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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

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

[…] 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 […]


Immunogenomics reveal molecular circuits of diclofenac induced liver injury in mice

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 […]


Improving Collaboration by Standardization Efforts in Systems Biology

Front Bioeng Biotechnol
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 […]


Monocyte to Macrophage Differentiation Goes along with Modulation of the Plasmalogen Pattern through Transcriptional Regulation

PLoS One
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 […]


Conversion of KEGG metabolic pathways to SBGN maps including automatic layout

BMC Bioinformatics
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 […]


Programming biological models in Python using PySB

Mol Syst Biol
PMCID: 3588907
PMID: 23423320
DOI: 10.1038/msb.2013.1

[…] as high-level languages are more widely adopted by the modeling community., graphical tools represent an alternative approach to making biological models easier to understand. celldesigner () and biouml () employ visual interfaces and graphical languages for model creation, interpretation, and revision. our experience has been that purely visual approaches to model creation do not scale well […]

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