BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
02 07 2019
02 07 2019
Historique:
accepted:
11
05
2019
revised:
02
05
2019
received:
13
03
2019
pubmed:
28
5
2019
medline:
27
5
2020
entrez:
28
5
2019
Statut:
ppublish
Résumé
BioUML (homepage: http://www.biouml.org, main public server: https://ict.biouml.org) is a web-based integrated environment (platform) for systems biology and the analysis of biomedical data generated by omics technologies. The BioUML vision is to provide a computational platform to build virtual cell, virtual physiological human and virtual patient. BioUML spans a comprehensive range of capabilities, including access to biological databases, powerful tools for systems biology (visual modelling, simulation, parameters fitting and analyses), a genome browser, scripting (R, JavaScript) and a workflow engine. Due to integration with the Galaxy platform and R/Bioconductor, BioUML provides powerful possibilities for the analyses of omics data. The plug-in-based architecture allows the user to add new functionalities using plug-ins. To facilitate a user focus on a particular task or database, we have developed several predefined perspectives that display only those web interface elements that are needed for a specific task. To support collaborative work on scientific projects, there is a central authentication and authorization system (https://bio-store.org). The diagram editor enables several remote users to simultaneously edit diagrams.
Identifiants
pubmed: 31131402
pii: 5498754
doi: 10.1093/nar/gkz440
pmc: PMC6602424
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
W225-W233Informations de copyright
© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.
Références
Bioinformatics. 1999 Jul-Aug;15(7-8):713-4
pubmed: 10487877
Nucleic Acids Res. 2003 Jan 1;31(1):97-100
pubmed: 12519957
Nucleic Acids Res. 2003 Jan 1;31(1):334-41
pubmed: 12520017
Bioinformatics. 2003 Mar 1;19(4):524-31
pubmed: 12611808
Nucleic Acids Res. 2003 Jul 1;31(13):3576-9
pubmed: 12824369
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
Biophys Chem. 2004 Apr 1;109(1):1-15
pubmed: 15059656
Ann Biomed Eng. 2005 Nov;33(11):1607-30
pubmed: 16341927
Bioinformatics. 2006 Dec 15;22(24):3067-74
pubmed: 17032683
Annu Rev Phys Chem. 2007;58:35-55
pubmed: 17037977
Nucleic Acids Res. 2007 Jan;35(Database issue):D550-6
pubmed: 17202170
Bioinformatics. 2008 Jun 15;24(12):1433-41
pubmed: 18424458
Brief Bioinform. 2008 Jul;9(4):326-32
pubmed: 18436575
BMC Bioinformatics. 2008 Aug 12;9:338
pubmed: 18694523
Am J Physiol Cell Physiol. 2009 Jan;296(1):C25-46
pubmed: 18829894
Brief Bioinform. 2008 Nov;9(6):518-31
pubmed: 19073714
Bioinformatics. 2009 Aug 1;25(15):1923-9
pubmed: 19505944
Bioinformatics. 2009 Sep 15;25(18):2452-4
pubmed: 19578039
Nat Biotechnol. 2009 Aug;27(8):735-41
pubmed: 19668183
Nat Biotechnol. 2010 Sep;28(9):935-42
pubmed: 20829833
Nucleic Acids Res. 2011 Jan;39(Database issue):D691-7
pubmed: 21067998
Chaos. 2010 Dec;20(4):045105
pubmed: 21198117
Adv Exp Med Biol. 2012;736:235-45
pubmed: 22161332
BMC Syst Biol. 2011 Dec 15;5:198
pubmed: 22172142
Cell. 2012 Jul 20;150(2):389-401
pubmed: 22817898
BMC Syst Biol. 2013 Feb 15;7:13
pubmed: 23409788
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W557-61
pubmed: 23640334
Am J Physiol Regul Integr Comp Physiol. 2014 May;306(9):R647-62
pubmed: 24500431
Nat Methods. 2015 Feb;12(2):115-21
pubmed: 25633503
J Integr Bioinform. 2015 Sep 04;12(2):268
pubmed: 26528566
IEEE Trans Biomed Eng. 2016 Oct;63(10):2007-14
pubmed: 27305665
Nucleic Acids Res. 2017 Jan 4;45(D1):D61-D67
pubmed: 27924024
Cancer Res. 2017 Nov 1;77(21):e39-e42
pubmed: 29092936
J Integr Bioinform. 2018 Mar 9;15(1):null
pubmed: 29522419
Nucleic Acids Res. 2018 Jul 2;46(W1):W537-W544
pubmed: 29790989
EuPA Open Proteom. 2016 Sep 09;13:1-13
pubmed: 29900117
ACS Synth Biol. 2018 Jul 11;:null
pubmed: 29944839
Biosystems. 2018 Sep;171:74-79
pubmed: 30053414
Nature. 2018 Nov;563(7729):145-146
pubmed: 30375502
Nucleic Acids Res. 2019 Jan 8;47(D1):D100-D105
pubmed: 30445619
J Theor Biol. 1988 Nov 21;135(2):175-201
pubmed: 3267767
Annu Rev Physiol. 1972;34:13-46
pubmed: 4334846
Bioinformatics. 1998;14(6):529-37
pubmed: 9694992