VectorBase Hands-on Workshop

VectorBase Hands-on Workshop

June 3 - 5, 2019

Universidad del Valle

Guatemala city, Guatemala




Instructor

Gloria I. Giraldo-Calderón, PhD
VectorBase Scientific Liaison/Outreach Manager

Official language

The official language of the workshop will be English, but the instructor is also able to speak in Spanish if needed.


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 and vector biology, hands-on practical sessions with VectorBase data, tools and resources.

Below you will find a link to apply. During the three days of the workshop, we aim to provide opportunities for hands-on activities, discussions and practice exercises, for each of the tools and topics listed in the agenda below.The outcome of this training relies heavily on your dedication and effort, which includes the time invested during and after the workshop. After the workshop, you are invited to send follow up questions to the instructor, via info@vectorbase.org.


Schedule and Location

June 3 - 5, 8:30 am to 5:30 pm.

Universidad del Valle

18 Avenida 11-95, Guatemala 01015

Guatemala City, Guatemala

Agenda

(subject to change)


Day 1, 8:30 am – 5:30 pm


Introduction, finding data/information

8:30-9:00 am: General introduction to omics (lecture)

9:00-9:30 am: Attendees introductions and turbo talks: who I am? what I do? why I am here? Depending on the number of participants you can have 1, 2 or 3 minutes.

9:30-10:00 am: Overview of VectorBase's remit, data, tools and resources (lecture)

10:00-10:30 am: Genome browser: gene, transcript, protein and location pages (lecture)

10:30-10:50 am: Coffee Break

10:50-12:00 pm: Finding data

12:00 - 1:00 pm: Lunch

1:00-2:00 pm: Finding data:

  • Clustal and Hmmer

Comparative genomics

2:00-3:00 pm:
  • Genomic alignments
  • Gene trees, orthology & paralogy

3:00-3:20 pm: Coffee Break

Next Generation Sequencing (NGS) & Galaxy

3:20-5:30 pm:
  • Analysis of a list of differentially expressed genes (we will start from the end!)
  • Intro to NGS: technologies, data processing and, RNAseq terminology and concepts (lecture)
  • Galaxy basics (demo)
  • RNAseq differential expression workflow (launch jobs)

Day 2, 8:30 am – 5:30 pm


Visualization and analyses of NGS data

8:30-10:30 am:
  • Differential expression workflow (view results from jobs launched yesterday)
  • Viewing alignment coverage in Galaxy and the genome browser
  • Analysis of a list of SNPs (again, starting from the end!)
  • Viewing SNP calls (precomputed results) and their genomic consequences in VectorBase genome browser

10:30-10:50 am:Coffee Break

Gene automatic and manual annotations

10:50-12:00 pm:
  • Automatic annotation of genomes at VectorBase: gene set predictions, functional annotation and projecting gene descriptions (lecture)
  • Apollo demo and test in sand boxes

12:00-1:00 pm: Lunch

Functional genomics

1:00-2:00 pm:
  • Introductory Concepts: microarray and RNAseq data (lecture)
  • Expression Browser and Map
  • Expression tracks (from the track hub registry) in the Genome Browser

Variation and Population data

2:00-3:00 pm:
  • Introductory Concepts: Single Nucleotide Polymorphisms (SNPs), insertions and deletions (INDELs) and microsatellites (lecture)
  • Finding and browsing variation data

3:00-3:20 pm: Coffee Break

3:20-4:00 pm: Seminar speaker name and title to be announced soon

4:00-5:30 pm: Form teams for a group project. Decide on a research question and experimental strategy to solve it. Start to work on it. You can use your own data, data from VectorBase or GenBank.


Day 3, 8:30 am – 4:00 pm


Population biology

8:30-10:30 am:
  • Simple Search and Browse
  • Map-based search and analysis of insecticide resistance (IR) data
  • Advanced Search

10:30-10:50 am: Coffee Break

10:50-12:00 pm: Teams to finish project and create 5 to 10 slides to present.

12:00-1:00 pm: Lunch

1:00-3:00 pm: Teams to present projects: 10-15 minutes each, depending on the number of participants, 2 or 4 people per team. During the presentation each member has to participate.

3:00-3:20 pm: Coffee Break

Wrap up

3:20 – 4:00 pm:

  • Group photo
  • Exit questionnaire
  • Workshop certificates: will be provided in digital format, no later than Monday, June 10th.


Computer and Internet access

A room with computers will be provided. If you bring your own laptop, it should have the latest Firefox, Google Chrome, Safari or Internet Explorer version installed.


Registration

  • Number of course participants: maximum 30 people
  • Applications will open on February 21, 2019
  • Applications may be made via this web form. This (Google) registration form is used to customize the workshop agenda and examples to the participants research interest. This information is confidential.
  • Application deadline: While there is no deadline for registration, registrations will be taken on a first-register, first-pay basis until we fill the workshop at 30 people. We do expect the workshop to fill up quickly.
  • 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

Costs and fees

The registration fee is $35 US dollars for attendees coming from developing countries and $150 for attendees from developed countries; after May 3, cost increases to $50 and $200 respectively. Payments should be made directly to the host, not to VectorBase. All payments, including paying the first day of the workshop, will be made in US Dollars through this link; the link also has information about the cancellation policy. If you register in the form above but do not make a payment, we will assume that you are unable to attend and will award your place to another applicant. The registration fee includes all workshop sessions, materials, computer access, morning and afternoon coffee breaks and lunches.

You are responsible for your own transportation, lodging and other meals (breakfast and dinner). At your request, we can email to you a letter to facilitate the solicitation of outside travel funds or scholarships.


Hotel Accommodations

If you are accepted to participate and need a hotel, let us know to provide you with recommendations.


Questions?

Please direct inquiries or comments to info@vectorbase.org


Sponsored and organized by:

Dr. Patricia L. Dorn, William and Audrey Hutchinson Distinguished Professor of Biological Sciences. Loyola University New Orleans.

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

Guatemala city, Guatemala
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