Artimo P Duvaud S Pachkov M Ioannidis V van Nimwegen E Stockinger H 2016 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. application/pdf https://sonar.ch/global/documents/124547 eng info:eu-repo/semantics/altIdentifier/doi/10.12688/f1000research.9794.1 info:eu-repo/semantics/altIdentifier/pmid/28232860 info:eu-repo/semantics/openAccess F1000Research. - 2016 Graphical User Interface bioinformatics command line tool data analysis genome motif activity response analysis The ISMARA client. http://purl.org/coar/resource_type/c_6501