Status and Challenges of Reproducibility in Computational Systems and Synthetic Biology

[1]  Matthew R. Pocock,et al.  Synthetic Biology Open Language (SBOL) Version 2.3 , 2019, J. Integr. Bioinform..

[2]  Kevin R. DeMarco,et al.  A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows , 2019, PLoS Comput. Biol..

[3]  Radu Grosu,et al.  c302: a multiscale framework for modelling the nervous system of Caenorhabditis elegans , 2018, Philosophical Transactions of the Royal Society B: Biological Sciences.

[4]  Herbert M. Sauro,et al.  Tellurium: An extensible python-based modeling environment for systems and synthetic biology , 2018, Biosyst..

[5]  Marcus J. Tindall,et al.  Multi-scale, whole-system models of liver metabolic adaptation to fat and sugar in non-alcoholic fatty liver disease , 2018, npj Systems Biology and Applications.

[6]  Steffen Klamt,et al.  Memote: A community driven effort towards a standardized genome-scale metabolic model test suite , 2018, bioRxiv.

[7]  Herbert M. Sauro,et al.  Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology , 2018, PLoS Comput. Biol..

[8]  Ozgur B. Akan,et al.  Controlled Information Transfer Through An In Vivo Nervous System , 2018, Scientific Reports.

[9]  James Alastair McLaughlin,et al.  SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology. , 2018, ACS synthetic biology.

[10]  Chris J. Myers,et al.  Harmonizing semantic annotations for computational models in biology , 2018, bioRxiv.

[11]  Jan Hasenauer,et al.  Evaluation of epidermal growth factor receptor signaling effects in gastric cancer cell lines by detailed motility-focused phenotypic characterization linked with molecular analysis , 2017, BMC Cancer.

[12]  David J. Gavaghan,et al.  The zoon r package for reproducible and shareable species distribution modelling , 2017 .

[13]  James Alastair McLaughlin,et al.  SBOLDesigner 2: An Intuitive Tool for Structural Genetic Design. , 2017, ACS synthetic biology.

[14]  Mary Goldman,et al.  Toil enables reproducible, open source, big biomedical data analyses , 2017, Nature Biotechnology.

[15]  Gary R. Mirams,et al.  Sinusoidal voltage protocols for rapid characterisation of ion channel kinetics , 2018, The Journal of physiology.

[16]  Jason A. Papin,et al.  Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions , 2017, Nature Communications.

[17]  Jeremy Leipzig,et al.  A review of bioinformatic pipeline frameworks , 2016, Briefings Bioinform..

[18]  Lucian P. Smith,et al.  phraSED-ML: A paraphrased, human-readable adaptation of SED-ML , 2016, J. Bioinform. Comput. Biol..

[19]  Olaf Wolkenhauer,et al.  COMODI: an ontology to characterise differences in versions of computational models in biology , 2016, Journal of Biomedical Semantics.

[20]  M. Baker.  1,500 scientists lift the lid on reproducibility , 2016, Nature.

[21]  Gary R. Mirams,et al.  The Cardiac Electrophysiology Web Lab , 2016, Biophysical journal.

[22]  Aurélien Naldi,et al.  Geometric analysis of pathways dynamics: Application to versatility of TGF-β receptors , 2015, Biosyst..

[23]  Melissa Haendel,et al.  SEPIO: A Semantic Model for the Integration and Analysis of Scientific Evidence , 2016, ICBO/BioCreative.

[24]  Matthew R. Pocock,et al.  SBOL Visual: A Graphical Language for Genetic Designs , 2015, PLoS biology.

[25]  Nathan D. Price,et al.  Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction , 2015, PLoS Comput. Biol..

[26]  J Chard,et al.  Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development , 2015, CPT: pharmacometrics & systems pharmacology.

[27]  Peter J. Hunter,et al.  OpenCOR: a modular and interoperable approach to computational biology , 2015, Front. Physiol..

[28]  Gary R. Mirams,et al.  Cellular cardiac electrophysiology modeling with Chaste and CellML , 2014, Front. Physiol..

[29]  Nicolas Le Novère,et al.  COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project , 2014, BMC Bioinformatics.

[30]  Stephen D. Larson,et al.  OpenWorm: an open-science approach to modeling Caenorhabditis elegans , 2014, Front. Comput. Neurosci..

[31]  Allan Kuchinsky,et al.  The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology , 2014, Nature Biotechnology.

[32]  Richard C. Gerkin,et al.  Collaborative infrastructure for test-driven scientific model validation , 2014, ICSE Companion.

[33]  A. Uhrmacher,et al.  SESSL , 2014 .

[34]  M. Uhlén,et al.  Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease , 2014, Nature Communications.

[35]  Yolanda Gil,et al.  Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome , 2013, PloS one.

[36]  Carole A. Goble,et al.  The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud , 2013, Nucleic Acids Res..

[37]  James Cheney,et al.  The W3C PROV family of specifications for modelling provenance metadata , 2013, EDBT '13.

[38]  Carole A. Goble,et al.  Why workflows break — Understanding and combating decay in Taverna workflows , 2012, 2012 IEEE 8th International Conference on E-Science.

[39]  Steffen Borchers,et al.  Integrating Cellular Metabolism into a Multiscale Whole-Body Model , 2012, PLoS Comput. Biol..

[40]  Bill Howe,et al.  Virtual Appliances, Cloud Computing, and Reproducible Research , 2012, Computing in Science & Engineering.

[41]  Natapol Pornputtapong,et al.  Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT , 2012, PLoS Comput. Biol..

[42]  C. Begley,et al.  Drug development: Raise standards for preclinical cancer research , 2012, Nature.

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

[44]  Michel Dumontier,et al.  Controlled vocabularies and semantics in systems biology , 2011, Molecular systems biology.

[45]  F. Prinz,et al.  Believe it or not: how much can we rely on published data on potential drug targets? , 2011, Nature Reviews Drug Discovery.

[46]  H. Sauro,et al.  Standard Biological Parts Knowledgebase , 2011, PloS one.

[47]  C. Gille,et al.  HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology , 2010, Molecular systems biology.

[48]  A. Nekrutenko,et al.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.

[49]  Michael L. Hines,et al.  NeuroML: A Language for Describing Data Driven Models of Neurons and Networks with a High Degree of Biological Detail , 2010, PLoS Comput. Biol..

[50]  Carole A. Goble,et al.  myExperiment: a repository and social network for the sharing of bioinformatics workflows , 2010, Nucleic Acids Res..

[51]  Norman W. Paton,et al.  SBRML: a markup language for associating systems biology data with models , 2010, Bioinform..

[52]  Chris J. Myers,et al.  Tablet—next generation sequence assembly visualization , 2009, Bioinform..

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

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

[55]  Deepak Chandran,et al.  TinkerCell: modular CAD tool for synthetic biology , 2009, Journal of biological engineering.

[56]  N. Kikuchi,et al.  CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks , 2008, Proceedings of the IEEE.

[57]  Giorgio Valle,et al.  The Gene Ontology project in 2008 , 2007, Nucleic Acids Res..

[58]  M. Ashburner,et al.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration , 2007, Nature Biotechnology.

[59]  Mudita Singhal,et al.  COPASI - a COmplex PAthway SImulator , 2006, Bioinform..

[60]  Herbert M. Sauro,et al.  SBW - A Modular Framework for Systems Biology , 2006, Proceedings of the 2006 Winter Simulation Conference.

[61]  Edward A. Lee,et al.  Scientific workflow management and the Kepler system , 2006, Concurr. Comput. Pract. Exp..

[62]  Jan-Hendrik S. Hofmeyr,et al.  Modelling cellular systems with PySCeS , 2005, Bioinform..

[63]  Jacky L. Snoep,et al.  Web-based kinetic modelling using JWS Online , 2004, Bioinform..

[64]  Catherine M Lloyd,et al.  CellML: its future, present and past. , 2004, Progress in biophysics and molecular biology.

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