© 2017 by Eduardo Gade Gusmao

The value of a nationwide community

January 7, 2018

This post has as a main goal to show the benefits of a nationwide community-driven effort to establish quality research. I will summarize (and put in some of my comments) the great publication by Dr. van Gelder et al. [1]. The case scenario here is: Bioinformatics in the Netherlands.

 

The early days

 

As early as the 70s, Dr. Pauilen Hogweg [2] realized that information processing could serve as a useful metaphor for understanding living systems. Therefore, she concluded that it was useful to distinguish bioinformatics as a research field in addition to biophysics and biochemistry. This was followed in the 80s by seminal groups in the University of Groningen with researchers such as: Dr. Herman Berendsen [3], Dr. Wilfred van Gunsteren [4] and Dr. Jan Drenth and Wim Hol [5].

 

From left to right: Dr. Pauilen Hogweg, Dr. Herman Berendsen, Dr. Wilfred van Gunsteren & Dr. Jan Drenth and Wim Hol.

 

NBIC: Bioinformatics under the Netherlands Genomics Initiative

 

NBIC was established in 2003, receiving, in the period of 2003-2013 over 38M euros (a big part from the NGI [Netherlands Genomics Initiative] funded by the NWO [Netherlands Organization for Scientific Research]). Seminal scientists at the cradle of NBIC were Dr. Gert Vriend, Dr. Bob Hertzberger and Dr. Jacob de Vlieg.

 

From left to right: Dr. Gert Vriend, Dr. Bob Hertzberger & Dr. Jacob de Vlieg.

 

Most interestingly, the NBIC established an integrated model of research, support and education, which were organized in the three NBIC programes: BioRange, BioAssist and BioWise, respectively. 

 

BioRange has as its main goal the distribution of PhDs and postdocs at universities and medical centers in the Netherlands, focused in four bioinformatics topics: sequence-based bioinformatics, genotype–phenotype modeling, proteomics and metabolomics and systems bioinformatics.

 

BioAssist provided software infrastructure support by having a short (20 - 25) scientific programmers permanently stationed at NBIC's partners for a short period of time. The main goal here was to "make other people's data work". The BioAssist programe was regarded as a crucial element for the success of the NBIC model's sustainability.

 

Finally, the BioWise's goal was to train the current and next generation of bioinformaticians and biologists; with target audience ranging from high school pupils to senior researchers.

 

A very interesting example of one of BioWise's outreach activities is the high school project Bioinformatics@school. This project started in 2006 as part of the national programe called Traveling DNA labs, where teaching assistants physically visit high schools throughout the country. They turn the classroom into a laboratory and bring modern life science and bioinformatics research alive for high school students and teachers. To date, more than 23000 high school pupils have attended a Bioinformatics@school practical at their own school. In my humble opinion, this is the highest level you can get regarding a countries' interest for its bright future.

 

Reorganization without central funding

 

What happens when your central public resources are gone and you are in a country where research is regarded as a benefit to the society (instead of dog-eat-dog "I have to publish first before this other group" type of country)? Join forces with other initiatives. In this case, NBIC joined forces with the Proteomics Centre, Netherlands Metabolomics Centre and Netherlands Consortium for Systems Biology (NCSB); which was named Dutch Techcentre for Life Sciences (DTL) and became the Dutch node of the European Life-Science Research Infrastructure ELIXIR (ELIXIR-NL). ELIXIR has a hub hosted in the European Bioinformatics Institute (EMBL-EBI; Hinxton, UK) and several hubs, coordinating and sustaining bioinformatics resources across its member states.

 

As of the summer of 2017, DTL had grown into a partnership of 50 life science organizations (> 120 expert groups). DTL's success was a result of its public-private network. Although in my opinion, it is research is an end-task towards any countries development; sometimes there are other end-tasks which are also urgent. I like to think as the (ideal) public resources' usage as a personal's computer processor: processing power is given in an alternate fashion to a certain number of tasks, which gives the user the sense of a larger multiprocessing interface.

 

Summary and Future

 

After 10 years of active bioinformatics community and programes coordinated by the NBIC, the Dutch bioinformatics community has now embedded its activities in three new initiatives that are strongly intertwined:


- DTL, the Dutch Techcentre for Life Sciences.


- ELIXIR-NL, the Dutch node of ELIXIR, which is hosted by DTL.


- BioSB, Netherlands Bioinformatics and Systems Biology Research School.

 

As mentioned in [1]:

 

"We envisage a type of infrastructure that allows researchers to flexibly combine data sets, bioinformatics tools, computational models and ICT platforms. The infrastructure should operate as a virtual workspace to collaborate and execute data-intensive analytics. It will be established and maintained by a broad range of public and private Dutch research and technology organizations and will form the data ‘backbone’ of topical life sciences infrastructures. This model underlies the nascent national infrastructure for personalized medicine and health research (Health-RI)."

 

Goed gedaan Nederland! Tulp?

 

 

References:
1. van Gelder C.W.G. et al. (2017) Briefings in Bioinformatics, bbx087.
2. https://en.wikipedia.org/wiki/Paulien_Hogeweg
3. https://en.wikipedia.org/wiki/Herman_Berendsen
4. Hünenberger P.H. et al. (2012) Journal of Chemical Theory and Computation, 8(10):3425-3429.
5. http://www.washington.edu/news/2007/05/03/may-10-science-in-medicine-lecture-structural-biology-and-tropical-diseases/
6. https://www.nbic.nl/about-nbic/nbic-faculty/details/prof-dr-gert-vriend/index.html
7. https://www.nbic.nl/en/about-nbic/who-is-who/pages1/1/details/prof-dr-lo-bob-hertzberger
8. https://www.nbic.nl/about-nbic/nbic-faculty/jacob-de-vlieg/index.html

 

Figure Sources:
Fig.1. http://kerdowney.com/destinations/netherlands/
Fig.2. http://www-binf.bio.uu.nl/ph/
          https://www.researchgate.net
          Hünenberger P.H. et al. (2012) Journal of Chemical Theory and Computation,

              8(10):3425-3429.
          http://www.washington.edu/news/2007/05/03/may-10-science-in-medicine-lecture-structural-biology-and-tropical-diseases/
Fig.3. https://www.nbic.nl/about-nbic/nbic-faculty/details/prof-dr-gert-vriend/index.html
          http://www.jvanpelt.nl/neuroinformatics/workshop30jan04/Pictures.html
          https://www.nbic.nl/about-nbic/nbic-faculty/jacob-de-vlieg/index.html

 

Further Related Links:
1. Overview of DTL's Technology Hotels and what they have to offer.
2. Bring your own data workshops.
3. Data FAIRport.
4. The personal health train project.
5. The European Open Science Cloud Initiative.
6. The ELIXIR training portal TeSS.
7. YoungCB (Young Computational Biologists).
8. Bioinformatics Training Network (BTN).
9. Galaxy.
10. The Global Organisation for Bioinformatics Learning Education and Training (GOBLET).
11. NLeSC: Netherlands eScience Center.
12. The collaborative ICT organization for Dutch education and research.
13. Software Carpentry and Data Carpentry (SWC/DC).
14. The online training portal of ELIXIR (TeSS).
15. The Netherlands Organization for Health Research and Development (ZonMw).

Share on Facebook
Share on Twitter
Share on LinkedIn
Awesome!
Please reload

Please reload

Tags
Please reload

Archive