Hands-on VectorBase and Vector Genomics Workshop

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Hands-on VectorBase and Vector Genomics Workshop

  •  
  • Application deadline: July 11, 2017
  • Acceptance notification: July 18, 2017
  • When: September 18th to 22nd, 8:00 am to 5:00 pm.
  • Location:

    Duduville Campus

    International Centre for Insect Physiology and Ecology (ICIPE)

    Nairobi, Kenya

Workshop Programme:

 

Day 1, 8:00 am – 5:00 pm

 

Introduction, finding data/information

8:00 – 8:30 am: General introduction to omics (lecture)

8:30 – 9:00 am: Overview of VectorBase's remit, tools and data (lecture):

  • website navigation and
  • available data types & downloads

9:00 – 9:20 am: Coffee Break

9:20: - 9:50 am: Genome Browser: gene, transcript, protein and location pages. Exporting data (lecture)

9:50 – 12:00 pm: Data mining

  • Search
  • BioMart

12:00 - 1:00 pm: Lunch

Sequence tools

1:00 - 3:00 pm: Finding data:

  • BLAST
  • Clustal and Hmmer

3:00 - 3:20 pm: Coffee Break

Next Generation Sequencing (NGS) & Galaxy

3:20 - 5:00 pm: NGS & Galaxy

  • Introduction to NGS (lecture)
  • Intro to NGS for transcriptomics (lecture)
  • Galaxy basics (demo)
  • Differential expression workflow (launch jobs)

 

 

Day 2, 8:00 am – 5:00 pm

 

Visualizing NGS data

8:00 - 10:00 am: NGS data analyses:

  • Differential expression workflow (view results)
  • Viewing alignment coverage in Galaxy and the genome browser
  • Viewing SNP calls (precomputed results) and their genomic consequences

 

10:00 – 10:20 am: Coffee Break

Comparative & functional genomics

10:20 – 12:00 pm: Comparative genomics

  • Genomic alignments
  • Gene trees, orthology & paralogy

12:00 – 1:00 pm: Lunch

1:00 - 3:00 pm: Functional genomics

  • Introductory Concepts: microarray and RNAseq data (lecture)
  • Expression Browser and Map
  • Expression tracks in the Genome Browser

 

3:00 – 3:20 pm: Coffee Break

Population biology

3:20 – 5:00 pm: Finding and browsing genomic variation data

  • Introductory Concepts: Single Nucleotide Polymorphisms (SNPs), insertions and deletions (INDELs) and microsatellites (lecture)
  • Sample Explorer

 

 

Day 3, 8:00 am – 5:00 pm

 

Population biology

8:00 - 9:00 am: Simple Search and Browse

9:00 – 10:00 am: Map-based search and analysis of insecticide resistance (IR) data

10:00 – 10:20 am: Coffee Break

10:20 - 12:00 pm: Advanced Search

12:00 – 1:00 pm: Lunch

Genome and Gene annotations

  • 1:00 – 1:30 pm: Automatic annotation of genomes at VectorBase: gene set predictions, functional annotation and projecting gene descriptions (lecture)

  • 1:30 – 2:30 pm: Web Apollo Demo and test in sand boxes

2:30 - 2:50 pm: Coffee Break

Wrap up

2:50 – 5:00 pm:

  • Q&A including a selection of pre-workshop research-related questions answered
  • Forthcoming tools and data
  • Group photo
  • Exit questionnaire
  • Workshop certificates

 

 

Day 4, Research Ethics, 8:00 am – 5:00 pm

 

Responsible conduct of research

Scientific Writing

  • Manuscript Writing Guidelines
  • Abstract Writing

 

Day 5, Modeling, 8:00 am – 5:00 pm

 

  • Modeling
  • Geographic Information System, GIS

Search

Community Outreach

CONTACTS

P. O. Box 30197 - 00100 G.P.O
College of Biological and Physical Sciences,

Chiromo Campus, University of Nairobi
Tel: +254-20-4449004/5
Email: cebib@uonbi.ac.ke

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