Portal:Bioinformatics

From GPNWiki

---

Bioinformatics

Contents 1 About 1.1 Mission/Goals 1.2 Leadership 2 Tools 2.1 Registration to Use Tools 2.2 Subscribe to Email List 3 Upcoming Activities 4 Meeting Notes 5 Related Sites

About

The Great Plains Network Bioinformatics and Computational Biology Group is a cooperative undertaking of member Great Plains Network universities. The group seek to use existing programs and regional initiatives to advance educational and research objectives at the intersection of biology and computer science.

Mission/Goals

• Computing Resources. Make available through a common site regional computing resources, applications, and data sets which can be used for applicable research. Computing resources also include storage and networking.
• Educational Resources. Make available through a common site a suite of resources available from members and affiliates which can be used for bioinformatics graduate education.
• Educational Partnerships. Create partnership opportunities across campuses for training of graduate students, and course-sharing opportunities. This is currently done through the Bioinformatics and Computational Biology Visiting Students program. Offerings of bioinformatics and computational biology courses via a campus’ distance education activities may be possible in the future. Ask about it if interested.
• Research Partnerships. Create partnership opportunities to develop and test new tools and discover new knowledge of use to the scientific and commercial community, such as for example those relating to development and testing new drug interventions.
• Regional Organization. Keep scientists and educators in the region aware of regional activities and opportunities in the field.
• International and Industrial Affiliations. Build mutually beneficial ties with international and industrial affiliates. These ties can be educational, research, and service oriented. Educational ties include student exchanges, distance education courses, and visiting speakers, and instructors. Research ties include collaborative and sponsored projects. Service ties include recruitment and advisory committee memberships.

Leadership

• Daniel Berleant, Ph.D., Leader, Department of Information Science, University of Arkansas at Little Rock, Little Rock, AR, 501-683-7265, berleant@gmail.com
• Gordon Springer, Ph.D., Department of Computer Science and Scientific Director UM Bioinformatics Consortium, University of Missouri, Columbia, MO, springer@cs.missouri.edu

Tools

To use the computational tools, you will have to register (below).

Available with registration: Portal to access the following tools:

• Clustal
• MPIBlast
• WWWBlast

is here.

Documentation is here.

Also Available:

Medkit: A Helper Toolkit for Automatic Mining of MEDLINE/PubMed Citations

GeneNarrator: A Text-Mining System

PathBinder: a repository of sentences containing biomolecule name cooccurrences

Registration to Use Tools

Register here.

Subscribe to Email List

Membership (in gp-bioscience at greatplains dot net) is open to all interested parties. Subscribe here.

Upcoming Activities

Bioinformatics and Computational Biology Teleconference: First Thursday of every month at 3:00 p.m.

Annual Conference of the MidSouth Bioinformatics and Computational Biology Society: Each spring.

Meeting Notes

• June 6, 2007: The conversation continued the discussion of the session at GPN2007.
  • What are the problems that require massive computation/distributed computing, remote sensing, and transferring large amounts of data? One type of problem might be in the area of ecological informatics. Are there others?
  • Steve recommends taking a long view to plan for a day long meeting at the next annual meeting in KC to engage researchers, listen to research problems and help problem solve.
  • Action Item: Sam - Find out next life science conference in KC area so we can see about attending adding a presentation or BoF.
  • Action Item: Greg—find some solicitations that we may want to buy into.
  • Action Item: Plan on a session on fairly focused theme at the next McBios meeting (http://www.mcbios.org/) in early 2008.
  • ***Greg would like to know, what about inviting people doing this work, e.g., at KSU, to spend part of a teleconference explaining what they do? (Volunteers?)
  • Next meeting: August (skip July unless something comes up).

• December, 2006:
  • Dan and Gordon are up and running with Blast on the MU resource. **Dan is identifying categories of folks to notify about the resource, Rahul will be making a bioinformatics registration page to get a name/password.
  • Rahul is also porting the web site over to the WIKI.
  • Samuel will be emailing folks to invite them to get an account on the MU resource once he does some searches and gets some verbage from Dan.
  • Gordon is also creating some documentation for the resource.
  • Next meeting: January 3, 2007 at 2PM.

Related Sites

• MidSouth Computational Biology and Bioinformatics Society (MCBIOS)
• The Bioinformatics Center at KSU is directed by Prof. Susan Brown who also directs the Arthropod Genomics Center. Additional information on the research being done here is located at http://bioinformatics.ksu.edu/web/research.shtml

New Wiki Account

GPN Member Web Site

Great Plains Network Home Page