Swiss Prot / South Africa Protein
Bioinformatics Workshop, South African Medical
Research Council, 17 to 18 November, Durban, South
Africa. The first day of the workshop will also be presented at the
University of Cape Town on the 23th November, 2010.
On behalf of the Swiss South African Joint Research
Programme (SSJRP), a programme leaded by the University of Basel in
Switzerland and the Council for Scientific and Industrial Research
(CSIR) in South Africa, we are pleased to invite you to participate in the
Swiss Prot / South Africa Protein Bioinformatics Workshop. This workshop will be presented at
the South African Medical Research Council, Durban, South
Africa from 17 to 18 November 2010 and at the University of Cape Town on the 23th November 2010.
DEADLINE for application: 5th
programme will include theoretical lectures and practical sessions on
the use and
interpretation of bioinformatics programs at the Uniprot, ViralZone,
RegaDB and the Stanford HIV Drug Resistance Databases.
The workshop is targeted at post-graduate students
and researchers working on bioinformatics, protein annotation, TB and HIV drug resistance
studies in Southern Africa. Southern African Treatment and Resistance
(SATuRN) members are encouraged to participate.
Workshop dates: 17-18 Nov 2010 (two days
program) at MRC, Durban, South Africa & 23 Nov 2010 (one day
program) at UCT, Cape Town, South Africa.
submit application forms to Dr. Tulio de Oliveira (Durban
workshop) or Prof. Nicola Mulder (Cape Town workshop).
+27 35 550 7542 (Dr. de Oliveira), +27 21 406 6058 (Prof. Mulder),
Costs: Attendance at the
applicants are responsible for all accommodation and travel costs).
Organizers: Marc Feuermann, Tulio de
Oliveira, Nicola Mulder, Philippe Le Mercier and Lydie
by: Swiss South African Joint
Programme (SSJRP) research grant entitled "Swiss Prot / South Africa:
Protein Bioinformatics Resource Development for Important
Health-related Pathogens " awarded to the Africa
Centre for Health and Population Studies, University of KwaZulu-Natal
(UKZN), University of Cape Town (UCT) and Swiss-Prot group at the Swiss
Institute of Bioinformatics (SIB).
Dr. Tulio de
Oliveira, Africa Centre for Health and Population
Studies, University of KwaZulu-Natal, South Africa and University
College of London, U.K.
Dr. Marc Feuermann,
Ph.D., Swiss-Prot Group, Swiss Institute of Bioinformatics, Geneva,
Dr. Michelle Gordon,
Pathogenesis Programme, Doris Duke Medical Research Institute,
University of KwaZulu-Natal, South Africa.
Mr. Justen Manasa, Ph.D. candidate, Africa Centre for Health and Population
Studies, University of KwaZulu-Natal, South Africa.
Assoc. Prof. Nicola Mulder,
Computational Biology Group, IIDMM, University of Cape Town, Cape Town,
Mr. Wayne Naidoo, School of Computer Science, University of KwaZulu-Natal and Jembi Health Systems, Durban, South Africa.
|Workshop Program and Protein Databases
to be presented Links:
Day 1 – Morning
1 – Introduction: UniProtKB, an encyclopedia for proteins.
2 – Sequence curation at UniProtKB
3 – Biological data curation at UniProtKB (which kind of data are
integrated, from what sources ?).
Day 1 – Afternoon
4 – Access to UniProt (detailed view of the website)
5 – UniProt statistics.
6 – ViralZone (this part could be optional at Nicky’s place in the case
we organize two workshops).
Day 2 – Morning
1 – Introduction: Usage of HIV proteins for the detection of drug
resistance to anti-retroviral therapy (ART).
2 – HIV Drug resistance databases and interpretation programs.
– Practical exercise: HIV drug resistance analysis using RegaDB.
Day 2 – Afternoon
4 – HIV Sequence Databases (Los Alamos, Stanford, GenBank).
7 – OpenMRS and RegaDB.
8 – Practical exercises
|Links to Protein databases, which will be
presented in the workshop:
UniProt (Universal Protein Resource)
is a catalog of information on proteins. The mission
of UniProt is to provide the scientific community with a comprehensive,
high-quality and freely accessible resource of protein sequence and
ViralZone - ViralZone is a
Swiss Institute of Bioinformatics web-resource for all viral genus and
families, providing general molecular and epidemiological information,
along with virion and genome figures.
Southern African Mirror of the
Stanford HIV Drug Resistance Database - A curated public
to represent, store, and analyze the divergent forms of data underlying
HIV drug resistance.
SATuRN RegaDB *
This copy of the database is accessible to SATuRN collaborators. RegaDB
is a clinical management bioinformatics database that can be used to
manage patients on ARVs and to do research on HIV-1 drug resistance
Datasets for the practical session on the 18 November 2010:
|Page last updated by Tulio de Oliveira.