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MSI Principal Investigator John Ohlfest (Masonic Cancer Center, Departments of Pediatrics and Neurosurgery) passed away on January 21, 2013. Professor Ohlfest’s research concerned the treatment of brain tumors using gene therapy and novel immunotherapies intended to boost a patient’s immune system to attack cancer. He used MSI for bioinformatics tools and sequencing software to support this research.
An obituary of Professor Ohlfest appears on the Masonic Cancer Center website. The staff at MSI extends their deepest condolences to his family, friends, and colleagues.
Distinguished McKnight Professor and MSI Principal Investigator Claudia Schmidt-Dannert (BMBB) was profiled recently in the OVPR Research blog. Professor Schmidt-Dannert engineers microbial cells for the production of chemicals and natural products. Part of the work requires that the researchers obtain and analyze genome sequences of the organisms they are studying. The group is using resources available through the MSI laboratories for sequence analysis and refinement and modeling of protein structures.
The OVPR Business blog also highlights Professor Schmidt-Dannert's work, in this case with the development of a new method of synthesizing biodiesel.
On January 9, 2013, MSI installed a Panasas ActivStor 14 to provide high-speed, high-capacity storage for home directories and project space.
We want you to know that there may be some effort required on your part. We have created documentation to assist you in determining what you will need to do and instructions on how to do that. This change does not affect Koronis users.
Complete information about the migration can be found on the Panasas Migration Guide webpage.
General questions about MSI’s storage and systems can be found on the FAQ page.
Important Information for Command-line Users of MSI Bioinformatics Software
On January 14, 2013 several bioinformatics software packages installed at MSI will be upgraded to new versions that are not backward compatible with previous releases. This may potentially affect user workflows, scripts, or pipelines that were operational prior to the upgrade. Scheduled software packages are listed below.
Please note that these upgrades only impact software used in command-line mode. Tools and workflows in Galaxy will not be affected.
These new versions are to become the default loaded version when using the "module load" function at MSI when no version is specified. Please note that the previous version will still be available to the user. You can use the "module load" command to specify which version of the software you want to use. To identify which software versions are available, type "module avail" on the system of interest.
Please contact email@example.com if you have questions or problems with this change. Please include "RISS" in the subject line of your message.
Software package: Bowtie
Current default version loaded by "module load bowtie": 0.12.8
New version loaded by "module load bowtie" after upgrade: 2.0.5
To continue using the old version use: module load bowtie/0.12.8
Compatibility issues: Bowtie genome indexes built using 0.X versions are not compatible with indexes built using 2.X versions. Bowtie 2.X genome indexes are available at /project/db/genomes/[SPECIES]/[BUILD]/bowtie2/ (i.e.
/project/db/genomes/Hsapiens/hg19/bowtie2). Significant changes
(improvements) have been made to Bowtie command-line options, and to how Bowtie performs alignments. The Bowtie programs have been renamed from "bowtie" to "bowtie2".
Software package: Tophat
Current default version loaded by "module load tophat": 1.4.1
New version loaded by "module load tophat" after upgrade: 2.0.5
To continue loading the old version use: module load tophat/1.4.1
Compatibility issue: The new version of Tophat uses Bowtie 2.X instead of Bowtie 0.X, and therefore uses Bowtie 2.X genome indexes.
Significant changes (improvements) have been made to Tophat command-line options, and to how Tophat performs alignments.
Software package: Cufflinks
Current default version loaded by "module load cufflinks": 1.3.0
New version loaded by "module load cufflinks" after upgrade: 2.0.2
To continue using the old version use: module load cufflinks/1.3.0
Compatibility issue: Significant changes (improvements) have been made to Cufflinks command-line options, and to how Cufflinks calculates differential expression. Output file formats have been changed.
Software package: GATK
Current default version loaded by "module load gatk": 1.6
New version loaded by "module load gatk" after upgrade: 2.3
To continue using the old version use: module load gatk/1.6
Compatibility issues: The GATK 2.X releases include both the addition of brand-new (and often still experimental) tools and updates to the existing stable tools. These updates will require users to change how they are using GATK tools. GATK 2.X is released under a different license that places restrictions on commercial usage.