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Practically Genomic – Bioinformatics IAP

Day 1 – January 26, 2009, 11 AM - 1 PM
Day 2 –
January 28, 2009, 11 AM - 1 PM
Day 3 –
January 30, 2009, 11 AM - 1 PM

Location: The DIRC 14N-132 (map)


Charlie Whittaker, AJ Bhutkar and Courtney Crummett

Microsoft Researchhttp://research.microsoft.com/en-us/default.aspx We are grateful to Microsoft Corporation and Microsoft Research for their generous support of our educational activities. Microsoft

Setup for the sessions:

The goal of this IAP is to expose attendees to a variety of methods and tools that will facilitate genomics-related research. Please take care of the following preparations prior to the sessions.

1) We will use the supplemental material from the following paper to illustrate different points throughout the sessions and it may be useful to take a look at the paper ahead of time:

2) Members of the MIT community have access to the Biobase products. Access the tools by searching Vera with the term "Biobase".

3) A MySQL server is available to members of the MIT commuity. Signup for access HERE.

4) The Gene Ontology Tree Machine and Webgestalt are free tools useful for functional analysis of gene lists. For access register HERE.

5) Affymetrix provides annotations and tools relating to their microarray platforms on their NetAffx website. For access register HERE.


6) Galaxy provides tools for working with genomic data. Create your free account HERE.

Additional Information regarding setup can be found HERE.

Specifically for attendees who will be bringing their own laptops:

  1. Download ClustalX
  2. Download NJplot
  3. Download Argo



Introductory Presentation

Topic 1 – Advanced Excel Usage Topic 2 – Genomics Topic 3 – Gene Annotation
Topic Materials Topic Materials Topic Materials
Databases:
NetAffx (registration required)
UniProt
NCBI Protein
IPI

Tools:
Compare 2 Lists
Draw Venn Diagrams
DAVID
Links:
UCSC Genome Informatics
Galaxy
Galaxy Screencast Tutorials
Ensembl
The Broad Institute
DOE Joint Genome Institute (JGI)
NCBI Entrez
Links:
Argo
Topic 4 – Multiple Sequence Alignment and Phylogenetic Analysis Topic 5 – Protein Domain and Motifs Topic 6 – Functional Annotation
Topic Materials
Introductory Presentation
Topic Materials Topic Materials
Links:
Uniprot
Clustal
Web-Based Clustalw
NJ Plot2) andaa
(
Phylip
Links:
SMART
InterPro
Scansite

Links:
GO Tree Machine
Biobase Bioknowledge Library
DAVID
GSEA
Topic 7 - Relational Databases Topic 8 - Unix Utilities Topic 9 - Perl Scripts
Topic Materials Topic Materials Topic Materials
Links:
Galaxy
MySQL
Wikipedia Join Entry
Links:
Emacs
EMBOSS
Blastall


Links:
Perl
Wikipedia Perl Entry
Topic 10 - R Topic 11 - Bioconductor Topic 12 - Microarray Data Processing
Topic Materials Topic Materials Topic Materials
Links:
R
Harvard-MIT Data Center
Links:
Bioconductor

Links:
Public Repositories of Array Data
GenePattern
Biobase Explain