GSoC 2020 project idea 10: Open source, cross simulator, large scale cortical models

An increasing number of studies are using large scale network models incorporating realistic connectivity to understand information processing in cortical structures. High performance computational resources are becoming more widely available to computational neuroscientists for this type of modelling and general purpose, well tested simulation environments such as NEURON and NEST are widely used. New, well annotated experimental data and detailed compartmental models are becoming available from the large scale brain initiatives. However, the majority of neuronal models which have been published over the past number of years are only available in simulator specific formats, illustrating a subset of features associated with the original studies.

This work will involve converting a number of published large scale network models into open, simulator independent formats such as NeuroML and PyNN and testing them across multiple simulator implementations. They will be made freely available to the community through the Open Source Brain repository (http://www.opensourcebrain.org) for reuse, modification and extension.

Skills required: Python; XML; open source development; computational modelling experience.

Desirable: Java experience; a background in theoretical neuroscience and/or large scale modelling.

Aims:

  1. Select a number of large scale cortical network models for the conversion & testing process.

  2. Convert network structure and cell/synaptic properties to NeuroML and/or PyNN. Where appropriate use the simulator independent specification in LEMS to specify cell/synapse dynamics & to allow mapping to simulators. Implementing extensions to PyNN, NeuroML or other tools may be required.

  3. Make models available on the Open Source Brain repository, along with documentation and references.

Mentor: Padraig Gleeson, Jessica Dafflon

Keywords: Python, XML, networks, modelling, simulation

Hi @pgleeson,
Hi, I am Hsueh Cheng-Hsun, a medical student at National Yang-Ming University in Taiwan. I have research experience in natural language generation, and have developed ecological model in international genetic engineering machine (iGEM) competition. I am really interested in this project! I am looking for a starting point so that I can understand more about this project. Thank you!

Advice for OSB GSoC 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:

Mejias et al. 2016

del Molino et al. 2017

WilsonCowan

CA1 network

Thalamocortical column

Migliore et al. 2014, Olfactory Bulb 3D

Izhikevich model

Pinsky Rinzel CA3 model

Pospischil et al. 2008

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:

  1. The list of potential models to convert as discussed above
  2. Details on the course currently being followed and a link to the course webpage.
  3. 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?
  4. How many hours per week will you be able to spend on this project?
  5. 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.
  6. Details of any previous experience in computational modelling.

Hi @jimHsueh,
Thanks for your interest in the project. I hope the pointers above are helpful for some background information.
Padraig

@pgleeson thanks so much! The pointers above are very helpful. I am drafting for the proposal, and looking forward to sending you recently!

Hi! I found that past GSoC project usually implemented one model. I am not sure if one single model or more models should be implemented for this project. Which would be more preferred? Thank you!

Hi @jimHsueh, If you’re new to NeuroML, it would be best to start with a smaller scale, simpler project (maybe just one cell) and convert that fully to NeuroML first. The main project could be a more detailed network model.

@pgleeson Thank you for the advice! I have finished my application draft. Where should I share the link to? Thank you!

You can email the link to me.

Hi @pgleeson. I am Raunak Swarnkar, MSc Cognitive Science student at the Centre for Cognitive & Brain Sciences, Indian Institute of Technology Gandhinagar, India. I was introduced to computational models of neuron (such as Leaky-Integrate & Fire, Hodgkin-Huxley) and the brain as part of my coursework and have been fascinated since then to work in this area. This project has presented itself as a perfect opportunity to spend time reading computational modelling papers and code (at the same time!) this summer. I look forward to reading and following the materials posted by you above. I will prepare the proposal draft and send it across for review/feedback. Thank you!

Hi @rauswarn, thanks for your interest. I look forward to your draft application.

I’m interested in the project. I’ve sent you an invitation to the proposal for feedback.

Hi @pgleeson !

I am Asmita Narang, currently enrolled in M.Sc. Cognitive systems at Ulm University, Germany. I did my Bachelors in Applied psychology at Delhi University, Delhi. I am currently specializing in Neurotechnology. I have extensively worked with EEG data preprocessing and machine learning.

My course encompasses knowledge in data mining, machine learning, mathematical modelling of cognitive systems. I have worked with java, Matlab(extensively), python, Arduino and presentation(neurobehavioral toolbox).

I am interested in cross simulator and large scale cortical models project and I am aware of the fact that I am running out of time. I discovered about the google summer school of code today only. Do you think my profile matches for the project and will the given background knowledge can I work in the project?

And if yes then where I can send the draft !

Thank you for your time.

Any suggestions and information would be of great value to me. Have a good day.

Best Regards,
Asmita Narang

Hi Asmita,
It does seem you have a good background for the project (although have you contributed to open source projects before?). However it is pretty close to the deadline. There are some pointers above in Advice for OSB GSoC applicants, and you should familiarise yourself with all of the Google/INCF requirements for the process too.
Regards,
Padraig

Hi @pgleeson

Thank you for your inputs. I understand that I am running out fo time but I am really interested in the project. And I will try to put my best in the proposal submit. Can I share my draft with you over email? I couldn’t find you email address mentioned.

Also, I haven’t worked in open source projects before this. I have looked at the guidelines and I will follow them. Thank you in advance for your time and consideration.

Best regards,
Asmita

Hi @pgleeson

I have shared my draft for the proposal. Kindly have a look if possible.

Thank you for your time and consideration.

Best Regards,
Asmita

Thank you for the review @pgleeson. Dr. Gunay and I eagerly await the announcement of the new models to start preparation for OSB’s repository!

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