BioUML statistics

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Citations per year

Citations chart

Popular tool citations

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Tool usage distribution map

Tool usage distribution map

Associated diseases

Associated diseases

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 No


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BioUML in publications

PMCID: 5836833
PMID: 29504919
DOI: 10.1186/s12920-018-0330-5

[…] 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 […]

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

[…] term respective p-values were calculated using the genexplain platform, version 3.0., 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 […]

PMCID: 4259112
PMID: 25538939
DOI: 10.3389/fbioe.2014.00061

[…] optimization framework eva2 (kronfeld, ) in a self-explanatory user interface and provides a complete implementation of the sbml standard in terms of an ode framework., the stand-alone desktop tool biouml (kolpakov et al., ) is among the few tools that provide a full implementation of the sbml standard in terms of ode systems and also provides its functions as javascript api., the stand-alone […]

PMCID: 3979739
PMID: 24714687
DOI: 10.1371/journal.pone.0094102

[…] with calculated values <−4 or >+4 were considered significantly regulated. gene ontology enrichment analysis was performed on a ranked set of transcripts from microarray data with the biouml software platform. for visualization only level 4 and level 5 categories were considered, primarily lipid related categories were chosen for visualization., significantly expressed […]

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

[…] 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 […]

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