ISMARA client: a standalone application to locally pre-process expression or ChIP-seq data
ISMARA (Integrated System for Motif Actitivity Response Analysis) is an online tool that models genome-wide expression or ChIP-seq data, in terms of computationally predicted regulatory sites for transcription factors (TFs) and micro-RNAS (miRNAs).
The input required for running ISMARA is either expression data (microarray or RNA-seq data), or ChIP-seq data from a set of biological samples.
Developed by the Genome Systems Biology (SIB Swiss Institute of Bioinformatics), ISMARA is a valuable tool, which has been successfully used by numerous scientists worldwide.
However, there is a potential problem with the ISMARA online tool since the input files can be very big (several GBs) and thus their upload to the server could require a lot of time depending on the user's network connection speed and reliability.
ISMARA client is a standalone application developed by the SIB Swiss Institute of Bioinformatics, which can be installed on a user's computer in order to locally pre-process expression or ChIP-seq data. The pre-processed data is significantly smaller in size and can be uploaded in reasonable time even with slow Internet connection speed.
More extensive documentation and sample input data are provided under the "Usage" link. Please also note ISMARA's "Terms of use"
The ISMARA client package was created at the SIB Swiss Institute of Bioinformatics by the groups:
ISMARA client is a standalone application developed by the SIB Swiss Institute of Bioinformatics, which can be installed on a user's computer in order to locally pre-process expression or ChIP-seq data. The pre-processed data is significantly smaller in size and can be uploaded in reasonable time even with slow Internet connection speed.
In order to ease the user experience, the user interface of the ISMARA-client application follows the ISMARA web site's look and feel. Indeed, the user starts by selecting the data type (microarray, RNA-seq or ChIP-seq). For RNA-seq and ChIP-seq, the user is also requested to select a genome assembly (human genome versions 18 and 19 (hg18, hg19) or mouse genome version 9 (mm9)). By default, if the user selects microarray or RNA-seq, miRNA are used to run the analysis. The default behavior can of course be changed.
Once the options of the pipeline are chosen, the user adds some files (2 files minimum required, in compressed format or not):
and starts the pre-processing.
In ISMARA-client, like on the ISMARA web site, it is recommended (although not mandatory) to specify a project name. It is also a good practice to provide an email address to be notified when the ISMARA sever has finished analyzing the data.
In ISMARA-client, all the jobs (i.e. individual requests) are stored in a table, with their status and a link to the corresponding ISMARA reports (which prevents the user from bookmarking each ISMARA result page). A detailed log information is also available and can be copy/pasted for further communication with the ISMARA team in case of problems or for questions.
Further information on usage examples and result interpretation of ISMARA can be found on the ISMARA web site in "Usage" section.
This section inteded fro Windows users who could not use ISMAR client. The reason is that some bioinformatics tools used in the file preprocessing are not available on Windows platform.
sudo yum install -y epel-release
sudo yum update -y
sudo yum install -y R
It might take a while.
Any feedback is welcome! If you expreince problems please report it to us. We try to fix it as soon as possible.
Sample data to test the client:
The developers of ISMARA give permission to you and your institution to use the ISMARA webserver for internal, research purposes, on the following conditions:
Commercial users should contact us for licensing arrangements.
The ISMARA client package was created at the SIB Swiss Institute of Bioinformatics by the groups