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Future Perspectives in Computational Pan-Genomics
“Future Perspectives in Computational Pan-Genomics”
V. Guryev, Groningen; T. Marschall, Saarbrücken; A. Schönhuth, Amsterdam; F. Vandin, Odense; K. Ye, St. Louis
8 – 12 June 2015
Aims and Description: Pan-genomics studies, which are concerned with research on large, coherent collections of genomes have particularly profited from the drastic increase in throughput and the drastic cost reduction of sequencing experiments. In fact, the era of pan-genomics has just begun. Sequencing data from genome collections is massive (‘big’), noisy and poses complex computational questions. The corresponding issues affect several communities, such as population, cancer and pathogen biologists. The driving idea underlying this workshop was to systematically create maximum synergy among the communities in this exciting fresh new area of research. The goal was to survey existing and anticipate future computational challenges, and to identify both common denominators and discipline-specific challenges.
Tangible Outcome: As an incentive for active participation, we have been writing a white paper that documents and summarizes the ideas raised during the workshop. Writing this white paper proceded (extremely!) favorably – nearly everyone made major efforts to contribute. Participants are still actively editing this paper and at this point, nearly 50 valuable pages have been written. The goal is that this white paper will serve as a 'roadmap' for the forming community of 'computational pan-genomics' for the coming 2-3 years. We are aiming at publishing this paper in a high-impact journal.
Scientific Breakthroughs: Pan-genomics need novel data structures, indices and compression schemes, as well as the corresponding algorithms that allow for arranging (sometimes exhaustive) collections of genomes efficiently. Many ideas were raised during the workshop. Once implemented, scientific breakthroughs in several areas of biological research, often concerned with health-related questions, will be “unavoidable”. Computational pan-genomics is interdisciplinary research. While new inspiration is to be expected also for computer science, real breakthroughs, in terms of scientific relevance, are to be expected in particular in biomedical research, which depends on underlying “data infrastructure”.
“Aha” Moments: We realized already before the workshop that the interest would be enormous. Several “big shots” (e.g. Evan Eichler, Jan Korbel, two leading genomicists of our times) agreed on participating. During the workshop, the “Aha” effect consisted in watching the great momentum during the discussions. It was obvious that the majority of participants was “burning” to contribute. We believe that, as a topic selected, “computational pan-genomics” was just perfectly right, both in terms of topic and point in time. By mere coincidence, another workshop concerned with similar topics, also taking place in Leiden, organized by the “Global Alliance for Genomics and Health” (run by globally leading institutions such as the Sanger Institute, Cambridge), was running in parallel. Several participants (from renowned institutions) of this workshop got aware of our workshop and joined ours (and not the other way round), actively participating by giving spontaneous short talks, and (still) actively contributing to the white paper.
In summary, the “Aha” moment was to observe the huge interest and the currently enormous momentum of the newly forming field of “computational pan-genomics”. The workshop seemed to happen perfectly right in time.
Format of the workshop: The “Lorentz format” was just absolutely perfect for this workshop – there could not have been a better platform for this. Ample room for discussions and work/writing sessions,
also in combination with lots of free time to reflect and interact with others on a more private basis were key to success for this workshop!