This will be a short practical course on Bioinformatics for biologists, molecular biologists or young researchers working in the field of biomedical or biological sciences who are interested in learning, in a practical way, how to build and explore gene and protein networks and how to place in a relational context (i.e. in a network-based context) the lists of genes or proteins, often derived from genomic or proteomic analyses. The course will be held for two days in Cape Town (South Africa) at the University of Cape Town Medical School, hosted by the Computational Biology Group (CBIO). It will be given by Professor Dr. Javier De Las Rivas, from the University of Salamanca and the Spanish National Research Council (USAL/CSIC, Spain).

The course will be divided in four sessions with the following topics: 
(1) Bioinformatics tools for functional enrichment analysis; 
(2) Construction of gene functional networks; 
(3) Protein interaction networks; 
(4) Construction and analysis of gene/protein networks.

The students attending do not need to know programming, but should be familiar with working on computers and keen to learn how to use Bioinformatics tools and concepts.

Dates:    Monday 23rd and Tuesday 24th of November 2015 
Place:     Cape Town, South Africa 
Venue:   Health Teaching Labs 1-2, Basement of Anatomy Building, UCT Medical School, Anzio Rd, Observatory
Time:     9:30 to 16:30

Lecturer: Dr. Javier De Las Rivas
Bioinformatics and Functional Genomics Group
Cancer Research Center (CiC-IBMCC, CSIC/USAL)
University of Salamanca, Spain
See scientific profile at: 
http://scholar.google.com/citations?user=VY2k-EQAAAAJ&hl=en
https://www.linkedin.com/profile/view?id=68956567

Workshop curriculm and materials

Attachments:

2015-CapeTownUCT-JDeLasRivas-23Nov2015_s1s2.pdf	[ ]	11576 Kb
2015-CapeTownUCT-JDeLasRivas-24Nov2015_s3s4.pdf	[ ]	20194 Kb
Material4Students.zip	[ ]	48408 Kb

Venue of workshop: Uganda Virus Research Institute, Entebbe Uganda

Dates for the workshop: 6th to 10th July 2015.

Workshop organisers:  MUII, THRiVE, Africa Centre for Health and Population Studies Wellcome Trust Programs, H3ABioNet , MRC/UVRI Uganda Research Unit on AIDS, and the Uganda Virus Research Institute

Registration opens:  8th May, 2015

Registration closes: 8th June, 2015

Notification date: 12th June, 2015

Link to application form: http://www.muii.org.ug

Participation: Application open to in-country H3Africa/H3ABioNet consortium and UVRI-Node research partners with selection, giving priority to those with demonstrated need for this training. A total of 25 participants from all the applications received will be selected.

Workshop Sponsors: MUII and THRiVE

Course Overview: The workshop involves theoretical lectures and practical sessions on analysis techniques for dealing with Next Generation Sequencing (NGS) data, including an introduction to programming for the study of large data sets of HIV and other genomic data. It will introduce working in Linux and R statistical programming. Various topics on NGS analysis e.g. de novo genome assembly, annotation, SNP calling, HIV-1 drug resistance mutation genotyping, population genetics/phylogenetics etc will be covered. Tools for data visualization and analysis e.g. Galaxy, e-Biokit among others will also be introduced. Usage of open source technologies will be encouraged.

Intended Audience: Designed for Scientists, graduate students, postdoctoral research fellows, and exceptional undergraduates in the region to become familiar with NGS data handling and analysis techniques.

Syllabus and Tools: Participants will learn about Linux, R programming, NGS assembly, annotation, and population genetics of genomes using various data visualization and analysis tools.

Trainers and support staff: 
Deo Ssemwanga, (MRC/UVRI, Entebbe, Uganda)
Jonathan Kayondo, (UVRI, Entebbe, Uganda)
Fred Lyagoba, (UVRI, Entebbe, Uganda)
Benard Kulohoma, (ICIPE, Nairobi, Kenya)
Justen Manasa, (WT Africa Centre for Health and Population Studies, South Africa)
Anne Derache, (WT Africa Centre for Health and Population Studies, South Africa) 
Etienne Villiers, (KEMRI/ Wellcome Trust, Kilifi, Kenya)
Miguel Quinones-Mateu,( Case Western Reserve University, Cleveland , USA)
Pontiano Kaleebu, (MRC/UVRI, Entebbe, Uganda)
Tulio de Oliveira (WT Africa Centre for Health and Population Studies, South Africa)

Prerequisites:  Participants will need to work through the following resources to enable them to gain the most from the workshop:
http://www.ee.surrey.ac.uk/Teaching/Unix/
http://www.r-tutor.com/r-introduction

Objectives:  The objective is to introduce bioinformatics analysis techniques for dealing with Next Generation Sequencing (NGS) data. After this workshop participants should be able to:
- Attempt using Linux based platforms for analysis
- Have a good familiarity with R and conducting statistical tests within R
- Assemble and analyze NGS genome data 
- Perform HIV-1 drug resistance mutation genotyping
- Perform various phylogentics analysis for viral transmission, evolution and other studies
- Use the e-Biokit and other resources for bioinformatics analysis

Workshop limitations: This workshop will only provide a foundation for continued learning in NGS bioinformatics and will not make you an expert in bioinformatics or NGS analysis.

Registration: All potential applicants must complete the application form and obtain and attach a motivation letter from their supervisor / Head of Department and submit the application form according to the instructions contained within it. Incomplete applications will NOT be reviewed. The successful applicants for the workshop will be contacted to complete a short biosketch with a recent picture and Participants will also be requested to come to the workshop with a poster describing their research.

Questions: If you may have any further queries, please contact Dr. Jonathan Kayondo

Venue of workshop: ICT Building, Covenant University, Ota, Ogun state, Nigeria

Dates for the workshop: 29th June to 1st July, 2015

Workshop organisers:Covenant University Bioinformatics Research Unit

Registration opens: 15th June, 2015

Registration closes: 23rd June, 2015

Notification date: 27th June, 2015

Link to workshop:http://cubre.covenantuniversity.edu.ng/index.php/covenant-university-gwas-workshop-for-complex-diseases-2015/

Participation: Successful applicants will be contacted on how to participate.

Workshop Sponsors:Covenant University Bioinformatics Research Unit

Course Overview: This workshop provides an overview on medical population genetics, PLINK and basic statistics and practicals in order to build a foundational knowledgebase for genome wide association testing. The workshop will consist of a series of theory lectures and a “hands on” practical lab session at the end.

Intended Audience: This workshop is aimed at H3Africa project members who will be involved in the design and analyses of population data and genome wide association testing and will be able to attend from the West African region within a virtual environment.

Syllabus and Tools: Participants will learn about PLINK, Quality Control and association testing.

Prerequisites: Participants are encouraged to work through the following resources to enable them to gain the most from the workshop:
•    http://www.ee.surrey.ac.uk/Teaching/Unix/
•    http://www.r-tutor.com/r-introduction
•    http://onlinestatbook.com/2/introduction/introduction.html
•    http://pngu.mgh.harvard.edu/~purcell/plink/

Objectives: After this workshop participants should be able to:
- Conduct genotype calling and association testing
- Conduct population structure and correct for population structure 
- Have a good familiarity with PLINK and conducting whole genome data analysis within PLINK
- Have a good background on the theory behind medical population genetics
- Be able to conduct a variety of population genetics statistical tests

Workshop limitations: This workshop will only provide a foundation for continued learning in GWAS study design and medical population genetics and will not make you an expert in medical population genetics and genome wide association testing and studies.

Registration: All potential applicants should send an email attaching a motivation letter and CV to and Cc  , with heading "YOUR NAME + admission-CU-GWAS workshop for complex diseases”. Once being successfully chosen for the workshop, participants will be contacted with details on how to access and attend the workshop.

Workshop Curriculum

Venue of workshop:The African Institute for Mathematical Sciences (AIMS),Cape Town, South Africa.

Dates for the workshop: 20^th-22^nd April, 2015, followed by a symposium from the 23^rd-24^th April, 2015

Workshop organisers: H3ABioNet, the African Institute for Mathematical Sciences (AIMS) and the CPGR node of H3ABioNet

Registration opens: 14^th January, 2015

Registration closes: 20^th February, 2015

Notification date: March, 2015

Link to application form:https://bioweb.cpgr.org.za/redcap/surveys/?s=4L3ANT998T

Workshop Sponsors: H3ABioNet and the African Institute for Mathematical Sciences

Workshop Overview: The workshop will be split into two tracks:

1. An introductory track that will cover fundamental assumptions, showcase recent successes and discuss limitations of current GWAS approaches in the field of complex diseases, particularly in the case of African populations with known low linkage disequilibrium (LD). It will also provide a ‘hands-on’ experience of data analysis and a stage for shaping the next generation of GWAS scientists/researchers.
2. An advanced track which will draw upon the audience’s interdisciplinary expertise in mathematics, simulation studies, statistics and machine learning to overcome present challenges and identify the most promising avenues of future research for effective phenotype–genotype association.

Intended Audience: The target audience includes H3Africa project members who will be involved in the design and analyses of population genetics data and genome wide association testing, technicians, graduate students, postdocs and established and young investigators entering the field of complex trait genetics from a variety of backgrounds such as biological, bioinformatics, statistics, mathematics and computer science.

Participation: Open application with selection for H3Africa consortium members, African Institute for Mathematical Sciences (AIMS) students and interested participants. The selection procedure will give priority to those with demonstrated need for this training, particularly those with data available or soon to be available. A total of 50 participants will be selected.

Syllabus and Tools: Participants will learn about the design and analyses of population data and genome wide association testing. On the second day, participants will be split into two groups

1. Hands on data processing, analysis and the interpretation of results
2. Advanced mathematical population genetics and disease scoring statistics

Objectives: This workshop aims to introduce an interdisciplinary audience to the potential of GWAS and to key strategic considerations in designing and performing Genome-wide Association studies, as well as to bring all participants up to speed on the basic principles of human genetic variation, genotyping and disease scoring statistics. In addition, this workshop aims to bridge the gap between statistics, bioinformatics and genetics. We envisage that researchers in machine learning and statistics who have an interest in genetic architecture of complex diseases, as well as statistical geneticists looking for using or improved tools for GWAS will benefit from participating in this workshop.

Workshop limitations: This workshop will provide a foundation for continued learning in medical genetics and GWAS studies for the introductory track and will not make one an expert in medical population genetics and genome wide association testing and studies. The advanced track will provide the cover current mathematical and statistical models and simulations methods used in population genetics and GWAS and will not make one an expert in simulations, mathematical and statistical modelling and methodology development for population genetics and GWAS studies.

Trainers and support staff:

1. Organizers: Prof. Nicola Mulder, Dr. Emile Chimusa, Dr. Judit Kumuthini and Dr. Gaston Kuzamunu
2. Trainers: Prof. Scott Hazelhurst, Dr. Noah Zaitlen, Dr. Bogdan Pasaniuc, Dr. Bjarni Vilhjalmsson and Shaun Aron

Prerequisites: Selected participants will need to work through the following resources to enable them to gain the most from the workshop:
http://www.ee.surrey.ac.uk/Teaching/Unix/
http://www.r-tutor.com/r-introduction
https://www.python.org/
http://onlinestatbook.com/2/ 
A pre-workshop course on an Introduction to Linux/R/python will take place on the 19^th April 2015.

Registration: All interested applicants must complete the application form and upload a motivation letter from their supervisor. Incomplete applications will NOT be reviewed. The successful applicants for the workshop, will be contacted to complete an airline ticket booking form, a short biosketch with a recent picture and the H3ABioNet workshop policy. The workshop will be followed by a symposium which workshop participants will automatically attend and are encouraged to submit an abstract for either oral or poster presentations.

H3ABioNet will cover the costs of a return economy air ticket to Cape Town. AIMS will cover the cost of accommodation from the night of the 19^th of April till the 24^th of April (departing on the 25^th) 2015 and meals from the 19^th of April to the morning of the 25^th of April 2015. H3ABioNet and AIMS will NOT cover the costs of visa fees, vaccinations, airport transfers from your local area or any other costs.

Please note, if a participant is unable to attend this workshop after acceptance, their place will be passed onto to applicants on the waiting list and not to other recommended members from their Institution or Research project.

If you would like any additional information, please do not hesitate to contact the symposium and workshop organizers: 

GWAS data analysis and results interpretation workshop

Advanced GWAS Modelling Workshop Program

Lecturers:

• Bogdan Pasaniuc (UCLA)
• Noah Zaitlen (UCSF)
• Bjarni Vilhjalmsson (HSPH)
• Shaun Aron (Wits)
• Scott Hazelhurst (Wits)