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5-6th February 2014 - EMBL-EBI
Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK

Description of the event/unit provided


This international workshop will be held at the European Bioinformatics Institute (EBI) at Hinxton, UK, as part of the INFRAVEC transnational access activities. The goal of the workshop is to offer a training and data analysis opportunity to external researchers and research teams applying via the INFRAVEC Access funding programme. The workshop will focus on the use of computational techniques for the exploration of vector genomics, especially programmatic access to data through VectorBase and analyses using high-throughput datasets including alignment of RNAseq or genome re-sequencing and subsequent measures of gene expression or variation respectively. This two-day course will be delivered using a mixture of lectures, hands-on practical sessions and an interactive session where users can discuss practical exercises with the trainers and fellow attendees. The trainers will be experienced vector bioinfomaticians and biologists from EBI and elsewhere.


Day 1 consists of a morning of introduction and summary talks with a guest lecture about the use of high-throughput genomic data sets in vector biology and then a walk through with exercises explaining programmatic access to VectorBase data using the Ensembl Application Programming Interface (API). Finally participants will initiate alignment of NGS dataset to a reference genome within the Galaxy platform


Day 2 explores builds on the aligned NGS data from Day 1 including the visualisation of the alignments and some simple analyses to get FPKM expression values for genes (to identify differential expression) and looking at calling variations (SNP detection). The session will end with discussion on how to improve data at VectorBase (community annotation efforts) and outreach activities (where to get help, what to expect from INFRAVEC/VectorBase).

Target audience: Researchers and research teams, including PhD students and postdocs. Participants will need to have experience of the Perl scripting language and a minimum of one year’s experience in the field of bioinformatics is preferable but not mandatory.

Prerequisites:The workshop is organised by the INFRAVEC Project as part of its Transnational Access activities aimed at providing funding to all researchers. Eligibility criteria for the provision of funding in the form of units of access are set by the EU Commission. In order to be considered for place on this course, applicants must register via the INFRAVEC web site and submit a short proposal describing their current position and research activities, explaining the reasons for requesting access to the workshop and how they plan to use and disseminate what they learn on the course. A recommendation letter signed by the applicant’s supervisor is highly recommended, though not mandatory. The deadline for registering and submitting proposals is 10th December 2013.




Proposals will be evaluated by the Workshop Scientific Committee before participation is granted and participants will be notified regarding acceptance by 20th December 2013. A £100 non-refundable registration fee is charged to successful applicants and must be paid within 15 days from receiving notification to EMBL-EBI (payment instructions will be sent to successfull applicants).  


The funding provided by INFRAVEC includes: participation to the workshop, course material, food and accommodation (max stay: 2 nights) for the length of the workshop. No cash funding is offered. The registration fee is not covered by the INFRAVEC funding. Further details are available on

Venue: The training workshop will take place at the EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK (approx. 10 miles south of the city of Cambridge).

Reception can be contacted on: +44 (0)1223 494 444

Further information and tips for getting to EMBL-EBI are available on

Download Programme.

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