BY4210

Biocomputing

Venue : Medical Informatics Computer Lab., Level 1 CRC

Lectures : 9.00 – 10.00 am

Practicals : 9.00 – 1.00 pm (except for 14/2/00)

Date

/

Topic

/ Mode of instruction / Staff-in-charge
Monday 31/1/00
9.00 – 10.00am / Use of computers in molecular biology
Internet services
Creating a web page
Searching literature using PubMed at NCBI / Lecture and demonstration / TTW/ MS
Tuesday
1/2/00
9.00-10.00 am / Biocomputing and bioinformatics at BIC (NUS):
BioMenu
BioAgent
BioPortal
BioKleisli / Lecture and demonstration / TTW/ MS
Thursday 3/2/00
9.00 am – 1.00pm / 3D structure graphics.
Use of SYBYL software for protein modeling and protein graphics.
Docking a ligand by shape matching, Computer simulation of motions of a biomolecule / Practical 1
(Blk S17, #07-11, Dept. of Computational Science) / CYZ
Friday
4/2/00
9.00am –10.00am / 1.1  Accessing biomedical databases.
1.2  Searching database using ENTREZ
1.3  Literature search using PubMed at NCBI
1.4  Using Editseq in DNAstar / Lecture and demonstration / CKL
Tuesday
8/2/00
9.00am –1.00 pm / 2.1  Using the Online Human Genetics Resources : Online Mendelian Inheritance in Man, HumanGenetic Maps , dbEST, dbSTS and genome databases.
2.2  Using the Taxonomy Browser at NCBI
2.3  Retrieving DNA and protein sequences from phlogenetically-related organisms
2.4  Compiling retrieved sequences into a file. / Practical 2 / EYPH
Thursday 10/2/00
9.00am – 1.00 pm / 3.1  Retrieval of a.a. and DNA sequences related to a protein of interest using ENTREZ.
3.2  Multiple sequence alignment of related a.a. and DNA sequences.
3.3  Phylogenetic analysis of sequences. .
3.4  Alignment decorations. / Practical 3 / CKL
Monday 14/2/00
12nn – 4 pm / 4.1  Using multiple alignment results for the design of PCR primers suitable for PCR amplification and DNA sequencing.
4.2  Design of primers for amplification and sequencing of a gene of interest – e.g. Hsp70 from B.pseudomallei.
4.3  Designing primers for Multiplex PCR / Practical 4 / EYPH
Tuesday 15/2/00
9.00am – 1.00pm / 5.1  Using SeqMan in DNAstar to assemble contigs using raw data from the ABI automated DNA sequencer.
5.2  Checking contig sequence for homology to DNA and a.a. sequences in databases by using BLAST at NCBI and BioKleisli
5.3  Using promoter scan and signal scan. / Practical 5 / CKL
Thursday 17/2/00
9.00am – 1.00pm / 6.1  Identify information on the databases regarding a specifc biochemical pathway, e.g. pigment synthesis, a metabolic pathway, or signal transduction pathway
6.2  Trace the flux.
6.3  Using Kyoto Encyclopedia of genes and genomes (KEGG) to obtain information regarding a particular enzyme of interest.
6.4  Using the Ligand Database to obtain information regarding reactions catalyzed and properrties of a protein involved in signal transducation, e.g. tyrosine phosphatase.
6.5  Using Enzyme Database to obtain information reactions catalyzed by an enzyme of interest. / Practical 6 / PK

Note: Each of the “Practical” sessions will comprise approximately 1 hour of instruction and 3 hours of hands-on exercises.

CKL - Dr Chua Kim Lee, Dept. of Biochemistry

TTW - Dr Tan Tin Wee, Director of IRDU and Bioinfomatics Center

MS - Ms Meena Sakharkar, Bioinformatics Center

CYZ - Dr Chen Yu Zhong, Dept. of Computational Science

EYPH - Dr Eric Yap Peng Huat, Defense Medical Research Institute

PK - Prasanna Kolatkar, Head, Resource Unit, Bioinformatics Centre.

Summary:

Lectures / : 3 hours
Practicals / : 24 hours
Mini-project / : 25 hours

Continuous assessment: 40%

This is based on exercises in Practicals 1-6. A report will be produced for each practical.

Mini-project: 60%