My goal is to help realize Charles Elton’s dream to “link up into some complete scheme the colossal store of facts about natural history” (Elton 1927 ) to enable biodiversity research and better understand the natural world around us.
I use my software engineering skills to develop new methods to solve “impossible” integration problems in biodiversity informatics. I use, or build, open source software to integrate, and study, open biodiversity data.
After spending about a decade in industry, I was re-introduced to academia in 2011 by attending the Ecological Integration Symposium at Texas A&M College Station. As an invited visual artist, I was asked to take a minute or two to introduce my video installation “Evidence of Use” to the conference attendees. I noticed the audience freeze when I suggested that all scientific data should be liberated for the unrestricted enjoyment of scientists and artists alike. Fortunately, after the talk, I was approached by an enthousiastic audience member who introduced me to his big dream and his excel spreadsheet with fish stomach diet data. This marked my unlikely entry into the field of ecological informatics and the start of my collaboration with Jim Simons, then marine biologist at Texas A&M Corpus Christi. Our complementary skills and shared enthusiasm led to the materialization of the Gulf of Mexico Species Interactions (GoMexSI, ) and Global Biotic Interactions (GloBI, https://globalbioticinteractions.org ) projects. Both projects re-purpose existing species datasets in an attempt to realize Charles Elton’s vision to “[…] provide conceptions which can link up into some complete scheme the colossal store of facts about natural history […]” (). GoMexSI focus is on synthesis of marine food webs in the Gulf of Mexico, while GloBI aims to make it easier to share and find any openly available species interaction (e.g., parasite-host, plant-pollinator, predator-prey) claim.
As a small, independent, open source and open data developer, I have no choice but to make use of openly available datasets, leverage cheap (or open) compute infrastructures, and establish a wide range of mutually beneficial research collaborations with institutional scientists. I have noticed that my frugal approach to software design, automation and collaborations have resulting in a sustained, economically viable, way of life with beneficial side effects such as:
1. Providing a de-facto continuous peer-review service of existing open datasets and -services ().
2. Developing pragmatic approaches to link biological data at scale (, ).
3. Engaging in, and enabling of, “risky” scientific studies that re-use existing datasets to answer (global) questions (, ).
4. Catalyzing discussions around data integration, frugal tools, data preservation, data standards and ontologies (, , ).
Over the years, I have come to realize that many of my contributions to the academic community cannot be measured in, or are often detrimental to, traditional metrics like citation indexes, grant moneys, institutional affiliation, and academic tenure. With this, I would like to think that, as a free-living parasite/ symbiont, I help my hosts evolve by transferring infectious new ideas across disciplinary and institutional boundaries.
You can reach me via jorrit.poelen at ronininstitute dot org . For more information, please see https://jhpoelen.nl .
References Simons JD, Yuan M, Carollo C, Vega-Cendejas M, Shirley T, Palomares ML, Roopnarine P, Gerardo Abarca Arenas L., Ibañez A. , Holmes J, Mazza Schoonard C, Hertog R, Reed D, and Poelen JH. 2013. Building a Fisheries Trophic Interaction Database for Management and Modeling Research in the Gulf of Mexico Large Marine Ecosystem. Bulletin of Marine Science; Jan 1;89(1):135–60. https://doi.org/10.5343/bms.2011.1130 .  Poelen JH, Simons JD, Mungall CJ. 2014. Global biotic interactions: An open infrastructure to share and analyze species-interaction datasets. Ecological Informatics. Nov;24:148–59. Available from: https://doi.org/10.1016/j.ecoinf.2014.08.005 .  Elton CS. 1927. Animal Ecology. https://doi.org/10.5962/bhl.title.7435 .  Poelen JH, et al. 2019 . GloBI GitHub Issues Archive 2013-2019 . GitHub. https://github.com/globalbioticinteractions/globalbioticinteractions/issues accessed at 2019-10-14 .  Thessen AE, Poelen JH, Collins M, Hammock J. 2018. 20 GB in 10 minutes: a case for linking major biodiversity databases using an open socio-technical infrastructure and a pragmatic, cross-institutional collaboration. PeerJ Computer Science 4:e164 https://doi.org/10.7717/peerj-cs.164  Grüss A, Palomares MLD, Poelen JH, Barile JR, Aldemita CD, Ortiz SR, et al. 2019 Building bridges between global information systems on marine organisms and ecosystem models. Ecological Modelling. Apr;398:1–19. https://doi.org/10.1016/j.ecolmodel.2019.01.023  Hayden B, Palomares MLD, Smith BE, Poelen JH. 2019. Biological and environmental drivers of trophic ecology in marine fishes – a global perspective. Sci Rep. Aug 6;9(1):11415. https://doi.org/10.1038/s41598-019-47618-2 .  Olivier, P. et al., 2019. Exploring the temporal variability of a food web using long?term biomonitoring data. Ecography. Available at: https://doi.org/10.1111/ecog.04461 .  Pauli JN, Newsome SD, Cook JA, Harrod C, Steffan SA, Baker CJO, … Poelen JH … 2017. Opinion: Why we need a centralized repository for isotopic data. Proceedings of the National Academy of Sciences [Internet]. Proceedings of the National Academy of Sciences; Mar 21;114(12):2997–3001. Available from: http://dx.doi.org/10.1073/pnas.1701742114  Hardisty AR, Michener WK, Agosti D, Alonso García E, Bastin L, Belbin L, … Poelen JH … 2019. The Bari Manifesto: An interoperability framework for essential biodiversity variables. Ecological Informatics. Jan;49:22–31. Available from: https://doi.org/10.1016/j.ecoinf.2018.11.003 .  Gallagher, R., Falster, D. S., Maitner, B., Salguero-Gomez, R., Vandvik, V., Pearse, W., … Poelen JH … Enquist, B. 2019. The Open Traits Network: Using Open Science principles to accelerate trait-based science across the Tree of Life. Pre-print. https://doi.org/10.32942/osf.io/kac45