Article (Scientific journals)
FALCON: A Toolbox for the Fast Contextualisation of Logical Networks.
DE LANDTSHEER, Sébastien; TRAIRATPHISAN, Panuwat; LUCARELLI, Philippe et al.
2017In Bioinformatics
Peer reviewed
 

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Abstract :
[en] Motivation: Mathematical modelling of regulatory networks allows for the discovery of knowledge at the system level. However, existing modelling tools are often computation-heavy and do not offer intuitive ways to explore the model, to test hypotheses or to interpret the results biologically. Results: We have developed a computational approach to contextualise logical models of regulatory networks with biological measurements based on a probabilistic description of rule-based interactions between the different molecules. Here, we propose a Matlab toolbox, FALCON, to automatically and efficiently build and contextualise networks, which includes a pipeline for conducting parameter analysis, knockouts, and easy and fast model investigation. The contextualised models could then provide qualitative and quantitative information about the network and suggest hypotheses about biological processes. Availability and implementation: FALCON is freely available for non-commercial users on GitHub under the GPLv3 licence. The toolbox, installation instructions, full documentation and test datasets are available at https://github.com/sysbiolux/FALCON . FALCON runs under Matlab (MathWorks) and requires the Optimization Toolbox. Contact: thomas.sauter@uni.lu. Supplementary information: Supplementary data are available at Bioinformatics online.
Research center :
University of Luxembourg: The Faculty of Science, Technology and Communication (FSTC)
Disciplines :
Life sciences: Multidisciplinary, general & others
Author, co-author :
DE LANDTSHEER, Sébastien 
TRAIRATPHISAN, Panuwat 
LUCARELLI, Philippe ;  University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit
SAUTER, Thomas ;  University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit
External co-authors :
no
Language :
English
Title :
FALCON: A Toolbox for the Fast Contextualisation of Logical Networks.
Publication date :
July 2017
Journal title :
Bioinformatics
ISSN :
1367-4803
eISSN :
1367-4811
Publisher :
Bioinformatics, United Kingdom
Peer reviewed :
Peer reviewed
European Projects :
H2020 - 642295 - MEL-PLEX - Exploiting MELanoma disease comPLEXity to address European research training needs in translational cancer systems biology and cancer systems medicine
FnR Project :
FNR7643621 - Predicting Individual Sensitivity Of Malignant Melanoma To Combination Therapies By Statistical And Network Modeling On Innovative 3d Organotypic Screening Models, 2013 (01/05/2015-30/04/2018) - Thomas Sauter
Funders :
FNR - Fonds National de la Recherche [LU]
Horizon 2020
CE - Commission Européenne [BE]
Available on ORBilu :
since 06 July 2017

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