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Integrating Bioinformatics into Information and Library Science Education

This article explores the challenges and approaches to incorporating bioinformatics into information and library science education, with examples from various universities and programs.

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Integrating Bioinformatics into Information and Library Science Education

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  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 SummarySchool Details

  2. 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.

  3. 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)

  4. 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).

  5. 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

  7. 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 • Peterson’s Graduate Schools and Programs search (course of study: bioinformatics)

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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

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

  15. 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.)

  16. 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

  17. 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

  18. Informatics Programs – University of Pennsylvania • Program: U Penn • Degree: BS, MS, PhD • Host Department: Biology, Computer Science, Mathematics • Program EntranceRequirements: variable • Program Completion Requirements:

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

  20. 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

  21. 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.

  22. 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

  23. 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.

  24. 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).

  25. ILS and Informatics Programs

  26. ILS and Informatics Programs

  27. Other Bioinformatics Programs

  28. Other Bioinformatics Programs

  29. Other Bioinformatics Programs

  30. Other Bioinformatics Programs

  31. Other Bioinformatics Programs

  32. Other Bioinformatics Programs

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