NSTDA Institute (NI)
National Science and Technology Development Agency (NSTDA)
Faculty of Graduate Studies, Mahidol University
Course Announcement
GRID617 Hypercourse on Bioinformatics (2 credits)
13-16 October 2009
NSTDA Institute (NI), National Science and Technology Development
Agency (NSTDA) in collaboration with Faculty of Graduate
studies, Mahidol University will offer a hypercourse on
Bioinformatics in the second semester of the academic year
2009. It is a 2-credit course, intended for graduate students
and researchers in sciences, computer sciences and science-related
disciplines from Mahidol University and other institutions.
Course description
Use of computers to store, retrieve, analyze biological
information; implement and use web service workflow in bioinformatics;
genomics-transcriptonomics-proteomics, bioinformatics at
DNA level; bioinformatics of gene cloning and expression,
biological database and NCBI, sequence alignment and similarity
searching, PCR primer and probe design, principle of nucleic
acid analysis & sequence alignment algorithms, phylogenetic
analysis, bioinformatics at SNP level; single nucleotide
polymorphism and its' application, SNP database for investigation
of human genome, pharmacogenomics/pharmacogenetics resources,
an interactive SNP visualization tool, selection of SNP
markers for disease association studies, bioinformatics
at proteomics level; protein bioinformatics, protein expression,
protein purification, introductory to proteomics, protein
identification, proteomic modeling and drug design, chat
room for hypercourse on bioinformatics.
Course objectives
- To provide an opportunity in self education utilizing
WWW resources so as to assist students in understanding
the principle and concept of Bioinformatics.
- To apply knowledge of bioinformatics (information and
automation) to various problems e.g., genome projects.
Prerequisites : The student should be able to use Internet
and must pass at least one course in biological sciences.
Course format
- Lecturer presentation and demonstration by using virtual
multimedia simulation and interactive animation
- Self study by using WWW
Duration and schedule : The 4-day course will be offered
during 13-16 October 2009
at 8.30-17.00 h
Venue : Room L-02, Faculty of Science, Mahidol University
Further information :
Please contact
Dr.Pintip Ruenwongsa <scprw@mahidol.ac.th>
Institute for Innovative Learning
Mahidol University, Rama 6 Rd, BKK 10400
Tel (02) 4419020-4 # 1300-9 Fax (02) 4410479
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Date
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Time |
Lecture/Demonstration
Topic |
Lecturers/Instructors |
| Oct
13 |
Lecture |
|
|
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9.00-9.30 |
Course orientation |
Wasun Chantratita
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|
Bioinformatics lecture tools; S* Alliance
and ASEAN Virtual University in Science and Technology |
Pintip Ruenwongsa (Fac. Science Mahidol) |
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Bioinformatics tools;
- BIO-IT (multimedia learning program of how to use bioinformatics
tools, step by step)
- คู่มือสอนการใช้โปรแกรมชีวสารสนเทศเบื้องต้น (text book)
|
|
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9.30-10:30 |
An Overview of Bioinformatics;
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Genomics-Transcriptonomics-Proteomics |
Wasun Chantratita (RAMA) |
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10.30-10.45 |
Break |
|
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11.00-12.00 |
Translational Bioinformatics;
- The development of storage, analytic, and interpretive
methods to optimize the transformation of increasingly voluminous
biomedical data, and genomic data in particular, into proactive,
predictive, preventive, and participatory health
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|
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12.00-13.00 |
Lunch |
|
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13.00-15.00 |
Bioinformatics at DNA level
- Principle of nucleic acid analysis & sequence alignment
algorithms
|
Prasit Palittapongarnpim |
| |
15.00-15.15 |
Break |
|
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Demonstration |
|
|
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15.15-15.45 |
Biological database and NCBI e-Utilities Web Service
- NCBI tour
- Entrez
- Bioinformatics sequence formats
- Reference sequence
- How to get the interesting sequence/gene from the database
|
Soranan Chantarangsu (Chula) |
| |
15.45-16.30 |
Sequence alignment and similarity searching
- BLAST
- Multiple alignment
- Consensus sequence
|
Ekawat Pasomsub (RAMA) |
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16.30-17.00 |
Taverna: Tool for designing and executing bioinformatics
workflows |
Ekawat Pasomsub (RAMA) |
| Oct
14 |
Lecture |
|
|
| |
9.00-10.00 |
Bioinformatics of gene cloning and expression |
Wasun Chantratita (RAMA) |
| |
10.00-10.10 |
Break |
|
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10.10-12.00 |
Phylogenetic analysis |
Sirawut Klinbunga (BIOTEC) |
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12.00-13.00 |
Lunch |
|
| |
Demonstration |
|
|
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13.00-14.00 |
Phylogenetic tree reconstruction with Phylip |
Ekawat Pasomsub (RAMA) |
| |
14.00-15.00 |
PCR primer and probe design
Primer check
- BLAST
- OligoCalc
- OligoAnalyzer
|
Ekawat Pasomsub (RAMA) |
| |
15.00-15.15 |
Break |
|
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15.15-15.45 |
- Restriction enzyme analysis
- Cloning analysis
|
Chuphong Thongnak
(RAMA)
|
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15.45-16.30 |
Bioedit - Biological Sequence Alignment Editors |
Chuphong Thongnak (RAMA) |
| |
16.30-17.00 |
- DNA fragment assembly
- Gene finding (ORF)
- DNA translation
|
Soranan Chantarangsu (Chula) |
| Oct
15 |
Lecture |
|
|
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|
Bioinformatics at SNP level |
|
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9.00-10.30 |
Overview: Single nucleotide polymorphism and its'
applications
- SNP, LD bin and haplotype block, haplotype Tagging SNPs,
- Linkage analysis and whole-genome disease association
studies SNP genotyping;
|
Surakameth Mahasirimongkol (Thailand MOPH) |
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SNP genotyping;
- High throughput
- Medium throughput
- Low throughput
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|
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10.30-10.45 |
Break |
|
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10.45-12.00 |
Genome Wide Association (GWAS) Data analysis |
Soranan Chantarangsu (Chula) |
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12.00-13.00 |
Lunch |
|
| |
Demonstration |
|
|
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13.00-14.30 |
SNP database for the investigation
of the human genome (online): The browsers used to view the
SNPs, linkage disequilibrium bins, and haplotype blocks across
all populations
- dbSNP (SNP database from NCBI)
- Perlegen (Perlegen Sciences, Inc)
- HapMap and HapMart (The International HapMap Project)
- SNPper (Retrieve known SNPs by position or by association
with a gene)
|
Chuphong Thongnak (RAMA),
Ekawat Pasomsub (RAMA)
|
| |
14.30-15.00 |
An interactive SNP visualization
tool (off-line tools);
- Genalys (powerful program which allows one to align multiple
sequences)
- SNPbrowsers (knowledge-guided selection of optimal sets
of SNPs for association and fine mapping studies)
|
Ekawat Pasomsub/ Soranan Chantarangsu (Chula) |
| |
15.00-15.30 |
Sample size calculation tools
(Minsage and Quanto) R-package for SNPs (handling genetic data)
|
Ekawat Pasomsub (RAMA) |
| |
15.30-15.45 |
Break |
|
| |
15.45-16.30 |
An interactive SNP visualization tool (off-line
tools);
- Haploview (simplify and expedite the process of haplotype
analysis)
|
Ekawat Pasomsub (RAMA) |
| |
16.30-17.00 |
Pharmacogenomics/Pharmacogenetics resources
|
Soranan Chantarangsu (Chula) |
| Oct
16 |
Lecture |
|
|
| |
|
Clinical Genomics Level Seven (CGL7) |
|
| |
9.00-10.00 |
The Clinical Genomics Informatics System (CGIS)
- Clinical genomics is an interdisciplinary field dealing
with the use of genetic data in clinical practice, such
as the prescription of drugs based on a patient's genetic
profile.
- Clinical Genomics Level Seven (CGL7) enables the exchange
of clinical and personalized genomic data between interested
parties. It is a set of Web services for clinical-genomics
decision-support applications that follow the HL7? (Health
Level 7?) Clinical Genomics standard for the representation
and exchange
of clinical genomics data.
- CGIS is the Future-proof and audit trail system for phamacogenomics
projects and clinical trails
- Applications will support Future Changes
- Applications are aware of future changes and gracefully
adjust to changes in either the amount of services
or in the exchange format. The application and the
data exchange format support both extensions, removed
elements and version controls. The system is to
use XML with an XML Schema.
- Application level audit trail allows us to track
changes at the detailed level. With the database to
build detailed records on changes, additions, and deletions
at the database level.
|
Dr. Harold H. Hibbert (Bioinfogen) |
| |
|
Bioinformatics at Proteomics
level |
|
| |
10.00-12.00 |
Overview: Protein bioinformatics
- Database
- Gene expression and webtools
- Protein and webtools
- Protein purification
|
Sittiruk Roytrakul (Biotec) |
| |
|
Protein expression
- Data retrieve
- Prediction of posttranslational modification
- Gene cloning
|
|
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Protein purification
- Physico-chemical of protein
- Protein structure
- Protein purification
|
|
| |
|
Introductory to Proteomics
- 2D-Gel and 2D-LC
- Maldi-Tof and ESI Mass Spectrometer
- Application
|
|
| |
|
Protein Identification
- Protein and proteome databases
- Peptide Mass Fingerprint
- De Novo sequencing
|
|
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12:00-13:00 |
Lunch |
|
| |
14:00-15:30 |
Proteomic modeling and drug design |
Supa Hannongbua (Kaset) |
| |
15:30-16.30 |
System Biology |
Santitham Prom-on (KMITT) |
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