MAGE-STK specifications


Unique identifier OMICS_27709
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C#, Java, Perl, Python
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline Paul Spellman

Publication for MAGE-STK

MAGE-STK citations


Trends in modeling Biomedical Complex Systems

BMC Bioinformatics
PMCID: 2762057
PMID: 19828068
DOI: 10.1186/1471-2105-10-S12-I1

[…] then defined. Formats are specified as spreadsheets (MAGE-TAB) and as an XML language (MAGE-ML). In addition, the MGED Ontology was developed for the description of key concepts. A software toolkit (MAGE-STK) was finally developed to facilitate the adoption of MAGE-OM and MAGE-ML.Along these lines, many 'Minimum Information' datasets have been defined in other biological domains. Currently, the M […]


A software framework for microarray and gene expression object model (MAGE OM) array design annotation

BMC Genomics
PMCID: 2358904
PMID: 18366695
DOI: 10.1186/1471-2164-9-133

[…] plexity of the ArrayDesigns being annotated, but the use of EhCache ensures that large ArrayDesigns can be edited on a typical Desktop machine with 1 Gb of RAM. The software makes use of the Jena and MAGE-stk libraries which are released under the GNU-licence and the software itself is released under the same open-source licence.The interface components have been structured to collect all the data […]

MAGE-STK institution(s)
Department of Cell and Molecular Biology, University of California at Berkeley, Berkeley, CA, USA; Rosetta Biosoftware, Kirkland, WA, USA; Open Informatics, Albuquerque, NM, USA; Bioscience Research - Agilent Technologies, Palo Alto, CA, USA; European Bioinformatics Institute, EMBL Hinxton Outstation, Cambridge, UK; Affymetrix, Inc., Emeryville, CA, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Molecular Mining Corporation, Kingston, ON, Canada; Imaging Research Inc., St. Catharines, ON, Canada; Iobion Informatics LLC, La Jolla, CA, USA; LION bioscience Inc., San Diego, CA, USA; Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA; The Institute for Genomic Research, Rockville, MD, USA; Computational Biology, Institute for Systems Biology, Seattle, WA, USA; CHRF, University of Cincinnati College of Medicine, Cincinnati, OH, USA
MAGE-STK funding source(s)
Supported by grant DE-FG02-00ER62893 from the DOE and an NSF biocomputing post-doctoral fellowship.

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