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 November  2010.

Workshop information:

The workshop 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.

Please submit application forms to Dr. Tulio de Oliveira (Durban workshop) or Prof. Nicola Mulder (Cape Town workshop).

Tel: +27 35 550 7542 (Dr. de Oliveira), +27 21 406 6058 (Prof. Mulder),


Costs: Attendance at the Workshop is Free*

(*However applicants are responsible for all accommodation and travel costs).

Organizers:  Marc Feuermann, Tulio de Oliveira, Nicola Mulder, Philippe Le Mercier and  Lydie Bougueleret.

Funded by: Swiss South African Joint Research 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).

Workshop Presenters:

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, Switzerland.

Dr. Michelle Gordon, HIV 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, South Africa.

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.
3 – 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 functional information.

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 database designed 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 clinical cases.

Datasets for the practical session on the 18 November 2010:

Page last updated by Tulio de Oliveira.