The Coordinated Laboratory for Computational Genomics (CLCG) was founded in 1996 and has been engaged in a variety of research topics in bioinformatics and computational biology.
The CLCG is a charter member lab of the CBCB.
Leadership
Thomas Casavant, Ph.D. (Roy J. Carver, Jr. Chair in Bioinformatics and Computational Biology): CBCB Director
Terry Braun, Ph.D.: CLCG Director
Todd Scheetz, Ph.D.: Director of Bioinformatics for the Institute for Vision Research (IVR) in the College of Medicine.
Research Topics
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Gene and mutation discovery
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Expression analysis and functional genomics
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Genetic and physical mapping
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Genome-scale analyses
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Information management.
CBCB
The Center for Bioinformatics and Computational Biology encompasses the Coordinated Laboratory for Computational Genomics.
The Center for Bioinformatics and Computational Biology (CBCB) was established in 2002 to expand the involvement of research in Bioinformatics and Computational Biology on the University of Iowa campus, and to coalesce efforts of current investigators.
Computing Facilities and Space
The CLCG is in the Center of Bioinformatics and Computational Biology (CBCB).
The CBCB consists of approximately 30 full-time faculty, post-docs, staff, and students occupying 3,000 sq.ft. housed in the Seamans Center for the Engineering Arts and Sciences Building on the University of Iowa main campus.
This recently remodeled facility is wired for high-speed networking (10- and 100-megabit, and gigabit ethernet – hardwired and wireless), and includes a dedicated Linux cluster optimized for next-generation sequence mapping and analysis (large memory and multi-core nodes), more than 100 computing systems (workstations and servers), 120 CPUs, (450 cores) more than 500 gigabytes of RAM, 192 gigabytes of server disk space, and 70 terabytes of disk space, 40 terabytes of spinning backup disk space, and 192 terabytes of tape backup space.
Many of the high-performance workstations in the lab are part of a computational grid to provide extra capacity during off-peak hours.
Office and laboratory space is available for all Principal Investigators, co-investigators, post-docs, staff and students. Convenient meeting space is also available. Offices are equipped with computers and printers, video-conferencing, and telephone conferencing. PI offices are equipped with video projection capabilities for small to medium-sized collaborative meetings, and for multi-site video conferencing.
All computers are connected to a 100Mbit switched Ethernet backbone, and most space is covered by 802.11N standard wireless ethernet. All key personnel involved in this project have Linux and/or Mac/PC computers (desktop and portable) connected to the network. Many of the faculty and staff have high-speed connections at home as well.
Available Computer Resources
- A dedicated compute cluster of 10 Linux systems (48 cores per node and 64 GB of RAM per node) connected with a dedicated, switched, copper Gigabit Ethernet intranet.
- 35 dedicated servers (web servers, database servers, file servers, application servers and project specific servers).
- 40 desktops, workstations, laptops and developmental machines.
- University of Iowa “App Store” for distribution of custom applications.
- Dedicated tape robot and server for backups.
- Dedicated “spinning” backup disk array and server.
- Substantial computing infrastructure is currently in place for development and monitoring of production computing.
- Sophisticated backup system that includes “spinning backups”, daily snapshots of changing data, off-site storage and archival of static data.
University of Iowa Computing Resources
To meet the computing needs of research, the University of Iowa has invested in and developed a computing resource facility.
The “Helium” Cluster consists of 200 “Investor Nodes” comprised of 2.66 GHz X5650 Xenon processors with 8 cores and 24 GB ram (1600 cores total). Investor nodes simply mean that the owners of these nodes have priority for compute jobs and non-investor jobs are killed on demand.
A phase 2 expansion of the cluster includes 150 compute nodes (2.66 GHz X5650 Xeon processors) with 12 cores each, and 24 GB or 144 GB RAM (1800 cores in Phase 2). There are 3400 cores combined.
The Phase 2 nodes are available campus-wide to investigators. The investor nodes are also available campus-wide, however jobs submitted to the investor nodes may be halted in favor of investor jobs.
The network provides access to 40 Gbs of Infiniband, 80 TB of NFS home account storage, and 140 TB of Luster scratch storage.
In collaboration with the Iowa Institute for Human Genetics (IIHG) and Information Technology Services (ITS) at the University of Iowa, the CLCG has deployed a Galaxy installation on the Helium Cluster and made the resource available to all investigators on campus.
Figure 1 shows the architecture of the installation. A next-generation sequence analysis pipeline has also been deployed on the Galaxy instance and is available to University of Iowa investigators. Jobs are submitted by the Galaxy web interface on the Galaxy Head Node.
These jobs are distributed on the Helium compute nodes by the Sun Grid Engine and are queued in a way that gives priority in order of submission (with a limit of 25 jobs per user). Additional jobs are queued until previous jobs finish.
All nodes have shared disk space via a Luster file system cluster via Infiniband Network that provides fast I/O access for high-I/O jobs (such as processing large exome-capture files).
Figure 1: Galaxy instance at University of Iowa installed on Helium Computer Cluster. The Galaxy instance and Helium Cluster is available to all investigators at the University of Iowa.