COMSTECH-SIUT WORKSHOP ON BIOINFORMATICS December 16 - 18, 2014

i. Title ENSEMBL DATABASE MINING AND WHOLE GENOME SEQUENCING ANALYSES
 
ii. Focal Person Dr. Syed Qasim Mehdi
HEC Distinguished National Professor and Chairman Centre for Human Genetics and Molecular Medicine

Sindh Institute of Urology and Transplantation (SIUT)
Karachi 74200, Pakistan
Email: sqmehdi@gmail.com
 
iii. Instructors Dr. Qasim Ayub
Staff Scientist
Wellcome Trust Sanger Institute
Hinxton, United Kingdom
http://www.sanger.ac.uk/research/projects/humanevolution/
 
  Dr. Vincenza Colonna
Research Scientist

National Research Council
Institute of Genetics and Biophysics, Naples, Italy
OBiLab http://www.igb.cnr.it/obilab
 
  Dr. Luca Pagani
Postdoctoral Fellow

Division of Biological Anthropology
University of Cambridge, United Kingdom
http://www.sanger.ac.uk/research/projects/humanevolution/
 
  Dr. Denise Carvalho-Silva (Virtual Lecturer)
Ensembl Outreach Officer

EMBL-European Bioinformatics Institute
Hinxton, United Kingdom
http://www.ebi.ac.uk/about/people/denise-carvalho-silva/
 
iv. Date/Venue December 16 - 18, 2014
COMSTECH Building, 33 Constitution Avenue
Sector G-5/2, Islamabad, Pakistan

December 20 – 22, 2014
Sindh Institute of Urology and Transplantation (SIUT)
Civil Hospital, Karachi, Pakistan

Course Objectives:

The main objective of the training course is to present a hands-on approach to the online Ensembl bioinformatics resources and introduce command line based options for analyses of whole genome sequencing data for students, post-doctoral fellows and teachers involved in biological research. The training course will include an introduction to the Ensembl Genome Browser with practical demonstrations and exercises using the human genome as reference. Analyses of high throughput genotyping and whole genome human sequencing data will also be presented with the overall aim of promoting the use of bioinformatics for health and research in the life sciences. Only human genomic sequencing data will be analysed during the training, but the same techniques can be used to analyze any data generated by next generation sequencing

Selection Criteria:

Candidates meeting the following criteria will be selected for the course:

a) Post-doctoral fellows, doctoral or medical students near completion of their studies with knowledge of at least one or more of the following fields: biochemistry, molecular biology, genetics, proteomics or biotechnology. Candidates that are employed by a university, or an institute, as a faculty member and who have research experience supported by research publications in peer reviewed journals will be preferred.

b) The candidate should have a working knowledge of computer, statistics, and internet applications related to bioinformatics

Course Content:

The main objective of the training course is to present a hands-on approach to the online Ensembl bioinformat All modules will consist of an introductory and a practical part, both carried out in a computer-equipped facility. The candidates will have ample time to go through the exercises independently. The instructors will be available between 9:00 a.m. to 5:00 p.m. for guidance and assistance while the candidates are carrying out their training.

Content Overview:

Day 1: Module I The Ensembl Genome Browser.
  Module II Introduction to Genomic Variation.
  Module III Ensembl: BioMart (Virtual Lecture).
Day 2: Module IV Introduction to UNIX/Linux.
  Module V Introduction to Next Generation Sequencing.
  Module VI PLINK.
Day 3: Module VII VCFtools
  Module VIII Ensembl VEP Tool.
  Module IX 1000 Genomes Browser.
  Conclusion Course Review and Discussion


Registration Fee for the Workshop in Islamabad

Registration fee for foreign participants is US$ 50.00 and for local participants Pak rupees 2,500.00. Full time students can avail 80% fee discount.

Local Hospitality and Travel

COMSTECH will provide free accommodation and meals to a limited number of selected participants. Travel grants are not available. Pick and drop service on arrival and departure will be provided to only those who are travelling by air.

There will be no registration fee and no lodging facilities for the event in Karachi.

Registration Process:

Step 1: Download application form from here
Step 2: Read instructions in the application form carefully and submit properly filled form to hanifa@comstech.org and comstech@comstech.org (Islamabad) or sqmehdi@gmail.com (Karachi). You do not need to deposit registration fee at this stage.

Step 3:  If you are selected we will notify you by email. Instructions for fee submission will be provided in the acceptance e-mail.

Last Date for Applications: October 25, 2014

For queries, please contact:


Islamabad:
Ms. Hanifa Beg

Programme Manager
Tel: +92-51-9220681-3
Fax: +92-51-9205264, +92-51-9220265
Email: 
hanifa@comstech.org
;
comstech@comstech.org
 

Karachi:
Prof. Syed Qasim Mehdi

SIUT, Karachi 74200, Pakistan
Tel:
+92-21-9215752, +92-21-9215718
Fax:
+92-21-9215469, +92-21-9215362
Email: sqmehdi@gmail.com

 

COMSTECH General Assembly Meeting


COMSTECH Secretariat, 33-Constitution Avenue, G-5/2, Islamabad Phone: (+92 51) 9220681 - Fax: (+92 51) 9211115 - COMSTECH Official Email