BioUML statistics

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Citations per year

Number of citations per year for the bioinformatics software tool BioUML

Tool usage distribution map

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


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


No version available

Publication for BioUML

BioUML citations


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

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” ( implemented using BioUML driven systems biology platform (, geneXplain platform: We revealed a number of differentially expressed genes (DEGs) between sensitive and insensitive cell l […]


Immunogenomics reveal molecular circuits of diclofenac induced liver injury in mice

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

[…] Regulatory gene networks were constructed with an analysis tool of the GeneWays database [] 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 […]


Conversion of KEGG metabolic pathways to SBGN maps including automatic layout

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 […]


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

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 […]


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

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, whose support for the costs of publication we gratefully acknowledge. […]

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