Towards open science: the myExperiment approach

Autor: David De Roure, Carole Goble, Sergejs Aleksejevs, Sean Bechhofer, Jiten Bhagat, Don Cruickshank, Paul Fisher, Duncan Hull, Danius Michaelides, David Newman, Rob Procter, Yuwei Lin, Meik Poschen

Publikováno v: Concurrency and Computation: Practice and Experience. 22:2335-2353

By making research content more reusable, and providing a social infrastructure that facilitates sharing, the human aspects of the scholarly knowledge cycle may be accelerated and -time-to-discovery' reduced. We propose that the key to this is the sh

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c3490f1c6db4afb076f0d95ad40425d6
https://doi.org/10.1002/cpe.1601

Taverna: lessons in creating a workflow environment for the life sciences

Autor: R. Mark Greenwood, Duncan Hull, Carole Goble, Matthew Pocock, Anil Wipat, Justin Ferris, Antoon Goderis, Matthew Addis, Phillip Lord, Martin Senger, M. Nedim Alpdemir, Darren Marvin, Robert Stevens, Tom Oinn, Kevin Glover, Chris Wroe, Peter Li

Publikováno v: Concurrency and Computation: Practice and Experience. 18:1067-1100

Life sciences research is based on individuals, often with diverse skills, assembled into research groups. These groups use their specialist expertise to address scientific problems. The in silico experiments undertaken by these research groups can b

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b7555056c55871b635c4a62cb18d8a2f
https://doi.org/10.1002/cpe.993

A community-driven global reconstruction of human metabolism

Autor: Hulda S. Haraldsdóttir, Douglas B. Kell, Andreas Hoppe, Duncan Hull, Miranda D. Stobbe, Daniel Jameson, Lukas Endler, Swagatika Sahoo, Warwick B. Dunn, Jens Nielsen, Bernhard O. Palsson, Kieran Smallbone, Neema Jamshidi, Stefan Gretar Thorleifsson, David Hala, Hans V. Westerhoff, Ottar Rolfsson, Nikolaus Sonnenschein, Arvind K. Chavali, Ines Thiele, Alexander Mazein, Dieter Weichart, Evgeni Selkov, Sergio Bordel, Michael Hucka, Intawat Nookaew, Nick Juty, Jason A. Papin, Paul D. Dobson, Ronan M. T. Fleming, Jon J. Jonsson, Neil Swainston, Anatoly Sorokin, Maike K. Aurich, Sarah M. Keating, Rasmus Agren, Monica L. Mo, Igor Goryanin, Nathan D. Price, Christian Bölling, Pedro Mendes, Evangelos Simeonidis, Johannes H. G. M. van Beek, Martin I. Sigurdsson, Naglis Malys, Nicolas Le Novère

Publikováno v: Thiele, I, Swainston, N, Fleming, R M T, Hoppe, A, Sahoo, S, Aurich, M K, Haraldsdottir, H, Mo, M L, Rolfsson, O, Stobbe, M D, Thorleifsson, S G, Agren, R, Bölling, C, Bordel, S, Chavali, A K, Dobson, P, Dunn, W B, Endler, L, Hala, D, Hucka, M, Hull, D, Jameson, D, Jamshidi, N, Jonsson, J J, Juty, N, Keating, S, Nookaew, I, Le Novère, N, Malys, N, Mazein, A, Papin, J A, Price, N D, Selkov, E, Sigurdsson, M I, Simeonidis, E, Sonnenschein, N, Smallbone, K, Sorokin, A, Van Beek, J H G M, Weichart, D, Goryanin, I, Nielsen, J, Westerhoff, H V, Kell, D B, Mendes, P & Palsson, B O 2013, ' A community-driven global reconstruction of human metabolism ', Nature biotechnology, vol. 31, no. 5, pp. 419-425 . https://doi.org/10.1038/nbt.2488
Nature Biotechnology, 31, 419-425. Nature (2013).
Nature Biotechnology; Vol 31
Thiele, I, Swainston, N, Fleming, R M, Hoppe, A, Sahoo, S, Aurich, M K, Haraldsdottir, H, Mo, M L, Rolfsson, O, Stobbe, M D, Thorleifsson, S G, Agren, R, Bölling, C, Bordel, S, Chavali, A K, Dobson, P, Dunn, W B, Endler, L, Hala, D, Hucka, M, Hull, D, Jameson, D, Jamshidi, N, Jonsson, J J, Juty, N, Keating, S, Nokaew, I, Le Novère, N, Malys, N, Mazein, A, Papin, J A, Price, N D, Selkov, E, Sigurdsson, M I, Simeonidis, E, Sonnenschein, N, Smallbone, K, Sorokin, A, van Beek, J H G M, Weichart, D, Goryanin, I, Nielsen, J, Westerhoff, H V, Kell, D B, Mendes, P & Palsson, B O 2013, ' A community-driven global reconstruction of human metabolism ', Nature Biotechnology, vol. 31, no. 5, pp. 419-425 . https://doi.org/10.1038/nbt.2488
Nature Biotechnology, 31(5), 419-25. Nature Publishing Group
Thiele, I, Swainston, N, Fleming, R M T, Hoppe, A, Sahoo, S, Aurich, M K, Haraldsdottir, H, Mo, M L, Rolfsson, O, Stobbe, M D, Thorleifsson, S G, Agren, R, Bölling, C, Bordel, S, Chavali, A K, Dobson, P, Dunn, W B, Endler, L, Hala, D, Hucka, M, Hull, D, Jameson, D, Jamshidi, N, Jonsson, J J, Juty, N, Keating, S, Nookaew, I, Le Novère, N, Malys, N, Mazein, A, Papin, J A, Price, N D, Selkov, E, Sigurdsson, M I, Simeonidis, E, Sonnenschein, N, Smallbone, K, Sorokin, A, Van Beek, J H G M, Weichart, D, Goryanin, I, Nielsen, J, Westerhoff, H V, Kell, D B, Mendes, P & Palsson, B O 2013, ' A community-driven global reconstruction of human metabolism ', Nature biotechnology, vol. 31, no. 5, pp. 419-427 . https://doi.org/10.1038/nbt.2488, https://doi.org/10.1038/nbt.2488
Thiele, I, Swainston, N, Fleming, R M T, Hoppe, A, Sahoo, S, Aurich, M K, Haraldsdottir, H, Mo, M L, Rolfsson, O, Stobbe, M D, Thorleifsson, S G, Agren, R, Bölling, C, Bordel, S, Chavali, A K, Dobson, P, Dunn, W B, Endler, L, Hala, D, Hucka, M, Hull, D, Jameson, D, Jamshidi, N, Jonsson, J J, Juty, N, Keating, S, Nookaew, I, Le Novère, N, Malys, N, Mazein, A, Papin, J A, Price, N D, Selkov, E, Sigurdsson, M I, Simeonidis, E, Sonnenschein, N, Smallbone, K, Sorokin, A, Van Beek, J H G M, Weichart, D, Goryanin, I, Nielsen, J, Westerhoff, H V, Kell, D B, Mendes, P & Palsson, B O 2013, ' A community-driven global reconstruction of human metabolism ' Nature biotechnology, vol. 31, no. 5, pp. 419-425 . https://doi.org/10.1038/nbt.2488
Nature Biotechnology, 31(5), 419-425. Nature Publishing Group
Nature biotechnology, 31(5), 419-425. Nature Publishing Group

To access publisher's full text version of this article click on the hyperlink at the bottom of the page Multiple models of human metabolism have been reconstructed, but each represents only a subset of our knowledge. Here we describe Recon 2, a comm

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https://doi.org/10.1038/nbt.2488

ChEBI – an Open-access Chemistry Resource for the Life Sciences:*Facilities for On-line Submission and Curation

Autor: Marcus Ennis, Nico Adams, Adriano Dekker, Paula de Matos, Janna Hastings, Kenneth Haug, Duncan Hull, Zara Josephs, Gareth Owen, Steve Turner, Christoph Steinbeck

Publikováno v: Nature Precedings.

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::5517c9c445f183c2b55032dbc81b08b1
https://doi.org/10.1038/npre.2010.5089

Further developments towards a genome-scale metabolic model of yeast

Autor: Ross D. King, Marie Brown, Evangelos Simeonidis, Paul R. Fisher, Robert Stevens, Paul D. Dobson, Pedro Mendes, Douglas B. Kell, Stephen G. Oliver, Daniel Jameson, Pınar Pir, Kieran Smallbone, Olusegun Oshota, Chuan-Zhen Lu, Neil Swainston, Duncan Hull, Natalie J. Stanford, Warwick B. Dunn, Karin Lanthaler

Publikováno v: BMC Systems Biology
Dobson, P D, Smallbone, K, Jameson, D, Simeonidis, E, Lanthaler, K, Pir, P, Lu, C, Swainston, N, Dunn, W B, Fisher, P, Hull, D, Brown, M, Oshota, O, Stanford, N J, Kell, D B, King, R D, Oliver, S G, Stevens, R D & Mendes, P 2010, ' Further developments towards a genome-scale metabolic model of yeast ', BMC Systems Biology, vol. 4, 145 . https://doi.org/10.1186/1752-0509-4-145, https://doi.org/10.1186/1752-0509-4-145
BMC Systems Biology; Vol 4
BMC Systems Biology, Vol 4, Iss 1, p 145 (2010)

Background To date, several genome-scale network reconstructions have been used to describe the metabolism of the yeast Saccharomyces cerevisiae, each differing in scope and content. The recent community-driven reconstruction, while rigorously eviden

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5689d0c69b03c40ccc32e2605ab1abba
https://pubmed.ncbi.nlm.nih.gov/21029416