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PETE JOKINEN
From 10 years to one week
SNS Europe talks to Pete Jokinen, Head of IT at the European Bioinformatics Institute (EMBL-EBI) in the UK, about how his role has changed to keep pace with the ever present, and ever increasing, need to collect, store and curate the information associated with technologies such as genome-sequencing, microarrays, proteomics and structural genomics. As Pete explains, the major challenge is to ensure that the ‘high-throughput revolution’ doesn’t drown the IT resource in data!
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SNS: Can you provide a brief professional autobiography, with reference to how your job has evolved over the years?
PJ: I completed a Masters in Computer Science at Helsinki University, involving one year of research under the supervision of Prof Ukkonen (studying approximate string matching). I then joined the National Public Health Institute in Helsinki as a senior analyst and worked on cancer prevention for approximately 5 years.
In 1996, I joined the EBI and in 1998 became the group leader of the systems team. In 1996 the team consisted of 3 people looking after about 70 EBI staff. We now have a systems team of 20, serving over 450 EBI staff.
SNS: Can you give some background as to the work carried out by the EBI?
PJ: As we move towards understanding biology at the systems level, access to large data sets of many different types has become crucial. Technologies such as genome- sequencing, microarrays, proteomics and structural genomics have provided parts lists for many living organisms,
and researchers are now focusing on how the individual components fit together to build systems.
The hope is that scientists will be able to translate their new insights into improving the quality of life for everyone. However, the high-throughput revolution also threatens to drown us in data. There is an ongoing, and growing, need to collect, store and curate all this information in ways that allow its efficient retrieval and exploitation.
The European Bioinformatics Institute (EMBL-EBI), which is part of the European Molecular Biology Laboratory (EMBL), is one of the few places in the world that has the resources and expertise to fulfill this important task.
Our mission To provide freely available data and bioinformatic services to all facets of the scientific community in ways that promote scientific progress.
To contribute to the advancement of biology through basic investigator driven research in bioinformatics
To provide advanced bioinformatics training to scientists at all levels, from PhD students to independent investigators
To help disseminate cutting-edge technologies to industry
SNS: Please give a flavour of the research projects carried out and their typical (if possible) IT/storage requirements
PJ: The EMBL-EBI provides a unique environment for bioinformatics research: we have a broad palette of research interests that complement our data resources, and these two strands of activity at the EMBL-EBI are mutually supportive. Areas of research include genomic analysis of developmental pathways and regulatory systems, evolutionary analysis of sequence data, computational systems biology of signalling pathways, text mining of the scientific literature, and protein structure and function. The services teams, who develop and maintain our data resources, also perform research to develop powerful new tools to handle the flood of data. The 1000 Genomes Project is a prime example to illustrate the scale
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