VectorBase Hands-on Workshops

VectorBase is a Bioinformatics Resource Center (BRC) focused on invertebrate vectors of human pathogens. VectorBase 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 the workshops is to offer the opportunity to scientists working in medical entomology, vector biology or control, hands-on practical sessions with VectorBase data, tools and resources.

Registered and accepted participants receive information about the required homework via email. A few short video tutorials will be assigned to watch and the understanding of them will be tested with a brief questionnaire with a some additionally molecular biology, bioinformatics and omics general questions. Participant responses are due eight business days before the first day of the workshop. The homework is not optional because is meant to provide an introduction to the material to be covered during the workshop, which will facilitate to start the work and discussion on site. During the workshop, the instructor(s) will give an introduction to each of the tools and topics listed in the agenda. All the material used, including the slide lectures, will be available to participants. Most segments will include hands-on exercises and an opportunity to ask questions to the VectorBase team.

Depending on the length of the workshop (one, two or three days), attendees will be introduced to some or all VectorBase’s tools for searching, browsing and retrieving data. Data submission routes will also be discussed including metadata annotation approaches. The workshops conclude with a Q&A, a discussion regarding future community needs for all VectorBase data, tools and resources, an exit survey and distribution of workshop certificates.


Hosting a workshop

If you are interested in hosting a standard (in-person) workshop or want more information, please contact us at info@vectorbase.org. Have a look at the most recent ones to get a better idea of what the agenda could be like. Our workshops are free of charge to research and academic institutions. However we request that travel and accommodation costs of the instructor(s), students handouts and certificates to be covered by the host. Is up to the host to decide if a small registration fee would be charged to attendees to cover some costs. Is the host responsibility to take care of the advertising and ensure a group of attendees of 15-30 people. Workshops can be taught by one, two or three instructors, depending on the length and budget of the host. We strongly encourage the host to provide a computer room, if not possible attendees should bring their own laptops.


Computer and Internet access

Computers must have a web browser that meets the following requirements, 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.


Content

The agenda of the workshop is put together with the list of topics below. Most topics consist of a short presentation and a demonstration of the tools, followed by hands-on exercises. Attendees are encouraged to bring their own your data and/or any questions they may have. The time expend in each topic depends on the interest of the participants, based on the information provided in the registration form. Host are welcome to suggest new topics to the agenda, we are always open to customize each workshop to the host and attendees needs.


Introduction, finding data/information:

  • general introduction to omics; overview of VectorBase's remit, tools and data; website navigation and available data types; automatic annotation of genomes at VectorBase (gene set predictions, functional annotation and projecting gene descriptions); genome browser (gene, transcript, protein and location pages)
  • data mining with Search and BioMart: retrieving information from a few genes or genome wide using a web interface (no programming required).

Sequence tools:

  • finding data with BLAST
  • finding data with Clustal and Hmmer

Comparative genomics:

  • genomic alignments
  • gene trees, orthology & paralogy

Functional genomics:

(microarray and RNAseq data)

  • expression browser and map
  • expression tracks in the genome browser

Next Generation Sequencing (NGS) & Galaxy:

  • introduction to NGS, transcriptomics, Galaxy basics
  • differential expression workflow; visualizing NGS data; alignment coverage; SNP calls and their genomic consequences

Population biology:

(data from lab and field samples: insecticide resistance; population abundance and any biology, ecology or behavior trait)

  • simple search and browse; map-based search and analysis; advanced Search
  • finding and browsing genomic variation data

Gene manual annotations:

  • community annotation with Apollo

Wrap up:

  • Q&A including a selection of pre-workshop research-related questions answered
  • Exit questionnaire
  • Workshop certificates (Optional. Only if the host wishes to do this, in which case we have our own template)


Registration

Host will decide if a fee will be charged and the amount of it. We create an individual page per workshop. In that page we provide a link to the registration form. If you have been accepted to attend, please reply to your acceptance notification with a short email to info@vectorbase.org in the deadline provided. 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. Prerequisites? None. Previous knowledge in molecular biology, bioinformatics and omics is preferred but not required.


Official language

The official language of the workshops is English and applications must be submitted in this language too. The website and handout materials are in English. If requested by the host, and depending on the audience and the assigned instructor, the language spoken during the workshop may potentially be Spanish.


Sponsors/Financial support

VectorBase personnel is supported by NIH/NIAID to produce workshop content and deliver the materials. Because of this, the project does not charge for these services to workshop hosts. The other costs, which we ask the host to cover, may be paid in part charging a minimal fee to participants.


Live and free webinars

For those of you that want to learn more about VectorBase data, tools, and resources but are unable to host or attend a VectorBase workshop, we have created VectorBase webinars. Follow this link for details.


Questions?

Please direct inquiries or comments to info@vectorbase.org