ECCB 2014 tutorial T01

Access

Tutorial announcement http://www.eccb14.org/program/tutorials/cis-r
Location Faculté de Médecine, Building Forum, Room 4, rue Kirschleger, 67085 Strasbourg
Map
Access instructions (in French) http://med.unistra.fr/fre/La-faculte/Localisation/Acces-au-Campus-Medecine
Maps of the buildings http://med.unistra.fr/fre/La-faculte/Les-plans-des-Amphitheatres-et-des-salles-de-cours

Requirements for hands-on

  • Hardware

    Participants are expected to bring their laptop for the practical sessions.

  • Software to install before the tutorial
    • Putty (only for Windows) secure shell connection. Only required for Windows, since Linux and Mac OSX have ssh included in the terminal. Will be used for command-line use of RSAT: ssh connection for Window users. http://www.putty.org/
    Filezilla Secured file transfer (graphical user interface). Will be used for command-line use of RSAT: retrieve the result files and folders. https://filezilla-project.org/
    Python version 2.7 (not 3) Programming language. Will be used for Web services: run the client script. https://www.python.org/download/
    Code editor (for the programming session) Will be used for Web services to edit the client scripts. Sublime text or Notepad++

Schedule

08:00-09:00 Registration and configuration of participants' laptops (network access)
  1. Laptop configuration.
  2. Checking your access to the IFB cloud
    (ideally: account should have been obtained before the tutorial).
  3. Opening your own RSAT server on the IFB cloud.
  4. Installing an RSAT Virtual Machine on your computer
    (optional, only for participants who wish to hold an RSAT VM on their own laptop).
09:00-10:30 Session 1: Analysis of cis-regulatory elements with the Regulatory Sequence Analysis Tools (RSAT): methods and website utilization (http://www.rsat.eu/).
  1. Retrieving sequences from a set of peak coordinates (fetch-sequences)
  2. Discovering motifs from peak sequences (peak-motifs)
  3. Visualizing the sites in the context of genome annotations (UCSC genome browser)
  4. Measure the enrichment of peaks for the expected motif (matrix-quality)
  5. A quick tour of utility tools on RSAT
10:30-10:45 Coffee break
10:45-12:00Session 1 (continued)
12:00-13:30Lunch
13:30-16:00Session 2: Using RSAT in command-line (Unix terminal via ssh connection)
  1. Technical overview (Access modes for RSAT)
  2. First RSAT command-line ((fetch-sequences)
  3. Motif scanning in peaks (matrix-scan)
  4. Testing the tools with negative controls (random-seq, random-genomic-fragments)
16:00-16:20Coffee break
16:20-18:00Session 3: programming SOAP/WSDL clients for RSAT
  1. Fetching sequences corresponding to peak coordinates (fetch-sequences)
  2. Motif scanning in peaks (matrix-scan)