1. 1 Bioinformatics: A New Vision for Academics 2 nd International Conference on Frontiers of Information Technology (FIT) 2006 Islamabad Pakistan December 20 - 21, 2006 Mudasser F. Wyne, Ph.D. Computer Science University of Michigan - Flint Computer Science Department Email: mfwyne@umflint.edu

2. FIT-2006Mudasser F. Wyne University of Michigan-Flint USA 2 Bioinformatics?? Classically known Computational biology Definition The storage and analysis of biological data using certain algorithms and computer software The application of tools of computation and analysis to the capture and interpretation of biological data Emphasis Use of computer and statistical methods to understand biological data

3. FIT-2006Mudasser F. Wyne University of Michigan-Flint USA 3 Bioinformatics A multifaceted discipline Biology Genetics and microbiology Biochemistry Mathematics Statistics Computer science AI, Database, Algorithms, Pattern recognition

4. FIT-2006Mudasser F. Wyne University of Michigan-Flint USA 4 Bioinformatics Bioinformatics is a new and rapidly evolving discipline that has emerged from the fields of experimental molecular biology and biochemistry, and from the artificial intelligence, database, pattern recognition, and algorithms disciplines of computer science.

5. FIT-2006Mudasser F. Wyne University of Michigan-Flint USA 5 Why Bioinformatics? Gene information at NCBI doubles every 14 months Computer scientists are needed to Analyze Index Represent Model Display Process Mine Search

6. FIT-2006Mudasser F. Wyne University of Michigan-Flint USA 6 Why a new Program? Non of the traditional programs serve the needs of the new demand Fundamental challenge Life science curricula have historically shared very little common ground with computer and IT curricula Traditional science programs in Computer Science and Biochemistry Information systems are the lifeblood of the new century A positive feedback cycle where the need for new genomics and biomedical discoveries Push the development of information systems

7. FIT-2006Mudasser F. Wyne University of Michigan-Flint USA 7 Why a new Program? Largely because of the inherently interdisciplinary nature of bioinformatics research, academia has been slow to respond to strong industry and government demands for trained scientists to develop and apply novel bioinformatics techniques to the rapidly growing freely available repositories of genetic data.

8. FIT-2006Mudasser F. Wyne University of Michigan-Flint USA 8 Another Reason Decrease in enrollment in computer science programs USA From 2000 the drop is around 35 to 50% Labor statistics forecast job growth 20% to 50% by 2012 UK From 2000 the drop is around 20% to 35% Electronics and Electrical engineering enrollment increased Europe Enrollments decreasing and jobs are rising

9. FIT-2006Mudasser F. Wyne University of Michigan-Flint USA 9 Interdisciplinary or Multidisciplinary Multidisciplinary Involvement of several different professional areas Not necessarily in an integrated manner Interdisciplinary Integration of multidisciplinary knowledge across a central program theme or focus Creates knowledge that is more holistic than knowledge built in discipline specific studies

10. FIT-2006Mudasser F. Wyne University of Michigan-Flint USA 10 Why Not Graduate Degree? Entrance barriers for these programs are high, Significant amount of prerequisite knowledge in the fields of biochemistry and computer science B.Sc. Computer Science Remedial courses in chemistry, biochemistry, molecular biology and genetics B.Sc. Biology Remedial courses in programming, data structure, database and artificial intelligence

11. FIT-2006Mudasser F. Wyne University of Michigan-Flint USA 11 Why Not Graduate Degree? I will present an undergraduate-level bioinformatics curriculum in computer science designed for the baccalaureate student. This program is designed to be tailored easily to the needs and resources of a variety of institutions.

12. FIT-2006Mudasser F. Wyne University of Michigan-Flint USA 12 Variations A challenge to discover Mostly offered as subprograms or specializations of existing programs Several terms Bioinformatics Medical informatics, Informatics, Health informatics, Computational biology Most programs have started in just the last 3 years and have not been entered into a program directory.

13. FIT-2006Mudasser F. Wyne University of Michigan-Flint USA 13 Web Search

14. FIT-2006Mudasser F. Wyne University of Michigan-Flint USA 14 School Statistics MichiganNational Schools with undergraduate degrees in Bioinformatics114 Schools with undergraduate tracks in1 Schools with Masters degrees in Bioinformatics39 Schools with Doctorial degrees in Bioinformatics11 Schools with Graduate tracks in Bioinformatics11 Schools with an undergraduate course in Bioinformatics2 TOTAL 925

15. FIT-2006Mudasser F. Wyne University of Michigan-Flint USA 15 Structural Learning Model Pre-Structural Level Learner is distracted by an irrelevant aspect belonging to a previous mode Uni-Structural Level Learner focuses on a relevant discipline Multi-Structural Level The learner acquires knowledge is several disciplines But does not integrate them Relational Level Learner integrates knowledge from several discilpines around a central theme

16. FIT-2006Mudasser F. Wyne University of Michigan-Flint USA 16 Bioethics (3) Biostatistics (3) Bioinformat ics (3) Adv. bioinformatics (3) Paper/ Project (3) Genomics (3-4) Genetics (4) Cell & Molecular Biology (4) General Biology II (4) General Biology I (4) MTH121 (4) MTH122 (4) MTH321 (3) DS & AA (3) Object Oriented Prog. (4) Organic Chemistry II (4) Organic Chemistry I (4) General Chemistry I (4) General Chemistry II (3) Prog. (4) Physics II (4) Physics I (4) Database Design (3) AI (3) Data Mining (3) Program Flow -1

17. FIT-2006Mudasser F. Wyne University of Michigan-Flint USA 17 Program Flow -2 Bioethics (3) Biostats (3) Statistics (3) Bioinformat ics (3) Adv. Bioinfor. (3) Paper/ Project (3) Genomics (3-4) Cell & Molecular Biology (4) Genetics (4) General Biology II (4) General Biology I (4) MTH121 (4) MTH122 (4) MTH321 (3) DS & AA (3) OO Prog. (4) BioChemistry (3) Organic Chemistry II (4) Organic Chemistry I (4) General Chemistry I (4) General Chemistry II (3) Prog. (4) Database Design (3) AI (3) Data Mining (3) VB (3) ICS (2) SW (1)

18. FIT-2006Mudasser F. Wyne University of Michigan-Flint USA 18 Sample Course Contents Bioinformatics Applications of computer-based tools to the representation, annotation, and analysis of DNA and protein sequences.computer-based tools Computer lab-oriented exercises employing software packages used to evaluate structural, functional, and evolutionary characteristics of animal and microbial genomes. Topics Fundamentals of Gene Structure and Function, Molecular Biology Databases, Information Retrieval, Database Searches, Molecular Sequence Analysis Tools, Gene Identification and Protein Structure-Function Predictions. Computational analysis of DNA data; Introduction to bioinformatics database using Pearl and SQL; configuration of UNIX workstations for bioinformatics analyses.

19. FIT-2006Mudasser F. Wyne University of Michigan-Flint USA 19 Sample Course Contents Adv. Bioinformatics This course presents an algorithmic focus to problems in computational biology. Problems and solutions covered in this course include Gene Hunting, Sequence Comparison, Multiple Alignment, Gene Prediction, Trees and Sequences, Databases and Rapid sequence analysis. Also known as: Bioinformatics, Computational Bioinformatics, Principles of Bioinformatics II, Advanced Bioinformatics Computing,

20. FIT-2006Mudasser F. Wyne University of Michigan-Flint USA 20 Sample Course Contents Bioethics Discussions of major ethical questions having arisen from research in genetics, medicine, and industries supported by this knowledge. Topics General scientific ethics, biological research ethics, governmental and research policy issues. Course work I primarily reading and writing

21. FIT-2006Mudasser F. Wyne University of Michigan-Flint USA 21 Credit Hours Maths:11 Biology:19 +3 (Biostatistics) + 3 (Bioinformatics) Chemistry:18 CS:23 + 3 (Project) Philosophy3 (Bioethics) Total hours:83

22. FIT-2006Mudasser F. Wyne University of Michigan-Flint USA 22 Accreditation This model program can be modified to meet CSAB requirements ABET Computer science topics at least 40 semester hours Mathematics and science at least 30 semester hours Humanities, social sciences, arts and other disciplines that serve to broaden the background of the student at least 30 semester hours.

23. FIT-2006Mudasser F. Wyne University of Michigan-Flint USA 23 QUERIES

24. FIT-2006Mudasser F. Wyne University of Michigan-Flint USA 24 2nd International Workshop on Web-Based Learning: Innovation and Challenges (WeLearn-2007) Amman, Jordan, 17–20 April 2007 Aims and Scope The focus of this workshop is on web based issues in both teaching and learning. We would also like to stimulate interest in this area, expose natural collaboration among the participants, inform the larger research community of the interest and importance of this topic and create a permanent forum for evaluating innovations and relevant research activities. Paper submission deadline: January 20, 2007. Send you submissions to mfwyne@umflint.edu.mfwyne@umflint.edu