroscience Meeting: CNS*2012. 13(Suppl 1)

Juty N et al. (2015). BioModels: Content, Features, Functionality, and Use. CPT: pharmacometrics & systems pharmacology. 4 [PubMed]

Juty N, Le Novère N, Laibe C. (2012). Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. Nucleic acids research. 40 [PubMed]

Kell DB, Ohagan S. (2015). Software review: The KNIME work- flow environment and its applications in genetic programming and machine learning Genetic Program. Evolvable Mach.. 16(3)

Krause F et al. (2010). Annotation and merging of SBML models with semanticSBML. Bioinformatics (Oxford, England). 26 [PubMed]

Le Novère N. (2006). Model storage, exchange and integration. BMC neuroscience. 7 Suppl 1 [PubMed]

Le Novère N et al. (2005). Minimum information requested in the annotation of biochemical models (MIRIAM). Nature biotechnology. 23 [PubMed]

Le Novère N et al. (2009). The Systems Biology Graphical Notation. Nature biotechnology. 27 [PubMed]

Leek JT, Peng RD. (2015). Opinion: Reproducible research can still be wrong: adopting a prevention approach. Proceedings of the National Academy of Sciences of the United States of America. 112 [PubMed]

Lehrer J. (2010). The truth wears off New Yorker. 13

Li C et al. (2010). BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC systems biology. 4 [PubMed]

MacCoun R, Perlmutter S. (2015). Blind analysis: Hide results to seek the truth. Nature. 526 [PubMed]

Machné R et al. (2006). The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks. Bioinformatics (Oxford, England). 22 [PubMed]

Mobley A, Linder SK, Braeuer R, Ellis LM, Zwelling L. (2013). A survey on data reproducibility in cancer research provides insights into our limited ability to translate findings from the laboratory to the clinic. PloS one. 8 [PubMed]

Mons B. (2005). Which gene did you mean? BMC bioinformatics. 6 [PubMed]

Mullard A. (2011). Reliability of 'new drug target' claims called into question. Nature reviews. Drug discovery. 10 [PubMed]

Murphy SN et al. (2010). Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2). Journal of the American Medical Informatics Association : JAMIA. 17 [PubMed]

Nosek BA et al. (2015). SCIENTIFIC STANDARDS. Promoting an open research culture. Science (New York, N.Y.). 348 [PubMed]

Nuzzo R. (2015). How scientists fool themselves - and how they can stop. Nature. 526 [PubMed]

Olivier BG, Snoep JL. (2004). Web-based kinetic modelling using JWS Online. Bioinformatics (Oxford, England). 20 [PubMed]

Pattinson D. (2014). PLOS ONE launches reproducibility initiative PLOS ONE Community Blog http://blogs.plos. org/everyone/2012/08/14/plos-one-launches-reproducibility-initiative/.

Peng RD. (2011). Reproducible research in computational science. Science (New York, N.Y.). 334 [PubMed]

Penkler G et al. (2015). Construction and validation of a detailed kinetic model of glycolysis in Plasmodium falciparum. The FEBS journal. 282 [PubMed]

Piwowar HA, Day RS, Fridsma DB. (2007). Sharing detailed research data is associated with increased citation rate. PloS one. 2 [PubMed]

Piwowar HA, Vision TJ, Whitlock MC. (2011). Data archiving is a good investment. Nature. 473 [PubMed]

Popper K. (2005). The Logic of Scientific Discovery.

Prinz F, Schlange T, Asadullah K. (2011). Believe it or not: how much can we rely on published data on potential drug targets? Nature reviews. Drug discovery. 10 [PubMed]

Richard B. (2014). Reproducibility undergoes scrutiny BioScience. 64(4)

Rodriguez N et al. (2016). The systems biology format converter. BMC bioinformatics. 17 [PubMed]

Ronald P. (2013). Lab life: The anatomy of a retraction Scientific American, OCT. 2013, last accessed online: 2015-08-07 http://blogs.scientificamerican.com/food-matters/lab-life-the-anatomy-of-a-retraction/.

Sandve GK, Nekrutenko A, Taylor J, Hovig E. (2013). Ten simple rules for reproducible computational research. PLoS computational biology. 9 [PubMed]

Sansone SA et al. (2012). Toward interoperable bioscience data. Nature genetics. 44 [PubMed]

Sauro HM, Bergmann FT. (2006). SBW—A modular framework for systems biology Proc. 38th Conf. Winter Simul..

Scharm M. (2015). Combine archive show case,” University of Rostock, ostock, Germany, Tech. Rep., https://github.com/SemsProject/CombineArchiveShowCase.

Scharm M, Wolkenhauer O, Waltemath D. (2016). An algorithm to detect and communicate the differences in computational models describing biological systems. Bioinformatics (Oxford, England). 32 [PubMed]

Schnell S. (2015). Ten Simple Rules for a Computational Biologist's Laboratory Notebook. PLoS computational biology. 11 [PubMed]

Sneddon TP et al. (2014). GigaDB: promoting data dissemination and reproducibility. Database : the journal of biological databases and curation. 2014 [PubMed]

Stodden . (2013). Setting the default to reproducible Comput. Sci. Res. SIAM News. 46

Stodden V, Guo P, Ma Z. (2013). Toward Reproducible Computational Research: An Empirical Analysis of Data and Code Policy Adoption by Journals. PloS one. 8 [PubMed]

Swat MJ et al. (2015). Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development. CPT: pharmacometrics & systems pharmacology. 4 [PubMed]

The Reproducibility Initiative. (2015). Replication best practices last accessed 2015-08-03.

Topalidou M, Leblois A, Boraud T, Rougier NP. (2015). A long journey into reproducible computational neuroscience. Frontiers in computational neuroscience. 9 [PubMed]

Waltemath D. (2013). Reproducibility of model-based results in systems biology System Biology.

Waltemath D. (2014). Meeting report from the fourth meeting of the computational modeling in biology network (COMBINE) Standards Genomic Sci.. 9(3)

Waltemath D et al. (2011). Minimum Information About a Simulation Experiment (MIASE). PLoS computational biology. 7 [PubMed]

Waltemath D et al. (2011). Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language. BMC systems biology. 5 [PubMed]

Waltemath D et al. (2016). Toward Community Standards and Software for Whole-Cell Modeling. IEEE transactions on bio-medical engineering. 63 [PubMed]

Waltemath D, Scharm M. (2015). Extracting reproducible simulation stud- ies from model repositories using the combinearchive toolkit Datenbanksysteme fur Business, Technologie und Web.

Weidemann A et al. (2008). SYCAMORE--a systems biology computational analysis and modeling research environment. Bioinformatics (Oxford, England). 24 [PubMed]

Wolstencroft K et al. (2015). SEEK: a systems biology data and model management platform. BMC systems biology. 9 [PubMed]

Wruck W, Peuker M, Regenbrecht CR. (2014). Data management strategies for multinational large-scale systems biology projects. Briefings in bioinformatics. 15 [PubMed]

Yu T et al. (2011). The Physiome Model Repository 2. Bioinformatics (Oxford, England). 27 [PubMed]