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