VectorBase Hands-on Workshop

VectorBase Hands-on Workshop

March 19-20, 2018

SIU - Universidad de Antioquia

Medellín, Colombia




Instructor

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

Official language

The official language of the workshop will be Spanish. Because the handout material is in English, excellent 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 two-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. If you are accepted to participate, via email you will receive information about the required pre-workshop homework. The assignment may include: short videos (of up to 15 min each) with a few questions to asses your understanding of them; omics background questions; up to four scientific papers and activities to asses your understanding of some of their important key points. Your responses are due on Thursday, March 1, 2018. The homework is not optional because is meant to provide you with an introduction and foundation to the material to be covered during the workshop, which will facilitate to start the work and discussion on site. During the two 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 before and during the workshop. After the workshop, you are invited to send follow up questions to the instructor, via info@vectorbase.org.


Schedule and Location

March 19th to 20th, 8:00 am to 5:30 pm.

SIU-Sede de Investigación Universitaria - Universidad de Antioquia

Calle 62 No 52-59, Auditorio No 3

Medellín, Colombia

At the bottom of the page, in the attached file section, find a pdf with a Google map locating the SIU and other information of interest

Agenda

(subject to change)


Day 1, 8:00 am – 5:30 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, data, tools and reources (lecture)

9:00 – 9:30 am: Automatic annotation of genomes at VectorBase: gene set predictions, functional annotation and projecting gene descriptions (lecture)

9:30 - 10:00 am: Genome browser: gene, transcript, protein and location pages (lecture)


10:00 – 10:20 am: Coffee Break


10:20 am – 12:00 pm: Finding data

  • Search
  • BLAST
  • BioMart

12:00 - 1:00 pm: Group lunch provided


1:00 - 1:30 pm: Finding data:

  • Clustal and Hmmer

Comparative genomics


1:30 – 2:30 pm: Comparative genomics

  • Genomic alignments
  • Gene trees, orthology & paralogy

Gene manual annotations


  • 2:30 – 3:00 pm: Apollo demo and test in sand boxes


3:00 - 3:20 pm: Coffee Break



Next Generation Sequencing (NGS) & Galaxy


3:20 - 5:30 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 – 5:30 pm



Visualizing NGS data


8:00 - 10:00 pm: 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 pm: Coffee Break


10:20 - 12:00 pm: Functional genomics

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


12:00 – 1:00 pm: Group lunch provided



Variation and Population data


1:00 – 3:00 pm: Finding and browsing genomic variation data

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


3:00 – 3:20 pm: Coffee Break



Population biology


3:20 - 4:00 pm: Simple Search and Browse

4:00 – 4:30 pm: Map-based search and analysis of insecticide resistance (IR) data

4:30 - 5:00 pm: Advanced Search


Wrap up


5:00 – 5:30 pm:


Computer and Internet access

A room with computers will not be provided, please bring your own laptop. You 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 December 11, 2017
  • Applications may be made via this web form.
  • Application deadline: February 9, 2018
  • Acceptance notification: February 12, 2018
  • Acceptance confirmation: February 16, 2018. If you have been accepted to attend, please reply to your acceptance notification with a short email to info@vectorbase.org by February 16, 2018. 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

The registration fee is $150.000 Colombian pesos for students and $200.000 Colombian pesos for professionals. There are two payment options:

  • Deposit: A deposit can be made with a unique code that will be send to your email, to the Davivienda checking account 0016-6999-9433. Only available for Colombian residents. Contact oficina@socolen.org.co for any questions.
  • Online payment: This option has an additional 10% fee, but the transaction can be done from anywhere in the world with a Colombian debit card or international credit card. The links to the SOCOLEN website with the PAYU links are available here.
The registation fee includes the cost of the hand-out materials and meals during the training (coffee breaks and lunches).

Each attendee is expected to provide their own accommodation (hotel or other) and transportation. 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, we will provide a list of recommended ones in January.


Questions?

Please direct inquiries or comments to info@vectorbase.org


Sponsored and organized by:

Yesica Paola Ardila Ríos, Dirección Ejecutiva. Junta Directiva Socolen 2016-2018. Sociedad Colombiana de Entomologia, Socolen

Carlos Muskus López. Profesor titular Universidad de Antioquia, Facultad de Medicina, Coordinador de la Unidad de Biología Molecular y Computacional del

Programa de Estudio y Control de Enfermedades Tropicales-PECET.

Andres Puerta. Estudiante de Posgrado en Ciencias Básicas Biomédicas, Universidad de Antioquia

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

Medellín, Colombia
Meeting Date: 
Monday, March 19, 2018 - 11:00 to Tuesday, March 20, 2018 - 23:00
Attached or inlined images: 
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