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SBMLR specifications


Unique identifier OMICS_21542
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.76.0
Stability Stable
XML, rsbml, deSolve
Maintained Yes




No version available



  • person_outline Tomas Radivoyevitch <>

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SBMLR citations


Evaluating Cell Processes, Quality, and Biomarkers in Pluripotent Stem Cells Using Video Bioinformatics

PMCID: 4743914
PMID: 26848582
DOI: 10.1371/journal.pone.0148642

[…] correlation-based feature selection (cfs) [], chi square (chi2) [], fast correlation-based filter (fcbf) [], fisher 9 [], gini index 16 [], infogain 6 [], sparse multinomial logistic regression (sbmlr 3) [], t-test [], kruskal wallis [], and minimal-redundancy-maximal-relevance []. the inputs for the feature selection algorithms are the average slope of each feature. the slope (incremental […]


R Based Software for the Integration of Pathway Data into Bioinformatic Algorithms

PMCID: 4009765
PMID: 24833336
DOI: 10.3390/biology3010085

[…] package []. the pathview package [] loads kgml encoded files using the kegggraph package and also features a download function, which is able to automatically retrieve kegg pathways via the web. the sbmlr package [] parses sbml up to level 2 using the r xml package. the package rsbml uses the system library libsbml [] to parse, validate and convert sbml data to r graphs, objects and currently […]


On systems and control approaches to therapeutic gain

PMCID: 1484487
PMID: 16638124
DOI: 10.1186/1471-2407-6-104

[…] (but not solve) two systems and control oriented, biochemical system model-based therapeutic gain strategies as abstractions of two conceptually distinct, specific cancer treatment strategies., sbmlr [-] was used with a folate model [] to map the childhood leukemia diagnostic bone marrow microarray data of yeoh et al [] into predicted steady state fluxes of de novo purine synthesis (dnps) […]


Folate system correlations in DNA microarray data

PMCID: 1198223
PMID: 16080796
DOI: 10.1186/1471-2407-5-95

[…] r [] was used with r packages of bioconductor [] to implement this study. specifically, the package biobase was used to manipulate microarray data as expression set (class eset) objects and sbmlr [,] was used to simulate a systems biology markup language (sbml) [-] representation of the folate metabolism model []. r scripts reproducing figures , , , , , , are included with sbmlr […]

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