How do I become a CBI member?
Just send a mail including your affiliations to lax.iyer@tufts.edu

How do I access the Tufts Cluster?
Instructions for applying for a cluster account
Note: Don’t be daunted by the application process if you are not officially a Tufts student or employee. UIT is dedicated to making the cluster’s resources available to all the Tufts community including Tufts Medical Center and other affiliates, and has broad leeway to accept applications in the ‘grey area’. If you have any troubles getting an account contact Lax Iyer at the address above.

[coming soon] Instructions for getting a Tufts UTLN if you do not already have one.
[coming soon] Instructions for getting additional storage space on the cluster.

I’ve got my account on the cluster, how do I use it?
A basic tutorial for getting around in UNIX

Key UNIX commands An alphabetical list of useful UNIX commands as an MSWord .doc downloadable file

[coming soon] A guide to running programs on the cluster & downloading/uploading files

[coming soon] A guide to bioinformatics and genomics programs installed on the cluster.

[coming soon] A brief guide for running programs in R

How do I join the Tufts and Tufts Medical Center Ingenuity Pathway Analysis (IPA) License ?

  • Visit IPA signup site
  • Use your Tufts or Tufts Medical Center e-mail and choose a password
  • Choose “Academic” for Institution type
  • Enter “Tufts University” or “Tufts Medical Center” for institution or company
  • Fill in the rest of the details and you are all set

To install Bioconductor packages and start microarray and next generation sequencing analysis follow this link

R/Bioconductor packages from NuGO (Nutrigenomics Organisation) can be found here. There you can find support libraries, annotation libraries, CDF libraries, pdInfo files and other information for the NuGO arrays, custom Affymetrix arrays used in many human and mouse nutrigenomics experiments.

 BEDTOOLS:bedtools support a wide range of operations for interrogating and manipulating genomic features

Coming soon…

How to plan a genomics scale experiment – gene expression, genetic variation, etc.

How to get started analyzing genomics data on the Tufts computing cluster

Methods for specific genomics/bioinformatics challenges and whom to contact for help

Lecture slides and other material from the Tufts/CBI Short Courses in Bioinformatics and Genomics

Methods for specific genomics/bioinformatics challenges and whom to contact for help

Protocol  for Identifying ChIP-seq enrichment using MACS
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

 
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