COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

Integrated metabolic spatial-temporal model for the prediction of ammonia detoxification during liver damage and regeneration

(2014) Freimut Schliess et al.   HEPATOLOGY

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology

(2014) Michal Galdzicki et al.   NATURE BIOTECHNOLOGY

Structuring research methods and data with the research object model: genomics workflows as a case study

(2014) Kristina M Hettne et al.   Journal of Biomedical Semantics

Improving the reuse of computational models through version control

(2013) D. Waltemath et al.   BIOINFORMATICS

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

Integration of Biochemical and Electrical Signaling-Multiscale Model of the Medium Spiny Neuron of the Striatum

(2013) Michele Mattioni et al.   PLoS One

Ten Simple Rules for Reproducible Computational Research

(2013) Geir Kjetil Sandve et al.   PLoS Computational Biology

Software support for SBGN maps: SBGN-ML and LibSBGN

(2012) M. P. van Iersel et al.   BIOINFORMATICS

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Revision history aware repositories of computational models of biological systems

(2011) Andrew K Miller et al.   BMC BIOINFORMATICS

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

(2011) Dagmar Waltemath et al.   BMC Systems Biology

Controlled vocabularies and semantics in systems biology

(2011) M. Courtot et al.   Molecular Systems Biology

Identifiers.org and MIRIAM Registry: community resources to provide persistent identification

(2011) N. Juty et al.   NUCLEIC ACIDS RESEARCH

High-throughput functional curation of cellular electrophysiology models

(2011) Jonathan Cooper et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Minimum Information About a Simulation Experiment (MIASE)

(2011) Dagmar Waltemath et al.   PLoS Computational Biology

SBRML: a markup language for associating systems biology data with models

(2010) Joseph O. Dada et al.   BIOINFORMATICS

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

(2010) Chen Li et al.   BMC Systems Biology

Accessible Reproducible Research

(2010) J. P. Mesirov   SCIENCE

The Systems Biology Graphical Notation

(2009) Nicolas Le Novère et al.   NATURE BIOTECHNOLOGY

FieldML: concepts and implementation

(2009) G. R. Christie et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Practical application of CellML 1.1: The integration of new mechanisms into a human ventricular myocyte model

(2008) David Nickerson et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY