Bioinformatics Working Group:

Harvard University's ABCD Committee offers a Bioinformatics Working Group and listserv; contact them.

Scripting Resources:

1. Scriptome is a toolbox helping biologists explore and manipulate their data.  The main niche of targeted users are biologists with little or no programming experience, who may be only occasional users. Others who may find Scriptome useful are biologists currently in the process of learning programming.  The tools consist mostly of Perl scripts. 

2. Do you need a central repository for your source code? Bug-tracking, mailing-lists, forums? Simply want to offload file release bandwidth? The ABCD group is proud to announce the launch of the "Harvard ABCD Forge" implementation of GForge:

http://forge.abcd.harvard.edu

GForge is an open source fork of the Sourceforge tools and provides a flexible feature list which includes:

CVS Repository
Mailing Lists
Discussion Forums
Bug Tracking
Feature Tracking
Task delegation
Project Management and Reporting

Project administrators can choose what feature(s) they want to use and disable unnecessary ones. Just want surveys? Forums? Bandwidth for File-Releases? Everything? ABCD Forge is whatever you want to make it.

Projects can be either public or private (restricted to selected registered users). Public projects can select a number of licenses to distribute code.

Visit http://forge.abcd.harvard.edu/ to create your account. All ABCD members are eligible to create projects. Simply select 'Register Project' on log in.

http://forge.abcd.harvard.edu is funded by the office of Senior Associate Provost and CIO, Dan Moriarty and is supported by a group of ABCD volunteers. Both ABCD and the Provost's office seek ways to reduce costs by addressing needs that extend beyond department and school boundaries. Our hope is to reduce the local sysadmin effort while raising the quality and frequency of software development at Harvard.

Esmond Kane, Harvard University Art Museums
Mark Diggory, Harvard/MIT Data Center
Norton Allen, Anderson Group, DEAS/Chemistry

Hosted Computational Biology Packages:

Information regarding the former Helix SeqWeb and GCG programs.

The SeqWeb program on helix.mgh.harvard.edu has been terminated and replaced by newer, more widely used open source programs such as command-line and web-based EMBOSS and command-line GCG (also called shell access or telnet and ssh access). We also are running an open source w2h web-based interface to GCG, described below, which you might also consider as a substitute for SeqWeb.

Partners - Dana Farber Cancer Institute Research Bioinformatics Computer - newmbcrr.dfci.harvard.edu

The Partners - Dana Farber Cancer Institute Research Bioinformatics Computer, newmbcrr.dfci.harvard.edu, is a Sun Solaris UNIX system with a basic UNIX command structure similar to what you used on Helix or Genetics. It is on the Partners network and can be reached with either of two names: newmbcrr.dfci.harvard.edu or gene.dfci.harvard.edu.

How to get an account on newmbcrr.dfci.harvard.edu or gene.dfci.harvard.edu

If you already have an account on gene.dfci.harvard.edu (for example, from the helix migration), you do not need another one. Proceed directly to the section titled Access to Web-based Bioinformatics Programs on newmbcrr.dfci.harvard.edu unless you wish to email us at HELIX@PARTNERS.ORG to copy your SeqWeb files into your home directory on newmbcrr for use with programs there.

Any DFCI or MGH researcher can get an account on gene.dfci.harvard.edu. This is a two-step process:

Step 1 If you know that your PI is listed with gene.dfci.harvard.edu, go directly to step 2. If you are not sure if your PI is already listed in the Principal Investigator file for gene.dfci.harvard.edu please send email to systems@mbcrr.dfci.harvard.edu which includes:

1. PI Name
2. PI Department
3. PI Institution (MGH, BWH, DFCI, etc.)
4. PI Office Address (room/floor/building/street number/city, etc.)
5. PI phone number

Step 2 SSH to newmbcrr.dfci.harvard.edu with the account name "new". If you do not have SSH (the encrypted successor to telnet) see the SSH section below.

1. Use df6i36uu when asked for password
2. Answer the questions written to the screen, NOTE: for the PI, use lower case last name
3. After completing the information, we will process the request, usually within a day, and your account will be activated, or you will be contacted if there is a problem.
4. Now that you have your own account, SSH to newmbcrr using your account name. Create a file that automatically forwards any email from the newmbcrr system admins, or any batch jobs you submit, to an email account that you read regularly. Such a file must be in your home directory and called .forward. Please note the dot in front of the word forward. You can use the command pico .forward to get the simple pico word processor. Just make a 1-line file with your correct address, for example: aeinstein@partners.org and then type <control>x to exit. The program will ask you if you want to save the file. Just say y and then hit Return to accept the name .forward if you typed it in correctly to begin with.

The Open Source EMBOSS package

We recommend that users migrate to the EMBOSS package that is installed on newmbcrr. EMBOSS is fast becoming the open source substitute for GCG. There are Web interfaces to EMBOSS that are installed on newmbcrr that will substitute for SeqWeb as well. Please see a description of EMBOSS at http://emboss.sourceforge.net. There is a tutorial and manual available on the web site describing the command-line EMBOSS package. All EMBOSS commands are installed on newmbcrr and you just have to type the commands to run them. You can also run GCG version 10.2 by typing (in all lower case letters), gcg. This initializes the GCG environment. Then just enter the GCG command names.

Access to Web-based Bioinformatics Programs on newmbcrr.dfci.harvard.edu.

Once you have a username and password on newmbcrr, you can use the same username and password to try out the web-based EMBOSS and GCG bioinformatics programs at the URL http://newmbcrr.dfci.harvard.edu/w2h-emboss/.

Other UNIX Bioinformatics Programs and other Partners Research Computing Resources.

There are other bioinformatics programs available on newmbcrr which we will try to present on the website at http://newmbcrr.dfci.harvard.edu/. The GCG help pages are online at:

http://newmbcrr.dfci.harvard.edu/gcghelp/gcgmanual.html

and the EMBOSS help pages are online at:

http://emboss.sourceforge.net/apps

If you have requests for other UNIX bioinformatics programs that would be of use to Partners researchers, please send suggestions to systems@mbcrr.harvard.edu. We have expanded the research computing facilities to possibly include high performance computing resources like a Linux cluster running NCBI Blast and web blast: http://www.partners.org/rescomputing/

SSH, SFTP and Administrative Contact Information

Note that telnet and ftp are no longer provided due to security reasons. SSH is very similar to telnet, and sftp, secure ftp, is very similar to ftp. But the sessions are encrypted. If you're using a PC, you can get SSH by going to

http://www.ssh.com/support/downloads/secureshellwks/non-commercial.html

and following the link to the Official Download Site for the non-commercial version, which, for Windows is SSHSecureShellClient-3.2.9.exe. Right click over the icon and select "copy to folder". The program provides both SSH and SFTP.

For MAC users, similar software can be downloaded from http://www.macssh.com if you're using OS9. If you're using MAC OS10, you already have SSH and SFTP in the UNIX shell program "Terminal" which is in the Applications:Utilities folder. Just type the command "ssh new@newmbcrr.dfci.harvard.edu" to log on as the user "new". When you have your own username, you can substitute your username in front of the "@" sign.

The general help address that sends copies of your message to all system administrators for newmbcrr issues is systems@mbcrr.harvard.edu although the specific system administrators are as follows:

For most MGH users
Dennis Gurgul, Systems Specialist
617.724.3169
dgurgul@partners.org

For MGH Molecular Biology Dept users
Norman tenBroek tenbroek@molbio.mgh.harvard.edu
Deverie Bongard bongard@molbio.mgh.harvard.edu

For Dana Farber users
Tom Graf tom@mbcrr.harvard.edu
Jeremy Zucker zucker@research.dfci.harvard.edu