4.6 Article

BioLQM: A Java Toolkit for the Manipulation and Conversion of Logical Qualitative Models of Biological Networks

Related references

Note: Only part of the references are listed.
Article Physiology

Logical Modeling and Analysis of Cellular Regulatory Networks With GINsim 3.0

Aurelien Naldi et al.

FRONTIERS IN PHYSIOLOGY (2018)

Article Biochemical Research Methods

PyBoolNet: a python package for the generation, analysis and visualization of boolean networks

Hannes Klarner et al.

BIOINFORMATICS (2017)

Article Biochemical Research Methods

MaBoSS 2.0: an environment for stochastic Boolean modeling

Gautier Stoll et al.

BIOINFORMATICS (2017)

Review Genetics & Heredity

Logical Modeling and Dynamical Analysis of Cellular Networks

Wassim Abou-Jaoude et al.

FRONTIERS IN GENETICS (2016)

Article Biochemical Research Methods

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

Nicolas Rodriguez et al.

BIOINFORMATICS (2015)

Article Biochemical Research Methods

Cooperative development of logical modelling standards and tools with CoLoMoTo

Aurelien Naldi et al.

BIOINFORMATICS (2015)

Review Cell Biology

Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks

Regina Samaga et al.

CELL COMMUNICATION AND SIGNALING (2013)

Article Biochemical Research Methods

Boolean modeling of biological regulatory networks: A methodology tutorial

Assieh Saadatpour et al.

METHODS (2013)

Article Mathematics, Applied

A Reduction Method for Boolean Network Models Proven to Conserve Attractors

Assieh Saadatpour et al.

SIAM JOURNAL ON APPLIED DYNAMICAL SYSTEMS (2013)

Article Mathematical & Computational Biology

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

Camille Terfve et al.

BMC SYSTEMS BIOLOGY (2012)

Article Mathematical & Computational Biology

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

Tomas Helikar et al.

BMC SYSTEMS BIOLOGY (2012)

Article Biochemical Research Methods

A SAT-Based Algorithm for Finding Attractors in Synchronous Boolean Networks

Elena Dubrova et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2011)

Article Biology

Reduction of Boolean network models

Alan Veliz-Cuba

JOURNAL OF THEORETICAL BIOLOGY (2011)

Article Biology

Mapping multivalued onto Boolean dynamics

Gilles Didier et al.

JOURNAL OF THEORETICAL BIOLOGY (2011)

Article Biochemistry & Molecular Biology

Controlled vocabularies and semantics in systems biology

Melanie Courtot et al.

MOLECULAR SYSTEMS BIOLOGY (2011)

Article Computer Science, Artificial Intelligence

Petri net representation of multi-valued logical regulatory graphs

C. Chaouiya et al.

NATURAL COMPUTING (2011)

Article Computer Science, Theory & Methods

Dynamically consistent reduction of logical regulatory graphs

Aurelien Naldi et al.

THEORETICAL COMPUTER SCIENCE (2011)

Article Computer Science, Artificial Intelligence

Potassco: The Potsdam Answer Set Solving Collection

Martin Gebser et al.

AI COMMUNICATIONS (2011)

Article Biochemical Research Methods

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

Christoph Muessel et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling

Aurelien Naldi et al.

PLOS COMPUTATIONAL BIOLOGY (2010)

Article Biochemical Research Methods

Synchronous versus asynchronous modeling of gene regulatory networks

Abhishek Garg et al.

BIOINFORMATICS (2008)

Article Mathematical & Computational Biology

Boolean network simulations for life scientists

Istvan Albert et al.

SOURCE CODE FOR BIOLOGY AND MEDICINE (2008)

Article Biochemical Research Methods

A logical model provides insights into T cell receptor signaling

Julio Saez-Rodriguez et al.

PLOS COMPUTATIONAL BIOLOGY (2007)

Article Biochemical Research Methods

Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle

Adrien Faure et al.

BIOINFORMATICS (2006)