BioCommons Publications

Some outputs from Australian BioCommons projects, events and presentations, including organisational documentation, project reports and research infrastructure roadmaps are self published and can be found in the Australian BioCommons document repository.

For metadata and training materials associated with our training events, please visit Australian BioCommons - Training Materials.

Peer reviewed publications from BioCommons team members:

  1. Al Bkhetan Z, Wang S. mgikit: demultiplexing toolkit for MGI fastq files. Bioinformatics. 2024 Sep;40(9):btae554.

  2. Goonasekera, N, Mahmoud, A, Suderman, K, Afgan, E. Galaxy Helm chart: a standardized method for deploying production Galaxy servers. Bioinformatics, 2024. btae486.

  3. Gareth Price (corresponding author) and the Galaxy community (including Australian contributors Olivier Allart, Madeline Bassetti, Catherine J Bromhead, Melissa L Burke, Patrick K Capon, Nuwan A Goonasekera, Ove Johan Ragnar Gustafsson, Christina Hall, Thomas W Harrop, Cameron J Hyde, Ross Lazarus, Justin Lee, Igor Makunin, Winnie Mok, Tiffanie M Nelson, Anna E Syme, Wai Cheng (Mike) Thang and Uwe Winter. The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update. Nucleic Acids Research, 2024 52(W1):W83-94.

  4. Brennan IG, Singhal S, Al Bkhetan Z. pipesnake: Generalized software for the assembly and analysis of phylogenomic datasets from conserved genomic loci. Bioinformatics, 2024 40(5):btae195.

  5. Williams JJ, Tractenberg RE, Batut B, Becker EA, Brown AM, Burke ML, Busby B, Cooch NK, Dillman AA, Donovan SS, Doyle MA, van Gelder CWG, Hall CR, Hertweck KL, Jordan KL, Jungck JR, Latour AR, Lindvall JM, Lloret-Llinares M, McDowell GS, Morris R, Mourad T, Nisselle A, Ordóñez P, Paladin L, Palagi PM, Sukhai MA, Teal TK, Woodley L. An international consensus on effective, inclusive, and career-spanning short-format training in the life sciences and beyond. PloS one. 2023 18(11):e0293879.

  6. Mehta S, Bernt M, Chambers M, Fahrner M, Föll MC, Gruening B, Horro C, Johnson JE, Loux V, Rajczewski AT, Schilling O, Vandenbrouck Y, Gustafsson OJR, Thang WCM, Hyde C, Price G, Jagtap PD, Griffin TJ. A Galaxy of informatics resources for MS-based proteomics. Expert Rev Proteomics 2023 20(11): 251-266.

  7. Hiltemann S, Rasche H, Gladman S, Hotz HR, Larivière D, Blankenberg D, Jagtap PD, Wollmann T, Bretaudeau A, Goué N, Griffin TJ. Galaxy Training: A powerful framework for teaching! PLoS Comput Biol. 2023 19(1): e1010752.

  8. Hall CR, Griffin PC, Lonie AJ, Christiansen JH. Application of a bioinformatics training delivery method for reaching dispersed and distant trainees. PLoS Comput Biol. 2021 17(3): e1008715.

  9. Baker D, van den Beek M, Blankenberg D, Bouvier D, Chilton J, Coraor N, Coppens F, Eguinoa I, Gladman S, Grüning B, Keener N, Larivière D, Lonie A, Kosakovsky Pond S, Maier W, Nekrutenko A, Taylor J, Weaver S. No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics. PLoS Pathog 2020 16(8): e1008643.

Pre-prints from BioCommons team members:

  1. da Silva RF, Bard D, Chard K, de Witt S, Foster IT, Gibbs T, Goble C, Godoy W, Gustafsson J, Haus UU, Hudson S et al. Workflows Community Summit 2024: Future Trends and Challenges in Scientific Workflows. arXiv preprint arXiv:2410.14943. 2024 Oct 19.

  2. Gilligan J, Inwood SN, Harrop TW, Keddell P, McPhail K, Sproston CJ, Williams DW, Petersen G, Hovius A, Kaspar J, Guhlin JG. Rapid and cost-effective production of high-quality insect genome sequences. bioRxiv. 2024:2024-10.

  3. Gustafsson, O J R, Wilkinson, S R, Bacall, F, Pireddu, L, Soiland-Reyes, S, Leo, S, Owen, S, Juty, N, Fernández, J M, Grüning, B, Brown, T, Ménager, H, Capella-Gutierrez, S, Coppens, F, Goble, C. WorkflowHub: a registry for computational workflows. arXiv. October 99, 2024.

  4. Wilkinson, S R, Aloqalaa, M, Belhajjame, K, Crusoe, M R, de Paula Kinoshita, B, Gadelha, L, Garijo, D, Gustafsson, O J R, Juty, N, Kanwal, S, Khan, F Z, Köster, J, Peters-von Gehlen, K, Pouchard, L, Rannow, R K, Soiland-Reyes, S, Soranzo, N, Sufi, S, Sun, Z, Vilne, B, Wouters, M A, Yuen, D, Goble, C. Applying the FAIR Principles to Computational Workflows. arXiv. October 4, 2024.

  5. Simpson, L, Cantrill, D, Byrne, M, Allnutt, T, King, G, Lum, M, Al Bkhetan, Z, Andrew, R, Baker, W, Barrett, M, Batley, J, Berry, O, Binks, R, Bragg, J G, Broadhurst, L, Brown, G, Bruhl, J, Edwards, R, Ferguson, S, Forest, F, Gustafsson, J, Hammer, T A, Holmes, G, Jackson, C, James, E, Jones, A, Kersey, P, Leitch, I, Maurin, O, McLay, T G B, Murphy, D, Nargar, K, Nauheimer, L, Sauquet, H, Schmidt-Lebuhn, A N, Shepherd, K, Syme, A, Waycott, M, Wilson, T, Crayn, D M. The Genomics for Australian Plants (GAP) framework initiative–developing genomic resources for understanding the evolution and conservation of the Australian flora. July 8, 2024.

  6. Batut B, Bernt M, Ansari MH, Kalaš M, Klemm P, Libouban R, Nasr E, Rioualen C, Thang WC, Zoabi R, Zierep P. How to improve the annotation of Galaxy resources? Outcomes of an online hackathon for improving the annotation of Galaxy resources for microbial data resources. BioHackrXiv. February 29, 2024

  7. Zierep P, Batut B, Kalaš M, Kayikcioglu T, Nasr E, Soranzo N, Thang WC, Wang J, Gustafsson OJR. How to increase the findability, visibility, and impact of Galaxy tools for your scientific community. BioHackrXiv. April 2, 2024.

  8. Lamothe L, Jensen JRB, Ienasescu H, Gustafsson OJR, Gaignard A, Repchevsky D, Svobodová R, et al. 2023. An Evaluation of EDAM Coverage in the Tools Ecosystem and Prototype Integration of Galaxy and Workflowhub Systems. BioHackrXiv. February 15, 2023.