BioUML statistics

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Citations per year

Number of citations per year for the bioinformatics software tool BioUML
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Tool usage distribution map

This map represents all the scientific publications referring to BioUML per scientific context
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BioUML specifications

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Unique identifier OMICS_21502
Name BioUML
Software type Framework/Library
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Medium
Stability Stable
Registration required Yes
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/BioUML

Versioning


No version available

Publication for BioUML

BioUML citations

 (5)
library_books

Computational master regulator search reveals mTOR and PI3K pathways responsible for low sensitivity of NCI H292 and A427 lung cancer cell lines to cytotoxic action of p53 activator Nutlin 3

2018
BMC Med Genomics
PMCID: 5836833
PMID: 29504919
DOI: 10.1186/s12920-018-0330-5

[…] nsitive cell lines. Comparative analysis of microarray data of these three cell lines was done using a computational pipeline “From genome to target” (http://my-genome-enhancer.com) implemented using BioUML driven systems biology platform (www.biouml.org, geneXplain platform: www.genexplain.com). We revealed a number of differentially expressed genes (DEGs) between sensitive and insensitive cell l […]

library_books

Immunogenomics reveal molecular circuits of diclofenac induced liver injury in mice

2016
Oncotarget
PMCID: 4924767
PMID: 26934552
DOI: 10.18632/oncotarget.7698

[…] Regulatory gene networks were constructed with an analysis tool of the GeneWays database [http://wiki.biouml.org/index.php/Geneways] available within the GeneXplain platform Version 3.0. A default cut-off score of 0.2, a FDR < 0.05 and a Z-score at 1.0 with a maximum radius of 4 steps upstream of an i […]

library_books

Conversion of KEGG metabolic pathways to SBGN maps including automatic layout

2013
BMC Bioinformatics
PMCID: 3765910
PMID: 23953132
DOI: 10.1186/1471-2105-14-250

[…] phical formats like SBGN. Some examples for SBML are Arcadia [], which uses GraphViz [] for layout and the SBML Layout Extension []. BioPAX to SBGN conversion is done, for example, by Paxtools [] and BioUML []. However, these approaches can’t translate the widely used KEGG maps into SBGN, and they mostly compute entirely new layouts rather than utilizing layout information derived from the origina […]

library_books

PathCase SB: integrating data sources and providing tools for systems biology research

2012
BMC Syst Biol
PMCID: 3410775
PMID: 22697505
DOI: 10.1186/1752-0509-6-67

[…] The results of each simulation are given either in a time course table, SBML or Copasi Native text format; no plots are shown on a graph. CopasiWeb also provides a simulation service, like RoadRunner.BioUML [] is open source integrated Java platform for building virtual cell and virtual physiological human. The web edition provides model visualization, editable model description (both visual and t […]

library_books

Functional classification of proteins based on projection of amino acid sequences: application for prediction of protein kinase substrates

2010
BMC Bioinformatics
PMCID: 3098073
PMID: 20537135
DOI: 10.1186/1471-2105-11-313

[…] on for Basic Research (Grant N 09-04-01281). We thank BIOBASE GmbH for providing access to TRANSPATH® database and ExPlain™ system. We would like also to thank Institute of Systems Biology http://www.biouml.org, whose support for the costs of publication we gratefully acknowledge. […]


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