Hackathons

Hackathons

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https://doi.org/10.12688/f1000research.156917.1
Case Study metrics
A libraries reproducibility hackathon: connecting students to University research and testing the longevity of published code
[version 1; peer review: 1 approved, 1 approved with reservations]
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
PUBLISHED 31 Oct 2024
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.138059.1
Method Article metrics
A tutorial hub for realising the potential of tools within the SPARC ecosystem
[version 1; peer review: 2 approved with reservations]
Niloofar Shahidi, Omkar Athavale, Yuda Munarko, Mathias Roesler, Kenneth Tran
Peer Reviewers Bhavesh Patel; Andrey Andreev
PUBLISHED 08 Jan 2024
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.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.75071.1
Software Tool Article metrics
SPARClink: an interactive tool to visualize the impact of the SPARC program
[version 1; peer review: 2 approved, 1 approved with reservations]
Sanjay Soundarajan, Sachira Kuruppu, Ashutosh Singh, Jongchan Kim, Monalisa Achalla
Peer Reviewers Tao Zeng; Karim Fouad and Abel Torres-Espin; Angela Pinot de Moira
PUBLISHED 31 Jan 2022
https://doi.org/10.12688/f1000research.73492.1
Software Tool Article metrics
KnowMore: an automated knowledge discovery tool for the FAIR SPARC datasets
[version 1; peer review: 2 approved with reservations]
Ryan Quey, Matthew A. Schiefer, Anmol Kiran, Bhavesh Patel
Peer Reviewers Thomas Donoghue; Ammar Ammar
PUBLISHED 09 Nov 2021
https://doi.org/10.12688/f1000research.73018.1
Software Tool Article metrics
AQUA: an Advanced QUery Architecture for the SPARC Portal
[version 1; peer review: 1 approved with reservations, 1 not approved]
Niloofar Shahidi, Xuanzhi Lin, Yuda Munarko, Laila Rasmy, Tram Ngo
Peer Reviewers Vijay Rajagopal; Maryann E. Martone
PUBLISHED 16 Sep 2021
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.26459.1
Software Tool Article metrics PEER REVIEW DISCONTINUED
Uncovering host-microbiome interactions in global systems with collaborative programming: a novel approach integrating social and data sciences
[version 1; peer review: 1 approved with reservations]
Jenna Oberstaller, Swamy Rakesh Adapa, Guy W. Dayhoff II, Justin Gibbons, Thomas E. Keller, Chang Li, Jean Lim, Minh Pham, Anujit Sarkar, Ravi Sharma, Agaz H. Wani, Andrea Vianello, Linh M. Duong, Chenggi Wang, Celine Grace F. Atkinson, Madeleine Barrow, Nathan W. Van Bibber, Jan Dahrendorff, David A. E. Dean, Omkar Dokur, Gloria C. Ferreira, Mitchell Hastings, Gregory S. Herbert, Khandaker Tasnim Huq, Youngchul Kim, Xiangyun Liao, XiaoMing Liu, Fahad Mansuri, Lynn B. Martin, Elizabeth M. Miller, Ojas Natarajan, Jinyong Pang, Francesca Prieto, Peter W. Radulovic, Vyoma Sheth, Matthew Sumpter, Desirae Sutherland, Nisha Vijayakumar, Rays H. Y. Jiang
Peer Reviewers Sucheta Tripathy
  • Funder
  • University of South Florida
PUBLISHED 17 Dec 2020
https://doi.org/10.12688/f1000research.23773.1
Software Tool Article metrics
Methods developed during the first National Center for Biotechnology Information Structural Variation Codeathon at Baylor College of Medicine
[version 1; peer review: 1 approved, 1 approved with reservations]
Medhat Mahmoud, Alejandro Rafael Gener, Michael M. Khayat, Adam C. English, Advait Balaji, Anbo Zhou, Andreas Hehn, Arkarachai Fungtammasan, Brianna Sierra Chrisman, Chen-Shan Chin, Chiao-Feng Lin, Chun-Hsuan Lo, Chunxiao Liao, Claudia M. B. Carvalho, Colin Diesh, David E. Symer, Divya Kalra, Dreycey Albin, Elbay Aliyev, Eric T. Dawson, Eric Venner, Fernanda Foertter, Gigon Bae, Haowei Du, Joyjit Daw, Junzhou Wang, Keiko Akagi, Lon Phan, Michael Jochum, Mohammadamin Edrisi, Nirav N. Shah, Qi Wang, Robert Fullem, Rong Zheng, Sara E Kalla, Shakuntala Mitra, Todd J. Treangen, Vaidhyanathan Mahaganapathy, Venkat Sai Malladi, Vipin K Menon, Yilei Fu, Yongze Yin, Yuanqing Feng, Tim Hefferon, Fritz J. Sedlazeck, Ben Busby
Peer Reviewers Istvan Albert; Yuriy Orlov
  • Funders
  • National Institute of Neurological Disorders and Stroke
  • Eunice Kennedy Shriver National Institute of Child Health and Human Development
  • U.S. National Library of Medicine
  • National Cancer Institute
  • National Institutes of Health
  • National Institute of General Medical Sciences
PUBLISHED 16 Sep 2020
https://doi.org/10.12688/f1000research.23180.2
Software Tool Article metrics
Revised
Jupyter notebook-based tools for building structured datasets from the Sequence Read Archive
[version 2; peer review: 2 approved]
Matthew N. Bernstein, Ariella Gladstein, Khun Zaw Latt, Emily Clough, Ben Busby, Allissa Dillman
Peer Reviewers Zichen Wang; Shannon Ellis
  • Funders
  • National Library of Medicine, National Institutes of Health
  • Chan Zuckerberg Initiative
LATEST VERSION PUBLISHED 04 Aug 2020
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.18238.1
Opinion Article metrics
BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services
[version 1; peer review: 2 approved with reservations]
Toshiaki Katayama, Shuichi Kawashima, Gos Micklem, Shin Kawano, Jin-Dong Kim, Simon Kocbek, Shinobu Okamoto, Yue Wang, Hongyan Wu, Atsuko Yamaguchi, Yasunori Yamamoto, Erick Antezana, Kiyoko F. Aoki-Kinoshita, Kazuharu Arakawa, Masaki Banno, Joachim Baran, Jerven T. Bolleman, Raoul J. P. Bonnal, Hidemasa Bono, Jesualdo T. Fernández-Breis, Robert Buels, Matthew P. Campbell, Hirokazu Chiba, Peter J. A. Cock, Kevin B. Cohen, Michel Dumontier, Takatomo Fujisawa, Toyofumi Fujiwara, Leyla Garcia, Pascale Gaudet, Emi Hattori, Robert Hoehndorf, Kotone Itaya, Maori Ito, Daniel Jamieson, Simon Jupp, Nick Juty, Alex Kalderimis, Fumihiro Kato, Hideya Kawaji, Takeshi Kawashima, Akira R. Kinjo, Yusuke Komiyama, Masaaki Kotera, Tatsuya Kushida, James Malone, Masaaki Matsubara, Satoshi Mizuno, Sayaka Mizutani, Hiroshi Mori, Yuki Moriya, Katsuhiko Murakami, Takeru Nakazato, Hiroyo Nishide, Yosuke Nishimura, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Hiromasa Ono, Yasset Perez-Riverol, Daisuke Shinmachi, Andrea Splendiani, Francesco Strozzi, Shinya Suzuki, Junichi Takehara, Mark Thompson, Toshiaki Tokimatsu, Ikuo Uchiyama, Karin Verspoor, Mark D. Wilkinson, Sarala Wimalaratne, Issaku Yamada, Nozomi Yamamoto, Masayuki Yarimizu, Shoko Kawamoto, Toshihisa Takagi
Peer Reviewers Todd J. Vision; João Moreira
  • Funder
  • National Bioscience Database Center, the Japan Science and Technology Agency (JST)
PUBLISHED 23 Sep 2019
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.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.15895.2
Software Tool Article metrics
Revised
NovoGraph: Human genome graph construction from multiple long-read de novo assemblies
[version 2; peer review: 2 approved]
Evan Biederstedt, Jeffrey C. Oliver, Nancy F. Hansen, Aarti Jajoo, Nathan Dunn, Andrew Olson, Ben Busby, Alexander T. Dilthey
Peer Reviewers Bjarni V. Halldorsson; Korbinian Schneeberger and Manish Goel
  • Funders
  • U.S. National Library of Medicine
  • Jürgen Manchot Stiftung
  • National Institutes of Health
  • National Human Genome Research Institute
LATEST VERSION PUBLISHED 10 Dec 2018
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.11389.2
Software Tool Article metrics
Revised
PubRunner: A light-weight framework for updating text mining results
[version 2; peer review: 1 approved, 2 approved with reservations]
Kishore R. Anekalla, J.P. Courneya, Nicolas Fiorini, Jake Lever, Michael Muchow, Ben Busby
Peer Reviewers Jin-Dong Kim; Fabio Rinaldi; Julien Gobeill
  • Funders
  • National Institutes of Health
  • Vanier Canada
LATEST VERSION PUBLISHED 13 Oct 2017
1-20 of 29 ARTICLES
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