Difference between revisions of "FedCloudRSAT"
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FCUC_Status = | | FCUC_Status = Preparatory| | ||
FCUC_StartDate = | | FCUC_StartDate = 08/10/2014| | ||
FCUC_EndDate = -| | FCUC_EndDate = -| | ||
FCUC_EGIName = | | FCUC_EGIName = Nuno Ferreira / nuno.ferreira@egi.eu, Diego Scardaci / diego.scardaci@egi.eu| | ||
FCUC_EXTName = | | FCUC_EXTName = Jacques.van-Helden / Jacques.van-Helden@univ-amu.fr | | ||
FCUC_ShortDesc = | FCUC_ShortDesc = | ||
[http://rsat.ulb.ac.be/ RSAT] (Regulatory Sequence Analysis Tools) offers a series of tools dedicated to the detection of regulatory signals in non-coding sequences. The only input required is a list of genes of interest (e.g. a family of co-regulated genes). From this information, you can retrieve the upstream sequences over a desired distance, discover putative regulatory signals, search the matching positions for these signals in your original dataset or in whole genomes, and display the results graphically in the form of a feature map. Each tool is presented as a form to fill. For each form, a manual page provides detailed information about the parameters. RSAT usally processes data-sets extracted by the [http://www.ensembl.org/index.html Ensembl] databases | | |||
FCUC_Tasks = | FCUC_Tasks = | ||
A VM image embedding RSAT is already available. As a first test we would like to deploy one instance of this VM on the EGI Federated Cloud. | |||
Requirements to run the RSAT VM: | |||
* 1 Core | |||
* 2 GB of RAM | |||
* 12 GB of storage | |||
RSAT Data-sets can be huge, first tests will be done with a couple of genomes (about 4 GB). Later we will test RSAT with bigger data-sets. | |||
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FCUC_Files = | FCUC_Files = | ||
RSAT web site: http://rsat.ulb.ac.be/ | |||
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Latest revision as of 16:29, 7 May 2015
Overview | For users | For resource providers | Infrastructure status | Site-specific configuration | Architecture |
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General Information
- Status: Preparatory
- Start Date: 08/10/2014
- End Date: -
- EGI.eu contact: Nuno Ferreira / nuno.ferreira@egi.eu, Diego Scardaci / diego.scardaci@egi.eu
- External contact: Jacques.van-Helden / Jacques.van-Helden@univ-amu.fr
Short Description
RSAT (Regulatory Sequence Analysis Tools) offers a series of tools dedicated to the detection of regulatory signals in non-coding sequences. The only input required is a list of genes of interest (e.g. a family of co-regulated genes). From this information, you can retrieve the upstream sequences over a desired distance, discover putative regulatory signals, search the matching positions for these signals in your original dataset or in whole genomes, and display the results graphically in the form of a feature map. Each tool is presented as a form to fill. For each form, a manual page provides detailed information about the parameters. RSAT usally processes data-sets extracted by the Ensembl databases
Use Case
A VM image embedding RSAT is already available. As a first test we would like to deploy one instance of this VM on the EGI Federated Cloud.
Requirements to run the RSAT VM:
- 1 Core
- 2 GB of RAM
- 12 GB of storage
RSAT Data-sets can be huge, first tests will be done with a couple of genomes (about 4 GB). Later we will test RSAT with bigger data-sets.
Additional Files
RSAT web site: http://rsat.ulb.ac.be/