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1 -20 of 27 ARTICLES
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Featured Article
https://doi.org/10.12688/f1000research.12989.2
Research Article metrics
Revised
Funding knowledgebases: Towards a sustainable funding model for the UniProt use case [version 2; referees: 3 approved]
Chiara Gabella, Christine Durinx, Ron Appel
Referees Helen Berman and John Westbrook; Eva Huala and Tanya Z. Berardini; Judith A. Blake
  • Funder
  • ELIXIR
PUBLISHED 22 Mar 2018
https://doi.org/10.12688/f1000research.15708.1
Software Tool Article metrics
Providing gene-to-variant and variant-to-gene database identifier mappings to use with BridgeDb mapping services. [version 1; referees: 1 approved, 1 not approved]
Friederike Ehrhart, Jonathan Melius, Elisa Cirillo, Martina Kutmon, Egon L. Willighagen, Susan L. Coort, Leopold M.G. Curfs, Chris T. Evelo
Referees Patrice Godard; Osman Ugur Sezerman
  • Funder
  • ELIXIR
PUBLISHED 03 Sep 2018
https://doi.org/10.12688/f1000research.15161.1
Method Article metrics
Common ELIXIR Service for Researcher Authentication and Authorisation [version 1; referees: 3 approved, 1 approved with reservations]
Mikael Linden, Michal Prochazka, Ilkka Lappalainen, Dominik Bucik, Pavel Vyskocil, Martin Kuba, Sami Silén, Peter Belmann, Alexander Sczyrba, Steven Newhouse, Ludek Matyska, Tommi Nyrönen
Referees Bengt Persson; Dixie Baker; Nicolas Liampotis; Marcus Hardt
  • Funders
  • Academy of Finland
  • ELIXIR
  • Horizon 2020
PUBLISHED 06 Aug 2018
https://doi.org/10.12688/f1000research.15119.1
Software Tool Article metrics
Norwegian e-Infrastructure for Life Sciences (NeLS) [version 1; referees: 2 approved]
Kidane M. Tekle, Sveinung Gundersen, Kjetil Klepper, Lars Ailo Bongo, Inge Alexander Raknes, Xiaxi Li, Wei Zhang, Christian Andreetta, Teshome Dagne Mulugeta, Matúš Kalaš, Morten B. Rye, Erik Hjerde, Jeevan Karloss Antony Samy, Ghislain Fornous, Abdulrahman Azab, Dag Inge Våge, Eivind Hovig, Nils Peder Willassen, Finn Drabløs, Ståle Nygård, Kjell Petersen, Inge Jonassen
Referees Olivier Collin; Wolfgang Mueller
  • Funders
  • Norges Forskningsråd
  • NordForsk
PUBLISHED 29 Jun 2018
https://doi.org/10.12688/f1000research.14613.1
Software Tool Article metrics
CyTargetLinker app update: A flexible solution for network extension in Cytoscape [version 1; referees: 1 approved, 1 not approved]
Martina Kutmon, Friederike Ehrhart, Egon L. Willighagen, Chris T. Evelo, Susan L. Coort
Referees Alex Gutteridge; John H. Morris
  • Funders
  • ELIXIR
  • Dutch Province of Limburg
PUBLISHED 14 Jun 2018
https://doi.org/10.12688/f1000research.15140.1
Opinion Article metrics
Recommendations for the packaging and containerizing of bioinformatics software [version 1; referees: 2 approved with reservations]
Bjorn Gruening, Olivier Sallou, Pablo Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes Röst, Timo Sachsenberg, Brian O'Connor, Fábio Madeira, Victoria Dominguez Del Angel, Michael R. Crusoe, Susheel Varma, Daniel Blankenberg, Rafael C. Jimenez, BioContainers Community, Yasset Perez-Riverol
Referees Ka Yee Yeung and Daniel Kristiyanto; Monther Alhamdoosh
  • Funder
  • Horizon 2020
PUBLISHED 14 Jun 2018
https://doi.org/10.12688/f1000research.13256.2
Method Article metrics
Revised
META-pipe Authorization service [version 2; referees: 2 approved]
Inge Alexander Raknes, Lars Ailo Bongo
Referees Mikael Linden; Frank Oliver Glöckner
  • Funders
  • Norges Forskningsråd
  • Horizon 2020 Framework Programme
PUBLISHED 01 Jun 2018
https://doi.org/10.12688/f1000research.13598.1
Opinion Article metrics
Ten steps to get started in Genome Assembly and Annotation [version 1; referees: 2 approved]
Victoria Dominguez Del Angel, Erik Hjerde, Lieven Sterck, Salvadors Capella-Gutierrez, Cederic Notredame F1000Prime Faculty Member
, Olga Vinnere Pettersson, Joelle Amselem, Laurent Bouri, Stephanie Bocs, Christophe Klopp, Jean-Francois Gibrat, Anna Vlasova, Brane L. Leskosek, Lucile Soler, Mahesh Binzer-Panchal, Henrik Lantz
Referees Bruno Contreras-Moreira; Dave Clements
  • Funder
  • Horizon 2020
PUBLISHED 05 Feb 2018
https://doi.org/10.12688/f1000research.13204.2
Method Article metrics
Revised
META-pipe cloud setup and execution [version 2; referees: 1 approved, 1 approved with reservations]
Aleksandr Agafonov, Kimmo Mattila, Cuong Duong Tuan, Lars Tiede, Inge Alexander Raknes, Lars Ailo Bongo
Referees Olivier Collin; Kang Ning
  • Funders
  • Norges Forskningsråd
  • UiT The Arctic University of Norway
  • EGI-Engage
  • Horizon 2020
PUBLISHED 18 Jan 2018
https://doi.org/10.12688/f1000research.12974.1
Software Tool Article metrics
Using bio.tools to generate and annotate workbench tool descriptions [version 1; referees: 4 approved]
Kenzo-Hugo Hillion, Ivan Kuzmin, Anton Khodak, Eric Rasche, Michael Crusoe, Hedi Peterson, Jon Ison, Hervé Ménager
Referees Michael L. Heuer; Christopher J. Fields; Manuel Corpas F1000Prime Faculty Member
; Brian O'Connor
  • Funder
  • Horizon 2020
PUBLISHED 30 Nov 2017
https://doi.org/10.12688/f1000research.12342.2
Opinion Article metrics
Revised
The future of metabolomics in ELIXIR [version 2; referees: 3 approved]
Merlijn van Rijswijk, Charlie Beirnaert, Christophe Caron, Marta Cascante, Victoria Dominguez, Warwick B. Dunn, Timothy M. D. Ebbels, Franck Giacomoni, Alejandra Gonzalez-Beltran, Thomas Hankemeier, Kenneth Haug, Jose L. Izquierdo-Garcia, Rafael C. Jimenez, Fabien Jourdan, Namrata Kale, Maria I. Klapa, Oliver Kohlbacher, Kairi Koort, Kim Kultima, Gildas Le Corguillé, Pablo Moreno, Nicholas K. Moschonas, Steffen Neumann, Claire O’Donovan, Martin Reczko, Philippe Rocca-Serra, Antonio Rosato F1000Prime Faculty Member
, Reza M. Salek, Susanna-Assunta Sansone, Venkata Satagopam, Daniel Schober, Ruth Shimmo, Rachel A. Spicer, Ola Spjuth, Etienne A. Thévenot, Mark R. Viant, Ralf J. M. Weber, Egon L. Willighagen, Gianluigi Zanetti, Christoph Steinbeck
Referees Charles F. Burant; Carl Brunius; Emmanuel Mikros
  • Funder
  • Horizon 2020 Framework Programme
PUBLISHED 30 Oct 2017
https://doi.org/10.12688/f1000research.12332.1
Opinion Article metrics
The ELIXIR-EXCELERATE Train-the-Trainer pilot programme: empower researchers to deliver high-quality training [version 1; referees: 2 approved]
Sarah L Morgan, Patricia M Palagi, Pedro L Fernandes, Eija Koperlainen, Jure Dimec, Diana Marek, Lee Larcombe, Gabriella Rustici, Teresa K Attwood, Allegra Via
Referees Jason J. Williams; Kim T. Gurwitz
  • Funder
  • ELIXIR-EXCELERATE
PUBLISHED 24 Aug 2017
https://doi.org/10.12688/f1000research.12168.1
Method Article metrics
Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data [version 1; referees: 2 approved]
Chao Zhang, Jochem Bijlard, Christine Staiger, Serena Scollen F1000Prime Faculty Member
, David van Enckevort, Youri Hoogstrate, Alexander Senf, Saskia Hiltemann, Susanna Repo, Wibo Pipping, Mariska Bierkens, Stefan Payralbe, Bas Stringer, Jaap Heringa, Andrew Stubbs, Luiz Olavo Bonino Da Silva Santos, Jeroen Belien, Ward Weistra, Rita Azevedo, Kees van Bochove, Gerrit Meijer, Jan-Willem Boiten, Jordi Rambla, Remond Fijneman, J. Dylan Spalding, Sanne Abeln
Referees Hervé Ménager; Gilbert S. Omenn
  • Funders
  • CTMM-TraIT
  • Horizon 2020
PUBLISHED 16 Aug 2017
https://doi.org/10.12688/f1000research.11718.1
Opinion Article metrics
Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action [version 1; referees: 3 approved]
Aleksandra Pawlik, Celia W.G. van Gelder, Aleksandra Nenadic, Patricia M. Palagi, Eija Korpelainen, Philip Lijnzaad, Diana Marek, Susanna-Assunta Sansone, John Hancock, Carole Goble F1000Research Advisory Board member
Referees Erin A. Becker; Anelda P. van der Walt and Juan Steyn; Laurent Gatto
  • Funders
  • Horizon 2020
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 03 Jul 2017
https://doi.org/10.12688/f1000research.11837.1
Opinion Article metrics
ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR [version 1; referees: 4 approved, 1 approved with reservations]
L. Larcombe, R. Hendricusdottir, T.K. Attwood, F. Bacall, N. Beard, L.J. Bellis, W.B. Dunn, J.M. Hancock, A. Nenadic, C. Orengo F1000Prime Section Head
, B. Overduin, S-A Sansone, M. Thurston, M.R. Viant, C.L. Winder, C.A. Goble F1000Research Advisory Board member
, C.P. Ponting, G. Rustici
Referees Michelle D. Brazas; Patricia M. Palagi; Celia W.G. van Gelder; Nicola J. Mulder F1000Research Advisory Board member
F1000Prime Faculty Member
; Manuel Corpas F1000Prime Faculty Member
  • Funders
  • Horizon 2020
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 21 Jun 2017
https://doi.org/10.12688/f1000research.11407.1
Opinion Article metrics
Four simple recommendations to encourage best practices in research software [version 1; referees: 3 approved]
Rafael C. Jiménez, Mateusz Kuzak, Monther Alhamdoosh, Michelle Barker, Bérénice Batut, Mikael Borg, Salvador Capella-Gutierrez, Neil Chue Hong, Martin Cook, Manuel Corpas F1000Prime Faculty Member
, Madison Flannery, Leyla Garcia, Josep Ll. Gelpí, Simon Gladman, Carole Goble F1000Research Advisory Board member
, Montserrat González Ferreiro, Alejandra Gonzalez-Beltran, Philippa C. Griffin, Björn Grüning, Jonas Hagberg, Petr Holub, Rob Hooft, Jon Ison, Daniel S. Katz, Brane Leskošek, Federico López Gómez, Luis J. Oliveira, David Mellor, Rowland Mosbergen, Nicola Mulder F1000Research Advisory Board member
F1000Prime Faculty Member
, Yasset Perez-Riverol, Robert Pergl, Horst Pichler, Bernard Pope, Ferran Sanz, Maria V. Schneider, Victoria Stodden, Radosław Suchecki, Radka Svobodová Vařeková, Harry-Anton Talvik, Ilian Todorov, Andrew Treloar, Sonika Tyagi, Maarten van Gompel, Daniel Vaughan, Allegra Via, Xiaochuan Wang, Nathan S. Watson-Haigh, Steve Crouch
Referees Roberto Di Cosmo; Greg (Gregory V.) Wilson; Stefanie Betz
  • Funders
  • ELIXIR-EXCELERATE
  • EMBL-ABR
  • Netherlands eScience Center
  • CORBEL
  • Software Sustainability Institute
PUBLISHED 13 Jun 2017
https://doi.org/10.12688/f1000research.11751.1
Opinion Article metrics
A community proposal to integrate proteomics activities in ELIXIR [version 1; referees: 2 approved]
Juan Antonio Vizcaíno, Mathias Walzer, Rafael C. Jiménez, Wout Bittremieux, David Bouyssié, Christine Carapito, Fernando Corrales, Myriam Ferro, Albert J.R. Heck, Peter Horvatovich, Martin Hubalek, Lydie Lane, Kris Laukens, Fredrik Levander, Frederique Lisacek, Petr Novak, Magnus Palmblad, Damiano Piovesan, Alfred Pühler, Veit Schwämmle, Dirk Valkenborg, Merlijn van Rijswijk, Jiri Vondrasek, Martin Eisenacher, Lennart Martens, Oliver Kohlbacher
Referees Felix Elortza; Chuming Chen
  • Funder
  • Horizon 2020
PUBLISHED 13 Jun 2017
https://doi.org/10.12688/f1000research.10473.2
Method Article metrics
Revised
An open and transparent process to select ELIXIR Node Services as implemented by ELIXIR-UK [version 2; referees: 2 approved, 1 approved with reservations]
John M. Hancock, Alf Game, Chris P. Ponting, Carole A. Goble F1000Research Advisory Board member
Referees Christine Durinx; Alfonso Valencia F1000Prime Head of Faculty
; Janet Kelso
  • Funders
  • Medical Research Council
  • Natural Environment Research Council
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 20 Mar 2017
https://doi.org/10.12688/f1000research.9656.2
Method Article metrics
Revised
Identifying ELIXIR Core Data Resources [version 2; referees: 2 approved]
Christine Durinx, Jo McEntyre, Ron Appel, Rolf Apweiler, Mary Barlow, Niklas Blomberg, Chuck Cook, Elisabeth Gasteiger, Jee-Hyub Kim, Rodrigo Lopez, Nicole Redaschi, Heinz Stockinger, Daniel Teixeira, Alfonso Valencia
Referees Helen Berman; Maryann E. Martone
PUBLISHED 09 Mar 2017
https://doi.org/10.12688/f1000research.10443.1
Method Article metrics
ELIXIR pilot action: Marine metagenomics – towards a domain specific set of sustainable services [version 1; referees: 1 approved, 2 approved with reservations]
Espen Mikal Robertsen, Hubert Denise, Alex Mitchell, Robert D. Finn, Lars Ailo Bongo, Nils Peder Willassen
Referees Marla I. Trindade and Leonardo van Zyl; Takashi Gojobori; Anders Blomberg
  • Funders
  • ELIXIR
  • EMBL-EBI
  • Universitetet i Tromsø
PUBLISHED 23 Jan 2017
1 -20 of 27 ARTICLES
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