FlexFlux: combining metabolic flux and regulatory network analyses

Cooperative development of logical modelling standards and tools with CoLoMoTo

(2015) A. Naldi et al.   BIOINFORMATICS

Quantitative and logic modelling of molecular and gene networks

(2015) Nicolas Le Novère   NATURE REVIEWS GENETICS

Optimizing genome-scale network reconstructions

(2014) Jonathan Monk et al.   NATURE BIOTECHNOLOGY

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

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim 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

Software applications for flux balance analysis

(2012) M. Lakshmanan et al.   BRIEFINGS IN BIOINFORMATICS

Modeling Regulatory Networks to Understand Plant Development: Small Is Beautiful

(2012) Alistair M. Middleton et al.   PLANT CELL

Multidimensional Optimality of Microbial Metabolism

(2012) R. Schuetz et al.   SCIENCE

Global Network Reorganization During Dynamic Adaptations of Bacillus subtilis Metabolism

(2012) J. M. Buescher et al.   SCIENCE

JSBML: a flexible Java library for working with SBML

(2011) Andreas Dräger et al.   BIOINFORMATICS

FASIMU: flexible software for flux-balance computation series in large metabolic networks

(2011) Andreas Hoppe et al.   BMC BIOINFORMATICS

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

(2011) Jan Schellenberger et al.   Nature Protocols

Logic-Based Models for the Analysis of Cell Signaling Networks

(2010) Melody K. Morris et al.   BIOCHEMISTRY

SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks

(2010) A. Gevorgyan et al.   BIOINFORMATICS

BoolNet—an R package for generation, reconstruction and analysis of Boolean networks

(2010) Christoph Müssel et al.   BIOINFORMATICS

Computationally efficient flux variability analysis

(2010) Steinn Gudmundsson et al.   BMC BIOINFORMATICS

OptFlux: an open-source software platform for in silico metabolic engineering

(2010) Isabel Rocha et al.   BMC Systems Biology

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

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

(2010) Ines Thiele et al.   Nature Protocols

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks inEscherichia coliandMycobacterium tuberculosis

(2010) Sriram Chandrasekaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Logical modelling of regulatory networks with GINsim 2.3

(2009) A. Naldi et al.   BIOSYSTEMS

Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli

(2008) Markus W. Covert et al.   BIOINFORMATICS

The Systems Biology Research Tool: evolvable open-source software

(2008) Jeremiah Wright et al.   BMC Systems Biology

Carbon catabolite repression in bacteria: many ways to make the most out of nutrients

(2008) Boris Görke et al.   NATURE REVIEWS MICROBIOLOGY

Modelling and analysis of gene regulatory networks

(2008) Guy Karlebach et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Emergent decision-making in biological signal transduction networks

(2008) T. Helikar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA