VectorBase Hands-on Workshop

VectorBase Hands-on Workshop

April 29, 2019

Universidad Nacional de la Amazonia Peruana, UNAP

Iquitos, Perú




Instructor

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

Official language

The official language of the workshop will be Spanish, but the instructor is also able to speak in English if needed. All the handout material will be provided in English, reading proficiency in this language is expected.


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 one-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 day 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

April 29th 2019, 8:00 am to 5:15 pm.

Dirección Vicerrectorado de Investigación - Universidad Nacional de la Amazonia Peruana, UNAP

Pasaje Los Paujiles s/n, Nuevo San Lorenzo,

San Juan Bautista, Maynas, Perú

Iquitos, Perú

Agenda - 8:00 am – 5:15 pm

(subject to change)

All are hands-on sessions except when marked as 'lecture'


Introduction

8:00-9:00 am (lecture):

  • General introduction to omics
  • Gene automatic and manual annotations:
    • gene set predictions, functional annotation and projecting gene descriptions
    • Apollo demo and test in sand boxes
  • Overview of VectorBase's remit, data, tools and resources
  • VectorBase Genome browser: gene, transcript, protein and location pages

Population biology

9:00-10:00 am:
  • Map-based search and analysis of population data:
    • population abundance
    • insecticide resistance (IR) genotypes and phenotypes
    • pathogen infection status
    • blood meal source
  • Simple Search and Browse
  • Advanced Search

10:00-10:20 am: Coffee Break

Population biology

10:20 - 12:00 m: continue with exercises

12:00 - 1:00 pm: Lunch

Finding data and information

1:00-2:30 pm:

  • Search
  • BLAST
  • BioMart
  • Clustal and Hmmer
  • Downloads: data files and images

Comparative genomics

2:30-3:00 pm:
  • Genomic alignments
  • Gene trees, orthology & paralogy

3:00-3:20 pm: Coffee Break

Functional genomics

3:20-4:30 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

4:30-5:00 pm:
  • Introductory Concepts: Single Nucleotide Polymorphisms (SNPs), insertions and deletions (INDELs) and microsatellites (lecture)
  • Finding and browsing variation data

Wrap up

5:00 – 5:15 pm:

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


Computer and Internet access

A room with computers will not be provided, please bring your own laptop, it should have the latest Firefox, Google Chrome, Safari or Internet Explorer version installed.


Registration

  • Number of course participants: maximum 20 people
  • Applications will open on March 28, 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 come, first served basis until we fill the workshop at 20 people. We do expect the workshop to fill up quickly.
  • Acceptance confirmation: If you have been accepted to attend, please reply to your acceptance notification with a short email to info@vectorbase.org within two business days of receiving the message. If you do not reply we will assume that you are unable to attend and will award your place to another applicant. This is an honor system, if you say you are coming we trust in your word. If you have last minute plan changes, please let us know as soon as possible with a brief email to info@vectorbase.org, no explanations required, just a notification so we may offer your seat to an applicant in the wait-list.
  • 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 S/50 Soles (Peruvian currency) for all attendees, except from the ones coming from the local host UPCH. Payments should be made directly to the host, not to VectorBase. The payment can only be made in cash, on the day of the event. The registration fee includes all workshop sessions, materials, morning and afternoon coffee breaks and lunch.

You are responsible for your own transportation, lodging and other meals (breakfast and dinner). At your request, we can email to you a registration acceptance 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:

Centro de Excelencia en Investigación de Malaria (ICEMR) de la Amazonía

Laboratorio Malaria de la Universidad Peruana Cayetano Heredia (UPCH)

Translational Research Development for Endemic Infectious Diseases of Amazonia - FOGARTY. Grant number: 2D43TW007120-11A1

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

Iquitos, Perú
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