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Path2Models specifications

Information


Unique identifier OMICS_20089
Name Path2Models
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Nicolas Le Novère

Publication for Path2Models

Path2Models citations

 (6)
library_books

SABIO RK: an updated resource for manually curated biochemical reaction kinetics

2017
Nucleic Acids Res
PMCID: 5753344
PMID: 29092055
DOI: 10.1093/nar/gkx1065

[…] etics data by third-party software tools and data workflows. These tools include CellDesigner (), VirtualCell (), Sycamore (), SBMLsqueezer (), cy3sabiork (http://apps.cytoscape.org/apps/cy3sabiork), Path2Models (), LigDig (), FAIRDOMHub (). Currently SABIO-RK is accessed mostly (ca. 90%) via web services, which underlines the importance of its integration in modelling and visualization tools.Stan […]

library_books

Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction

2015
PLoS Comput Biol
PMCID: 4643975
PMID: 26566239
DOI: 10.1371/journal.pcbi.1004530

[…] supplemental data to model structure, copy KEGG IDs from Yeast 7 model using common ChEBI identifiers.Yeast 6—downloaded from yeast.sf.netYeast 7—downloaded from yeast.sf.netBiomodels.db—generated by path2models software [], downloaded 11/21/13 from biomodels database [] at https://www.ebi.ac.uk/biomodels-main/BMID000000141353 Each of the models is provided in , formatted as.mat files containing t […]

library_books

BioModels: Content, Features, Functionality, and Use

2015
PMCID: 4360671
PMID: 26225232
DOI: 10.1002/psp4.3

[…] ly the SBML files of the literature models, all the model files (all formats in addition to the SBML files) of the literature models, all the RDF/XML files for the curated models, and all models from Path2Models (in three archives for the metabolic, nonmetabolic, and whole genome metabolism models). In addition to the full database releases, some of the archives are automatically generated on a we […]

library_books

Integration of a constraint based metabolic model of Brassica napus developing seeds with 13C metabolic flux analysis

2014
Front Plant Sci
PMCID: 4271587
PMID: 25566296
DOI: 10.3389/fpls.2014.00724

[…] ta used in systems biology. Various software platforms exist to automate initial steps in the reconstruction process (Hamilton and Reed, ). For example, the SuBliMinaL (Swainston et al., ) toolbox of path2models (Buchel et al., ) in the BioModels database outputs a draft reconstruction of 1672 reactions and 2032 genes for Arabidopsis, leaving the arduous task of model refinement to the reconstruct […]

library_books

A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories

2014
Comput Struct Biotechnol J
PMCID: 4212277
PMID: 25379147
DOI: 10.1016/j.csbj.2014.08.010

[…] luation of multiple potential MCF hosts to see which best accommodates a biosynthetic pathway of interest. In particular, automated methods of genome-scale model building, such as the Model SEED and Path2Models , have produced models for thousands of potential MCF hosts. Database resources such as MetaNetX enable the direct incorporation of new de novo biosynthetic pathways into existing genome- […]

library_books

BioModels linked dataset

2014
BMC Syst Biol
PMCID: 4423647
PMID: 25182954
DOI: 10.1186/s12918-014-0091-5

[…] ogies used for annotating resources []. This allows users to run complex queries, such as ‘find all models which have annotations to some part of membrane’.Future plans include the integration of the Path2Models [] branches of BioModels Database into the BioModels Linked Dataset. […]

Citations

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Path2Models institution(s)
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany; Babraham Institute, Babraham Research Campus, Cambridge, UK; Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK; Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany; HITS gGmbH, Heidelberg, Germany; Caulfield School of Information Technology, Monash University, VIC, Australia; Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA; School of Chemistry, The University of Manchester, Manchester, UK; School of Computer Science, The University of Manchester, Manchester, UK; Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA; Instituto Gulbenkian de Ciência (IGC), Portugal; Institute of Computer Science, University of Halle-Wittenberg, Halle, Germany
Path2Models funding source(s)
Supported by the European Union FP7 project UNICELLSYS (grant number: 201142); the EU project BioPreDyn (ECFP7-KBBE-2011-5 Grant number 289434); the US National Institute of General Medical Sciences (grant number GM070923); the Federal Ministry of Education and Research (BMBF, Germany) in the projects Virtual Liver Network (grant number 0315756) and National Genome Research Network (NGFN-Plus, grant number 01GS08134); Marie Curie International Outgoing Fellowship within FP7 (project AMBiCon, 332020); the US National Institute of General Medical Sciences (grant number GM080219) and the BBSRC (grant number BB/J019259/1); the EMBL-EBI; the Innovative Medicines Initiative Joint Undertaking under grant agreement no. 115156.

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