Hands-on VectorBase and Vector Genomics Workshop





Instructors

Daniel Lawson, PhD
VectorBase Principal Investigator
Imperial College London

Amie Jaye, MSc
Bioinformatician for the VectorBase Expression resources
Imperial College London

Remote Instructor - Gloria I. Giraldo-Calderón, Ph.D.
VectorBase Scientific Liaison/Outreach Manager

Official language

The official language of the workshop will be English and applications must be submitted in this language too. Applications submitted in any other language will not be taken into account.


About the workshop

VectorBase is a Bioinformatics Resource Center (BRC) focused on invertebrate vectors of human pathogens. This BRC currently hosts sequence data from 40 genomes. VectorBase also provides transcriptomic, proteomic and population biology data from colony and field specimens for an even broader selection of species. The goal of this three-day workshop is to offer the opportunity to scientists working in medical entomology, hands-on practical sessions with VectorBase data, tools and resources.

Below you will find a link to apply. If you are accepted to participate, via email you will receive information about the required pre-workshop homework. Five short video tutorials (6 to 15 min each), will be assigned for you to watch. Your understanding of the videos and of some additional background information will be assed with a few questions. Your responses are due on Friday, September 1, 2017. The homework is not optional because is meant to provide you with a brief introduction to the material to be covered during the workshop, which will facilitate to start the work and discussion on site. During the three days of the workshop, we aim to give an introduction to each of the tools and topics listed in the agenda below, all the material used, including the slide lectures, will be available to you. Most segments will include hands-on exercises and an opportunity to ask questions to the VectorBase team.


Schedule and Location

September 18th to 22nd, 8:00 am to 5:00 pm.

Duduville Campus

International Centre for Insect Physiology and Ecology (icipe)

Nairobi, Kenya

Follow this link for more information

Agenda

(subject to change)


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 & Genotype Explorers

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: 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 and Guest Talks, 8:00 am – 5:00 pm

Scientific Writing: Serap Aksoy (Yale University) & Daniel Masiga (icipe)

  • 8:00 - 10:00 am: Lecture and example discussion

10:00 – 10:20 am: Coffee Break

  • 10:20 - 12:00 pm: Discussion to be continued. Please feel free to bing the draft of your most recent manuscript or paper.

12:00 – 1:00 pm: Lunch

Responsible conduct of research: Guiyun Yan (University of California Irvine)

  • 1:00 - 3:00 pm: Lecture and discussion

3:00 - 3:20 pm: Coffee Break

  • 3:20 - 5:00 pm: Discussion to be continued.

Day 5, Modeling and GIS, 8:00 am – 5:00 pm

Modeling: Caitlin Bever ( Institute for Disease Modeling, http://idmod.org/team/bio/28 )

  • 8:00 - 9:00 am: Introduction to modeling: Basic concepts and example applications
  • 9:00 – 10:00 am: Modeling malaria

10:00 - 10:20 am: Coffee Break

  • 10:20 - 12:00 pm: How to read a modeling paper with hands-on exercise in Excel
  • 12:00 - 1:00 pm: Lunch

    Geographic Information System, GIS: Jackson Kimani ( icipe - International Centre of Insect Physiology and Ecology, http://www.icipe.org/research/research-support-units/geo-information )

    • 1:00 - 1:30 pm: Introduction to GIS; Basic concepts and applications
    • 1:30 - 2:00pm - Coordinate reference systems and projections
    • 2:00 - 2:30pm - GIS data overlay;point, vector, raster

    2:30 - 2:50pm: Coffee Break

    • 3:00 - 4:00pm - Spatial analysis; clipping, buffering
    • 4:00 - 5:00pm - Map making, Q & A

    The software to be used during the GIS session will be QGIS, which is an open-Source GIS program (link: http://www.qgis.org/en/site/forusers/download.html , for both windows and Mac users. Participants should have the software installed on their machines/laptop before the session. If in need of any assistance, feel free to contact us.

    Computer and Internet access

    A room with computers will be provided. If you bring your own laptop ensure your web browser meets the following requirements. You should either have the latest Firefox or Google Chrome browser installed, or, if using a system-provided browser, please note that Mac users will need Safari 7 or higher (available since OS X 10.9 "Mavericks") and Windows users will require Internet Explorer 11.


    Registration

    • Number of course participants: maximum 30 people
    • Applications will open on April 25, 2017
    • Applications may be made via this web form.
    • Application deadline: July 11, 2017
    • Acceptance notification: July 18, 2017
    • Acceptance confirmation: July 25, 2017. If you have been accepted to attend, please reply to your acceptance notification with a short email to info@vectorbase.org by July 25, 2017. If you do not reply we will assume that you are unable to attend and will award your place to another applicant
    • Who should apply: The ideal candidate should have a need to learn how to use VectorBase and presumably has a research question that involves this database to help to solve it
    • Evaluation of applications will focus heavily on applicants' responses to the questionnaire in the application form

    Costs and fees

    Thanks to the event organizers and sponsors listed below, all training materials, certificates and lunches are provided at no cost to you. Attendees are expected to provide their own transportation to the course and pay for their own breakfasts and dinners. We can email to you a letter of acceptance to facilitate the solicitation of outside travel funds.


    Hotel Accommodations

    If you are accepted to participate and need a hotel, the recommended hotel is located on the icipe campus. The price per-night for single and double occupancy is $70 and $110, respectively and it includes Bed and Breakfast. For reservations please contact the course organizers at shenson@icipe.org.


    Questions?

    Please direct inquiries or comments to info@vectorbase.org


    Sponsored and organized by:

    Sonal Henson, Daniel Masiga, Robert Skilton and Jandouwe Villinger (International Centre of Insect Physiology and Ecology, icipe, Nairobi, Kenya)

    Guiyun Yan (University of California, Irvine, US), NIH D43 TW001505

    Serap Aksoy and Gisella Caccone (Yale University), NIH D43 TW007391

    VectorBase, Bioinformatics Resource for Invertebrate Vectors of Human Pathogens. VectorBase have been funded in whole or in part with Federal funds from the National Institute of Allergy and Infectious Diseases and National Institutes of Health, NIAID/NIH

    Nairobi, Kenya
    Meeting Date: 
    Tuesday, September 19, 2017 - 01:00 to Saturday, September 23, 2017 - 01:00
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