Bioinformatics awareness through training provision in Portugal

Pedro L Fernandes, Instituto Gulbenkian de Ciência, Oeiras, PT     and    Cath Brooksbank, European Bioinformatics Institute (EMBL Outstation), Hinxton, UK

Introduction

Biologists have to adapt to changes in

methodology, some of them quite drastic,

more often than in other fields of science.

Not surprisingly, the availability of sequences

from Molecular Biology created new needs in

the area of using biological information to

know more. The field of Bioinformatics was

born and grew in this environment.

Modern Biologists need to manipulate

information and perform experiments with

data, as Biology became an information

science as well.

Skills

Preparing a community of biomedical

researchers to use Bioinformatics is

nowadays imperative, as the job of dealing

with data is not easily outsources to

specialists. Researchers should be as capable

as possible to address this type of needs on

their own.

Bioinformatics practitioners require skills that

can be acquired by self tuition, help from

colleagues and training.

The Instituto Gulbenkian de Ciência (IGC) has

started to provide Bioinformatics training to

MSc students in 1986. Very soon it became

clear that other researchers were needing

similar training, mostly at the PhD

preparation phase. The IGC started to provide

training courses on a yearly basis

Early experiments

Local provision of training became cost

effective quite quickly, avoiding travel

costs, time expenditure, etc. At the same

time, the accumulation of experience in

the community started to create additional

needs and a collection of themes emerged.

It was time to create a more solid offer

than sporadic events in this area.

Early Bioinformatics learners and

instructors at the IGC, in 1996

GTPB

The Gulbenkian Training Programme in

Bioinformatics (GTPB) was established in

1999 [1]. It aims at providing a continuous

stream of Bioinformatics training courses,

aimed at meeting the needs of the

portuguese research community. All the

courses are hands-on, taught in English, fully

documented in digital media and made

available to the international community as

well. More than 3000 researchers at all levels

have participated in GTPB courses.

Collaboration with the EBI

EMBL and in particular its Outstation in

Hinxton, UK, the European Bioinformatics

Institute (EBI) has been collaborating with IGC

and GTPB since the beginning. Data

resources, software tools, instructors, all

merged together to make the GTPB offer

much more comprehensive and articulated.

An ad-hoc system of cross referencing

training course offers has resulted in

numerous exchanges of referrals, ultimately

resulting in actual presence in events.

Methods

The GTPB has progressed in enhancing its

methods and adjusting to the evolving

needs

The present Bioinformatics Training Room,

where improvements in interaction and

learner engagement are continuously

tested.

Improvements

Enhancements in Bioinformatics training is

nowadays a subject of extensive discussion in

several expert networks where the IGC and

the EBI contribute regularly:

- EMBnet

- Bioinformatics Trainers Network [2]

- GOBLET [3]

- ELIXIR

The results of this work are published in

papers and reports that are publicly available.

The impact is also monitored and made public

[4].

Outreach

The IGC has hosted several “Road Shows”,

a BioSapiens Summer School and

occasional workshops to display EMBL

developments. This activity is mainly

outreach, but played a major role at

creating awareness and preparing

researchers for the upcoming needs.

References[1] Fernandes PL, “”The GTPB training programme in Portugal””, Brief Bioinform (2010) 11(6): 626-634, first

published online October 21, 2010 doi:10.13/bib/bbq063.

[2] Schneider MV, et al, Bioinformatics Training Network (BTN): a community resource for bioinformatics

trainers.Brief Bioinform. 2012 May,13(3):383-9. Doi: 10.1093/bib/bbr064. Epub 2011 Nov 22. Review.

[3] Via A, et al, “”Best practices in bioinformatics training for life scientists”” Brief Bioinform. 2013 Jun 25. [Epub

ahead of print] doi:10.1093/bib/bbt043

[4]Fernandes P, et al “”Training Experimental Biologists in Bioinformatics”” Advances in Bioinformatics (open

access), Volume 2012, Article ID 672749, doi:10.1155/2012/672749”

Acknowledgements

The activities described above have been

possible with the support of a wide variety

of sponsoring resources, of which we

highlight Fundação Calouste Gulbenkian,

EMBL, Brenda, BioSapiens, Elixir (ESFRI)

and SLING.