Hi @Claudio and @Sarah Narrowe Danielsson 👋🏻 Thought I'd kick off a thread here to get you started. 'cc @Jose Espinosa-Carrasco and other #C0351A8S487 users / devs 🙏🏻 Pasting from email thread:

Claudio and Sarah are working on a very efficient pipeline to run massive screens of protein-protein interactions using AlphaFold. Their pipeline uses several clever tricks (such as precompiling JAX code) and might be of value to a broader community. Do you think it might be of interest to include it in NF-core (there is currently a proteinfold pipeline, but it seems to primarily be aimed at running single predictions).

https://www.scilifelab.se/wp-content/uploads/2023/02/BeyondFold-–-Advancing-structural-biology-with-deep-learning-approaches.pdf

Not sure if there's any source code to look at? But question here is whether there's scope for a #CE6SDEDAA proposal, or whether there's any way for you to join forces on the #C0351A8S487 pipeline. I'll let you all take it from here 🧵 Thanks all :)

Thank you @Phil Ewels! Just like you mentioned, we are currently working on a Nextflow pipeline that could let you run millions of protein-protein interactions more efficiently. We were simply wondering if it'd be of interest to the nf-core community to include it in nf-core and if that's case we'd like more specifics on how to implement our pipeline there. We appreciate any thoughts/ideas you all might have!

Hi @Sarah Narrowe Danielsson! We are currently working in the release of proteinfold 2.0.0 and our plan is after the release try to make possible to perform these kind of high-througput analyses. If I am not wrong, @Thomas Litfin, @Joshua and @Keiran Rowell have already some in-house developments. We have a weekly pipeline development meeting, the only issue is that today we decided to have a winter break ☃️ until the 7th of January. So next meetings will be the 7th of January at 9:00 CET, will it work for you?

Ok, sounds like a good idea to have a meeting then! Yes, I should be able to attend the one on the 7th. 🙂

Would it be possible for @Thomas Litfin @Joshua or @Keiran Rowell to attend? Add a 👍🏻 to this message if yes, please

The meeting is today right? At the rediris Zoom link?

Yeah, sorry I am connecting also now, I forgot about the meeting

Thank you all for a nice meeting!