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https://doi.org/10.12688/f1000research.8382.2
Editorial metrics NOT PEER REVIEWED
Revised
Closing gaps between open software and public data in a hackathon setting: User-centered software prototyping
[version 2; peer review: not peer reviewed]
Ben Busby, Matthew Lesko, August 2015 and January 2016 Hackathon participants, Lisa Federer
LATEST VERSION PUBLISHED 09 May 2016
https://doi.org/10.12688/f1000research.11429.1
Research Article metrics
Community and Code: Nine Lessons from Nine NESCent Hackathons
[version 1; peer review: 1 approved, 1 approved with reservations]
Arlin Stoltzfus, Michael Rosenberg, Hilmar Lapp, Aidan Budd, Karen Cranston, Enrico Pontelli, Shann Oliver, Rutger A. Vos
Peer Reviewers Eva Amsen; Cameron Neylon
  • Funder
  • National Evolutionary Synthesis Center
PUBLISHED 06 Jun 2017
https://doi.org/10.12688/f1000research.16959.1
Opinion Article metrics
Hackathon-driven tutorial development
[version 1; peer review: 1 approved, 1 approved with reservations]
Bruno M. Grande, Arjun Baghela, Anna Cavalla, Florian Privé, Peter Zhang, Yisong Zhen
Peer Reviewers Ming Tang; Brad A. Chapman
PUBLISHED 24 Dec 2018
https://doi.org/10.12688/f1000research.156917.2
Case Study metrics
Revised
A libraries reproducibility hackathon: connecting students to university research and testing the longevity of published code
[version 2; peer review: 3 approved]
Chasz Griego, Kristen Scotti, Elizabeth Terveen, Joseph Chan, Daisy Sheng, Alfredo González-Espinoza, Christopher Warren
Peer Reviewers Benjamin Antunes; Teresa Gomez-Diaz and Tomas Recio; Stephen J Eglen
LATEST VERSION PUBLISHED 09 Sep 2025
https://doi.org/10.12688/f1000research.10964.2
Opinion Article metrics
Revised
hackseq: Catalyzing collaboration between biological and computational scientists via hackathon
[version 2; peer review: 2 approved]
hackseq Organizing Committee 2016
Peer Reviewers Kate L. Hertweck; Jiarong Guo
LATEST VERSION PUBLISHED 10 Apr 2017
https://doi.org/10.12688/f1000research.9762.1
Software Tool Article metrics
Viewing RNA-seq data on the entire human genome
[version 1; peer review: 3 approved]
Eric M. Weitz, Lorena Pantano, Jingzhi Zhu, Bennett Upton, Ben Busby
Peer Reviewers Chase A. Miller; Christopher J. Fields; Philip Ewels
  • Funder
  • National Institutes of Health
PUBLISHED 28 Apr 2017
https://doi.org/10.12688/f1000research.8288.1
Software Tool Article metrics
MetaNetVar: Pipeline for applying network analysis tools for genomic variants analysis
[version 1; peer review: 3 approved]
Eric Moyer, Megan Hagenauer, Matthew Lesko, Felix Francis, Oscar Rodriguez, Vijayaraj Nagarajan, Vojtech Huser, Ben Busby
Peer Reviewers John Didion; Sahar Al Seesi; Tomasz Adamusiak
PUBLISHED 13 Apr 2016
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; peer review: 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
Peer Reviewers 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.26452.1
Software Tool Article metrics
Lessons learned in virulence factor identification and data management from a hackathon on microbial virulence
[version 1; peer review: 1 approved, 1 approved with reservations]
Brett E. Pickett, Ryan Connor, Tamiru Berhanu-Denka, Sherry Bhalla, Vyacheslav Brover, Michael James Chambers, Kumardeep Chaudhary, Ousmane H. Cissé, Allissa Dillman, Moamen M. Elmassry, Michael Feldgarden, Eric Holloway, Xin Huang, William Klimke, Catarina Inês Mendes, S. Elizabeth Norred, Jonathan Parkinson, Samantha Sevilla, Monica Garcia Solache, Defne Surujon, Udana Torian, Vadim Zalunin, Ben Busby
Peer Reviewers Rick Stevens and James Davis; Kevin Tyler
  • Funders
  • Fundação para a Ciência e a Tecnologia
  • Scientific and Technological Research Council of Turkey
  • Intramural Research Program of the National Library of Medicine
PUBLISHED 09 Feb 2022
https://doi.org/10.12688/f1000research.8684.1
Software Tool Article metrics
A cloud-based learning environment for comparing RNA-seq aligners
[version 1; peer review: 2 approved with reservations]
Elizabeth Baskin, Peter DeFord, Allison F. Dennis, Ian Misner, Frederick J. Tan, Ben Busby
Peer Reviewers Malachi Griffith; Timothy I. Shaw
PUBLISHED 13 May 2016
https://doi.org/10.12688/f1000research.19140.1
Software Tool Article metrics
Iron Hack - A symposium/hackathon focused on porphyrias, Friedreich’s ataxia, and other rare iron-related diseases
[version 1; peer review: 2 approved]
Gloria C. Ferreira, Jenna Oberstaller, Renée Fonseca, Thomas E. Keller, Swamy Rakesh Adapa, Justin Gibbons, Chengqi Wang, Xiaoming Liu, Chang Li, Minh Pham, Guy W. Dayhoff II, Linh M. Duong, Luis Tañón Reyes, Luciano Enrique Laratelli, Douglas Franz, Segun Fatumo, ATM Golam Bari, Audrey Freischel, Lindsey Fiedler, Omkar Dokur, Krishna Sharma, Deborah Cragun, Ben Busby, Rays H.Y. Jiang
Peer Reviewers Karl E Anderson; Robert J. Desnick
  • Funders
  • American Cancer Society
  • WHC
  • U.S. National Library of Medicine
  • University of South Florida
  • National Science Foundation
PUBLISHED 19 Jul 2019
https://doi.org/10.12688/f1000research.110194.1
Software Tool Article metrics
The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms
[version 1; peer review: 1 approved, 3 approved with reservations]
Kimberly Walker, Divya Kalra, Rebecca Lowdon, Guangyi Chen, David Molik, Daniela C. Soto, Fawaz Dabbaghie, Ahmad Al Khleifat, Medhat Mahmoud, Luis F Paulin, Muhammad Sohail Raza, Susanne P. Pfeifer, Daniel Paiva Agustinho, Elbay Aliyev, Pavel Avdeyev, Enrico R. Barrozo, Sairam Behera, Kimberley Billingsley, Li Chuin Chong, Deepak Choubey, Wouter De Coster, Yilei Fu, Alejandro R. Gener, Timothy Hefferon, David Morgan Henke, Wolfram Höps, Anastasia Illarionova, Michael D. Jochum, Maria Jose, Rupesh K. Kesharwani, Sree Rohit Raj Kolora, Jędrzej Kubica, Priya Lakra, Damaris Lattimer, Chia-Sin Liew, Bai-Wei Lo, Chunhsuan Lo, Anneri Lötter, Sina Majidian, Suresh Kumar Mendem, Rajarshi Mondal, Hiroko Ohmiya, Nasrin Parvin, Carolina Peralta, Chi-Lam Poon, Ramanandan Prabhakaran, Marie Saitou, Aditi Sammi, Philippe Sanio, Nicolae Sapoval, Najeeb Syed, Todd Treangen, Gaojianyong Wang, Tiancheng Xu, Jianzhi Yang, Shangzhe Zhang, Weiyu Zhou, Fritz J Sedlazeck, Ben Busby
Peer Reviewers Rodolfo Aramayo; Nguyen Quoc Khanh Le; Pedro G. Ferreira; Quan Long
  • Funders
  • National Library of Medicine
  • Swiss National Science Foundation
  • USDA Agricultural Research Service HQ Research Associate program in Big Data
  • Centers for Disease Control and Prevention through the Association of Public Health Laboratories
  • ALS Association Milton Safenowitz Research
  • The Research Council of Norway
  • Large Facilities Office
  • China Scholarship Council PhD scholarship
  • NIHR Maudsley Biomedical Research Centre
  • The Motor Neurone Disease Association
  • FWO
PUBLISHED 16 May 2022
https://doi.org/10.12688/f1000research.148237.1
Software Tool Article metrics
The fifth international hackathon for developing computational cloud-based tools and resources for pan-structural variation and genomics
[version 1; peer review: 2 approved with reservations]
Sontosh K Deb, Divya Kalra, Jędrzej Kubica, Erik Stricker, Van Q. Truong, Qiandong Zeng, Christopher J. Fiscus, Daniel Paiva Agustinho, Adam Alexander, Marlon Arciniega-Sanchez, Lorianne Bosseau, Christian Brueffer, Astrid Canal, Joyjit Daw, David Enoma, Alison Diaz-Cuevas, Colin Diesh, Janet M. Doolittle-Hall, Luis Fernandez-Luna, Tina Han, Wolfram Höps, Peiming Peter Huang, Tony Huang, Michal Bogumil Izydorczyk, Farhang Jaryani, Rupesh K. Kesharwani, Shaheerah Khan, Sina Majidian, Ayan Malakar, Tania Girão Mangolini, Sejal Modha, Mauricio Moldes, Rajarshi Mondal, Abdullah Al Nahid, Chi-Lam Poon, Sagayamary Sagayaradj, Philippe Sanio, Tania Sepulveda-Morales, Muhammad Shahzaib, Muhammad Sohail Raza, Trinh Tat, Ishaan Thota, Umran Yaman, Jason Yeung, Qiyi Yu, Xinchang Zheng, Medhat Mahmoud, Fritz J. Sedlazeck, Ben Busby
Peer Reviewers German Demidov; Istvan Albert
  • Funder
  • NIH
PUBLISHED 27 Jun 2024
https://doi.org/10.12688/f1000research.6349.2
Opinion Article metrics
Update
agINFRA: a research data hub for agriculture, food and the environment
[version 2; peer review: 2 approved]
Andreas Drakos, Vassilis Protonotarios, Nikos Manouselis
Peer Reviewers George Adamides; Christopher Brewster
LATEST VERSION PUBLISHED 15 Jun 2015
https://doi.org/10.12688/f1000research.51477.2
Software Tool Article metrics
Revised
An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates
[version 2; peer review: 1 approved, 3 approved with reservations]
Ann M. Mc Cartney, Medhat Mahmoud, Michael Jochum, Daniel Paiva Agustinho, Barry Zorman, Ahmad Al Khleifat, Fawaz Dabbaghie, Rupesh K Kesharwani, Moritz Smolka, Moez Dawood, Dreycey Albin, Elbay Aliyev, Hakeem Almabrazi, Ahmed Arslan, Advait Balaji, Sairam Behera, Kimberley Billingsley, Daniel L Cameron, Joyjit Daw, Eric T. Dawson, Wouter De Coster, Haowei Du, Christopher Dunn, Rocio Esteban, Angad Jolly, Divya Kalra, Chunxiao Liao, Yunxi Liu, Tsung-Yu Lu, James M Havrilla, Michael M Khayat, Maximillian Marin, Jean Monlong, Stephen Price, Alejandro Rafael Gener, Jingwen Ren, Sagayamary Sagayaradj, Nicolae Sapoval, Claude Sinner, Daniela C. Soto, Arda Soylev, Arun Subramaniyan, Najeeb Syed, Neha Tadimeti, Pamella Tater, Pankaj Vats, Justin Vaughn, Kimberly Walker, Gaojianyong Wang, Qiandong Zeng, Shangzhe Zhang, Tingting Zhao, Bryce Kille, Evan Biederstedt, Mark Chaisson, Adam English, Zev Kronenberg, Todd J. Treangen, Timothy Hefferon, Chen-Shan Chin, Ben Busby, Fritz J Sedlazeck
Peer Reviewers Francois Sabot; Kamil S. Jaron; Ricardo Assunção Vialle; Loren L. Flynn
  • Funders
  • NIH/NICHD
  • C3.ai Digital Transformation Institute COVID-19 award
  • Intramural Research Program of the National Library of Medicine
  • NHMRC
  • Intramural Research Program of NHGRI
  • NIHR Maudsley Biomedical Research Centre
  • NIH
  • The Motor Neurone Disease Association
  • FWO
LATEST VERSION PUBLISHED 03 Sep 2021
https://doi.org/10.12688/f1000research.19630.2
Software Tool Article metrics
Revised
A strategy for building and using a human reference pangenome
[version 2; peer review: 2 approved]
Bastien Llamas, Giuseppe Narzisi, Valerie Schneider, Peter A. Audano, Evan Biederstedt, Lon Blauvelt, Peter Bradbury, Xian Chang, Chen-Shan Chin, Arkarachai Fungtammasan, Wayne E. Clarke, Alan Cleary, Jana Ebler, Jordan Eizenga, Jonas A. Sibbesen, Charles J. Markello, Erik Garrison, Shilpa Garg, Glenn Hickey, Gerard R. Lazo, Michael F. Lin, Medhat Mahmoud, Tobias Marschall, Ilia Minkin, Jean Monlong, Rajeeva L. Musunuri, Sagayamary Sagayaradj, Adam M. Novak, Mikko Rautiainen, Allison Regier, Fritz J. Sedlazeck, Jouni Siren, Yassine Souilmi, Justin Wagner, Travis Wrightsman, Toshiyuki T. Yokoyama, Qiandong Zeng, Justin M. Zook, Benedict Paten, Ben Busby
Peer Reviewers Anna Kuosmanen; Robert A. Beagrie
  • Funders
  • Simons Foundation
  • Carlsbergfondet
  • U.S. National Library of Medicine
  • W. M. Keck Foundation
  • National Institutes of Health
  • Australian Research Council
LATEST VERSION PUBLISHED 29 Jul 2021
https://doi.org/10.12688/f1000research.18236.1
Opinion Article metrics
BioHackathon 2015: Semantics of data for life sciences and reproducible research
[version 1; peer review: 2 approved]
Rutger A. Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano, Shuichi Kawashima, Jin-Dong Kim, Yuki Moriya, Toshiaki Tokimatsu, Atsuko Yamaguchi, Yasunori Yamamoto, Hongyan Wu, Peter Amstutz, Erick Antezana, Nobuyuki P. Aoki, Kazuharu Arakawa, Jerven T. Bolleman, Evan E. Bolton, Raoul J. P. Bonnal, Hidemasa Bono, Kees Burger, Hirokazu Chiba, Kevin B. Cohen, Eric W. Deutsch, Jesualdo T. Fernández-Breis, Gang Fu, Takatomo Fujisawa, Atsushi Fukushima, Alexander García, Naohisa Goto, Tudor Groza, Colin Hercus, Robert Hoehndorf, Kotone Itaya, Nick Juty, Takeshi Kawashima, Jee-Hyub Kim, Akira R. Kinjo, Masaaki Kotera, Kouji Kozaki, Sadahiro Kumagai, Tatsuya Kushida, Thomas Lütteke, Masaaki Matsubara, Joe Miyamoto, Attayeb Mohsen, Hiroshi Mori, Yuki Naito, Takeru Nakazato, Jeremy Nguyen-Xuan, Kozo Nishida, Naoki Nishida, Hiroyo Nishide, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Benedict Paten, Jean-Luc Perret, Philip Prathipati, Pjotr Prins, Núria Queralt-Rosinach, Daisuke Shinmachi, Shinya Suzuki, Tsuyosi Tabata, Terue Takatsuki, Kieron Taylor, Mark Thompson, Ikuo Uchiyama, Bruno Vieira, Chih-Hsuan Wei, Mark Wilkinson, Issaku Yamada, Ryota Yamanaka, Kazutoshi Yoshitake, Akiyasu C. Yoshizawa, Michel Dumontier, Kenjiro Kosaki, Toshihisa Takagi
Peer Reviewers Jeremy G. Frey; James P. Balhoff and Gaurav Vaidya
  • Funder
  • National Bioscience Database Center, the Japan Science and Technology Agency (JST)
PUBLISHED 24 Feb 2020
https://doi.org/10.12688/f1000research.12516.1
Software Tool Article metrics
Tools for annotation and comparison of structural variation
[version 1; peer review: 1 approved, 2 approved with reservations]
Fritz J. Sedlazeck, Andi Dhroso, Dale L. Bodian, Justin Paschall, Farrah Hermes, Justin M. Zook
Peer Reviewers Mitchell A. Bekritsky; Andrew Carroll; Aaron R. Quinlan
  • Funders
  • Inova Health System
  • National Institutes of Health
  • National Science Foundation
PUBLISHED 03 Oct 2017
https://doi.org/10.12688/f1000research.12781.1
Software Tool Article metrics
NastyBugs: A simple method for extracting antimicrobial resistance information from metagenomes
[version 1; peer review: 2 approved with reservations]
Hsinyi Tsang, Matthew Moss, Greg Fedewa, Sharif Farag, Daniel Quang, Alexey V. Rakov, Ben Busby
Peer Reviewers Torsten Seemann; Tom J. B. de Man
  • Funders
  • U.S. National Library of Medicine
  • National Cancer Institute
PUBLISHED 08 Nov 2017
https://doi.org/10.12688/f1000research.9837.1
Software Tool Article metrics
Extending TCGA queries to automatically identify analogous genomic data from dbGaP
[version 1; peer review: 2 approved, 1 approved with reservations]
Erin K. Wagner, Satyajeet Raje, Liz Amos, Jessica Kurata, Abhijit S. Badve, Yingquan Li, Ben Busby
Peer Reviewers Yussanne Ma and Victoria Trinh; Konstantinos Krampis; Tsung-Jung Wu
  • Funders
  • U.S. National Library of Medicine
  • Frances Berger Foundation Fellowship
  • Ramesh Kesanupalli Family
  • Beckman Research Institute, City of Hope
PUBLISHED 24 Mar 2017
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