Channeling Community Contributions to Scientific Software: A Sprint Experience

by Michael R Crusoe, C. Titus Brown
Published 2016-07-01

Walking the Talk: Adopting and Adapting Sustainable Scientific Software Development processes in a Small Biology Lab

by Michael R. Crusoe, C. Titus Brown
Published 2016-11-01

Implementation of FAIR Practices in Computational Metabolomics Workflows—A Case Study

by Mahnoor Zulfiqar, Michael R. Crusoe, Birgitta König-Ries, Christoph Steinbeck, Kristian Peters, Luiz Gadelha
Published 2024-02-01

Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis

by Steffen Möller, Stuart W. Prescott, Lars Wirzenius, Petter Reinholdtsen, Brad Chapman, Pjotr Prins, Stian Soiland-Reyes, Fabian Klötzl, Andrea Bagnacani, Matúš Kalaš, Andreas Tille, Michael R. Crusoe
Published 2017-11-01

Recommendations for the packaging and containerizing of bioinformatics software [version 2; peer review: 2 approved, 1 approved with reservations]

by 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
Published 2019-03-01

Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience [version 2; peer review: 2 approved, 1 approved with reservations]

by Azza E. Ahmed, Phelelani T. Mpangase, Sumir Panji, Shakuntala Baichoo, Yassine Souilmi, Faisal M. Fadlelmola, Mustafa Alghali, Shaun Aron, Hocine Bendou, Eugene De Beste, Mamana Mbiyavanga, Oussema Souiai, Long Yi, Jennie Zermeno, Don Armstrong, Brian D. O'Connor, Liudmila Sergeevna Mainzer, Michael R. Crusoe, Ayton Meintjes, Peter Van Heusden, Gerrit Botha, Fourie Joubert, C. Victor Jongeneel, Scott Hazelhurst, Nicola Mulder
Published 2019-08-01

Perspectives on automated composition of workflows in the life sciences [version 1; peer review: 2 approved]

by Anna-Lena Lamprecht, Magnus Palmblad, Jon Ison, Veit Schwämmle, Mohammad Sadnan Al Manir, Ilkay Altintas, Christopher J. O. Baker, Ammar Ben Hadj Amor, Salvador Capella-Gutierrez, Paulos Charonyktakis, Michael R. Crusoe, Yolanda Gil, Carole Goble, Timothy J. Griffin, Paul Groth, Hans Ienasescu, Pratik Jagtap, Matúš Kalaš, Vedran Kasalica, Alireza Khanteymoori, Tobias Kuhn, Hailiang Mei, Hervé Ménager, Steffen Möller, Robin A. Richardson, Vincent Robert, Stian Soiland-Reyes, Robert Stevens, Szoke Szaniszlo, Suzan Verberne, Aswin Verhoeven, Katherine Wolstencroft
Published 2021-09-01

Enabling precision medicine via standard communication of HTS provenance, analysis, and results.

by Gil Alterovitz, Dennis Dean, Carole Goble, Michael R Crusoe, Stian Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Anjan Purkayastha, Charles H King, Dan Taylor, Elaine Johanson, Elaine E Thompson, Eric Donaldson, Hiroki Morizono, Hsinyi Tsang, Jeet K Vora, Jeremy Goecks, Jianchao Yao, Jonas S Almeida, Jonathon Keeney, KanakaDurga Addepalli, Konstantinos Krampis, Krista M Smith, Lydia Guo, Mark Walderhaug, Marco Schito, Matthew Ezewudo, Nuria Guimera, Paul Walsh, Robel Kahsay, Srikanth Gottipati, Timothy C Rodwell, Toby Bloom, Yuching Lai, Vahan Simonyan, Raja Mazumder
Published 2018-12-01

The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations]

by Michael R. Crusoe, Hussien F. Alameldin, Sherine Awad, Elmar Boucher, Adam Caldwell, Reed Cartwright, Amanda Charbonneau, Bede Constantinides, Greg Edvenson, Scott Fay, Jacob Fenton, Thomas Fenzl, Jordan Fish, Leonor Garcia-Gutierrez, Phillip Garland, Jonathan Gluck, Iván González, Sarah Guermond, Jiarong Guo, Aditi Gupta, Joshua R. Herr, Adina Howe, Alex Hyer, Andreas Härpfer, Luiz Irber, Rhys Kidd, David Lin, Justin Lippi, Tamer Mansour, Pamela McA'Nulty, Eric McDonald, Jessica Mizzi, Kevin D. Murray, Joshua R. Nahum, Kaben Nanlohy, Alexander Johan Nederbragt, Humberto Ortiz-Zuazaga, Jeramia Ory, Jason Pell, Charles Pepe-Ranney, Zachary N. Russ, Erich Schwarz, Camille Scott, Josiah Seaman, Scott Sievert, Jared Simpson, Connor T. Skennerton, James Spencer, Ramakrishnan Srinivasan, Daniel Standage, James A. Stapleton, Susan R. Steinman, Joe Stein, Benjamin Taylor, Will Trimble, Heather L. Wiencko, Michael Wright, Brian Wyss, Qingpeng Zhang, en zyme, C. Titus Brown
Published 2015-09-01