Mining biological pathways using WikiPathways web services.

Autor: Thomas Kelder, Alexander R Pico, Kristina Hanspers, Martijn P van Iersel, Chris Evelo, Bruce R Conklin

Publikováno v: PLoS ONE, Vol 4, Iss 7, p e6447 (2009)

WikiPathways is a platform for creating, updating, and sharing biological pathways [1]. Pathways can be edited and downloaded using the wiki-style website. Here we present a SOAP web service that provides programmatic access to WikiPathways that is c

Externí odkaz: https://doaj.org/article/d26135ccf4444b89931d591aec6ac7a5

The systems biology format converter

Autor: Piero Dalle Pezze, Lu Li, Nicolas Le Novère, Kedar Nath Natarajan, Martijn P. van Iersel, David Tolnay, Chris T. Evelo, Jean-Baptiste Pettit, Nicolas Rodriguez, Martina Kutmon, Gaël Jalowicki, Arnaud Henry, Melanie I. Stefan

Publikováno v: Rodriguez, N, Pettit, J-B, Dalle Pezze, P, Li, L, Henry, A, van Iersel, M P, Jalowicki, G, Kutmon, M, Natarajan, K N, Tolnay, D, Stefan, M I, Evelo, C T & Le Novère, N 2016, ' The systems biology format converter ', BMC Bioinformatics, vol. 17, no. 1, pp. 154 . https://doi.org/10.1186/s12859-016-1000-2
BMC Bioinformatics
BMC Bioinformatics, 17:154. BioMed Central Ltd

Background Interoperability between formats is a recurring problem in systems biology research. Many tools have been developed to convert computational models from one format to another. However, they have been developed independently, resulting in r

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a988dfd5913aaf358229ee0accf28bfb
https://www.pure.ed.ac.uk/ws/files/25019193/Rodriguez_et_al..pdf

Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment

Autor: Martina Kutmon, Chris T. Evelo, Anwesha Bohler, Egon Willighagen, Lars M. T. Eijssen, Magali Jaillard, Christ Leemans, Martijn P. van Iersel

Publikováno v: BMC Bioinformatics
BMC Bioinformatics, 16:267. BioMed Central Ltd

Background Biological pathways are descriptive diagrams of biological processes widely used for functional analysis of differentially expressed genes or proteins. Primary data analysis, such as quality control, normalisation, and statistical analysis

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5231dcf136aed8aeea2b07b90eb66d9f
https://doi.org/10.1186/s12859-015-0708-8

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

Autor: Claudine Chaouiya, Nicolas Le Novère, Sarah M. Keating, Duncan Berenguier, Martijn P. van Iersel, Tomáš Helikar, Aurélien Naldi, Denis Thieffry

Publikováno v: Journal of Integrative Bioinformatics, Vol 12, Iss 2, Pp 691-730 (2015)

Summary Quantitative methods for modelling biological networks require an in-depth knowledge of the biochemical reactions and their stoichiometric and kinetic parameters. In many practical cases, this knowledge is missing. This has led to the develop

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1fbed19be71a02f6388fd8d2534bcddd

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

Autor: Michel Page, Finja Büchel, Claudine Chaouiya, Benjamin Wicks, Nicolas Le Novère, Steffen Klamt, Bryan Kowal, Duncan Berenguier, Hidde de Jong, Axel von Kamp, Aurélien Naldi, Denis Thieffry, Andreas Dräger, Nicolas Rodriguez, Michael Hucka, Sarah M. Keating, Pedro T. Monteiro, Thomas Cokelaer, Julien Dorier, Emanuel Gonçalves, Julio Saez-Rodriguez, Ioannis Xenarios, Martijn P. van Iersel, Tomáš Helikar

Publikováno v: Repositório Científico de Acesso Aberto de Portugal
Repositório Científico de Acesso Aberto de Portugal (RCAAP)
instacron:RCAAP
BMC Systems Biology
BMC Systems Biology, 2013, 7 (1), pp.135. ⟨10.1186/1752-0509-7-135⟩
BMC Systems Biology, BioMed Central, 2013, 7 (1), pp.135. ⟨10.1186/1752-0509-7-135⟩
BMC Systems Biology, vol. 7, pp. 135
Chaouiya, Claudine; Bérenguier, Duncan; Keating, Sarah M; Naldi, Aurélien; van Iersel, Martijn P; Rodriguez, Nicolas; et al.(2013). SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Systems Biology, 7(1), 135. doi: http://dx.doi.org/10.1186/1752-0509-7-135. Retrieved from: http://www.escholarship.org/uc/item/6sk6h7r7

Background: Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative da

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::62037b78eaf3653e0e82af02e9792d86