Integrating Bioinformatics into Information and Library Science Education

1
Integrating Bioinformatics into Information and
Library Science Education

• Bradley Hemminger, Anne Bauers
• School of Information and Library Science,
  University of North Carolina, Chapel Hill
• http//ils.unc.edu/bioinfo
• Examples (Pittsburgh, UNC-CH) Complete
  Details (Word doc)
• School Summary
  School Details

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Challenges to Incorporating Bioinformatics

• Multidisciplinary field
• Primary field is usually not ILS
• (usually biological sciences or computer science
  based)
• ILS may not even be initially considered part of
  a biologically based bioinformatics program.

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Host Department Approaches

• Single department concentration. (Rice, George
  Mason, Arizona St)
• Interdisciplinary program that crosses
  departmental boundaries utilize courses from
  each participating dept. (UNC-CH, CMU, Iowa
  State, UCSD)
• Standalone program as Center or Institute (Boston
  Univ Bioinformatics, Pittsburgh CBMI)

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Degrees and Certificates

• A single department usually grants their degree
  (for example Master CS with concentration in
  bioinformatics).
• The interdisciplinary approach usually grants
  degrees from the students home department, and
  then a specialization in bioinformatics, earned
  by meeting the additional requirements of the
  bioinformatics program.
• Center institute programs generally grants a
  degree from that program (bioinformatics).

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Program Descriptions

• Integrated ILS schools, detailed examples
  (Pittsburgh, UNC-CH)
• Search Methodology
• School Summary (26 national schools)
• School Details
• Complete Details (Word Document)

6
Search Criteria

• Degree-granting program at a college or
  university
• Offering a focus, concentration, or degree in
  bioinformatics
• Preference for programs offering graduate degrees
• Focus on scientific, bioinformatics-specific
  programs
• Less interest in medicine or engineering focused
  programs
• Less interest in strict computational biology
  programs

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Search Methodology

• Google searches
• Bioinformatics degree programs
• Bioinformatics graduate PhD Masters
• Bioinformatics information science
• information science bioinformatics
• library science bioinformatics
• Other References and Searches
• NIH list of bioinformatics graduate programs
• University of Texas list of bioinformatics
  graduate programs
• Petersons Graduate Schools and Programs search
  (course of study bioinformatics)

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ILS Programs University of Pittsburgh

• Program University of Pittsburgh
• Degree MS, PhD, MS or PhD certificate, and
  postdoctoral fellowships
• Host Department Center for Biomedical
  Informatics (CBMI) School of Information
  Studies (SIS) is strongly affiliated with the
  program.
• Program Entrance Requirements Summarize
  background in medicine and computer science
  admissions committee will determine if
  prerequisites are required.
• Program Completion Requirements MS requires 44
  credits and Research Project/Thesis. PhD
  requires 71 credits, comprehensive exam, and
  dissertation.

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ILS Programs University of Pittsburgh

• Program University of Pittsburgh
• Courses
• Required Biomedical Informatics Core (8-11
  credits)
• BIOINF 2011 Introduction to Biomedical
  Informatics
• BIOINF 2013 Clinical Environments in Biomedical
  Informatics
• BIOINF 2031/BIOINF 2032 Biomedical Informatics
  Colloquium/Journal Club
• Required Information Science Core (12 credits)
• INFSCI 2610 Data Structures
• INFSCI 2710 Database Management
• INFSCI 2300 Human Information Processing

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ILS Programs UNC-Chapel Hill

• Program University of North Carolina Chapel
  Hill
• Degree PhD certificate of specialization
• Host Department Twenty-two participating
  departments including the School of Information
  and Library Science hosted by Genome Sciences
  Center.
• Program Entrance Requirements Formal coursework
  in computer science including programming,
  algorithms and data structures biochemistry,
  cellular biology, or genetics and statistics.
• Program Completion Requirements Core
  curriculum, plus six additional courses
  successful completion of examinations.

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ILS Programs UNC-Chapel Hill

• Program University of North Carolina Chapel
  Hill
• Courses
• SILS 110 Biological Information Storage and
  Retrieval - An introduction to databases and data
  mining in biology.
• BIOL 162 Computational Genetics - An introduction
  to the computational and statistical methods
  employed in sequence and genome analysis.
• BIOC 276 Structural Methods - An introduction to
  computational methods for protein structure
  analysis and prediction.
• BMME 231 Advanced Topics in Bioinformatics - A
  study of current bioinformatics applications with
  an emphasis on machine learning approaches.
• Bioinformatics and Computational Biology
  Colloquium - A weekly discussion and seminar
  series.

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Informatics Programs Boston University

• Program Boston University (cooperative with
  Northeastern)
• Degree MS, PhD
• Host Department Bioinformatics
• Program Entrance Requirements Intro to C, Intro
  to Probability and/or Statistics, Intro to
  Algorithms, Knowledge of PERL, Cell Biology,
  Physical Chemistry, and Biochemistry
• Program Completion Requirements MS requires 32
  credits and an industrial internship. PhD
  requires 64 credits and a collaborative research
  project.

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Informatics Programs Boston University

• Program Boston University (cooperative with
  Northeastern)
• Core Courses
• GRS CH525 Physical biochemistry
• GRS BI 552 Molecular Biology I
• ENG BE561 Protein and DNA Sequence Analysis
• ENG BE768 Biological Database Systems
• ENG BE777 Computational Genomics
• LAW JD933 Biotechnology Law and Ethics
• GRS BF 821 Bioinformatics Graduate Seminar

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Informatics Programs Indiana University

• Program Indiana University
• Degree BS, MS, PhD minor
• Host Department School of Informatics
• Program Entrance Requirements Introductory
  background in informatics/computer science and
  biology.
• Program Completion Requirements MS requires 36
  credit hours and thesis. PhD minor requires 12
  credits.

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Informatics Programs Indiana University

• Program Indiana University
• Core Courses(9 cr.)
• INFO I501 Introduction to Informatics (3 cr.)
• INFO I502 Information Management (3 cr.)
• AND choose one from among the following
• BIOL L519 Bioinformatics Theory and Application
  (3 cr.)
• BIOL L529 Bioinformatics in Molecular Biology and
  Genetics Practical Applications (4 cr.)
• INFO I531 Seminar in Bioinformatics (1-3 cr.)
• INFO I552 Independent Study in Bioinformatics
  (1-3 cr.)

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Informatics Programs - Northeastern

• Program Northeastern University (cooperative
  with Boston University)
• Host Department Bioinformatics
• Program Entrance Requirements Applicants to the
  MS Program must have earned a baccalaureate
  degree in a biological science, chemistry,
  computer science, pharmacy, engineering, nursing,
  or other related discipline from an accredited
  college or university.
• Program Completion Requirements All
  fundamental core courses, at least one
  elective, industrial internship

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Informatics Programs - Northeastern

• Program Northeastern University (cooperative
  with Boston University)
• Fundamental Courses
• BIO3564 General Biochemistry 4QH
• BIO3565 Molecular Biology 4QH
• MTH3580 Statistics for Bioinformatics 4QH
• COM3113 Fundamentals of Programming 4QH
• Core Courses
• BIO3566 Cellular Biochemistry 4QH
• COM3301 Database Systems 4QH
• COM3150 Algorithms and Data Structures 4QH
• BIO3580 Protein and DNA Sequence Analysis 5QH
• PCL3101 Concepts in Pharmacology 2QH
• BIO3581 Bioinformatics Seminar (this course
  should be taken 2 times) 2QH

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Informatics Programs University of Pennsylvania

• Program U Penn
• Degree BS, MS, PhD
• Host Department Biology, Computer Science,
  Mathematics
• Program Entrance Requirements variable
• Program Completion Requirements

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Informatics Programs University of the Sciences

• Program University of the Sciences in
  Philadelphia
• Degree BS, MS
• Host Department Bioinformatics
• Program Entrance Requirements BS or BA in a life
  science, Computer Science, or Chemistry
• Program Completion Requirements Required
  courses, electives, and a two-semester
  independent project.

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Informatics Programs University of the Sciences

• Program University of the Sciences in
  Philadelphia
• Courses
• BS 764 Biotechnology I 2 credits
• BS 765 Biotechnology Laboratory 2 credits
• BI 780 Advanced Systems Analysis and Design for
  Bioinformatics 3 credits
• BI 785 Advanced Algorithms for Bioinformatics 3
  credits
• BI 898 Graduate Seminar
• BI 790 Master's Project in Bioinformatics
• BI 450 Bioinformatics I (Genomics) 3 credits
• BI 451 Bioinformatics II (Methods and
  Applications) 3 credits

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Informatics Programs University of Washington

• Program University of Washington
• Degree MS
• Host Department Department of Medical Education
  and Biomedical Informatics (MEBI), with joint
  faculty from the Information School
• Program Entrance Requirements College-level
  mathematics, computer programming, and biology
  courses undergraduate GPA of 3.0 or above.
• Program Completion Requirements MS requires 60
  credits, Final Examination, and Thesis/Project.
  

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Informatics Programs University of Washington

• Program University of Washington
• Courses Basic Core
• MEDED 530 - Medical Informatics
• MEDED 531 - Computing Concepts for Medical
  Informatics
• MEDED 532 - Computing Concepts for Medical
  Informatics II
• MEDED 598/558 - Integrated Systems Technical and
  Sociopolitical Dimensions
• Two of the following three courses
• MEDED 534 - Biology for Informaticists
• MEDED 535 - Clinical Topics for Informaticists
• EPI/HSERV 503 - Public Health Informatics and
  Surveillance

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Informatics Programs Vanderbilt

• Program Vanderbilt University
• Degree MS, PhD concentration
• Host Department Biomedical Informatics
• Program Entrance Requirements Computer
  Programming, Design and Analysis of Algorithms
  and Data Structures (e.g., CS 250, or CS201),
  Networks (e.g., CS 283)
• Program Completion Requirements MS requires 27
  credit hours and a thesis. PhD concentration
  requires core courses, plus at least 2 elective
  courses and a reading list on 3 areas of
  concentration.

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Informatics Programs Vanderbilt

• Program Vanderbilt University
• Courses
• All students will take five core Biomedical
  Informatics courses (Foundations of Biomedical
  Informatics and Evidence-Based Medicine, Medical
  Decision-Support Systems and Machine Learning,
  Health Care Organization and Management,
  Bioinformatics for Molecular Biology, Clinical
  Information Systems). Those who are pursuing an
  M.S. degree will not be required to take the four
  associated laboratories, while those who pursue a
  Ph.D. must do so.
• All students will take core courses in the
  remaining three areas (3 courses for the methods
  area, 3 for the biomedicine area, and 3 for the
  informatics area).

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ILS and Informatics Programs
Program Degree Host Dept.
Boston University MS, PhD Bioinformatics
Indiana University School of Informatics MS School of Informatics
Northeastern MS Bioinformatics
Pittsburgh University MS, PhD Center for Biomedical Informatics (CBMI)
University of the Sciences in Philadelphia BS, MS Bioinformatics
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ILS and Informatics Programs
Program Degree Host Dept.
University of North Carolina School of Information Library Science PhD certifi-cate School of Pharmacy and the Department of Biomedical Engineering School of Information and Library Science is a participating program.
University of Washington Bioinformatics program MS Department of Medical Education and Biomedical Informatics (MEBI) Information School is closely affiliated
Vanderbilt University MS, PhD Biomedical Informatics
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Other Bioinformatics Programs
Program Degree Host Dept.
Arizona State MS Computational biosciences
Carnegie Mellon BS, MS, PhD Computer Science, Biology, Chemistry
George Mason School of Computational Studies MS, PhD Biology
Georgia Tech MS, PhD School of Biology
Harvard and MIT Bioinformatics and Integrated Genomics PhD Harvard/MIT division of Health Sciences and Technologys medical engineering and medical physics program
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Other Bioinformatics Programs
Program Degree Host Dept.
Iowa State Bioinformatics Computational Biology MS, PhD Participating departments include animal science, botany, chemical engineering, computer science, electrical computer engineering, math, physics astronomy, plant pathology, statistics, veterinary microbiology, zoology genetics
Medical College of Wisconsin Bioinformatics graduate program MS Departments included Mathematics, Statistics and Computer Science Electrical and Computer Engineering Biology and Biomedical Engineering at Marquette. Bioinformatics research at the Medical College of Wisconsin.
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Other Bioinformatics Programs
Program Degree Host Dept.
NC State statistical genetics bioinformatics MS, PhD Program in Genomic Science
Northern Illinois University MS special-ization Administered by the Dept. of Biological Sciences
U Penn BS,MS, PhD Biology, Computer Science, Mathematics
Renneselear bioinformatics and molecular biology BS, MS, PhD Rensselaer-Wadsworth Center for Bioinformatics (CB), Biology
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Other Bioinformatics Programs
Program Degree Host Dept.
Rice University MS Concen-tration Computer Science
Stanford bioinformatics certificate program Certificate program only Stanford Center for Professional Development
University of California, Irvine MS, PhD concen-tration Information and Computer Science
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Other Bioinformatics Programs
Program Degree Host Dept.
UCLA BS, MS, PhD Math / Statistics Computer Science Biological Sciences
UCSD Interdisciplinary Bioinformatics program PhD specializ-ation Bioengineering, biology, biomedical sciences, chemistry, biochemistry, computer science engineering, math, physics
UCSF Biological medical informatics MS, PhD Quantitative biology
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Other Bioinformatics Programs
Program Degree Host Dept.
University of Memphis MS concen-tration Computer Science
University of Minnesota BS minor, MS, PhD Biology, Computer Science
VA Tech Graduate Option in bioinformatics MS, PhD option Biochemistry, Biology, CS, Crop Soil Environ-mental Science, Genetics, Plant Pathology, Statistics