Statewide Bioinformatics in Kentucky

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Statewide Bioinformatics in Kentucky

• Eric C. Rouchka, D.Sc.
• University of Louisville
• Department of Computer Engineering and Computer
  Science
• Eric.rouchka_at_louisville.edu

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Current Status of Bioinformatics within UofL/KBRIN

• Overview of KBRIN
• Infrastructure
• Networking
• Research
• Education

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History

• October 2001 NIH/NCRR announced grant award for
  Kentucky BRIN (later INBRE)
• BRIN Biomedical Research Infrastructure Network
• Focus states with disproportionate share of NIH
  funding
• Purpose improve infrastructure to make them more
  competitive for NIH awards

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Participating Institutions

• BRIN/INBRE Network

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Computer Infrastructure
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Hardware Resources

• Computer Equipment
• Beowulf cluster computer (UofL)
• 16 node, 32 CPU
• 2 Terabyte RAID storage (NAS)
• Bellarmine cluster computer
• Classroom Laptops (WKU)

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Kentucky Biomedical Research Infrastructure
Network (KBRIN) Computational Cluster Facilities
CECS DepartmentBioinformatics Laboratory
KBRIN Computational ClusterDahlem Supercomputer
Laboratory
KBRIN Project Office
KBRIN Supercomputer (16) Compute Nodes Dual AMD
2400 2 GB memory40 GB hard drive1 gb NIC
Master Backup System Dual AMD 2400 Workstation2
GB memory(4) 70GB hard drives100 mb NIC
Dual AMD 2400 Workstation2 GB memory80 GB hard
drive100 mb and 1 gb NIC
Dual AMD 2400 Workstation2 GB memory80 GB hard
drive100 mb and 1 gb NIC
Web Srvr / Bkp masterDual AMD 2400 2 GB memory
CD RW drive(4) 70 GB hard drives100 mb and 1
gb NIC
Dual AMD 2400 Workstation2 GB memory80 GB hard
drive100 mb and 1 gb NIC
Gigabit Ethernet
100 mb Ethernet
KVM Switch
Monitor, Keyboard
Dual AMD 2400 Workstation2 GB memory80 GB hard
drive100 mb and 1 gb NIC
Master NodeDual AMD 2400 2 GB memory CD RW
drive(4) 70 GB hard drives100 mb and 1 gb NIC
HPLaser Printer
24 Port Gb Ethernet Switch
100 mb Ethernet
Campus Ethernet Network
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Bioinformatics Laboratory
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University of Kentucky Resources

• Mac XServe G5
• Workgroup Cluster
• BioInquiry
• Statistics Server
• Microarray Analysis
• BASE Microarray database

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Software

• Invitrogen/Informax Software Statewide Site
  license
• UK 200 licenses
• UofL 25 licenses
• Vector NTI
• Vector XPression

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Vector NTI Usage
Informax/Invitrogen Usage (University of
Louisville Dynamic License Server). 1This data
excludes the two highest users of
VectorNTI. 2This data includes all users of all
software packages.
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Vector NTI Usage
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Other Software Packages

• Accelrys GCG
• (No longer available)
• EMBOSS/EMBASSY
• Local BLAST Servers
• (NCBI and WU versions)

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Consolidating Software Licenses

• Discussing dynamic licenses (like vNTI) for other
  packages
• GeneSpring
• S, ArrayAnalyzer
• Renewal of GCG

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Networking
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Communication

• Only UK, UofL have internet-2 (and access grid)
  capabilities
• Working on solutions to hook up regional
  institutions
• Hosting AG Room at UofL
• Desktop headsets camera at regionals
• Looking into NetMeeting

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Bioinformatics Expertise

• Problem Not many bioinformatics experts in
  Kentucky
• Solution Pool resources generate list of
  bioinformatics expertise

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http//www.kbrin.louisville.edu/cores/experts.html
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Educational Opportunities
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Bioinformatics Seminars and Workshops

• Informax Workshop (Summer 02, 03)
• NCBI/Microarray Workshop (UofL June 04)
• Nearly 100 participants

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• Joint Tennessee/Kentucky Bioinformatics Meeting
• April 1-3, 2005
• Lake Barkley State Park
• Combinatorial Algorithms
• Sequence Based Analysis
• Gene Expression Networks
• Image/Visualization
• http//cgb.utmem.edu/summit_05/

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Bioinformatics Seminars

• UofL
• J. Quackenbush, TIGR (BMB)
• W. Gish, Wash U (KYBRIN)
• I. Shmulevich, MD Anderson (KYBRIN)
• R. Irizarry, Johns Hopkins (SPH)
• J. Cohen, Brandeis University (CECS)
• Other
• Bruce Rowe, OU-ACGT (Bellarmine)
• Dave Swofford, Florida State (EKU)

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Bioinformatics Courses at UofL

• CECS 660 Introduction to Bioinformatics (Spring)
• CECS 694 Bioinformatics Journal Club (Fall)
• PHBI 750 Statistics for Bioinformatics (Fall)
• PHBI 751 High Throughput Data Analysis (Spring)
• Informal Perl Programming for Biologists
• Spring, 2003

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Joint Masters Program

• MS in CS or Biology from EKU
• Course work at EKU
• Final Semester at UofL
• Research in Bioinformatics
• Introduction to Bioinformatics Course
• First Student Spring 2006

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Bioinformatics Certificate Program

• Currently considering in CECS department
• Collaboration with
• Bioinformatics and Biostatistics
• Biochemistry and Molecular Biology
• 12-18 credit hours required
• 9 core credits
• 1 statistics 1 molecular biology 1
  bioinformatics
• Hopefully will be submitted for review by Fall
  06
• Modeled after Data Mining Certificate (offered
  online)

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Proposed Ph.D. Tracks

• Ph.D. Concentrations in Bioinformatics
• 12 credit hours (4 courses)
• CECS 660 Introduction to Bioinformatics
• PHBI 750 Statistical Methods in Bioinformatics
• BIOC 641 Advanced Eukaryotic Genetics
• 1 Elective from CECS, PHBI, BIOC, MATH
• Two research Rotations
• HHMI-NIBIB Grant (Submitted in July)

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Research
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UofL Bioinformatics Research Group (BRG)

• Computer Engineering Computer Science
• School for Public Health
• School of Medicine
• School of Dentistry
• http//kbrin.a-bldg.louisville.edu/brg/

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Microarray Database Resource

• Design of Custom Arrays
• Selection of Genes Functional Groups
• Design of oligos and primer pairs
• Storage of Experimental Results
• Customized Analysis

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MPrime Multiple Primer Design

• Primer/oligonucleotide design program
• Web-based form
• Used with rat, mouse, human, zebrafish, fruitfly
  genes
• Returns primer pairs or oligonucleotides with
  lowest score deviating from constraints

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Locating Tandem Repeats

• Zebrafish genome highly polymorphic
• Mapping regions of tandem repeats
• Copy number at least 10
• Repeat size at least 5 base pairs long

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Motif Detection Algorithm

• Using novel approach to motif detection
• Locating similar regions within a set of
  DNA/protein sequences
• Preliminary results are promising

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Bioinformatics Service

• UofL Dept of Bioinformatics and Biostatistics
• Microarray data analysis
• UofL Center for Environmental Systems Biology
  (CESB)
• Part of Center for Genetics in Molecular Medicine
• UK StatsServer

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UofL Task Force on Bioinformatics

• Initiated by VP of Research
• Develop white paper Roadmap for bioinformatics
  at UofL (Due Nov)
• Education
• Research
• Infrastructure
• Outreach
• University-wide, multidisciplinary

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UofL Task Force on Bioinformatics

• Goals
• Establish management structure
• Provide resources for bioinformatics
• Including faculty slots
• All initiated by kbrin efforts

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Web Links

• KYBRIN Bioinformatics Core
• http//www.kbrin.louisville.edu/about/bioinform_co
  re.html
• UofL Bioinformatics Seminars
• http//kbrin.a-bldg.louisville.edu/Seminars/
• Introduction to Bioinformatics
• http//kbrin.a-bldg.louisville.edu/CECS694/
• Bioinformatics Journal Club
• http//kbrin.a-bldg.louisville.edu/JournalClub/

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Acknowledgements

• KBRIN-INBRE
• Nigel Cooper, UofL (PI)
• Chuck Staben, UK
• Pat Calie, EKU
• NCRR 2 P20 RR-16481
• Bioinformatics Research Group
• Dar-jen Chang
• Susmita Datta
• Ahmed Desoky
• Adel Elmaghraby
• Quiang He
• Ted Kalbfleisch
• Abdelnaby Khalyfa
• Ken Kundsen
• Tom Knudsen
• Rudy Parrish
• Amar Singh

• Students
• Vasuhandra Akkenini
• Elizabeth Cha
• Xiaohui Cui
• Ravishrikanth Gundlapalli
• Tim Hardin
• Josh Hornsby
• Support
• Stephanie Dearing
• Michelle Padgett
• Ed Birchler
• Nate Johnson
• Virtual Genomics Conference

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NCRR Grant Support

• 1P20RR016481-01
• 5P20RR016481-02
• 5P20RR016481-03
• 2P20RR016481-04
• 5P20RR016481-05
• 3P20RR016481-02S1
• 2P20RR016481-049003

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Questions?