|
Six Day CEP
Course on
Flood
of data on genomics, transcriptomics, proteomics, phenomics, and xxx-omics has
led to the emergence of a new inter-disciplinary field where organization,
analysis, and processing of this data has to be done efficiently. The biological
databases are of many different kinds and more and more are emerging with the
advent of the technology in the respective field. Although the different databases are related to each other, the
link is not always clear. The challenge
lies in understanding the link between these databases to glean new biological
information. Another avenue is to apply
systems science approach to understand biology better. The course introduces participants to
biological databases, tools to analyze and compare data, inter- and intra-
database relationships, various algorithms, verbal models, quantitative models,
etc. The course would cater to both
biologists as well as non-biologists.
The
course is mainly designed for those who wish to make a career (in industry /
research) in bioinformatics. Pharma /
IT companies and academicians (biologists as well as engineers) who would like
to venture into bioinformatics would benefit the most from the course. The course will help biologists expand the
scope of their research by employing bioinformatics tools.
1.
Organization of Biological Data: A bit of biology, the code, transcription, and translation.
genome, transcriptome, proteome, metabolome and phenotype.
2.
Databases: Raw databases and
Processed databases, Publicly available data; types levels of databases,
Querying in databases; tools for querying
3.
Relational Database concepts and
Data mining in Biology: Data modeling and representation, Data storage, retrieval,
creating your own database.
4.
DNA sequence analysis: Gene finding, Hidden
Markov Models, gene annotation, prediction of co-regulated genes from
sequences, prediction of regulatory elements for co-regulated genes.
5.
Protein sequence analysis: Pair-wise sequence
alignment, substitution matrices, local vs. global alignment, multiple sequence
alignment, Hierarchical clustering, prediction of protein function,
protein-protein interaction, gene fusion events, gene clusters, phylogenetic
analysis
evolutionary trace analysis, binding site
prediction.
6.
3-D structural databases: Homology, Algorithms for comparison
of protein structures, Comparison of
distance matrices, searching for patterns, The triads (catalytic, metal
binding, etc.), Evolution of protein
structure and sequences.
7.
A bird’s eye view of the Human
Genome:
Tools for analysis of human genome, gene finding, Alternative splicing models,
Probing with ESTs, Exon Microarray, Implications in Cancer genetics, drug
discovery, SNPs
8.
Gene expression profiling; The technology, Gene Chip,
The Databases, Tabulation and visualization of data, error models, Data
Analysis: Clustering, self organizing maps, correlations. Time dependent analysis, Patterns, bi-clustering,
wavelets, functional coupling.
9.
Applications of Gene expression
profiling:
Classification of genes, cancers and drugs; marker genes, monitoring of
treatment, integration of data, Co-regulated genes, regulatory motifs.
10.
Metabolic & Genetic
regulatory networks:
Reconstruction of metabolic networks, Basic architecture of genetic networks,
genetic switches and amplifiers, identification of new genetic networks, use of
the gene disruption data.
11.
Systems Engineering Approach: Defining metabolic
phenotype, virtual experiments (gene knockout, metabolic shift, etc.), metabolic engineering and functional genomics.
12.
Proteomics: The technology (2-D gels,
n-hybrid systems, etc.), The Databases, Proteomic definition of physiological
state, protein-protein interaction maps, protein chips, searching in
databases.
Course Material
The
course material includes lecture notes, transparencies, list of references,
instruction sheets for computational lab sessions, and a listing of about 200
web-sites for biological data.
Computational Lab
The participants will be
given hands on experience in bioinformatics through computer based assignments
for each module. The assignments would involve data-mining, analysis of data,
organization of data, etc. with
internet based tools as well as with programming (optional for those who are
conversant with C/C++). Clear
instruction sheets would be given for lab sessions.
Programming
knowledge is desirable but not essential for understanding the fundamentals
covered in the course. Programming
language will not be taught in this course.
Course
dates & Venue
The course dates are November 17-22, 2003. The venue would be conference Hall(Ground
floor), IIT Guest house (report here for registration) and Computer Lab,
Chemical Eng. Dept. IIT-Bombay.
Accommodation
Guest house
facility on the campus is available
for a limited number of
participants on payment as per actuals and with advance request.
Course Fee &
Registration
The course fee per
participant is :
Industry : Rs. 16,500/-
Academia* (faculty, staff
& students): Rs.
11,000/-
Foreign delegates# : US$ 800
(Fee
includes course material, working lunch & tea refreshments
#The
fee for foreign delegates includes airport pickup, drop and guest house
accommodation for 6 days)
*You
must send a certificate of affiliation with academic / govt. R&D institute
to avail the rate applicable for academia.
Fees must be paid
by a demand draft drawn in the favour of “Registrar, IIT Bombay (CEP A/c)”.
Kindly fill out
the attached registration form and mail it along with course fees to the course
coordinator.
Kindly note that
no income tax is to be deducted at source from course fee payments, as I.I.T.
Bombay is exempted from the same.
Deadline
for registration (with full payment):
October 27, 2003.
Address all
correspondence to:
Prof.
Pramod Wangikar, Course Coordinator,
Dept. of Chemical Engg.,
I. I. T. Bombay
Powai, Mumbai - 400 076.
India.
Tel :
(022) 2576 7060 (CEP cell), 2576 4215 (Mr. Bapat)
Fax : 2572 6895, 2572 3480
Email : pw-cep@che.iitb.ac.in
R E G I S T R A T I O N F
O R M
Six-day CEP Course on
November 17-22,
2003
NAME (PRINT) :
________________________________________________________
DESIGNATION :
_______________________________________
ORGANIZATION:
________________________________________________________
MAILING ADDRESS : _____________________________________
________________________________________________________
________________________________________________________
TELEPHONE :__________________ FAX: ___________________
EMAIL :
________________________________________________
QUALIFICATIONS
&Discipline :______________ _____
EXPERIENCE
: ______ Yrs.
BROAD
AREA OF YOUR RESEARCH / WORK :
Sex: M/F
Age: ____Years
Do you have basic familiarity with:
|
|
Y/N |
|
Y/N |
|
Molecular
Biology |
|
Computer/Internet |
|
|
Mathematics/Statistics |
|
Programming
Language |
|
IIT Guest House accommodation
required?* YES / NO
(*Guest House bill to be paid
directly by participant.)
PAYMENT:
D.D. No.: Dt. Rs.
[Demand draft should be drawn
in favour of "The Registrar, IIT Bombay (CEP A/c)"].
Date: Signature of
Applicant