Novel Bioinfromatics Problem RRS feed

  • Question

  • Greetings, 

    I am a member of lab at Oklahoma State University that works with Microbial Diversity. We work with a program called Arliquien that was devolved to analyze genetic diversity. We are attempting to use it with large data sets, larger then the typical user has used, it should be feasible to run however, the program states that it is input data size limited by the RAM of the computer running it. The best computer we have in a lab has 8GB of DDR2 RAM and when running our dataset, the memory is insufficient to run. The program does not have a cluster implementation version and is coded for Windows (Xp) and requires a GUI interface. What would be the best resource to run the program, do you know of any centers that have 64GB or 128GB shared RAM implementation that will support GUI use perhaps through Windows Server 2008? I am unaware what the final RAM requirement will be for our data set but the smallest one we are running (we have multiple ones, the others are larger) needed more than 8GB, so if these entities do not exist, can you direct me to the one that has the largest shared RAM possible.

    All the best,
    Matthew Brian Couger
    Graduate Student 
    Microbiology and Molecular Genetics Oklahoma State University 
    Biochemistry and Molecular Biology B.S. 2008
    Psychology B.S. 2008
    Saturday, December 5, 2009 8:35 PM


  • Dear Matthew,

      Have you had any luck with the OU Supercomputing Center for Education and Research (OSCER) (http://www.oscer.ou.edu/contact.php) ?  They might have some public resources that you could use with your research.  Looks like they also have some shared workstations where work can be scheduled.

      You might want to try some of the other US based supercomputing centers and see if you can use their resources as an external researcher.

    With Best Regards,

    Mark Staveley
    SDET II - US High Performance Computing
    • Proposed as answer by Mark Staveley Tuesday, December 29, 2009 7:51 PM
    • Marked as answer by Don Pattee Friday, January 29, 2010 7:38 AM
    Tuesday, December 29, 2009 7:51 PM