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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 help@msi.umn.edu if you have questions or problems with this change. Please include "RISS" in the subject line of your message.

 

Details:

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".

Find more information

 

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.

Find more information.

 

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.

Find more information

 

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.

Find more information

 

 

 

MSI Fellow and Principal Investigator Efi Foufoula-Georgiou (Civil Engineering, St. Anthony Falls Laboratory) is one of the lead investigators on a new $720,000 grant just awarded to the University of Minnesota by the National Science Foundation. The University will be the lead organization in an international, multi-university virtual institute, called Linked Institutions for Future Earth (LIFE), which will study Earth-surface systems with emphasis on watersheds and deltas.

 

Professor Foufoula-Georgiou uses MSI resources to support research studying precipitation and water systems. Using data received from a number of sources, the Foufoula-Georgiou research group is analyzing and modeling rainfall across large portions of the earth’s surface. The datasets for both the precipitation measurements and for geological features (river networks, channels, etc.) are very large, necessitating the use of powerful computing capabilities and parallel computational capacity. Besides being on the faculty at the St. Anthony Falls Laboratory, Professor Foufoula-Georgiou the director of the National Center for Earth-Surface Dynamics and is a Resident Fellow at the Institute on the Environment.

 

More information about this grant, including a description of the LIFE virtual institute, can be found at the UMNews release

 

The University News Service recently published a feature article about MSI PI Jaime Modiano (Veterinary Clinical Sciences) and his research into the genetics of cancer. Professor Modiano uses high-throughput, genome-wide technologies available through MSI to study the origin and progression of tumors in dogs, mice, and humans. Areas of his current research at MSI include osteosarcoma, non-Hodgkin lymphoma, soft tissue sarcomas (hemangiosarcoma), melanoma, and other tumors.

 

Professor Jane Davidson (Mechanical Engineering), a long-time Principal Investigator at MSI, has received the Frank Kreith Energy Award from the American Society of Mechanical Engineers. According to the ASME’s website, this award is presented to individuals for “significant contributions to a secure energy future with particular emphasis on innovations in conservation and/or renewable energy.” The award was presented at the 2012 ASME International Mechanical Engineering Congress and Exposition, held in Houston, Texas in November.

 

Professor Davidson is the director of the Solar Energy Laboratory at the University. Her research group uses MSI resources to model aspects of chemical reactions, fluid flow, and heat transfer both for analysis of experimental results and the design of prototype reactions.

 

You can read more about Professor Davidson and Kreith Award at the ASME website.

 

MSI Principal Investigators in the Department of Chemical Engineering and Materials Science were recently awarded a $1.8 million research grant. Michael Tsapatsis is the lead researcher; Prodromos Daoutidis is also on the research team.

 

The grant is from the Department of Energy’s Advanced Research Projects Agency (ARPA-E) and is for the development of membrane technologies that will enable energy-efficient separations in the chemical, petrochemical, water, fossil fuel, and renewable energy resources. The University’s award is intended specifically for improving the efficiencies of industrial processes.

 

Professors Tsapatsis and Daoutidis use MSI resources for their work in developing gas-separation technologies and related research. They published a paper in the journal Science in 2011 about their development of zeolite nanosheets. This project was featured in a Research Spotlight on the MSI homepage last summer.

 

The People section of the UMNews website has a story about this grant. You can also read the news release.

 

 

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