Educational Programs in Bioinformatics at UNO

Hesham H. AliHesham H. AliDepartment of Computer ScienceDepartment of Computer Science

College of Info Science and TechnologyCollege of Info Science and TechnologyUniversity of Nebraska at OmahaUniversity of Nebraska at Omaha

April 21April 21stst, 2004, 2004

What is Bioinformatics?

Source: British Medical JournalBayat, Ardeshir (2002) "Science, medicine, and the future: Bioinformatics" 324: 1018-1022.

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 Mid 1990s: The development of MS

Programs and short term certificate Programs and short term certificate programs.programs.

Late 1990s: The development of Ph. D. Late 1990s: The development of Ph. D. Programs and Postdoctoral Positions. Programs and Postdoctoral Positions.

Recently: The development of Recently: The development of Undergraduate Programs. Undergraduate Programs.

Challenges to Educational Programs

Too many prerequisitesToo many prerequisitescomputer science – math – stats – biology – computer science – math – stats – biology – chemistry – engineering chemistry – engineering

Students SupportStudents Supportmentors – peers – financial resources – mentors – peers – financial resources – administration help administration help

The Multidisciplinary FactorThe Multidisciplinary Factormaking sure everybody is on the same page 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 The process of speeding up Biosciences processes by automating what otherwise processes by automating what otherwise Biologists have to do manually.Biologists have to do manually.

Another application domain for Computer Another application domain for Computer Scientists to apply or employ their currently Scientists to apply or employ their currently available algorithms or theories.available algorithms or theories.

Current Steps in Nebraska

Interest from researchers/educators/studentsInterest from researchers/educators/students Support from the administrationSupport from the administration Infrastructure grants funded (Nebraska Center for Infrastructure grants funded (Nebraska Center for

Life Sciences) Life Sciences) Higher degree of communicationHigher degree of communication New innovative programs in BioinformaticsNew innovative programs in Bioinformatics Various interesting research projectsVarious interesting research projects Student organizations/societies in BioinformaticsStudent organizations/societies in Bioinformatics

Current Educational Programs

New coursesNew courses Bioinformatics tracks in existing degree Bioinformatics tracks in existing degree

programs programs New degreesNew degrees

MS and Ph.D. in BioinformaticsMS and Ph.D. in Bioinformatics Ph.D. in Information TechnologyPh.D. in Information Technology New undergraduate degree in New undergraduate degree in

Bioinformatics Bioinformatics

New Graduate Curricula

MS and Ph.D. tracks in Bioinformatics (joint MS and Ph.D. tracks in Bioinformatics (joint effort between UNO college of IS&T and UNMC effort between UNO college of IS&T and UNMC dept of Pathology and Microbiology)dept of Pathology and Microbiology)

New introductory interdisciplinary courses New introductory interdisciplinary courses Combination of foundation, core, elective and Combination of foundation, core, elective and

research coursesresearch courses A compromised formatA compromised format

Graduate Programs

Bioinformatics tracks in MS program in CSBioinformatics tracks in MS program in CS New Ph.D. program in ITNew Ph.D. program in IT

Started Fall 2003Started Fall 2003 Employed a new concept that balances breadth Employed a new concept that balances breadth

and depth as related to key disciplines in ITand depth as related to key disciplines in IT Bioinformatics has been identified as one of Bioinformatics has been identified as one of

the thematic areas of the programthe thematic areas of the program

New Undergraduate Degree

Joint Degree offered by IS&T and A&S at UNOJoint Degree offered by IS&T and A&S at UNO Prepare students for Bioinformatics-related Prepare students for Bioinformatics-related

positions in industry or research institutes positions in industry or research institutes Prepare students for graduate programs in Prepare students for graduate programs in

Bioinformatics or related areas Bioinformatics or related areas Provide strong training for students interested in Provide strong training for students interested in

the health professions and further education in the health professions and further education in allied areas of biomedical research/molecular allied areas of biomedical research/molecular biologybiology

Proposed Curriculum

Computer ScienceComputer Science Mathematics/StatisticsMathematics/Statistics BiologyBiology ChemistryChemistry New Courses in BioinformaticsNew Courses in Bioinformatics Internships – practical training Internships – practical training

New Degree in Bioinformatics

Computer Science: Computer Science: Intro to Computer Science IIntro to Computer Science IIntro to Computer Science IIIntro to Computer Science IIComputer Organization Computer Organization Data StructuresData Structures

Introduction to Software Engineering Introduction to Software Engineering Database Management Systems Database Management Systems Data Warehousing and Data Mining Data Warehousing and Data Mining

New Degree in Bioinformatics (cont.)

Mathematics/Statistics:Mathematics/Statistics:

Calculus I Calculus I

Calculus II Calculus II

Calculus IIICalculus III

Discrete MathematicsDiscrete Mathematics

Applied Probability and StatisticsApplied Probability and Statistics

Graph Theory & ApplicationsGraph Theory & Applications

New Degree in Bioinformatics (cont.)

Biology:Biology:

Principles of Biology Principles of Biology

Genetics Genetics

Molecular Biology of the Cell Molecular Biology of the Cell

Molecular Genetics Molecular Genetics

Cellular Biology Cellular Biology

New Degree in Bioinformatics (cont.)

Chemistry:Chemistry:

General Chemistry IGeneral Chemistry I

General Chemistry IIGeneral Chemistry II

Organic Chemistry IOrganic Chemistry I

Organic Chemistry IIOrganic Chemistry II

Biochemistry Biochemistry

New Degree in Bioinformatics (cont.)

Bioinformatics Courses:Bioinformatics Courses:

Introduction to Bioinformatics Introduction to Bioinformatics

Algorithms for Computational Biology Algorithms for Computational Biology

Database search and pattern discovery in Database search and pattern discovery in Bioinformatics Bioinformatics

LAMP for BioinformaticsLAMP for Bioinformatics

Senior Project in Bioinformatics Senior Project in Bioinformatics

Seminar in BioinformaticsSeminar in Bioinformatics

General Education and Electives - IS&T

Humanities and Ethics – 9 Credit HoursHumanities and Ethics – 9 Credit Hours Social Studies – 9 Credit HoursSocial Studies – 9 Credit Hours Cultural Diversity – 6 Credit Hours (May be Cultural Diversity – 6 Credit Hours (May be

satisfied using Humanities and/or social Studies)satisfied using Humanities and/or social Studies) English/Speech –12 Credit HoursEnglish/Speech –12 Credit Hours General Electives – 12 Credit HoursGeneral Electives – 12 Credit Hours

IS&T Degree versus A&S Degree

The IS&T curriculum includes 12 hours of electives, The IS&T curriculum includes 12 hours of electives, while the A&S curriculum includes an additional 12 while the A&S curriculum includes an additional 12 hours of general education requirements hours of general education requirements

The slight difference reflects the fact that A&S degrees The slight difference reflects the fact that A&S degrees have a larger liberal arts focus, while IS&T degree have a larger liberal arts focus, while IS&T degree offers more professional type degrees. offers more professional type degrees.

The elective hours can be used to take up to four The elective hours can be used to take up to four courses in one of the four basic disciplines (Computer courses in one of the four basic disciplines (Computer Science, Biology, Chemistry and Mathematics). This Science, Biology, Chemistry and Mathematics). This can provide the students the opportunity to have an can provide the students the opportunity to have an added focus in one of the four angles of Bioinformatics. 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 HoursSocial Studies – 12 Credit Hours Cultural Diversity – 6 Credit Hours (May be Cultural Diversity – 6 Credit Hours (May be

satisfied using Humanities and/or social Studies)satisfied using Humanities and/or social Studies) World Civilization – 6 Credit HoursWorld Civilization – 6 Credit Hours English/Speech –12 Credit HoursEnglish/Speech –12 Credit Hours

Complimentary Research Activities

Joint Research ProjectsJoint Research Projects Joint Grant Proposals (resources)Joint Grant Proposals (resources)

Advanced computing facilities Advanced computing facilities experimental and medical facilitiesexperimental and medical facilities Student support Student support

Service and Outreach Activities

BioInformatics Interest Group (BIIG)BioInformatics Interest Group (BIIG) Bioinformatics Resource LibBioinformatics Resource Lib Introductory/General SeminarsIntroductory/General Seminars Local BLAST ServerLocal BLAST Server General Advising/Networking General Advising/Networking

Summer Camps and Open House EventsSummer Camps and Open House Events High School Visits/WorkshopsHigh School Visits/Workshops Women in IT days – Diversity in IT daysWomen in IT days – Diversity in IT days