Workshop 4: Training

Bioinformatics Training for Life Scientists: Showcases and Challenges from Tutors’ Perspectives


Date & time: 9 September 2012, 9:00-17:00


Registration: Congress Center Basel, Messeplatz 21

Venue: Room "Geneva 1", Hotel Ramada, Messeplatz 12





The workshop focuses on training in bioinformatics for life scientists. Our days anyone embarking in biological research, from clinicians to evolutionary biologists, needs to address the explosive generation of molecular data and how to access and analyze/manage them in a biologically meaningful manner. To this aim, bioinformatics supplies resources and tools meant to be used by end users, which often are life scientists. Training, however, is not often on top of the priority list (which mostly includes research projects and publication turn over) of those developing resources and tools.


The several efforts in pushing bioinformatics training are mostly done independently, often as individual one-off efforts, and successful and problematic aspects (from structure to actual contents) are not necessarily shared among those involved in bioinformatics training. During the last few years the Bioinformatics Training Network (BTN, has been established, an initiative that has a two-fold ambition:


1. to bring together people involved in bioinformatics training to share experiences and best practices;
2. to offer a centralized repository of bioinformatics training material and information ( freely available to the community.


The BTN initiative has been very stimulating and enriching to its members, and this workshop would be the occasion to open the discussion to a wider audience composed of European and non-European trainers/scientists. This workshop represents a platform where those involved in bioinformatics training to life scientists can meet, confront and share experiences, as well as discuss future directions and collaboration in joint efforts.



Target Audience

The workshop is targeted at any level of trainers:
1) Both experienced and beginner trainers
2) Researchers who are involved in training 

When you participate in this workshop you will: 




Programme and schedule:


8:00   Registration at conference center

Welcome & opening lecture by the workshop organizers


How is bioinformatics training for life scientists coming along


Patricia Palagi (SIB Swiss Institute of Bioinformatics, Switzerland)

Allegra Via (Sapienza University of Rome, Italy)

Celia van Gelder (Netherlands Bioinformatics Centre, NBIC)

    Session I: Training Challenges in training life science researchers in bioinformatics

Challenges – Introduction

Anna Tramontano (Sapienza University of Rome, Italy)

10:15   Challenge: Defining your target group and your course objectives
Pedro Fernandes (Instituto Gulbenkian de Ciência, Portugal)
10:45   Coffee break
11:15   Challenge: Choosing the optimal training methodology
Kristian Rother (Science Trainer at Academis Training)
11:45   Challenge: Evaluating the quality of your course
Cath Brooksbank (Head of Outreach and Training, EBI)
12:15   Lunch
    Session II: Showcases in training life science researchers in bioinformatics

Showcases – Introduction

Fran Lewitter (Whitehead Institute for Biomedical Research)


Face-to-Face training

  • Kallio A, Hupponen T, Klemela P, Tuimala J, Gentile M, Scheinin I, Efficient bioinformatics training using biologist-friendly software.

    Korpelainen E.
  • Martin DMA, Procter JB, Barton GJ. Teaching versus Training – the Jalview conudrum.
  • Falquet L, Bertelli Lombardo C, Miyazaki R, Gharib W, Calderon-Copete S, Harshman K, Greub G, Robinson-Rechavi M, Van Der Meer J. Bioinformatics for a next generation class of experimental biologists.



  • Sehra M, Porras P, Laurent T, Brooksbank C, Schneider-Gricar V. Challenges involved in creating and maintaining online training courses for an EMBL-EBI molecular interaction resource.

  • Lisacek F, Koks P, Quadroni M, Kraehenbuhl JP. Article-based learning with e-learning platforms.

15:45   Coffee break

Panel discussion: Bioinformatics training for life scientists: where are we heading

Panel chairs:  the workshop organizers; 
Panel members: Anna Tramontano, Cath Brooksbank, Fran Lewitter, Kristian Rother & Pedro Fernandes.

Open discussion with the audience and the invited speakers on topics such as:

  • building and strengthening of a network of trainers,
  • possible collaborations,
  • international developments,
  • getting recognition for your training efforts,
  • and other issues related to training.


Send your questions and remarks to now, and we will have the pleasure to address them during this Panel discussion.

17:00   End of workshop.




Patricia Palagi

(SIB Swiss Institute of Bioinformatics, member BTN)

Vicky Schneider

(European Bioinformatics Institute, EBI, member BTN)

Allegra Via

(Dept of Physics, Sapienza University of Rome, chair BTN)

Celia van Gelder

(Netherlands Bioinformatics Centre, NBIC, secretary BTN)