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Bio
A decade of running NMR labs and accumulating data convinced me about the value that a vast amount of organised data represents for research. The same decade spent on developing strategies and tools to improve our capacity to store and mine these data for accelerating discovery showed me that the obstacles are not all technical, but are mainly consequences of how research is conducted. Therefore, I have been teaming up with Luc Patiny from EPFL (Switzerland) and back in 2012 we showcased https://www.mylims.org a database for spectroscopic data that allows users to request services, view and manipulate their data online so that the data will never leave the lab before being stored into a database. Features were added to promote its use, enabling the creation of interactive teaching material for online courses. The rationale was that students would learn with the same tools that they would later use in the lab. Although valid, this argument was far too simplistic and integrating everything into a single platform was too difficult to maintain. The java applet technology used by then got unsafe and deprecated, and our group migrated the code to JavaScript. This is a rather unusual choice for building scientific tools and was dictated by the fact that we believe browsers will become the fastest graphical interfaces, receiving a lot of effort from many giant companies. Moreover, inspired by software practices, the next iteration was built in three pillars that work independently, storage, processing engine and visualization. A working instance of it is available at https://www.c6h6.org, while all the necessary code is shared on https://www.github.com/cheminfo under the open source MIT license. The first mentioned database has been up and running at EPFL, at Universidad del Valle and in several industries (thanks to Luc) for 12 years. The smallest one, in Colombia, has more than 30'000 entries and 100 active users. This decade of work let us accumulate a useful number of experiences dealing with users, formats, technologies, and with libraries and platforms that are currently in use, such as simulation and prediction of NMR spectra. One of these websites (www.nmrdb.org) receives more than 2000 monthly visits and are ranked first in Google searches (NMR prediction, spectra simulation).
However, working on an automatic assignment pipeline showed us the limitation of not having access to large collections of curated data. It is, in my opinion, a pertinent example of how the access to high-quality data can improve the development of future algorithms that in turn can improve the quality of the same data, by simultaneously improving the quality of spectra assignment and prediction of NMR parameters.
The more recent collaborations with Elaine Holmes from Imperial College widened the aims of our research, and we are currently working to improve the identification of putative metabolites during untargeted analysis. A database is running at Imperial College that stores data of reference compounds and allows one to superimpose them over loading plots or spectra of mixtures. The identification is thus performed visually, using a JavaScript library developed over several projects and available at https://github.com/npellet/visualizer, while further work is ongoing to make this process fully automatic. A grasp of the possibilities offered by this package can be found at https://www.cheminfo.org. The c6h6.org platform was readily adapted to this new purpose, due to the above mentioned division into independent pillars.
In addition, I dedicated efforts to establishing and consolidating the NMR community in Colombia. Starting 2008 I have chaired 5 international NMR schools in Colombia. Starting in 2012, with the collaboration of Elaine Holmes, we fostered metabolic profiling events in Latin America that resulted in 3 events, in Lima (Peru), Rosario (Argentina) and Rio de Janeiro (Brasil). These activities were keys to establish an international network of collaborations for research and formation. Bringing top researchers to Colombia played an important role in the formation of local students and helped establish a network of laboratories that could play an important role in promoting this project in Latin America. In addition, my group trained 11 undergraduate students, 6 masters, 2 PhD and 2 postdocs. I led a collaboration effort between Switzerland (EPFL) and Colombia and received 22 Swiss students in our lab as interns. During the last years, I have been in charge of international relations and transfer of technology and am now in charge of restructuring the laboratories. This shows a genuine concern to build and participate in the construction of durable international networks and robust institutions in Latin America, beyond the short term agenda of research.
Research Interests
Papers共 7 篇Author StatisticsCo-AuthorSimilar Experts
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Andrew G. Ewing,David Joffe,Svetlana Blitshteyn, Anna E. S. Brooks,Julien Wist,Yaneer Bar-Yam,Stephane Bilodeau, Jennifer Curtin, Rae Duncan, Mark Faghy, Leo Galland, Etheresia Pretorius, Spela Salamon,Danilo Buonsenso,Claire Hastie,Binita Kane, M. Asad Khan,Amos Lal,Dennis Lau,Raina MacIntyre, Sammie McFarland,Daniel Munblit,Jeremy Nicholson, Hanna M. Ollila,David Putrino, Alberto Rosario, Timothy Tan
Annals of Clinical Microbiology and Antimicrobialsno. 1 (2025): 1-19
Julien Wist, Philipp Nitschke, Ricardo Conde, Angela de Diego, Maider Bizkarguenaga, Samantha Lodge, Drew Hall,Zhonglin Chai, Wenjun Wang, Sudhir Kowlessur, Marcio-Fernando Cobo, Niels Pompe, Birk Schütz, Hartmut Schäfer,Manfred Spraul, Claire Cannet,Tammo Diercks, Nieves Embade,Elaine Holmes,Oscar Millet,Jeremy K Nicholson
Analytical chemistryno. 12 (2025): 6399-6409
Maartje Cox, Aaron Raman, Timothy Fairchild, John P Beilby, Bu B Yeap, Jeremy K Nicholson,Julien Wist, Jeremiah Peiffer, Nathan G Lawler
Experimental physiology (2025)
Jurissa Lang, Andres Bernal,Julien Wist, Siobhon Egan, Sze How Bong,Oscar Millet, Monique Ryan, Aude-Claire Lee, Drew Hall, Philipp Nitschke, Reika Masuda,Allison Imrie,Elaine Holmes,Jeremy Nicholson,Ruey Leng Loo
Janonna Kadyrov, Samuele Sala, Lucy Grigoroff, Novia Minaee, Reika Masuda, Samantha Lodge, Timothy M Ebbels, Michael D Reily, Donald Robertson, Lois Lehman-McKeeman, John Shockcor, Bruce D Car,Glenn H Cantor, John C Lindon, Jeremy K Nicholson,Elaine Holmes,Julien Wist
Archives of toxicologyno. 6 (2025): 2669-2681
Alanah Grant-St James, Aude-Claire Lee, Alex J Lee,Julien Wist, Ferdous Sohel, Kok Wai Wong, Bu B Yeap,Ruey Leng Loo,Amanda Henry, Daniella Susic, Emad El-Omar, Jeremy K Nicholson,Elaine Holmes,Luke Whiley, Nicola Gray
Analytica chimica acta (2025): 344225-344225
Dana Hicks, Monique J Ryan, Amira Allahham, Lucy W Barrett,Silvia Lee, Benjamin Bartlett, Herbert Ludewick,Natalie C Ward,Ruey Leng Loo,Girish Dwivedi,Jeremy K Nicholson,Julien Wist,Elaine Holmes, Nicola Gray
Analytica chimica acta (2025): 343791-343791
Author Statistics
#Papers: 4
#Citation: 0
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Sociability: 3
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