(Q27499050)

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

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scholarly article

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

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applied mathematics

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structural biology

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1 reference

based on heuristic

inferred from title

Nicolas Le Novère

22

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Martijn P van Iersel

5

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Tomáš Helikar

object named as

Tomáš Helikar

24

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Nicolas Rodriguez

object named as

Nicolas Rodriguez

6

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Emanuel Gonçalves

object named as

Emanuel Gonçalves

12

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object named as

Pedro T Monteiro

15

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Thomas Cokelaer

object named as

Thomas Cokelaer

9

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object named as

Aurélien Naldi

4

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Claudine Chaouiya

object named as

Claudine Chaouiya

1

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object named as

Steffen Klamt

20

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object named as

Denis Thieffry

21

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Julio Saez-Rodriguez

object named as

Julio Saez-Rodriguez

23

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object named as

Finja Büchel

8

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Sarah M Keating

object named as

Sarah M Keating

3

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object named as

Julien Dorier

13

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object named as

Michael Hucka

19

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Andreas Dräger

object named as

Andreas Dräger

7

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Ioannis Xenarios

17

object named as

Ioannis Xenarios

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author name string

Duncan Bérenguier

2

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Bryan Kowal

10

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Benjamin Wicks

11

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Michel Page

14

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Axel von Kamp

16

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Hidde de Jong

18

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publication date

10 December 2013

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BMC Systems Biology

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7

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1

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135

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describes a project that uses

object named as

Cytoscape

2 references

Europe PubMed Central

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

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CZ Software Mentions: A large dataset of software mentions in the biomedical literature

Precise generation of systems biology models from KEGG pathways

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

20 March 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

20 March 2017

Minimum Information About a Simulation Experiment (MIASE)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

20 March 2017

Structural and functional analysis of cellular networks with CellNetAnalyzer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

20 March 2017

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

20 March 2017

A comprehensive, multi-scale dynamical model of ErbB receptor signal transduction in human mammary epithelial cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

20 March 2017

A cell simulator platform: the cell collective

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

20 March 2017

Ergodic sets as cell phenotype of budding yeast cell cycle

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

20 March 2017

Mathematical modelling of cell-fate decision in response to death receptor engagement

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

20 March 2017

Boolean network model predicts cell cycle sequence of fission yeast

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

20 March 2017

Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

20 March 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

20 March 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

20 March 2017

Controlled vocabularies and semantics in systems biology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

20 March 2017

Emergent decision-making in biological signal transduction networks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

7 April 2017

The yeast cell-cycle network is robustly designed

1 reference

https://api.crossref.org/works/10.1186/1752-0509-7-135

22 April 2017

The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster

1 reference

https://api.crossref.org/works/10.1186/1752-0509-7-135

22 April 2017

The Systems Biology Graphical Notation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

7 April 2017

The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

CySBGN: a Cytoscape plug-in to integrate SBGN maps

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

Boolean model of yeast apoptosis as a tool to study yeast and human apoptotic regulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

The TOL network of Pseudomonas putida mt-2 processes multiple environmental inputs into a narrow response space

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

Boolean modeling and fault diagnosis in oxidative stress response

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

Bio-logic builder: a non-technical tool for building dynamical, qualitative models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

A boolean model of the cardiac gene regulatory network determining first and second heart field identity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

State-time spectrum of signal transduction logic models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

Integrating literature-constrained and data-driven inference of signalling networks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

Digital clocks: simple Boolean models can quantitatively describe circadian systems

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

Information routing driven by background chatter in a signaling network

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

ADAM: analysis of discrete models of biological systems using computer algebra

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

Comparing signaling networks between normal and transformed hepatocytes using discrete logical models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

JSBML: a flexible Java library for working with SBML.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

A Boolean model of the gene regulatory network underlying Mammalian cortical area development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

Odefy--from discrete to continuous models.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

SimBoolNet--a Cytoscape plugin for dynamic simulation of signaling networks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

Logical modelling of regulatory networks with GINsim 2.3.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

Boolean network simulations for life scientists

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

LibSBML: an API library for SBML.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

Dynamic simulation of regulatory networks using SQUAD

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

Dynamical roles of biological regulatory circuits

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

Petri net modelling of biological networks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signaling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

A methodology for the structural and functional analysis of signaling and regulatory networks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

Modeling and simulation of molecular biology systems using petri nets: modeling goals of various approaches

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

29 September 2017

Dynamical modeling and analysis of large cellular regulatory networks.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

2 June 2018

BioModels Database: a repository of mathematical models of biological processes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

2 June 2018

An overview of existing modeling tools making use of model checking in the analysis of biochemical networks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

2 June 2018

Querying quantitative logic models (Q2LM) to study intracellular signaling networks and cell-cytokine interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

2 June 2018

A mathematical framework for describing and analysing gene regulatory networks.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

2 June 2018

Homeostasis and Differentiation in Random Genetic Control Networks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3892043

2 June 2018

Boolean network-based model of the Bcl-2 family mediated MOMP regulation

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-135

21 January 2018

Attractor analysis of asynchronous Boolean models of signal transduction networks

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-135

21 January 2018

Dynamics of influenza virus and human host interactions during infection and replication cycle

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-135

21 January 2018

Model-based analysis of an adaptive evolution experiment with Escherichia coli in a pyruvate limited continuous culture with glycerol

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-135

21 January 2018

Modular logical modelling of the budding yeast cell cycle

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-135

21 January 2018

Segmenting the fly embryo: logical analysis of the role of the segment polarity cross-regulatory module

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-135

21 January 2018

Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis.

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-135

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-135

21 January 2018

Temporal logic patterns for querying dynamic models of cellular interaction networks

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-135

21 January 2018

Ruleminer: a knowledge system for supporting high-throughput protein function annotations

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-135

21 January 2018

Logical modelling of gene regulatory networks with GINsim

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-135

21 January 2018

Genetic network analyzer: a tool for the qualitative modeling and simulation of bacterial regulatory networks.

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-135

21 January 2018

HSM - a hybrid system based approach for modelling intracellular networks.

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-135

21 January 2018

The logical analysis of continuous, non-linear biochemical control networks

1 reference

https://pubmed.ncbi.nlm.nih.gov/24321545

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Snoopy--a unifying Petri net framework to investigate biomolecular networks

1 reference

https://pubmed.ncbi.nlm.nih.gov/24321545

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Application of formal methods to biological regulatory networks: extending Thomas' asynchronous logical approach with temporal logic

1 reference

https://pubmed.ncbi.nlm.nih.gov/24321545

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

SBML Level 3 package: Qualitative Models, Version 1, Release 1.

1 reference

https://pubmed.ncbi.nlm.nih.gov/24321545

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1186/1752-0509-7-135

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

DBLP publication ID

journals/bmcsb/ChaouiyaBKNIRDBCKWGDPMKXJHKTNSH13

1 reference

DBLP Dataset 2021-01-02

28 January 2021

Dimensions Publication ID

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release_t5bqbcvifze4do5djgi4srvcxm

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OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

PMC publication ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

PubMed publication ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

ResearchGate publication ID

0 references

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