Linux Cluster

The Bauer Core hosts a cluster of more than 150 networked Linux computers, with many biological applications and databases installed, as well as some more general scientific and programming software.

Getting an Account

There is a fixed charge of $100 per month for each research group for access to the cluster.
This fee covers:

Up to 10 individual user accounts per research group
10 GB of disk storage space for each research group
Daily file backups
Access to applications and databases hosted and maintained on the cluster by the research computing group.
Access to web-based applications hosted by the research computing group.

Additional group or individual storage space is available for a fee.

Cluster account request form (requires Harvard PIN)

Using the Cluster

Users connect to the cluster by logging in to portal.cgr.harvard.edu. (Note: portal.cgr.harvard.edu is not a web page.) You can connect to the cluster using a secure shell program: ssh on UNIX, the Terminal application on Mac, or a program like PuTTY on Windows. Transfer files to and from the cluster with secure FTP. In order to run jobs (programs) on the cluster, you need to "submit" them to the LSF job queueing system. For more information on these topics, see below.

Logging in to the cluster
Transferring files to and from the cluster
Running jobs with the cluster's LSF queueing system

Resources Available on the Cluster

A large set of applications and databases have been installed on the Linux cluster and are available to Harvard research groups. A few of the popular applications are:

BLAST (NCBI and WU)
EMBOSS
Primer3
QRNA and SNOSCAN
Bioperl
GMEP
Mathematica (Bauer Lab only)

Databases include GenBank, UniProt (aka Swiss-Prot), NCBI blast databases, and more. The Resource List has more information on these and other computational resources provided by the Computational Biology Group.