title: The ISMARA client.
abstract: ISMARA ( ismara.unibas.ch) automatically infers the key regulators and regulatory interactions from high-throughput gene expression or chromatin state data. However, given the large sizes of current next generation sequencing (NGS) datasets, data uploading times are a major bottleneck. Additionally, for proprietary data, users may be uncomfortable with uploading entire raw datasets to an external server. Both these problems could be alleviated by providing a means by which users could pre-process their raw data locally, transferring only a small summary file to the ISMARA server. We developed a stand-alone client application that pre-processes large input files (RNA-seq or ChIP-seq data) on the user's computer for performing ISMARA analysis in a completely automated manner, including uploading of small processed summary files to the ISMARA server. This reduces file sizes by up to a factor of 1000, and upload times from many hours to mere seconds. The client application is available from ismara.unibas.ch/ISMARA/client.
authors.affiliation: SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Panu
authors.initials: P
authors.lastname: Artimo
authors.affiliation: SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Séverine
authors.initials: S
authors.lastname: Duvaud
authors.affiliation: Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
authors.forename: Mikhail
authors.initials: M
authors.lastname: Pachkov
authors.affiliation: SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Vassilios
authors.initials: V
authors.lastname: Ioannidis
authors.affiliation: Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
authors.forename: Erik
authors.initials: E
authors.lastname: van Nimwegen
authors.affiliation: SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Heinz
authors.initials: H
authors.lastname: Stockinger
keywords: Graphical User Interface; bioinformatics; command line tool; data analysis; genome; motif activity response analysis