Multi-campus high-performance computing infrastructure for research support Gary K. Allen University of Missouri System Copyright Gary K. Allen, This work is the intellectual property of the author. Permission is granted for this material to be shared for non- commercial, educational purposes, provided that this copyright statement appears on the reproduced materials and notice is given that the copying is by permission of the author. To disseminate otherwise or to republish requires written permission from the author.

University of Missouri System

Enrollment > 56,000 76% undergraduates 24% graduate and first professional students > 9,500 teaching and research staff

UM System Strategic Plan Organizational environment for continuous improvement in research and scholarly capacity, productivity, and funding Research targets that build on strengths and reflect future funding opportunity Internal and external intellectual alliances Complementary programmatic initiatives across the System that represent strengths not present on any one campus

UM System Life Sciences > $140 M in research expenditures (FY01) Being strategically strengthened through multi-year Mission Enhancement program - expected to add 75 new faculty hires Outstanding programs and investigators in medicine, molecular biology, genetics, structural biology, and molecular evolution

UM System Life Science Research Columbia – Oncology; Animal, plant, and microbial genomics; proteomics; health informatics Kansas City – Fungal genomics, Drosophila EST databases; proteomics; structural biology Rolla – Neural networks; artificial intelligence; algorithm development; visualization tools St. Louis – genomics; molecular electronics; intermolecular interactions

Chemistry Biology: Human Animal Plant Computer Science Agricultural Science Engineering Applied Optometry Basic Pharmacy Agriculture, Food, and Natural Resources Medicine Application and Commercialization Dentistry Veterinary Medicine Nursing Life Sciences

Central Dogma of Molecular BiologyDNARNA ProteinPhenotype

Generating the Data High-throughput methods, e.g., Cloning Sequence amplification tools (PCR) High-throughput sequencers Microarrays Structural analysis methods Imaging

“The Human Genome Project has catalyzed striking paradigm changes in biology - biology is an information science.” Leroy Hood, MD, PhD Institute for Systems Biology Seattle, Washington

What is Bioinformatics? Recently recognized as discipline Roots in early application of computers to biology in 1950’s and 60’s Hybrid of computer and informational sciences and biology

“Bioinformatics” Narrow usage Creation and management of genomics databases Broad usage All applications of computers and information sciences to problems in biology

Bioinformatics (per NIH) “Research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze, or visualize such data.”

Central Dogma of BioinformaticsGeneticInformationMolecularStructureBiochemicalFunctionSymptoms

Computational Subdisciplines Database Theory and Design Machine Learning Robotics Statistics & Probability Artificial Intelligence Information Theory Graph Theory Algorithms

Supporting Technologies Mass storage High-throughput networking Image analysis Retrieval methods High-performance computing

Bioinformatics Research Areas Sequence and multiple sequence alignments and searches Gene prediction Phylogenetic analysis Identification of patterns and profiles Protein sequence analysis

Bioinformatics Research Areas Structure prediction, property analysis, and comparison Biochemical simulations Whole genome analysis Microarray analysis Proteomics Pathway mapping

Genomes In Public Databases Published complete genomes: Ongoing prokaryotic genomes: Ongoing eukaryotic genomes: /4/01 10/3/

YearStructures Time my , hours ,593 American Scientist, 90(4), 2002

UM System Strategic Research Initiatives Nanotechnology and Materials Science Bioinformatics and Health Informatics

UM Bioinformatics Consortium UM System-wide resource for high- performance computational infrastructure Emphasizes and facilitates inter-campus communication and bioinformatics and related life-science research collaborations.

UMBC Strategy MOREnet Provide backbone transport and statewide GigaPop membership UM System Fund I2 subscription and connection fees Fund hardware infrastructure Individual Campuses Support faculty for research initiatives

Implementation System-wide needs assessment Architectural plan for core computational and storage resources Definition of service model and staffing plans Hardware and software acquisition and deployment

Collaborative Workspace

UMBC – Emphasis Areas Genomic & post-genomic life sciences Human & animal health & pharmacogenomics Food crop improvement Biomedical Sciences Health Informatics & Medical Decision Making Data Warehousing & Data Mining Mathematical Biology & Computational Modeling High-performance networking Bioethics

UMBC – Shared Infrastructure High-performance computational systems Mass storage devices High speed networking services New technical and grant development support staff New faculty hires tied to Mission Enhancement targets

Education and Outreach Web sites Seminars and workshops Conference presentations Publications Direct involvement with ongoing and developing research projects

UMBC – Impact Computational and database resources shared across the UM System System-wide enhancement of human, plant, and animal genome research Advanced information technology applications in the Life Sciences Platform for bioinformatics training Coordination of acquisition of additional funding from federal and foundation sources.

UMBC – Impact Collaboration with peer Internet2 institutions Collaborations with private sector through cooperative research and educational programs. Improved education and healthcare for Missourians

UMBC as a catalyst Culture of shared research resources Increased interactions between research and information technology Fostering curriculum development Enhanced external relationships

MLSRA Proposal: Missouri Bioinformatics Research Network UMSUMC UMR SLU WU / DDPSC UMSL KCASLICMH MAHI – SLH MRISIMR UHS–COM UHS – COMUMKC

MLSRA Proposal: MBRN Objectives Improve networking infrastructure Expand data storage and computational resources Increase collaboration Enhance educational opportunities

Redefining Biology “Molecular biology has entered a stage of maturity that requires its transformation into an engineering discipline. The wealth of data on cellular components and their interactions will promote an understanding of cellular behavior that is sufficient for prediction, control, and redesign.” -- A.P. Arkin, Synthetic Cell Biology Current Opinion in Biotechnology, 12:638, 2001

University of Missouri Bioinformatics Consortium