The ISMARA client

Artimo, Panu and Duvaud, Séverine and Pachkov, Mikhail and Ioannidis, Vassilios and van Nimwegen, Erik and Stockinger, Heinz. (2016) The ISMARA client. F1000Research, 5 (Elixir). p. 2851.

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Official URL: http://edoc.unibas.ch/54795/

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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.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Bioinformatics (van Nimwegen)
UniBasel Contributors:van Nimwegen, Erik and Pachkov, Mikhail
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:F1000 Research Ltd.
Note:Publication type according to Uni Basel Research Database: Journal article
Identification Number:
Last Modified:25 Oct 2017 12:48
Deposited On:25 Oct 2017 12:48

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