The Informatics Institue at UMDNJ provides a repository of bioinformatics software used within the university for both research and teaching . The repository is referred to as the BioRPMs Repository. The software we have choosen is based on requirements of research being done here in addition to specific requests from individuals, and represent a wide range of areas in bioinformatics (Sequence Analysis, Molecular Modeling, Microarray, Statistical Analysis, etc)

The software listed here is installed on all the Informatics Institute RedHat Linux workstations. All software is available from the command-line or shell. Any applications with a graphical user interface (GUI) is available from the Start Menu in the Bioinformatics Group.

All RPMs listed here meet certain usability requirements including:

1. All RPMs are built to run on RedHat Enterprise Linux and Fedora.
2. All RPMs are digitally signed. Import this key using "rpm -import".
3. Any/all environment variables are set in a shell script in /etc/profile.d with the package name as the script name. The scripts are run when a user logs in ensuring the applications are ready to run.
4. GUI applications include the neccessary files to display them from the Start Menu in the Bioinformatics Application Group.
5. All RPMs can be rebuilt from a self-contained source RPM or require other RPMs to be installed.

Downloads

We have divided the repository into two distinct sets: 1) GPL-licensed, and 2) non-GPL licensed software. GPL licensed software is available to anyone who wishes to use them. Non-GPL licensed software is only available to the UMDNJ community.

Click here to see a list of software available in the repository (registration required).

Mailing List

If you wish to be notified when new or updated RPMs become available, please send an email to the biorpms mailing list (listserv@lists.umdnj.edu) with the text "SUB biorpms".

Questions/Comments?

Please address all questions and comments to Ryan Golhar, PhD. (golharam@umdnj.edu)

News

October 28, 2008
We are in the process of upgrading our repository to support RHEL 5, 32-bit, 64-bit, and PPC. We are also working on a mechanism to automatically populate summary changes to the news feed, implementing a yum respository, and making it possible for users to upload their own source RPMs to include in the repository. Please subscribe to the mailing list (above) to keep posted on changes.

Updated Sybyl RPM available
- TA_BROWSWER is now defined to use /usr/bin/firefox

April 14, 2008
Updated NCBI RPM available
- NCBI (Blast) RPM has been updated to version 2.2.18
New naccess RPM available
- libmcrypt, mhash have been added (support for naccass)
- naccess has been added

February 14, 2008
Updated openbabel RPM available
- openbabel has been updated to version 2.1.1

February 4, 2008
Updated Sybyl RPM available
- Sybyl has been updated to version 8
Updated GOLD RPM available
- Gold has been updated to version 3.2
Updated repeatmasker RPM available
- RepeatMasker and associated database has been updated to v3.1.9

December 28, 2007
Updated MOE RPM available
- MOE has been updated to 2007.09

November 22 , 2007
Updated ClustalX RPM available
- ClustalX rpm has been updated to ClustaW/X v2.0

September 27 , 2007
Updated modeller and msms RPM available
- modeller was been updated to a new version
- There is a bug fix in the msms RPM

September 18 , 2007
Updated NCBI RPM available
- NCBI has been updated to version 2.2.17. It includes BLAST 2.2.17 and the program asn2all from the toolkit.

August 2, 2007
Updated chimera RPM available
- chimera from UCSF has been updated to version 1.2422

July 23 , 2007
Updated EMBOSS, EMBASSY RPMs available
- EMBOSS has been updated to 5.0.0 and all EMBASSY applications have been updated to support EMBOSS 5.0.0.

July 3 , 2007
Updated msms RPM available
- msms has been updated from 2.5-1 to 2.5-2

June 25 , 2007
New phred RPM available
- phred is now available

June 4 , 2007
Updated autodock and mgltools RPM available
- autodock has been updated from 3.0.5-6 to 4.0.1-1
- mgltools has been updated from 1.4-1 to 1.4-5

May 3 , 2007
Updated vmd RPM available
- amber has been updated from 1.8.5-2 to 1.8.6-1 with patches

April 16, 2007
Updated amber RPM available
- amber has been updated from 9.0-2 to 9.0-3 with patches

April 13, 2007
New pymol RPM available
- Pymol is a powerful viewer designed for viewing structures of proteins, nucleic acids and enzymes. This program is also useful for preparing publication quality images.

April 12, 2007
Updated NCBI (and NCBI-devel) RPM available
- NCBI has been updated from 2.2.15 to 2.2.16
Updated chimera RPM available
- chimera has been updated from v2205 to v2304

April 9, 2007
Updated UCSF dock RPM available
- dock has been updated from 6.0 to 6.1

March 7, 2007
Updated EMBOSS RPM available
- EMBOSS has been updated from 4.0.0 to 4.1.0
Update EMBASSY RPMs available
- All EMBASSY packages have been updated for EMBOSS 4.1.0

Feb 28, 2007
Updated GOLD RPM available
- gold RPM has been update to Gold v3.1.1 and Silver v1.1.1

Jan 24, 2007
Updated mgltools RPM available
- mgltools RPM has been updated to version 1.4

Jan 23, 2007
Updated modeller RPM available
- modeller RPM has been updated to version 9.

Jan 18, 2007
New apg RPM available
-A new RPM for "Automated Password Generator " version 2.2.3 is now available.

Jan 11, 2007
New libxml2 RPM available
Updated openbabel RPM available
- The new openbabel RPM fixes a problem where input types were not recognized. The new RPM also requires libxml2 >= 2.6.5 to be installed as well.

Nov 9, 2006
Updated EMBOSS RPMs available
- The EMBOSS RPMs have been updated to version 4.0.0-5. This fixes a problem involving the specification of mismatches in "the fuzzies" (i.e. fuzznuc etc).

Nov 7, 2006
Updated openbabel RPM available
- The openbabel RPM has been updated to version 2.0.2

Oct 25, 2006
Updated NCBI RPM available
-The NCBI RPM has been updated for BLAST 2.2.15 from NCBI.
-PAML RPM has been downgraded from 3.15 to 3.14 in order to work consistently with BioPerl v1.5.

Oct 11, 2006
Updated RepeatMasker RPM available
-The RepeatMasker RPM has been updated 3.1.6. The updated RPM also includes an updated version of the RepeatMasker database.

Sept 28, 2006
New R Statistical Language RPM available
-A new RPM for "R Statistical Language" version 2.3.1 is now available.

Sept 20, 2006
Update NCBI RPM available
-The NCBI RPM has been updated for BLAST 2.2.14 from NCBI.

Aug, 2006
Listed on EMBOSS Downloads
-The EMBOSS RPM is now available for EMBOSS v4.0.0 and associated EMBASSY applications.
-We are listed on the EMBOSS download page for EMBOSS and EMBASSY applications.

July, 2006
Noted in Nature Biotechnology
-Field, Tiwari, et. al. Nature Biotechnology 24, 801 - 803 (2006) uses our respository as an example in their paper.

Sometime, 2002-2003
BioRPMs Repository created
-The BioRPMs repository is created and made available.