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Include additional scripts and tutorials to generate the predicted disassembly units and key interacting regions associated with the new publication of pyCapsid ("Identifying disassembly units in viral capsid").
Due by May 15, 2026The initial version of pyCapsid associated with the publication in Bioinformatics (2024) didn't follow the standard lab project structure and included several bad coding practices. The code should be restructured, adapted to be object-oriented and give a more straightforward account of inputs used, data obtained, and outputs. Ideally, this milestone should be developed parallel to the `disassembly milestone`. That milestone focuses more on the work needed for the follow-up publication as an application of pyCapsid. This milestone would focus more on the computer science part and programming crafting.
Overdue by 1 year(s)•Due by June 30, 2024•0/4 issues closedIn the release and publication of pyCapsid in Bioinformatics (Colin et al. 2024, <https://doi.org/10.1093/bioinformatics/btad761>), we showed the potential application of pyCapsid to identify disassembly units in viral capsids. This was included in the supplementary materials of the article. The goal now is to go deeper into those analyses to clarify the insights of pyCapsid and the aspects that require new research in the future. The milestone opened here will coordinate the efforts towards this goal and, hopefully, a new peer-reviewed publication associated with pyCapsid.
Overdue by 1 year(s)•Due by May 31, 2024•1/7 issues closedThe goal of this milestone is to revise the documentation and GitHub documents so the repository and online materials are comprehensible for new users. This milestone is not intended for major changes, just for minor adjustments that guarantee that most information is up to date and any deprecated parts are removed.
Overdue by 1 year(s)•Due by January 25, 2024•4/5 issues closed