The ISMARA client.
- Artimo P SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Duvaud S SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Pachkov M Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
- Ioannidis V SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- van Nimwegen E Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
- Stockinger H SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- 2017-02-25
Published in:
- F1000Research. - 2016
Graphical User Interface
bioinformatics
command line tool
data analysis
genome
motif activity response analysis
English
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.
- Language
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- English
- Open access status
- gold
- Identifiers
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- DOI 10.12688/f1000research.9794.1
- PMID 28232860
- Persistent URL
- https://sonar.ch/global/documents/124547
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