GEMS specifications

Information


Unique identifier OMICS_24473
Name GEMS
Alternative name Gene Expression Model Selector
Software type Application/Script
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, MATLAB
Computer skills Medium
Version 2.0.2
Stability Stable
Registration required Yes
Maintained Yes

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Maintainer


  • person_outline Constantin Aliferis <>

Publications for Gene Expression Model Selector

GEMS in publications

 (6)
PMCID: 4870777
PMID: 27188717
DOI: 10.1186/s12967-016-0896-7

[…] by collett [] to analyze the prognostic value of potentially prognostic factors. support vector machines (svm)-based area under receiver operating characteristic (roc) curve method as implemented in gene expression model selector (gems) software utilizing ten-fold cross-validation and linear polynomial kernel for svm [] was used to evaluate the performance of the published gene signatures […]

PMCID: 4739337
PMID: 26842629
DOI: 10.1186/s12859-016-0900-5

[…] comes from the application of biology, and 11 from gene expression datasets except arcene and madelon, are obtained from a repository of the most widely studied gene expression sets (http://www.gems-system.org/) []. the dataset arcene, madelon and the rest are obtained from uci machine learning repository (http://archive.ics.uci.edu/ml/). table 1, four dataset indicators are used […]

PMCID: 3875537
PMID: 24386356
DOI: 10.1371/journal.pone.0084253

[…] feature selection methods such as bw , one-versus-rest s2n (ovr-s2n) , kw , and ovr-t-test as references to test the general performance of our method. ovrsvm was used as classifier as well. the gems system and spider software (http://people.kyb.tuebingen.mpg.de/spider/) in the matlab environment were employed to filter genes and fit classification model of ovrsvm., we first used […]

PMCID: 3865347
PMID: 24348903
DOI: 10.1371/journal.pone.0079843

[…] as age at diagnosis (≥12 months vs. <12 months), international neuroblastoma staging system (inss) stage (stage 4 vs. other stages), and mycn status (amplified vs. non-amplified) were tested. gems algorithm was used to construct support vector machine (svm) predictors using 20-fold cross-validation for each clinical factor: death event (de), relapse event (re), and inss stage. […]

PMCID: 2655631
PMID: 19300522
DOI: 10.1155/2009/403689

[…] method. the optimization is done by l1_ls matlab package, which is available online (http://www.stanford.edu/~boyd/l1_ls/). the results of svms are obtained by gene expression model selector (gems), a software with graphic user interface for classification of gene expression data, which is freely available at http://www.gems-system.org/ and used in [] for the comprehensive study […]


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GEMS institution(s)
Discovery Systems Laboratory, Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
GEMS funding source(s)
Supported by NIH grants RO1 LM007948-01 and P20 LM 007613-01.

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