Iowa State University

Blue Gene/L Supercomputer

The Blue Gene/L Supercomputer is the most powerful high performance computer at Iowa State University. It is available to all Iowa State faculty, professional staff, and graduate students for appropriate research projects that are computationally demanding and require the use of such a platform. The system has a peak speed of 5.7 Teraflops, 512 Gigabytes of total main memory, and 11 Terabytes of disk storage.

BOREAS-Net

BOREAS-Net connects the Iowa State University campus network to national and international research networks so Iowa State University researchers can collaborate with peers worldwide using high bandwidth applications.

GIS Support and Research Facility

The Geographic Information System (GIS) Support and Research Facility is a public computing facility providing a high level GIS research support laboratory for ISU students, faculty, and staff as well as providing GIS education and outreach to the ISU community and the state of Iowa.

High Performance Computing Group

The High Performance Computing (HPC) Group includes full-time staff as well as a number of graduate students and, from time to time, visiting scholars from other countries. The group provides training, assistance, and support for research and high performance computing as well as engaging in funded research projects.

High Performance Computing Partnership

The High Performance Computing (HPC) Partnership is a unique consortium of faculty who strive to provide high-capacity, high performane computational facilities and to keep them updated through active cost-sharing between the university, IT Services, colleges and departments, the faculty, and through supporting grants.

Internet2

Iowa State University is an active participant in Internet2, a consortium being led by 200 universities working in partnership with industry and government to develop and deploy advanced network applications and technologies, accelerating the creation of tomorrow's Internet.

Lightning Supercomputer

The Lightning Supercomputer is the second most powerful high performance computer at Iowa State University and was purchased by the faculty in the High Performance Computing (HPC) Partnership. It is available to all Iowa State faculty in the HPC Partnership as well as their students and collaborators. The system has a peak speed of 2.8 Teraflops, 1184 Gigabytes of total main memory, and 15 Terabytes of disk storage.

Scalable Computing Laboratory

The Scalable Computing Laboratory (SCL) enables parallel computing through clustering techniques for use in scientific and engineering computation.

Student Cluster

The Student Cluster exists for students and instructors to use for classes, or other high performance computing needs including personal educational interests.

Virtual Reality Applications Center

The Virtual Reality Applications Center (VRAC) is an interdisciplinary research center focusing on the rapidly expanding interface between humans and computers. Facilities include the C6 and C4 three-dimensional, full-immersion, synthetic environments.

Institutes at Iowa State University

A number of Institutes and Centers involved with the Life Sciences on campus engage in collaborative research efforts across many academic departments and disciplines. Just a few of these include:

Plant Sciences Institute
Institute for International Cooperation in Animal Biologics
Bioeconomy Institute

Centers at Iowa State University

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Laurence H. Baker Center for
Bioinformatics and Biological Statistics

The Laurence H. Baker Center is most closely associated with the BCB Graduate Program at Iowa State. Their mission is to facilitate the bioinformatics work of students and faculty by providing computer support, fostering communications among the students and faculty at ISU and with external laboratories and granting agencies, and providing leadership in bioinformatics activities.

Faculty in the Center are engaged in research that either: 1) produces large amounts of biological data or 2) develops computational, graphical, or algorithmic methods to interpret and glean information from large biological data sets. Such data sets stem from molecular, cellular, anatomical, physiological, population, and ecological studies. A number of tools are available through them located here: Baker Center's Bioinformatics Tools.

Bioinformatics Resources

A large number of bioinformatics-related resources are available at Iowa State which have resulted from the world-class research underway here.

Genome Projects and Databases

Iowa State University is a national center for agricultural bioinformatics, housing the USDA National Bioinformatics Coordinator for all animal species. In addition to the animal genome projects housed at ISU, internationally-recognized plant and microbial genome research projects are available to researchers as well.

Websites include:

• Animals - National Animal Genome Database
• Pig - The U.S. Pig Genome Project
• Plants - Plant Genome Date Base
• Barley - BarleyBase- a plant microarray data resource
• Maize - Maize Genome Database
• Soybean - SoyBase Home Page

• Metabolic Network Exchange

• http://www.ggobi.org/

• Yet Another Bioinformatics Index.

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The BCB Lab

Students in the BCB Graduate program can participate in the BCB Lab. This student-led group works with Life Science researchers at ISU to create and apply computational and bioinformatics solutions to biological problems. The BCB Lab showcases the wide range of research projects available at Iowa State in BCB.

Participants learn from the exchange of experience, knowledge, and resources with one another while making substantial contributions to on-going research efforts.

Projects range from porting legacy Fortran applications to PHP/MySQL, to structure determination and microarray analysis. The BCB Lab helped create the Iowa-mosquito.net, a web portal for mosquito surveillance information, 1969 to present.

A new BCB undergraduate program at ISU will further enhance opportunities for the BCB Lab in research and teaching.

BCBLab Cluster

The BCBlab has a cluster on which many bioinformatics resources reside. If you are a BCB student at Iowa State, many programs and much parallel computing power can be available to you !

The cluster consists of:

• 1 Head Node
• 1GB Memory
• 40GB HD (accessible by all the compute nodes)
• 8 Compute Nodes
• 512MB Memory
• 40GB temporary storage
• All Nodes have a single 1.5GHz Athlon XP 1700+ CPU

Access the Cluster:

• The cluster is accessible by HTTP and SSH at the following address:
  olympus.psi.iastate.edu
• Need an account setup by Fadi Towfic to login. Email ftowfic@iastate.edu to request access

Cluster Internals:

• The cluster runs the Rocks 5.0 GNU/Linux distribution
• Rocks is a slightly modified CentOS 5/RHEL 5 distribution
• Has GCC (GNU C(++) Compiler) version 3.4.6

Bioinformatics Software packages available:

• BLAST: Basic Local Alignment Search Tool
• NCBI-toolkit: For writing efficient sequence comparison algorithms
• mpiBLAST: Parallel implementation of BLAST
• HMMER: Sequence comparison/alignment using Hidden Markov Models
• ClustalW: Sequence Alignment
• GROMACS: Molecular dynamics simulation package
• EMBOSS: European Molecular Biology Open Software Suite
• TIGR Assembler: Genome assembly
• MeV: Microarray Analysis Tool
• Glimmer: Gene finder for microbial genomes
• FASTA: Database search program for protein/nucleotide sequences
• MrBayes: Bayesian inference of phylogeny
• Phylip: Package for inference of phylogenies
• T_Coffee: Multiple sequence alignment package
• Bioperl/BioPython: Programming libraries

What the BCBLab cluster offers ISU's BCB Graduate Students:

• 24/7 access to some of the most frequently used programs in Bioinformatics
• Ability to experiment with the programs in a safe environment
• Single point of entry for accessing help for all the diverse programs -
  http://olympus.psi.iastate.edu/roll-documentation/bio/4.3
• Ability to compile and test your own MPI code before deploying to a more strictly managed cluster

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Service Facilities for Research in Biotechnology

Iowa State has a wide span of Biotechnology Facilites. These are the instrumentation facilities for biotechnology-related research at Iowa State University. Go to this website for an updated list of these facilities. They are available to faculty at Iowa State University and individuals in other universities, government and industry who are interested in utilizing the facilities' services for their research projects.

• Animal Gene Transfer Facility
• Atmospheric Air Quality Laboratory
• Atomic Force Microscopy
• Chemical Instrumentation Facility
• Confocal Microscopy Facility
• Crop ProductsPilot Plant
• DNA Facility
• Environmental Engineering Research Laboratory
• Fermentation Facility
• Fitness and Metabolism Unit
• Flow Cytometry Facility
• Genomic Technologies Facility
• GeneChipFacility
• Grain Quality Laboratory
• Hybridoma Facility
• Image Analysis Facility
• Isothermal Titration Microcalorimetry Facility
• Macromolecular X-ray Crystallography Facility
• W.M. Keck Metabolomics Research Laboratory
• Microfabrication Facility
• Microscopy and NanoImaging Facility
• Nuclear Magnetic Resonance Facility
• Plant Transformation Facility
• Protein Facility
• Proteomics Facility
• Sensory Evaluation Unit
• Ultrahigh Resolution Biological Microscopy Lab

Campus-wide Computing Services

The Information Technology Services (ITS) at Iowa State manages a campus-wide computer network which augments the various departmental computing facilities. For general information about the computing facilities at Iowa State University contact ITS or call the ITS Solution Center located in 195 Durham, at 294-4000.

Access to Computers and Computer Labs on the ISU campus

Computer Labs on Campus
Laptop checkout is available at 195 Durham Hall
Communications Building Laptop checkout

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BCB Resources at the ISU Library

The ISU Library has an impressive list of resources available for BCB Graduate Students. The Bioinformatics and Computational Biology Resources guide provides a list of books, e-books, literature databases, and selected websites.

Andrea Dinkelman is BCB's Science and Technology Librarian. She conducts seminars on NCBI, literature databases, etc. See her September 2008 presentation for BCB here.

Andrea L. Dinkelman, PharmD, MS
Assistant Professor/Science & Technology Librarian
Iowa State University
152 Parks Library
2280 Veterinary Medical Library
Ames, IA 50011-2140
Parks Office: (515) 294-6943
Veterinary Medical Library: (515) 294-2233
adinkelm@iastate.edu
Andrea Dinkelman's website

Accessing Electronic Dissertations

If you would like to see the dissertations from BCB graduate students, see their titles and abstracts on our Alumni webpage. You can access complete dissertations from the Library homepage. Once there:

Go to Collections; Then to Indexes and Abstracts
There is an alphabetical list. Go to D's for Dissertations.
Under dissertations, go to Dissertations at ISU.
This takes you to the Proquest UMI site where you can do a search for the dissertation you wish to find:

Enter:
Author's last name, first name
Interdisciplinary database
Dissertations within last two years, etc.

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BCB Library Books