Sir, i was reading the last year idea which is related to this project.
After changing the model format with Neuro ML format need to make model available on Open Source Brain repository, along with documentation and references. I read the docs i want more deep dive into this. and also i want to contribute in this project gsoc 23. i am writing proposal for this i will send you as soon as possible.
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We don’t have a template specifically for us, but there is documentation like this that you can follow:
https://google.github.io/gsocguides/student/writing-a-proposal
How many issues need to solve for selection for this project i read all the documentation and i am writing the proposal for this project. any small contribution matters for selection.
Hey! I’m Arnab, I’m studying computer science student at the University of Edinburgh. I’ve been lurking on this forum and learning for the past few weeks since this project caught my attention.
I thought I’d properly introduce myself. I have made myself comfortable with NeuroML (creation and simulation) and am tackling the conversion of a model after talking to the professor.(GitHub - doorkn-b/Pituitary-GH-3-to-Neuro-ML: A model for pituitary GH(3) lactotroph (Wu and Chang 2005)).
Although I wasn’t sure this was the best way I could allocate my time and contribute to OSB. I’ve gone through the previous year’s projects and have understood the procedure but it seems daunting to take it on as a contribution before asking the mentors. What’s the best way I could spend my time while contributing and making myself a good fit for this project?
Thanks!
Arnab.
My Github for reference - doorkn-b (Arnab Mukherjee) · GitHub
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Sir where can i send my proposal for review please tell
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Folks, please feel free to e-mail me your proposals at ankur DOT sinha AT ucl DOT ac DOT uk if you’d like some feedback before submitting.
(We do not require you to have any PRs etc. merged before the application/contribution period for the OSB projects.)
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Advice for OSB GSoC 2023 applicants
Background reading
Read the Open Source Brain paper as well as the LEMS/NeuroML2 paper (have a look too at the libNeuroML, NeuroML v1 and PyNN papers).
Browse the OSB website, including help pages .
Have a good look at the outcomes of previous years’ OSB GSoC projects:
Migliore et al. 2014, Olfactory Bulb 3D
Suggested activities prior to application
Sign up to GitHub if you’re not already there.
Create an OSB user account & link your GitHub account to it.
Have a look at some of the OSB projects (either on http://www.opensourcebrain.org/projects or those mentioned above), and try cloning the model and installing associated simulators locally.
Make a minor pull request to an existing OSB project on GitHub that you find interesting (e.g. small update to README/documentation).
Assemble a list of cortical models from ModelDB or from the literature to include with your application, which you think would be of benefit to the community if they were converted to NeuroML/PyNN.
If you find a project there particularly relevant, feel free to set up a personal GitHub repository for it and start adding code/documentation there.
Please share the draft of your application early to allow feedback before the application deadline!
Essential information to include in your application:
- The list of potential models to convert as discussed above
- Details on the course currently being followed and a link to the course webpage.
- What are your time commitments during the coding period? Please be specific about this, work/exam commitments etc. Are you planning any vacations this summer? How many classes are you taking this summer?
- How many hours per week will you be able to spend on this project?
- If you have any evidence of your coding abilities (e.g. contributions to open-source projects) and/or background in neuroscience, please let us know about it. Send links to specific public repositories showing commits by you.
- Details of any previous experience in computational modelling.
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Hi @doorkn-b. Thanks for your interest.
This example would be highly relevant for you, as it has an XPP version of a model: PinskyRinzelModel/booth_bose.ode at master · OpenSourceBrain/PinskyRinzelModel · GitHub and the equivalent in LEMS: PinskyRinzelModel/pinskyRinzelCA3CellDL.xml at master · OpenSourceBrain/PinskyRinzelModel · GitHub, which has eventually ended up as a NML core cell type: Cells — NeuroML Documentation
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Hi @Aman123lug. Thanks for your interest in this project.
For this project it is very important for applicants to establish their knowledge of some aspects of computational neuroscience, or modelling in biology. You will need to be able to show you have an appreciation of the types of biological neuronal models that are out there and an idea of how these can be translated into NeuroML.
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I learned all the essential aspects of computational neuroscience, or modeling in biology. I am just reading the necessary documentation about this. One question I write a proposal for this project I want to feed back from mentors. Can you please review my proposal before sending to google?
Hi all. Please submit your proposals well before the deadline on the GSoC site, where you can upload a draft pdf, which we can see and comment on.
It is very important though to demonstrate a clear knowledge in that of the current state of computational modelling in neuroscience, and have identified a list of (recent) models of the cortex (cells and or networks) from ModelDB which would benefit from conversion into NeuroML/PyNN, and oultline how you would go about doing that. Example code in a GitHub repo that you have created, making a start on converting a model to NeuroML (or even creating a toy model based on our examples) would significantly benefit your application.
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Okay! Before that I send my proposal for review can you please you it before I send to Google.
I created a demo PyNN model for models. In my proposal, I mentioned the approach only how I work on this project
Hey!
Thanks for the example. I was able to make good progress on my XPP model conversion. For the models I select, is there any specific type that I must adhere to or could I choose any?
In the essential information to include in application, what exactly does ‘Details on course currently being followed…’ refer to?
Is it upto us to choose whether we do a large project (375 hours) or the other? Following up on that, how many models should I include in my proposal if I were to do a 375 hour project?
Thanks!
I send you my draft proposal please review it. and give feedback on how can I improve the implementation part or something else. I created a toy model which is on my GitHub I tried to convert it into NeuroML format.
My research and I am working on a toy model.
Also, I Successfully build Strong knowledge about computational modeling in neuroscience.
For converting I am going to choose NeuroML
Once I have identified a list of candidate models, I would evaluate each model based on its scientific significance, complexity, and feasibility for conversion into NeuroML/PyNN. Models that have already been published in NeuroML/PyNN format or have previously been used in simulations with these tools would be given higher priority.
To convert a model from ModelDB into NeuroML/PyNN, I would first obtain the source code for the model and analyze its structure and dependencies. I would then use a NeuroML editor or converter tool to create a NeuroML version of the model, making any necessary modifications or adjustments to ensure that the model is accurately represented in the new format.
If the model is particularly complex or requires custom modifications, I may need to create a Python script to generate the NeuroML code programmatically. In this case, I would use a tool like PyNN to create a template script for the model, and then customize the script to include the specific parameters and equations required by the original model.
Thank you!
I have submitted my proposal (draft). Would appreciate any feedback.
Thanks.
Thanks for submitting your draft proposals everyone. We are very excited to go through them all. We’ll be going through them in due time to provide feedback.
In the meantime we did want to note that we’re likely going to be able to accept only one candidate here (if we make it through the ranking system and so on and receive any slots), so we encourage all candidates to please also apply to other projects that they are interested in. We always receive lots of great candidates and each year, we can only select one or two.
I am Successfully able to Simulate the models in local machine
Hello!
Apologies for appearing late! I have submitted my proposal on GSoC portal before the due date, after carefully working out a schedule for the project. I have gone through NeuroML documentation for this purpose and am currently taking deeper dive into associated tools. The previous year project has been a useful resource. I have made an account on OSB and linked it to my GitHub account.
Currently, I am working on some basic models. I am also reviewing literature to shortlist the ones that I want to work on during the project. Please share your valuable guidance!
I am deeply interested in neuroscience and computational aspects. The fascinating diversity of neuron models was indeed intriguing. I fully comprehend the importance of the task taken up here. Hoping to contribute to this endeavor by INCF!!!
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Thanks for your interest in the project @YashvitaS. Out of fairness to all candidates we will be assessing the applications at the time of submission, and any subsequent work won’t be taken into consideration when we select a candidate for this project.
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Dear all,
Thank you so much for your excellent applications. Unfortunately, the INCF did not get as many slots as we’d hoped and so we did not get any slots alloted for this particular project in this round. We hope you picked up some useful information while writing your proposals. While we cannot work with you at GSoC, if you are still interested in converting any models to NeuroML (if it’s for your academic work, for example), please do get in touch and we will be happy to guide you.
Thanks very much