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

Precise generation of systems biology models from KEGG pathways

(2013) Clemens Wrzodek et al.   BMC Systems Biology

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes

(2013) Kieran Smallbone et al.   FEBS LETTERS

An analysis of a ‘community-driven’ reconstruction of the human metabolic network

(2013) Neil Swainston et al.   Metabolomics

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

(2013) Rasmus Agren et al.   PLoS Computational Biology

Software support for SBGN maps: SBGN-ML and LibSBGN

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

Qualitative translation of relations from BioPAX to SBML qual

(2012) Finja Büchel et al.   BIOINFORMATICS

Improving metabolic flux predictions using absolute gene expression data

(2012) Dave Lee et al.   BMC Systems Biology

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms

(2012) Camille Terfve et al.   BMC Systems Biology

The Cell Collective: Toward an open and collaborative approach to systems biology

(2012) Tomáš Helikar et al.   BMC Systems Biology

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

State–time spectrum of signal transduction logic models

(2012) Aidan MacNamara et al.   PHYSICAL BIOLOGY

The Units Ontology: a tool for integrating units of measurement in science

(2012) G. V. Gkoutos et al.   Database-The Journal of Biological Databases and Curation

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

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

(2011) Ines Thiele et al.   BMC Systems Biology

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

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

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis

(2011) Matthew A. Oberhardt et al.   PLoS Computational Biology

Logic-Based Models for the Analysis of Cell Signaling Networks

(2010) Melody K. Morris et al.   BIOCHEMISTRY

Editing, validating and translating of SBGN maps

(2010) T. Czauderna et al.   BIOINFORMATICS

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

(2010) Wolfram Liebermeister et al.   BIOINFORMATICS

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

(2010) Jan Schellenberger et al.   BMC BIOINFORMATICS

Integration of metabolic databases for the reconstruction of genome-scale metabolic networks

(2010) Karin Radrich et al.   BMC Systems Biology

Further developments towards a genome-scale metabolic model of yeast

(2010) Paul D Dobson et al.   BMC Systems Biology

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

(2010) Chen Li et al.   BMC Systems Biology

Towards a genome-scale kinetic model of cellular metabolism

(2010) Kieran Smallbone et al.   BMC Systems Biology

Mining metabolites: extracting the yeast metabolome from the literature

(2010) Chikashi Nobata et al.   Metabolomics

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

The BioPAX community standard for pathway data sharing

(2010) Emek Demir et al.   NATURE BIOTECHNOLOGY

A QconCAT informatics pipeline for the analysis, visualization and sharing of absolute quantitative proteomics data

(2010) Neil Swainston et al.   PROTEOMICS

Mass spectrometry tools and metabolite-specific databases for molecular identification in metabolomics

(2009) M. Brown et al.   ANALYST

libAnnotationSBML: a library for exploiting SBML annotations

(2009) N. Swainston et al.   BIOINFORMATICS

The Systems Biology Graphical Notation

(2009) Nicolas Le Novère et al.   NATURE BIOTECHNOLOGY

The CellML Model Repository

(2008) C. M. Lloyd et al.   BIOINFORMATICS

LibSBML: an API Library for SBML

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

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

(2008) Andreas Dräger et al.   BMC Systems Biology

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

(2008) Markus J Herrgård et al.   NATURE BIOTECHNOLOGY

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH

WikiPathways: Pathway Editing for the People

(2008) Alexander R Pico et al.   PLOS BIOLOGY