Sixth Annual BCM Hackathon on Structural Variation and Pangenomics

<ns3:p>Background Structural variants (SVs) and metagenomics remain challenging areas in genomics, requiring new tools and collaborative solutions. Hackathons provide a rapid, team-based approach to prototyping and innovation. Methods In August 2024, 48 scientists from six continents convened at Baylor College of Medicine for the Sixth Structural Variant Codeathon. Participants worked in interdisciplinary teams over three days, using public datasets and cloud-based infrastructure to design and implement computational tools. Results Eight projects were developed, addressing topics such as tandem repeat annotation, structural variant discovery, benchmarking, pangenome visualization, and machine learning applications. Each project produced open-source software, with repositories openly available on GitHub and archived on Zenodo. Conclusions The hackathon fostered global collaboration and generated reproducible, community-driven tools. These outputs provide new resources for structural variation and metagenomics research and demonstrate the effectiveness of hackathons in advancing genomic science.</ns3:p>

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Publication Details

Journal
F1000Research
Published
2025-11-07
DOI
https://doi.org/10.12688/f1000research.170665.1
Citations
1
Primary Topic
Biomedical and Engineering Education
Type
article
Field-Weighted Citation Impact
0.67

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article

Sixth Annual BCM Hackathon on Structural Variation and Pangenomics

Jędrzej Kubica, Sina Majidian, Meghana Ram, Callum MacPhillamy et al.
1 citations
F1000Research
Biomedical and Engineering Education
0.67
article

Sixth Annual BCM Hackathon on Structural Variation and Pangenomics

Jędrzej Kubica, Sina Majidian, Meghana Ram, Callum MacPhillamy, Mauricio Moldes, Farhang Jaryani, Michael Nute, Rajarshi Mondal, Jen‐Yu Wang, Saket Kumar, Siyuan Cheng, Fritz Joachim Sedlazeck, Iva Kotásková, Rosário Santos, Rupesh K. Kesharwani, Sam Stroupe, Abraham Moller, Moustafa Shokrof, Francesco Andreace, Philippe Sanio, Todd J. Treangen, Ümran Yaman, Kristen Curry, Christian Brueffer, Jonah N. Cullen, Tina Han, Ben Busby, Nha Van Huynh, Xinchang Zheng, Daniel Paiva Agustinho, Natali Gulbahce, Minal Jamsandekar, Ryan Doughty, Adam C. English, Michal Izydorczyk, Shaghayegh Beheshti, Divya Kalra, Neda Ghohabi Esfahani, Emrah Kacar, Abolhassan Bahari, Bishnu Adhikar, Arthur Shem Kasambula, Eleni Mourouzidou, Dmitrii Olisov, Anika Pallapothu, Sarah Fross, Marcus Chan Hua Rui, Michael Olufemi, Narges SangaraniPour, Gobikrishnan Subramaniam, Pankhuri Wanjari, Farha zain, Aanuoluwa Adekoya, Oluwaseun Akinsulire
article en
1 citations

Abstract

<ns3:p>Background Structural variants (SVs) and metagenomics remain challenging areas in genomics, requiring new tools and collaborative solutions. Hackathons provide a rapid, team-based approach to prototyping and innovation. Methods In August 2024, 48 scientists from six continents convened at Baylor College of Medicine for the Sixth Structural Variant Codeathon. Participants worked in interdisciplinary teams over three days, using public datasets and cloud-based infrastructure to design and implement computational tools. Results Eight projects were developed, addressing topics such as tandem repeat annotation, structural variant discovery, benchmarking, pangenome visualization, and machine learning applications. Each project produced open-source software, with repositories openly available on GitHub and archived on Zenodo. Conclusions The hackathon fostered global collaboration and generated reproducible, community-driven tools. These outputs provide new resources for structural variation and metagenomics research and demonstrate the effectiveness of hackathons in advancing genomic science.</ns3:p>

F1000ResearchVol. 14
Ain Shams University (EG), University of the Philippines Los Baños (PH), Louisiana State University (US), Queen's University Belfast (GB), Northeastern University (US), Centre National de la Recherche Scientifique (FR), National Institutes of Health (US), University of Minnesota (US), University of Massachusetts Lowell (US), University of Crete (GR), Johns Hopkins University (US), Institut Pasteur (FR), University of Alabama (US), Pondicherry University (IN), Baylor College of Medicine (US), Lund University (SE), University of California, Irvine (US), Université Paris Cité (FR), Trinity College Dublin (IE), Johns Hopkins Medicine (US), Knoxville College (US), Defence Science and Technology Agency (SG), University of Alabama at Birmingham (US), University of Chicago (US), Ministry of Health (UG), Kennedy Center (DK), University Hospital St. Marina (BG), Pediatric Nephrology of Alabama (US), Quantitative BioSciences (US), High Institute for Education and Research in Transfusion Medicine (IR), Nova Management (United States) (US), Twist Bioscience (United States) (US), UK Dementia Research Institute (GB), DNAnexus (United States) (US), Centre for Genomic Regulation (ES), Texas Children's Hospital (US), Children's Cancer Center (US), Oxford Nanopore Technologies (United Kingdom) (GB), Baylor Genetics (US), Data Management (Italy) (IT), University of Warsaw (PL), The University of Adelaide (AU), Shahid Beheshti University of Medical Sciences (IR), Rice University (US), University of Tennessee at Knoxville (US), Université Grenoble Alpes (FR), Texas A&M University (US), Icahn School of Medicine at Mount Sinai (US)
Cancer Prevention and Research Institute of Texas, Rice University, Agence Nationale de la Recherche, National Institutes of Health, National Human Genome Research Institute
Openalex Percentile: Top 25%
Biomedical and Engineering Education
0.67
DOIOpen Access PDFOpenAlex
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