{ * Smarty * } JCVI: GSC / Workshop

August 22-28, 2013: Advanced Bioinformatics Workshop, International Livestock Research Institute, Nairobi, Kenya


Day 1:
Basics of Bioinformatics Mark Wamalwa, Joyce Njuguna,
Dedan Githae, Nelson Ndegwa,
Koko Mutai
Introduction to Linux
Hands on command line LINUX
Day 2:
Bioinformatics Resources for data management. Mark Wamalwa, Joyce Njuguna,
Dedan Githae, Nelson Ndegwa,
Koko Mutai
Nucleotide and Protein sequence analysis resources
An introduction to the Ensembl database
Database search using NCBI’s Command Line BLAST
Day 3:
Introduction to genomics and applications to infectious diseases David Wentworth
Overview of viral projects, technologies, microbiome, phylogenetics, zoonotic infections (bacterial and viral)
Application of ‘Omics technology to research on infectious diseases and the Human microbiome Karen Nelson, Marcus Jones
Overview of Next Generation Sequencing Technologies Timothy Stockwell, Vivien Dugan
I have all this data- Now What? Introduction to Bioinformatics software and computing infrastructures
Bioinformatics for Viral Genomics – Sequencing, assembly and annotation Timothy Stockwell, Vivien Dugan, David Wentworth, Marcus Jones
Day 4:
Overview of NIH/NIAID and NIH H3Africa program Maria Y. Giovannis
Lessons learnt from emerging viruses David Wentworth
Synthetic genomics and its applications to bacterial infectious disease Sanjay Vashee
Comparative Genomics Analysis to Identify Genetic Determinants of Influenza virus human adaptation Richard Scheuermann
Overview of the NIAID Bioinformatics Resource Centers Program and use of the Virus Pathogen Resource (www.viprbrc) and Influenza Research Database (www.fludb.org)
Day 5:
Synthetic genomics and its applications to viral infectious diseases David Wentworth, Tim Stockwell
Immuno-informatics/Reverse Immunology Vish Nene
Introduction to gene expression analysis Marcus Jones

Primer Design for Microbial Genomes
Primer Design Exercise
Molecular Barcoding for Multiplexing
Processing NGS Data - Assembly Strategies
Assembly Exercise
Annotation Exercise
Submitting Data to GenBank
Synthetic Genomics and Its Application to Viral Infectious Diseases
Application of Omics Technology to Infectious Diseases and the Human Microbiome
Data Mining: Clustering and Statistical Analysis with MeV
Overview of Next Generation Sequencing (NGS) Technologies
Introduction to Bioinformatics Software and Computing Infrastructures
Synthetic Genomics and its Applications to Bacterial Infectious Diseases
Lessons Learnt from Emerging Viruses
Overview of viral projects: technology, microbiome, phylogenetics, zoonotic infections
Comparative Genomics Analysis to Identify Genetic Determinants of Influenza Virus Human Adaptation
Influenza Research Database & Virus Pathogen Resource Exercises

The workshop is funded by the JCVI and federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services under contract numbers N01-AI30071 and / or HHSN272200900007, Australian Agency for International Development (AusAID) through a partnership between Australia's Commonwealth Scientific and Industrial Research Organisation (CSIRO) and the BecA-ILRI Hub; the Syngenta Foundation for Sustainable Agriculture (SFSA); the Bill & Melinda Gates Foundation (BMGF); the Swedish Ministry for Foreign Affairs; and the Swedish International Development Cooperation Agency (Sida).

Presentation will be available after training.

Home   >  GSCID   >  Workshops