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MedVetNet Microarray Data Analysis Workshop

three-day workshop, May 14 - 16, 2008, held in Denmark

Course Programme



Organized by

The Center for Biological Analysis, Technical University of Denmark, Denmark
BfR - Bundesinstitut für Risikobewertung

Course organizers: Dave W. UsseryCarsten Friis, and Thomas Alter




Aim

The workshop will focus on the design and analysis of pan-genomic microarrays.

Due to the massive availability of sequences of genomes of microbes and other organisms, the degree of sequence variation is becomming measurable both across bacterial species, but also within different isolates of the same species. Indeed, the pan-genome, defined as the total number of unique genes observed in any isolates of a given species, can be much larger than the individual genome of any single isolate. For the microarray analyst, genetic variation between isolates of the same species presents new challenges since a traditional microarray designed to target one specific genome is likely to perform very poorly if used with another, different isolate.

As the number of fully sequenced genomes of indepentent isolates for each bacterial species increases, it becommes possible to design pan-genomic microarrays capable of targeting any and all unique genes ever observed in that species. The advantages of this technology includes not only a much broader coverage for traditional expression studies, but also the ability to differentiate between even highly related isolates of the same strain through comparative genomic hybridization (CGH).

Who should attend
The workshop is designed for participants with different educational backgrounds and different research interests to work together in cooperation. Thus, the workshop is suitable for all students and researchers in medical science, biological science, computer science, bioinformatics, biotechnology, and related fields. The participants should have a basic knowledge in molecular biology and some background in statistics. Those who have a computer science related background will be introduced to basic molecular biology to be able to perform the hands-on exercise.

The participants will have the opportunity to work in groups consisting of colleagues from different disciplines. Moreover, participants will be able to use the workshop as a forum to share and exchange their experiences and also to discuss and identify practical problems and solutions with the experts in the field of comparative microbial genomics, DNA microarrays and bioinformatics.




Practical information

The course will consist of lectures and computer exercises, where the students will be introduced to a range of computational methods used in the field.
Lectures and exercises will take place in Lyngby, Denmark, at The Danish Technical University. Building 208, room 062

Registration
Registration is now closed. Any questions pertaining to registration should be directed to Thomas Alter. The price of registration is 175 Euro which covers course materials as well as meals, but not accomodation. Although you must pay for it yourself, we can try to book a hotel for you allowing you to stay together with the other course participants. If you desire this, please specify this when you register for the course. CBS will organise and pay for lunch for all participants throughout the workshop and also cater for drinks and coffee breaks.

Limitation
The number of participants is restricted to 30 persons. Places will be given on a first come basis. Limited number of participants will allow the opportunity for the participants to access to all the facility and to work closely with the experts, or to work on their own data (if any). Upon acceptance, all participants will receive further information about the workshop as well as some course material.

Exercises
Will be performed in groups of two and supervised by one or more instructors. Exercises will be purely computational. Although computers will be available as needed during the workshop, it is possible to use your own portable Windows or Mac computer for the exercises with a minimum of preparation.

Lecture notes
As far as possible, we will put up the lecture notes on the course programme web-page linked to the lecture itself. Lecture notes will be in PDF format and will in many cases be preliminary, ie. the lecturer will provide the final notes after the talk and these will then replace the preliminary notes.




Transport & Accomodation

DTU is located in Lyngby, 10 km north of Copenhagen. You can get to DTU in Lyngby by car or by public transportation. Several busses stop almost at the door and Lyngby Station is just 3 km away with even more bus connections.

Public Transport
The Copenhagen Metro travels from the airport to Nørreport Station in the centre of Copenhagen. There is a service every 4 minutes. In addition, there is a train service every 20 minutes from the Copenhagen Airport train station to Nørreport. At Nørreport Station, bus no. 150 S leaves approximately every ten minutes and stops at DTU. The price of a ticket for this journey is around DKK 70. Alternatively, you can take the s-train (S-tog) from Copenhagen Central Station in the direction of Hillerød and Holte (line B or E). Both those trains will stop at Lyngby station from where you can get the bus 300 S in the direction of Nærum/Kokkedal and get off at DTU.

Taxi/Car
A taxi ride from Copenhagen Airport to DTU costs around DKK 400 and takes from 30 minutes, depending on traffic. From the centre of Copenhagen to DTU, a taxi ride also takes about 30 minutes and costs approximately DKK 200.

Accommodation
For participants accomodation will not be pre-booked; thus, the participants must ensure that they make these bookings themselves in good time. If you wish, we can try to book a room for you ensuring that you stay at the same hotel with other course participants. Please specify if you want this when you register. This offer is subject to the availability of rooms at the hotel.

If you prefer to book on your own then in Lyngby, Hotel Scandic Eremitage is the closest situated hotel to DTU. If you prefer staying in central Copenhagen it is worthwhile to check out the following website where cheaper accommodation can be found: Hotels in Copenhagen. If you book accommodation in Copenhagen, we recommend that you find a hotel close to Copenhagen central station or Nørreport station, from where transport to Lyngby is easy.

All travel, transport and accommodation costs will not be reimbursed by the organisers, but should be covered by participants' own budget.