SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks

JSBML 1.0: providing a smorgasbord of options to encode systems biology models: Table 1.

(2015) Nicolas Rodriguez et al.   BIOINFORMATICS

GRN2SBML: automated encoding and annotation of inferred gene regulatory networks complying with SBML

(2013) S. Vlaic et al.   BIOINFORMATICS

Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0

(2013) Michael Weber et al.   BMC Systems Biology

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

(2013) Claudine Chaouiya et al.   BMC Systems Biology

The systems biology simulation core algorithm

(2013) Roland Keller et al.   BMC Systems Biology

Precise generation of systems biology models from KEGG pathways

(2013) Clemens Wrzodek et al.   BMC Systems Biology

Path2Models: large-scale generation of computational models from biochemical pathway maps

(2013) Finja Büchel et al.   BMC Systems Biology

Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction

(2013) E. J. O{middle dot}Brien et al.   Molecular Systems Biology

Systems Modelling of NHEJ Reveals the Importance of Redox Regulation of Ku70/80 in the Dynamics of DNA Damage Foci

(2013) David Dolan et al.   PLoS One

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Biological network inference for drug discovery

(2012) Paola Lecca et al.   DRUG DISCOVERY TODAY

JSBML: a flexible Java library for working with SBML

(2011) Andreas Dräger et al.   BIOINFORMATICS

KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats

(2011) Clemens Wrzodek et al.   BIOINFORMATICS

Controlled vocabularies and semantics in systems biology

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

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

SABIO-RK--database for biochemical reaction kinetics

(2011) U. Wittig et al.   NUCLEIC ACIDS RESEARCH

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

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

A quantitative comparison of Calvin–Benson cycle models

(2011) Anne Arnold et al.   TRENDS IN PLANT SCIENCE

Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation

(2010) Wolfram Liebermeister et al.   BIOINFORMATICS

Odefy -- From discrete to continuous models

(2010) Jan Krumsiek et al.   BMC BIOINFORMATICS

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

(2010) Jan Schellenberger et al.   BMC BIOINFORMATICS

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

SBML2LATEX: Conversion of SBML files into human-readable reports

(2009) A. Drager et al.   BIOINFORMATICS

Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies

(2009) Andreas Dräger et al.   BMC Systems Biology

Designing and encoding models for synthetic biology

(2009) L. Endler et al.   Journal of the Royal Society Interface

The Systems Biology Graphical Notation

(2009) Nicolas Le Novère et al.   NATURE BIOTECHNOLOGY

Modeling of the Bacterial Mechanism of Methicillin-Resistance by a Systems Biology Approach

(2009) Ida Autiero et al.   PLoS One

LibSBML: an API Library for SBML

(2008) B. J. Bornstein et al.   BIOINFORMATICS

Gene regulatory network inference: Data integration in dynamic models—A review

(2008) Michael Hecker et al.   BIOSYSTEMS

SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks

(2008) Andreas Dräger et al.   BMC Systems Biology

CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks

(2008) A. Funahashi et al.   PROCEEDINGS OF THE IEEE