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Overview

 

 Cutting edge biological research presents the biologist with new bioinformatic and genomic opportunities and challenges.  The Institute for Cyber-Enabled Research (iCER) and the MSU High Performance Computing Center (HPCC) offer a variety of bioinformatics-related resources and support for MSU biologists, including: 

  • Commonly used bioinformatics packages which may be used on the HPCC cluster.

  • A bioinformatics "Help Desk" to serve as an interface between MSU researchers and the HPCC.  Through the Help Desk, we provide information on: 


    • Bioinformatics-related computing resources offered through HPCC; 
    • Vitual machine setups for BLAST, Galaxy, and the UCSC Genome Browser;
    • How-To's on utilizing HPCC resources;
    • One-on-one consultations on bioinformatics problems;
    • Limited on-site server setup and configuration; and,
    • Links to other MSU bioinformatics resources.
  • We offer up-to-date Information about seminars and training activities on campus.

How We Can Help  

Here are some areas in which we have been assisting biological researchers:

High-throughput Data Analysis

Genome Browsing & Short-Read Alignments

High-Level Biological Computation

  • Handling very large data sets
  • Working with data files in many different formats 
  • Using standard tools and custom scripts to
    sort and search these data
  • Cluster utilization
  • Genome browser setup & customization
  • Viewing reference data
  • Handling short-read alignments
  • Data parsing and manipulation
  • Algorithm optimization / tuning
  • Code customization
  • Adapting programs to utilize
    heavy-duty computational resources
  • Optimizing run speed

Pankaj A., Drosophila melanogaster


• Data parsing, analysis
• Python & perl scripting
• Cluster assistance
• Job optimization

Astrid V., Chlamydamonas reinhardtii


• GBrowse configuration
• Bowtie alignments
• Server setup and administration
• User training

Jackie D., Biological modeling


• Model optimization
• Cluster assistance
• Software configuration & installation

Database Services

MySQL

HPCC offers MySQL services through its "db-01" internal host.  Database access is currently restricted to users needing analytical tool "backend" services, such as those required by OrthoMCL.  Data set size is limited however, and large permanent sets cannot be accommodated.  Postgres services are also available. Contact us for more information.

Reference Data Sets

The HPCC offers a central data set repository for biological researchers via the "common-data" research space.  Sets currently available include those for:

We also provide properties templates for Blast2go Consed , PaCE , Primer3 , QIIME , Structure , and TransABySS .

How to Get Help


Research Specialists are available to provide a wide-range of bioinformatics support to MSU researchers.  Support services currently offered include:

  • Custom script development for data processing and analysis
  • HPC bioinformatics software support
  • Software selection and data management
  • Limited external systems administration support (e.g., setting up a customized GBrowse installation)

To request assistance or to setup a consultation, please  complete a ticket request .  (It is helpful to include the phrase "Bioinformatics Assistance" somewhere in your request.)  
We will generally respond to all requests within about 1-2 business days.

Training, Education, and Support

NextGen Bioinformatics Seminars - NextGen Seminars are scheduled on a roughly bi-monthly basis during Fall and Spring Semesters.  Topics deal specifically with data analysis and interpretation issues at a Grad-Postdoc level.  Refer to the NGS Seminar Page.

Tutorials - Tutorials and "howtos" are available which cover a wide range of Bioinformatics related topics.  From application use, to data management, format conversions, and parameter selection.

Summer Bioinformatics Training - Analyzing NextGen Sequencing Data (ANGUS) was offered at the MSU Kellogg Biological Station as a Summer course in 2010, 2011, 2012, and 2013.  See the ANGUS website for more information on training opportunities in 2014.

Tools

HPCC offers many bioinformatics applications that can be utilized on the HPCC cluster. You can view the current list for more information. If you do not see a particular application listed that you would like to use, please fill out a help ticket with the details.

Bioinformatics Resources

Research Technology Support Facility  (RTSF) - RTSF provides technical and analytical support for Biomedical and Agricultural research at MSU in Genomics, Structural Biology, Proteomics, Bioinformatics, and Mass Spectrometry.

Bioinformatics at MSU   - Faculty, research labs, and academic offerings.

ANGUS  - Analyzing NextGen Sequencing Data (tutorials).  Built around the course by the same name created by [Prof. Titus Brown|http://ged.msu.edu/].

Pygr - Modules for creating scalabable bioinformatics interfaces in Python.

GEDD - Gene Expression in Development & Disease Focus Group at MSU