GSoC Project Idea 1: Accessible High-Performance Computing with CBRAIN

GSoC
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Hi Davide, great to meet you.

I would recommend that you sign up for an account on our CBRAIN portal and familiarize yourself with our platform. You can sign up for an account at https://portal.cbrain.mcgill.ca. We have some documentation to get your started on our GitHub Wiki at https://github.com/aces/cbrain/wiki. And if you have any questions, you CBRAIN account will let you sign into our discussion forum at https://forum.cbrain.mcgill.ca/. I will have our developers publish the RestAPI on SwaggerHub and post in a subsequent method. Even though CBRAIN is in Ruby on Rails, you shouldn’t need to learn that as you will be working on clients and testing of the RESTFul API, which can really be in any language.

Thanks, looking forward to working with you.
Shawn

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I’ve just requested an account. Thanks!

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Update: I’ve read the wiki and played a little bit with the web app. It seems cool!
I’m wondering if there are more tutorials (e.g. something that gives you a list of files, a task and teach you how it works in a real scenario).
Let me know!
Thanks in advance.

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Here’s a copy of my brain: https://www.dropbox.com/s/7x65xi24v00qcj5/andrew_mri_nov_2015.nii.gz?dl=0

See if you can upload it to CBRAIN, register it, and launch a task to convert it to .mnc!

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@crocodoyle it works, thank you so much!

@shots47s is it possible to have the RestAPI docs?
Also, how the library should be designed? Does it have to cover the entire APIs or just a subset?

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There is a link to the docs in the project description. The bare minimum API coverage for the project would be the calls required to upload data, run a task, and download the results.

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I think that now I’ve enought information/knowledge to write a good proposal.
Thanks!

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Shawn and I are happy to give you feedback on your proposals before they are submitted to Google :slight_smile:

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Hi,

Should you be a registered student to take part in GSoC? I just graduated from McGill in December 2018. Will I be eligible?

Thank you

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Hi Shawn, Andrew, Malin, and team!

My name is Logan. I’m currently an M.S. CS student at Georgia Tech’s online (distance-learning) OMSCS program, and presently living in Montreal. As a recent B.Sc. (Hons) Soft. Eng. alum @McGill, I came across this opportunity through Ann Jack’s message to McGill grads, suggesting interested parties should reach out here.

Looking into the CBRAIN project, this opportunity is immensely appealing to me, builds on my strong affinity for projects in Bioinformatics / applied Data Eng., and could fit very well with my current plans!

As a brief pitch: my experience ranges across academic research (~12 months on McGill Bioinf. & NLP ML projects) & industry software development roles (~20 months: mix of MVC / REST development and, recently, Data Eng. heavy work in Python / Jupyter Notebooks at Shopify).

Linking to my profiles:

To familiarize myself with the CBRAIN platform, in anticipation of submitting a Google Summer of Code proposal, I’ve recently requested an account through the CBRAIN portal (note: applied with my GA Tech email, logan.martel@gatech.edu).

Hope to hear from you soon. I will also have a look at available documentation on the GitHub Wiki in the meantime :slightly_smiling_face:.

Best,
Logan

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Hello Shabirmean, this is what it says in the GSoC guidelines: “You must currently be a full or part-time student (or have been accepted and committed to the fall term) at an accredited university as of the date accepted student proposals are announced” (May 6). As I interpret that, you will not be eligible. However, some of the projects may also be looking for new project members, outside of GSoC.

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Hi Logan & others,

Thanks for your interest. Have you had your account approved yet Logan? Not a whole lot of time left to prepare an application. A good proposal would indicate some familiarity with the CBRAIN API and the workflows necessary to do the science :slight_smile:

What I have suggested to others is that they first use the web interface to run a tool on some data, try it again using the OpenAPI live docs, and document the steps.

If you can install CBRAIN locally, that could be verrry instructive (and might be difficult), but is not strictly necessary for the completion of the project.

Best,
Andrew

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Hi everyone
Sorry to bother you again
I’m writing the project proposal, but the website of the GSOC asks me an INCF proposal tag (screenshot down below).
What should I select?

OT: I’ve just submitted a draft, it would be great to have a feedback!

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I’m not sure, I can’t access that page. What are the options in that dropdown?

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The tags are:

  • genn_project;
  • tvb_project;
  • gnode_project;
  • catmaid_project;
  • openworm_project;
  • other_project;
  • brian_project.
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(Org admin here)

Hello Davide, you can select the other_project tag. (The relative low limit for number of tags, I think it is 10 doesn’t allow us to give a specific tag to all projects). The tags are not super important, but they help us keep track.

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Great, thanks.

One last thing: is there a way to have a feedback on the draft proposal before submitting it as final?

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Yes, please coordinate with the mentors. You can either submit as draft to the Google platform and have your discussions there, or share your draft with them for feedback through some other channel, before you submit.

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I’ve already submitted the draft to the GSoC website yesterday, because I don’t have any contact infos about the mentor unfortunately

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The mentors are Andrew Doyle and Shawn Brown. Andrew has his contact info on his website here http://crocodoyle.ca/#contact, Shawn can be reached on stbrown@mcin.ca,

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