ISMARA client

a standalone application to locally pre-process expression or ChIP-seq data
Dear Users, ISMARA client does not support yet FASTQ files processing. We are working on it.

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: Why?

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:

  • Genome Systems Biology: M. Pachkov and E. van Nimwegen
  • SIB Techonology: P. Artimo, S. Duvaud, V. Ioannidis and H. Stockinger

Citation:
ISMARA: Automated modeling of genomic signals as a democracy of regulatory motifs
Piotr J. Balwierz, Mikhail Pachkov, Phil Arnold, Andreas J. Gruber, Mihaela Zavolan & Erik van Nimwegen Genome Research 2014

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.

ISMARA client: How?

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):

  • CEL files for microarray
  • BAM, SAM or BED for RNA-seq and ChIP-seq

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.

Use of linux VirtialBox image for running the cleint

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.

Setup

  • Dwnload VirtualBox from its website.
  • Download VM image from osboxes.org. For this example we used CentOS7 image.
  • Load the image and install R by executing the follwoing commands:
                      sudo yum install -y epel-release
                      sudo yum update -y
                      sudo yum install -y R
                    
    It might take a while.
  • Download the client and start using it.

Sample data

Sample data to test the client:

ISMARA results

A description of the results that ISMARA provides is given here

The developers of ISMARA give permission to you and your institution to use the ISMARA webserver for internal, research purposes, on the following conditions:

  1. The ISMARA webserver will be used by you and/or your institution solely for non-commercial purposes, except with express permission from the authors.
  2. You may provide us with feedback on the use of the ISMARA webserver in your research, and we are permitted to use any information you provide in making changes to ISMARA.
  3. Any risk associated with using the ISMARA webserver is with you and your institution.
  4. The ISMARA webserver should be cited in any publication(s) reporting on data obtained by using it as:
    ISMARA: Automated modeling of genomic signals as a democracy of regulatory motifs Piotr J. Balwierz, Mikhail Pachkov, Phil Arnold, Andreas J. Gruber, Mihaela Zavolan & Erik van Nimwegen Genome Research 2014

Commercial users should contact us for licensing arrangements.

Contact

The ISMARA client package was created at the SIB Swiss Institute of Bioinformatics by the groups

  • Genome Systems Biology: M. Pachkov and E. van Nimwegen
  • SIB Techonology: P. Artimo, S. Duvaud, V. Ioannidis and H. Stockinger
    © 2015 - SIB Swiss Institute of Bioinformatics

Main developers

ISMARA client scripts + server

Project Management & Coordination

Furher information

SIB Swiss Institute of Bioinformatics - www.isb-sib.ch

Support/Contact:

www.expasy.org/support