BMC Systems Biology | |
Path2Models: large-scale generation of computational models from biochemical pathway maps | |
Nicolas Le Novère4  Andreas Dräger5  Camille Laibe9  Falk Schreiber1,10  Julio Saez-Rodriguez9  Claudine Chaouiya2  Andreas Zell5  Pedro Mendes8  Wolfgang Müller7  Douglas B Kell1  Michael Hucka3  Henning Hermjakob9  Michael Wybrow6  Matthias Rall5  Sarah Keating9  Martijn van Iersel9  Martin Golebiewski7  Mihai Glont9  Michael Schubert9  Florian Mittag5  Roland Keller5  Tobias Czauderna1,10  Clemens Wrzodek5  Neil Swainston8  Nicolas Rodriguez4  Finja Büchel5  | |
[1] School of Chemistry, The University of Manchester, Manchester M13 9PL, UK;Instituto Gulbenkian de Ciência (IGC), Oeiras P-2780-156, Portugal;Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125, USA;Babraham Institute, Babraham Research Campus, Cambridge, UK;Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen 72076, Germany;Caulfield School of Information Technology, Monash University, Victoria 3800, Australia;HITS gGmbH, D-69118, Heidelberg, Germany;Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK;European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK;Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben D-06466, Germany | |
关键词: SBML; SBGN; Logical models; Constraint based models; Modular rate law; | |
Others : 1141963 DOI : 10.1186/1752-0509-7-116 |
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received in 2013-07-19, accepted in 2013-10-23, 发布年份 2013 | |
【 摘 要 】
Background
Systems biology projects and omics technologies have led to a growing number of biochemical pathway models and reconstructions. However, the majority of these models are still created de novo, based on literature mining and the manual processing of pathway data.
Results
To increase the efficiency of model creation, the Path2Models project has automatically generated mathematical models from pathway representations using a suite of freely available software. Data sources include KEGG, BioCarta, MetaCyc and SABIO-RK. Depending on the source data, three types of models are provided: kinetic, logical and constraint-based. Models from over 2 600 organisms are encoded consistently in SBML, and are made freely available through BioModels Database at http://www.ebi.ac.uk/biomodels-main/path2models webcite. Each model contains the list of participants, their interactions, the relevant mathematical constructs, and initial parameter values. Most models are also available as easy-to-understand graphical SBGN maps.
Conclusions
To date, the project has resulted in more than 140 000 freely available models. Such a resource can tremendously accelerate the development of mathematical models by providing initial starting models for simulation and analysis, which can be subsequently curated and further parameterized.
【 授权许可】
2013 Büchel et al.; licensee BioMed Central Ltd.
【 预 览 】
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20150327180427936.pdf | 1539KB | download | |
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