Paul Medvedev 
#algorithmicbioinformatics what are the big challenges facing our field? What are the things we are doing well that we should keep on doing?
Luis Pedro Coelho@Pashadag a lot of tools require too much memory as they optimize for speed and it would be good to be able to trade those off more
Tommi Mäklin@luispedro @Pashadag adding onto this, many tools are also poorly maintained and/or unnecessarily difficult to use. We really should make sure that projects which result in widely used software do not rely on a single person to keep them running.
Eric Pelletier@themaklin @luispedro @Pashadag not only a question of maintainer, but also of funding: once your tool / database is published, it becomes harder to get fundings to maintain it.
@EricPelletier @themaklin @Pashadag
In my experience, maintenance as is "keeping it alive" can be done at very little cost if things are set up correctly ahead of time
We commit to supporting software 5 years post pub (https://www.big-data-biology.org/software/commitments/ — and, in practice, still support things from 15 years ago) and this mostly means that I have high standards on ensuring that things are maintainable after the original trainee leaves (some of this is learned from past experience)
@luispedro @EricPelletier @Pashadag This is great! Something similar is definitively something for other labs & individual researchers to consider.
@themaklin @EricPelletier @Pashadag I've thought of writing a commentary piece in a proper journal and this mastodon discussion makes me think there is a readership
@luispedro @EricPelletier @Pashadag I think it would be very useful, or at least make more PIs and funders realize the importance of planning maintenance and sustained development ahead of time.
At least for me reading this related paper https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02625-x made me spend more time looking for alternative solutions when deploying new pipelines rather than flocking to the most widely known ones, so communicating the issues (and solutions!) should help.
@themaklin @EricPelletier @Pashadag
This is now published at PLOS CB!
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011920