11
Bioinformatics: Bioinformatics: A New Vision for Academics A New Vision for Academics
2nd International Conference on Frontiers of Information Technology (FIT) 2006
IslamabadPakistan
December 20 - 21, 2006Mudasser F. Wyne, Ph.D.
Computer Science
University of Michigan - Flint
Computer Science Department
Email:
FIT-2006FIT-2006 Mudasser F. WyneMudasser F. Wyne University of Michigan-Flint University of Michigan-Flint
USAUSA
22
Bioinformatics??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-2006FIT-2006 Mudasser F. WyneMudasser F. Wyne University of Michigan-Flint University of Michigan-Flint
USAUSA
33
BioinformaticsBioinformatics A multifaceted discipline
Biology Genetics and microbiology
Biochemistry Mathematics Statistics Computer science
AI, Database, Algorithms, Pattern recognition
FIT-2006FIT-2006 Mudasser F. WyneMudasser F. Wyne University of Michigan-Flint University of Michigan-Flint
USAUSA
44
BioinformaticsBioinformatics 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-2006FIT-2006 Mudasser F. WyneMudasser F. Wyne University of Michigan-Flint University of Michigan-Flint
USAUSA
55
Why Bioinformatics?Why Bioinformatics?
Gene information at NCBI doubles every 14 months Computer scientists are needed to
Analyze Index Represent Model Display Process Mine Search
FIT-2006FIT-2006 Mudasser F. WyneMudasser F. Wyne University of Michigan-Flint University of Michigan-Flint
USAUSA
66
Why a new Program?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-2006FIT-2006 Mudasser F. WyneMudasser F. Wyne University of Michigan-Flint University of Michigan-Flint
USAUSA
77
Why a new Program?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-2006FIT-2006 Mudasser F. WyneMudasser F. Wyne University of Michigan-Flint University of Michigan-Flint
USAUSA
88
Another ReasonAnother 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-2006FIT-2006 Mudasser F. WyneMudasser F. Wyne University of Michigan-Flint University of Michigan-Flint
USAUSA
99
Interdisciplinary or MultidisciplinaryInterdisciplinary 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-2006FIT-2006 Mudasser F. WyneMudasser F. Wyne University of Michigan-Flint University of Michigan-Flint
USAUSA
1010
Why Not Graduate Degree?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-2006FIT-2006 Mudasser F. WyneMudasser F. Wyne University of Michigan-Flint University of Michigan-Flint
USAUSA
1111
Why Not Graduate Degree?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-2006FIT-2006 Mudasser F. WyneMudasser F. Wyne University of Michigan-Flint University of Michigan-Flint
USAUSA
1212
VariationsVariations
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-2006FIT-2006 Mudasser F. WyneMudasser F. Wyne University of Michigan-Flint University of Michigan-Flint
USAUSA
1313
Web SearchWeb Search
FIT-2006FIT-2006 Mudasser F. WyneMudasser F. Wyne University of Michigan-Flint University of Michigan-Flint
USAUSA
1414
School StatisticsSchool StatisticsMichigan National
Schools with undergraduate degrees in Bioinformatics 1 14
Schools with undergraduate tracks in 1
Schools with Masters degrees in Bioinformatics 3 9
Schools with Doctorial degrees in Bioinformatics 1 1
Schools with Graduate tracks in Bioinformatics 1 1
Schools with an undergraduate course in Bioinformatics 2
TOTAL 9 25
FIT-2006FIT-2006 Mudasser F. WyneMudasser F. Wyne University of Michigan-Flint University of Michigan-Flint
USAUSA
1515
Structural Learning ModelStructural 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-2006FIT-2006 Mudasser F. WyneMudasser F. Wyne University of Michigan-Flint University of Michigan-Flint
USAUSA
1616
Bioethics(3)
Biostatistics(3)
Bioinformatics(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 -1Program Flow -1
FIT-2006FIT-2006 Mudasser F. WyneMudasser F. Wyne University of Michigan-Flint University of Michigan-Flint
USAUSA
1717
Program Flow -2Program Flow -2Bioethics
(3)
Biostats(3)
Statistics (3)
Bioinformatics(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)
DataMining
(3)
VB(3)
ICS(2)
SW(1)
FIT-2006FIT-2006 Mudasser F. WyneMudasser F. Wyne University of Michigan-Flint University of Michigan-Flint
USAUSA
1818
Sample Course ContentsSample 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-2006FIT-2006 Mudasser F. WyneMudasser F. Wyne University of Michigan-Flint University of Michigan-Flint
USAUSA
1919
Sample Course ContentsSample 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-2006FIT-2006 Mudasser F. WyneMudasser F. Wyne University of Michigan-Flint University of Michigan-Flint
USAUSA
2020
Sample Course ContentsSample 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-2006FIT-2006 Mudasser F. WyneMudasser F. Wyne University of Michigan-Flint University of Michigan-Flint
USAUSA
2121
Credit HoursCredit Hours
Credit Hours Maths: 11 Biology: 19 +3 (Biostatistics) + 3
(Bioinformatics) Chemistry: 18 CS: 23 + 3 (Project) Philosophy 3 (Bioethics) Total hours: 83
FIT-2006FIT-2006 Mudasser F. WyneMudasser F. Wyne University of Michigan-Flint University of Michigan-Flint
USAUSA
2222
AccreditationAccreditation
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-2006FIT-2006 Mudasser F. WyneMudasser F. Wyne University of Michigan-Flint University of Michigan-Flint
USAUSA
2323
QUERIES QUERIES
FIT-2006FIT-2006 Mudasser F. WyneMudasser F. Wyne University of Michigan-Flint University of Michigan-Flint
USAUSA
2424
2nd International Workshop on 2nd International Workshop on Web-Based Learning: Innovation and ChallengesWeb-Based Learning: Innovation and Challenges
(WeLearn-2007) (WeLearn-2007)Amman, Jordan, Amman, Jordan, 17–20 April 200717–20 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].
Top Related