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Been looking at the open source bioinformatics ini...
# random
k
Been looking at the open source bioinformatics initiatives that are hosting interns for Google summer of code. Seems to me like nf-core would be a good fit, maybe applying to be a host next year wouldn't be a bad idea
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p
We've looked into GSoC a bunch of times, but nf-core isn't an organisation / institution. So nf-core itself can't really participate.
Institutions that have people working on nf-core can absolutely host GSoC students to work on nf-core projects though.
k
Aw! I see, how unfortunate
I did see EMBL-EBI is one of the choices, I'll look into that
p
Yes a bunch of people have done projects in the past before, or have expressed an interest in it. I think the person I spoke to most recently about it was @Chris Fields @Chris Fields
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Not sure if @Matthieu Muffato is also involved somehow? And many others who I won't ping, going back in my Slack history to around 2019 😆
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m
Hi. Yes, I am GSoC org admin for the Sanger Institute (and was GSoC mentor for EMBL-EBI in the past). We’re not doing GSoC this year though because we didn’t have enough project ideas that fit the remit of GSoC. I would actually think that nf-core is suitable as an org in GSoC. GSoC is for open-source groups. They don’t have to be backed by a physical org / institute. On the contrary, I feel like Sanger and EMBL-EBI are outliers within GSoC 🙂
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k
Sanger would have been nice too. It's unfortunate I've only begun to look into this this year🥲
p
@Matthieu Muffato you might be right, it's been years since I looked into it properly 👍🏻 I remember going quite deep into it and giving up anyway 😅
c
Open Bioinformatics Foundation has participated in GSoC in the past, but we ran into the same issue @Matthieu Muffato had re: project ideas as well as late recruitment for potential mentors.
Also 💯 w/ Matthieu: I don’t think you need an official org to participate though we found it helps for structure and organization. For example ‘Genome Informatics’ was one group that was accepted which acted as an umbrella ‘org’ of sorts for the various GMOD projects (GBrowse, JBrowse, etc). Run by the legendary Scott Cain
If you are interested for next year and doing it within nf-core or nextflow, I recommend finding potential GSoC leads this summer/early fall, then starting (fall 2026) in recruiting potential mentors and projects. Or plan to do it in coordination w/ another group like OBF. There is a fair bit o’ time commitment and 🐈 herding involved
k
@Chris Fields EMBL-EBI 's GSoC page has this nf-core oriented project as well as a few other Nextflow heavy ones I guess I'll apply to them
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Do you (@Chris Fields, @Matthieu Muffato) think it's too late fro me to start reaching out to mentors and getting a draft done given the deadline is March 31st?
p
Heads up that "publishing an nf-core/vep" pipeline is a bit of a risky ambition, as it needs to go through the #CE6SDEDAA process. We already have several VEP modules and a number of pipelines using them: https://nf-co.re/modules/ensemblvep_vep/
k
I guess I need to reach out to @Syed Hossain and discuss how exactly his proposed workflow will be different from the existing ones
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m
@Kurayi You can try but it may be too late, yes. Normally at this point there are already some good conversations and plans with prospective applicants.
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k
Well the mentors respond VERY fast, I just got my response in less than 3 minutes 😆
c
You really want a decent head-start: pick a lead with enough time to run the program, inform prospective mentors of prospective projects of expected time commitments, line up projects and mentors, write up a decent proposal, etc. And you’ll want a decent slate of projects: not all of them will be selected by a student if you get selected.
OBF had anywhere from 8-20 prospective projects lined up, of which maybe half make it through the ‘matchmaking’ process
Another thing: I’d have to check how the current GSoC runs (it’s changed), but another point is how funds are distributed. It used to be $5k or so per student prior to 2021, with the org getting 10% of that. If you already have some financial organization in place that helps considerably, which is another reason why having an org helps.
Just to be clear, I’m not dissuading you from trying. Just want to make sure you know what you are getting into 😉
And don’t get too down if you aren’t selected. We’ve been turned down a number of times.
k
Thanks Chris! All very helpful - if not for me this year then definitely when I help someone else out in the coming years
And don't worry, I've been receiving rejections from various summer programs non stop for the last 3 weeks 😆 I'm about as used to this now as one can get
Sort of scrambling to pull last minute tails all over the place and hoping something bites - I'll let you know if anything develops with GSoC
c
Good luck!
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p
Note that @Kurayi is approaching this as a student, not an organiser to be clear
k
True. But I'm sure it'll be useful in the event that I needed to convince an Organization to host ahead of time
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c
Ah, I missed that, thx @Phil Ewels! I saw all of the discussion re: mentors, writing up for GSoC, etc and assumed this was for someone writing up for the current one
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k
Should probably add (student) to my user name😂Not the first time this has happened
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