FA COST Action TD0801 StatSeq

BMBS COST Action BM1006 SeqAhead

Sequence Data Analysis Training School

Course Materials can be found here


Welcome to this training school, organised by the European Research Group EADGENE_S , and the COST Actions StatSeq (TD0801) and SeqAhead (BM1006). This page contains information and details on registration as well as application for COST travel grants.

Dates : December 10 - 14, 2012

The course will start on Monday December 10th after lunch at 1.00 pm, and will end with lunch on Friday 14th of December.

Aim :
The course is focussed on learning to analyse sequence data by applying the state of the art methods to real datasets. Data analysis exercises will be carried out by participants in a virtual server environment. Throughout the course the aim will be to learn useful approaches and strategies for analysing your data, to learn about the important algorithms and their software implementations, and to learn how to use scripting language(s) to connect different available software tools to construct a data analysis pipeline.

Outline :

Day 1
- Introduction to using the Linux operating system for large scale data analysis.
- Course dinner, followed by an invited presentation (TBA) and drinks.

Day 2
- Use of Cloud computing in sequence data analysis.
- Sequence data quality control and trimming of sequence data.
- Quality measures and filtering of sequence data to avoid downstream problems.

Day 3
- Mapping of next generation sequence reads.
- SNP discovery from NGS data.

Day 4
- sRNAseq (miRNA analysis)
- Measuring (differential) expression levels from RNA-seq
- Course dinner, followed by an invited presentation (TBA) and drinks.

Day 5
- De Novo assembly

Data standards (BAM etc.) will be discussed for all topics throughout the course. Exercises in a virtual server environment are an intricate part of the course.

Instructors :

- Christoph Klopp, INRA - Toulouse, France.
- Mick Watson, The Roslin Institute - Edinburgh, United Kingdom. website
- Hendrik-Jan Megens, Wageningen University - Wageningen, the Netherlands.

Target audience :

The course is designed for PhD students and postdoctoral fellows working with high volume next generation sequence data. Participants are expected to be familiar with sequence data and general genomics concepts. Although an introduction to working with sequence data in the Linux environment is part of the course, participants should prepare by learning the basic Linux skills if they do not already have them.
The aim of the course is to teach methods, algorithms and strategies that allow participants to turn next generation sequence data into biologically relevant information such as sequence variants and expression levels. Some examples of downstream analyses that makes use of this data will be included. A combination of lectures and exercises will allow participants to get a feeling of both theory and practical application.

Course Fee1 :
A. EADGENE_S2 and COST3,4 participants, and WIAS PhD's 200.00
B. Other PhD's, post-docs, academia and WU staff 400.00
C. Industry 800.00
1Fee include course materials, daily coffee, tea and lunch, and a course dinner. Hotel accommodation and traveling is not included.
2The European Research Group EADGENE_S (see www.eadgene.info ) participants qualify for the reduced rate. The list of partners in EADGENE_S can be found here .
3Subsidy for the COST Action STATSEQ participants: The EU COST Action StatSeq (see www.statseq.eu ) has funds for 10 travel grants of 1000,- (max.) This grant is meant for participants who are:
I. Early Stage Researcher, i.e., doing a PhD or recently completed a PhD (max. 8years ago)
II. Currently working in a country that is participating in (= signed the StatSeq Action MoU) the COST Action StatSeq. The list of participating countries can be found here .
4Subsidy for the COST Action SEQAHEAD participants: The EU COST Action SeqAhead (see www.seqahead.eu ) has funds for 10 travel grants of 1000,- (max.) This grant is meant for participants who are:
I. Early Stage Researcher, i.e., doing a PhD or recently completed a PhD (max. 8years ago)
II. Currently working in a country that is participating in (= signed the SeqAhead Action MoU) the COST Action SeqAhead. The list of participating countries can be found here .
NB. Candidates selected for travel grants of STATSEQ or SEQAHEAD qualify for the reduced registration fee.

Selection of candidates to be awarded the travel grant will be based on :
a.Letter of motivation to participate in the course, indicating the value to the research being done (max 10 lines)
b.Country of residence (there will be prioritization for Eastern Europe countries & the balance among COST countries will be considered)
c.Year of (expected) completion of PhD thesis
d.Gender (positive discrimination : favouring female participants)
e.Whether applicant is a StatSeq member (registered for user account at www.statseq.eu = affiliation to the COST Action)
f.Whether applicant is a SeqAhead member (registered for user account at www.seqahead.eu = affiliation to the COST Action)
To apply for a EU-COST Action travel grant, please send information regarding the above-mentioned criteria along with your application form. The application form contains a section where the required information can be filled. This is the same form as the one found below under "Registration" and can be downloaded here .
The application form, including the travel grant application, needs to be send to john.bastiaansen@wur.nl
For the travel grant application please note the following dates:
Deadline travel grant application (StatSeq OR SeqAhead) :October 31st 2012.
Decisions on selected applications by the COST Action :November 5th 2012.
Confirmation by the selected trainees :November 10th 2012.

Course location :

The course will be organized at the ZODIAC building of the Animal Sciences Group, on Wageningen Campus, Wageningen University, De Elst 1, 7608 WD Wageningen, the Netherlands.

Registration :

To register for the course please download the application form here and send it to john.bastiaansen@wur.nl. The top part of the form needs to be filled to apply for participation in the course. The bottom part of the form is only needed if you are applying for a COST travel grant (see section "Travel Grants" above).

Full registration only occurs once you have provided us with the requested information as stated above, and after you will receive an official registration confirmation by one of the course organizers.

Hotel Accommodation :

Wageningen has several hotels to choose from:
- Hotel Hof van Wageningen. Distance to the campus : 2.1 km (on foot)
- Hotel de Nieuwe Wereld. Distance to the campus : 2.3 km (on foot)
- Hotel de Wereld. Distance to the campus : 2.3 km (on foot)
- Hotel Nol in 't Bosch. Distance to the campus : 5.2 km
The first three hotels and the campus are easily accessible by public transport (Bus nr. 88, also called 'de Valleilijn'). These buses (blue-colored) operate within 7 minutes time-intervals and connect Wageningen center (bus terminal 'Stadsbrink') with the main rail road station Ede-Wageningen (train going to Nijmegen/Arnhem - via Utrecht - departing from Amsterdam or Airport Amsterdam (Schiphol) and the same for the way back).
The listed hotel nr. 4 is easily accessible by car, but hardly by public transportation.

The nearby town, Ede, has also some hotels to choose from:
- Hotel de Reehorst. Distance to the campus : 6.9 km
This hotel is conveniently located near main rail road station Ede-Wageningen.
- Hotel PTC+. Distance to the campus : 5.6 km

Additional information :

Course Organisation :Dr John BastiaansenDr Hendrik-Jan Megens
Tel. + 31 317483966Tel. + 31 317482469
john.bastiaansen@wur.nl hendrik-jan.megens@wur.nl

COST ACTION StatSeq :

Dr Marco Bink
Tel. +31 317481072
marco.bink@wur.nl

COST ACTION SeqAhead :

Dr Erik Bongcam-Rudloff
Tel. +46 18672121
erik.bongcam@slu.se