Transcript FIT-2006 - Fredonia
Bioinformatics: A New Vision for Academics
2 nd International Conference on Frontiers of Information Technology (FIT) 2006 Islamabad Pakistan
December 20 - 21, 2006 1
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
FIT-2006 Mudasser F. Wyne University of Michigan-Flint USA 2
Bioinformatics
A multifaceted discipline
Biology
Genetics and microbiology
Biochemistry
Mathematics
Statistics
Computer science
AI, Database, Algorithms, Pattern recognition
FIT-2006 Mudasser F. Wyne University of Michigan-Flint USA 3
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.
FIT-2006 Mudasser F. Wyne University of Michigan-Flint USA 4
Why Bioinformatics?
Gene information at NCBI doubles every 14 months Computer scientists are needed to
Analyze
Index
Represent
Model
Display
Process
Mine
Search
FIT-2006 Mudasser F. Wyne University of Michigan-Flint USA 5
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
FIT-2006 Mudasser F. Wyne University of Michigan-Flint USA 6
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.
FIT-2006 Mudasser F. Wyne University of Michigan-Flint USA 7
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
FIT-2006 Mudasser F. Wyne University of Michigan-Flint USA 8
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
FIT-2006 Mudasser F. Wyne University of Michigan-Flint USA 9
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
FIT-2006 Mudasser F. Wyne University of Michigan-Flint USA 10
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.
FIT-2006 Mudasser F. Wyne University of Michigan-Flint USA 11
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.
FIT-2006 Mudasser F. Wyne University of Michigan-Flint USA 12
Web Search
FIT-2006 Mudasser F. Wyne University of Michigan-Flint USA 13
School Statistics
Michigan National Schools with undergraduate degrees in Bioinformatics 1 14 Schools with undergraduate tracks in Schools with Masters degrees in Bioinformatics Schools with Doctorial degrees in Bioinformatics Schools with Graduate tracks in Bioinformatics Schools with an undergraduate course in Bioinformatics TOTAL 1 3 1 1 2 9 1 1 9 25
FIT-2006 Mudasser F. Wyne University of Michigan-Flint USA 14
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
FIT-2006 Mudasser F. Wyne University of Michigan-Flint USA 15
FIT-2006
Bioethics (3) Biostatistics (3) MTH321 (3) MTH122 (4) MTH121 (4)
Program Flow -1
Genomics (3-4) Paper/ Project (3) Adv.
bioinformatics (3) AI (3) Genetics (4)
Cell & Molecular Biology (4)
Bioinformat ics (3) DS & AA (3) Data Mining (3) Organic Chemistry II (4) Database Design (3) Organic Chemistry I (4) General Biology II (4) General Biology I (4) Physics II (4) Physics I (4) Object Oriented Prog.
(4) Prog.
(4) General Chemistry II (3) General Chemistry I (4)
Mudasser F. Wyne University of Michigan-Flint USA 16
Program Flow -2
FIT-2006
Biostats (3) Statistics (3) MTH321 (3) MTH122 (4) MTH121 (4) Bioethics (3) Genomics (3-4) Cell & Molecular Biology (4) Genetics (4) General Biology II (4) General Biology I (4) Paper/ Project (3) Adv.
Bioinfor.
(3) AI (3) BioChemistry (3) Bioinformat ics (3) DS & AA (3) Data Mining (3) Organic Chemistry II (4) OO Prog.
(4) Prog.
(4) VB (3) Database Design (3) SW (1) Organic Chemistry I (4) General Chemistry II (3) ICS (2) General Chemistry I (4)
Mudasser F. Wyne University of Michigan-Flint USA 17
Sample Course Contents
Bioinformatics
Applications of computer-based tools to the representation, annotation, and analysis of DNA and protein sequences.
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.
FIT-2006 Mudasser F. Wyne University of Michigan-Flint USA 18
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,
FIT-2006 Mudasser F. Wyne University of Michigan-Flint USA 19
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
FIT-2006 Mudasser F. Wyne University of Michigan-Flint USA 20
Credit Hours
Credit Hours
Maths: Biology: Chemistry: CS: Philosophy
Total hours:
11 19 +3 (Biostatistics) + 3 (Bioinformatics) 18 23 + 3 (Project) 3 (Bioethics)
83
FIT-2006 Mudasser F. Wyne University of Michigan-Flint USA 21
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.
FIT-2006 Mudasser F. Wyne University of Michigan-Flint USA 22
QUERIES
FIT-2006 Mudasser F. Wyne University of Michigan-Flint USA 23
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 [email protected]
.
FIT-2006 Mudasser F. Wyne University of Michigan-Flint USA 24