Educational Programs in Bioinformatics at UNO Hesham H. Ali Department of Computer Science College of Info Science and Technology University of Nebraska at Omaha April 21 st, 2004

What is Bioinformatics? Source: British Medical Journal Bayat, Ardeshir (2002) "Science, medicine, and the future: Bioinformatics" 324:

History of Education/Training in Bioinformatics Late 1980s to mid 1990s: Ad hoc activities. Late 1980s to mid 1990s: Ad hoc activities. Mid 1990s: The development of MS Programs and short term certificate programs. Mid 1990s: The development of MS Programs and short term certificate programs. Late 1990s: The development of Ph. D. Programs and Postdoctoral Positions. Late 1990s: The development of Ph. D. Programs and Postdoctoral Positions. Recently: The development of Undergraduate Programs. Recently: The development of Undergraduate Programs.

Challenges to Educational Programs Too many prerequisites Too many prerequisites computer science – math – stats – biology – chemistry – engineering Students Support Students Support mentors – peers – financial resources – administration help The Multidisciplinary Factor The Multidisciplinary Factor making sure everybody is on the same page Who is in charge? Who is in charge?

The Two Extremes The process of speeding up Biosciences processes by automating what otherwise Biologists have to do manually. The process of speeding up Biosciences processes by automating what otherwise Biologists have to do manually. Another application domain for Computer Scientists to apply or employ their currently available algorithms or theories. Another application domain for Computer Scientists to apply or employ their currently available algorithms or theories.

Current Steps in Nebraska Interest from researchers/educators/students Interest from researchers/educators/students Support from the administration Support from the administration Infrastructure grants funded (Nebraska Center for Life Sciences) Infrastructure grants funded (Nebraska Center for Life Sciences) Higher degree of communication Higher degree of communication New innovative programs in Bioinformatics New innovative programs in Bioinformatics Various interesting research projects Various interesting research projects Student organizations/societies in Bioinformatics Student organizations/societies in Bioinformatics

Current Educational Programs New courses New courses Bioinformatics tracks in existing degree programs Bioinformatics tracks in existing degree programs New degrees New degrees  MS and Ph.D. in Bioinformatics  Ph.D. in Information Technology  New undergraduate degree in Bioinformatics

New Graduate Curricula MS and Ph.D. tracks in Bioinformatics (joint effort between UNO college of IS&T and UNMC dept of Pathology and Microbiology) MS and Ph.D. tracks in Bioinformatics (joint effort between UNO college of IS&T and UNMC dept of Pathology and Microbiology) New introductory interdisciplinary courses New introductory interdisciplinary courses Combination of foundation, core, elective and research courses Combination of foundation, core, elective and research courses A compromised format A compromised format

Graduate Programs Bioinformatics tracks in MS program in CS Bioinformatics tracks in MS program in CS New Ph.D. program in IT New Ph.D. program in IT  Started Fall 2003  Employed a new concept that balances breadth and depth as related to key disciplines in IT  Bioinformatics has been identified as one of the thematic areas of the program

New Undergraduate Degree Joint Degree offered by IS&T and A&S at UNO Joint Degree offered by IS&T and A&S at UNO Prepare students for Bioinformatics-related positions in industry or research institutes Prepare students for Bioinformatics-related positions in industry or research institutes Prepare students for graduate programs in Bioinformatics or related areas Prepare students for graduate programs in Bioinformatics or related areas Provide strong training for students interested in the health professions and further education in allied areas of biomedical research/molecular biology Provide strong training for students interested in the health professions and further education in allied areas of biomedical research/molecular biology

Proposed Curriculum Computer Science Computer Science Mathematics/Statistics Mathematics/Statistics Biology Biology Chemistry Chemistry New Courses in Bioinformatics New Courses in Bioinformatics Internships – practical training Internships – practical training

New Degree in Bioinformatics Computer Science: Computer Science: Intro to Computer Science I Intro to Computer Science II Computer Organization Data Structures Introduction to Software Engineering Database Management Systems Data Warehousing and Data Mining

New Degree in Bioinformatics (cont.) Mathematics/Statistics: Mathematics/Statistics: Calculus I Calculus II Calculus III Discrete Mathematics Applied Probability and Statistics Graph Theory & Applications

New Degree in Bioinformatics (cont.) Biology: Biology: Principles of Biology Genetics Molecular Biology of the Cell Molecular Genetics Cellular Biology

New Degree in Bioinformatics (cont.) Chemistry: Chemistry: General Chemistry I General Chemistry II Organic Chemistry I Organic Chemistry II Biochemistry

New Degree in Bioinformatics (cont.) Bioinformatics Courses: Bioinformatics Courses: Introduction to Bioinformatics Algorithms for Computational Biology Database search and pattern discovery in Bioinformatics LAMP for Bioinformatics Senior Project in Bioinformatics Seminar in Bioinformatics

General Education and Electives - IS&T Humanities and Ethics – 9 Credit Hours Humanities and Ethics – 9 Credit Hours Social Studies – 9 Credit Hours Social Studies – 9 Credit Hours Cultural Diversity – 6 Credit Hours (May be satisfied using Humanities and/or social Studies) Cultural Diversity – 6 Credit Hours (May be satisfied using Humanities and/or social Studies) English/Speech –12 Credit Hours English/Speech –12 Credit Hours General Electives – 12 Credit Hours General Electives – 12 Credit Hours

IS&T Degree versus A&S Degree The IS&T curriculum includes 12 hours of electives, while the A&S curriculum includes an additional 12 hours of general education requirements The IS&T curriculum includes 12 hours of electives, while the A&S curriculum includes an additional 12 hours of general education requirements The slight difference reflects the fact that A&S degrees have a larger liberal arts focus, while IS&T degree offers more professional type degrees. The slight difference reflects the fact that A&S degrees have a larger liberal arts focus, while IS&T degree offers more professional type degrees. The elective hours can be used to take up to four courses in one of the four basic disciplines (Computer Science, Biology, Chemistry and Mathematics). This can provide the students the opportunity to have an added focus in one of the four angles of Bioinformatics. The elective hours can be used to take up to four courses in one of the four basic disciplines (Computer Science, Biology, Chemistry and Mathematics). This can provide the students the opportunity to have an added focus in one of the four angles of Bioinformatics.

General Education - A&S Humanities and Ethics – 12 Credit Hours Humanities and Ethics – 12 Credit Hours Social Studies – 12 Credit Hours Social Studies – 12 Credit Hours Cultural Diversity – 6 Credit Hours (May be satisfied using Humanities and/or social Studies) Cultural Diversity – 6 Credit Hours (May be satisfied using Humanities and/or social Studies) World Civilization – 6 Credit Hours World Civilization – 6 Credit Hours English/Speech –12 Credit Hours English/Speech –12 Credit Hours

Complimentary Research Activities Joint Research Projects Joint Research Projects Joint Grant Proposals (resources) Joint Grant Proposals (resources)  Advanced computing facilities  experimental and medical facilities  Student support

Service and Outreach Activities BioInformatics Interest Group (BIIG) BioInformatics Interest Group (BIIG)  Bioinformatics Resource Lib  Introductory/General Seminars  Local BLAST Server  General Advising/Networking Summer Camps and Open House Events Summer Camps and Open House Events High School Visits/Workshops High School Visits/Workshops Women in IT days – Diversity in IT days Women in IT days – Diversity in IT days