Merge pull request #24 from SIMEXP/lunebellec-patch-1

complete refactor using mystmd

Author: lunebellec

.github/workflows/deploy-book.yml

@@ -23,19 +23,14 @@ jobs:
       run: |
         pip install -r content/requirements.txt
 
-    # Fetch ORCID records
-    - name: Fetch ORCID records
-      run: |
-        cd content; python orcid_to_bib.py
-
     # Build the page
     - name: Build the book
       run: |
-        jupyter-book build content/
+        myst build --html
 
     # Push the book's HTML to github-pages
     - name: GitHub Pages action
       uses: peaceiris/actions-gh-pages@v4
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
-        publish_dir: ./content/_build/html
+        publish_dir: _build/html

.gitignore

@@ -0,0 +1,4 @@
+# MyST build outputs
+_build
+# for vim
+*.swp 

README.md

@@ -1,6 +1,6 @@
 # simexp.github.io
 Website of the laboratory for brain simulation and exploration (SIMEXP). The codebase of this website is licensed under a
-[Creative Commons Attribution 4.0 International License][cc-by].
+[Creative Commons Attribution 4.0 International License][cc-by] and is based on the [Myst Markdown](https://mystmd.org/) framework.
 
 ## Usage
 
@@ -11,18 +11,9 @@ If you'd like to develop and/or build the SIMEXP website, you should:
 1. Clone this repository
 2. Run `pip install -r content/requirements.txt` (it is recommended you do this within a virtual environment)
 3. (Optional) Edit the books source files located in the `content/` directory
-4. In a terminal, move to the `content` directory
-5. Run `python orcid_to_bib.py` to update the content of the publication section.
-4. Run `jupyter-book clean .` to remove any existing builds
-5. Run `jupyter-book build .` to create the book
+4. Run `myst build --html` to create the website
 
-A fully-rendered HTML version of the book will be built in `content/_build/html/`.
-
-### Hosting the book
-
-Please see the [Jupyter Book documentation](https://jupyterbook.org/publish/web.html) to discover options for deploying a book online using services such as GitHub, GitLab, or Netlify.
-
-For GitHub and GitLab deployment specifically, the [cookiecutter-jupyter-book](https://github.com/executablebooks/cookiecutter-jupyter-book) includes templates for, and information about, optional continuous integration (CI) workflow files to help easily and automatically deploy books online with GitHub or GitLab. For example, if you chose `github` for the `include_ci` cookiecutter option, your book template was created with a GitHub actions workflow file that, once pushed to GitHub, automatically renders and pushes your book to the `gh-pages` branch of your repo and hosts it on GitHub Pages when a push or pull request is made to the main branch.
+A fully-rendered HTML version of the book will be built in `_build/html/`. If a change is merged into `main`, a github action will automatically publish an updated version of the website. 
 
 ## Contributors
 

alliance_canada/quick_start.md

@@ -0,0 +1,38 @@
+# Let's get started
+
+The lab applies for storage space and compute time on Alliance Canada every year.
+These resources are limited and have to be shared fairly across members of the lab.
+Given that no member of the lab has privileged admin rights, this fairness relies on everyone adopting a clear code of conduct, and shared organization.
+
+## Get access 
+To get access to simexp resources in Alliance Canada, create an account on [CCDB](https://ccdb.alliancecan.ca/) and then apply for resources under tab "My Account",  select "Apply for a new role", then apply the appropriate role with CCRI `gsf-624-02`. Note that the main allocation of the lab is currently hosted on [rorqual](https://docs.alliancecan.ca/wiki/Rorqual/en). 
+
+## Submitting jobs
+You can learn more on high-performance computing (HPC) and the Digital Alliance using their [docs](https://docs.alliancecan.ca/wiki/Running_jobs). The compute allocation of the lab (only available on `rorqual`) can be accessed using the code `gsf-624-ab`. You can log on any HPC of the Alliance, but you will only have access to the default compute allocation there (`gsf-624-aa`). Note that each HPC is managed independently, so compute launched on, say, `beluga` does not affect our `rorqual` allocation. 
+
+## Setup your environment
+
+When you are new to Alliance Canada, we will ask you to run a setup script that will set data management access and give you access to utils for project management, including:
+
+- setup ACLs for the data admin to the project and nearline folders
+- add project management commands to your bash environment
+- generate SSH keys if not already created, and help you set them up on Github for easier access
+- configure the ssh agent and keychain to avoid typing your ssh key password each time you push to github or ssh to another server.
+- configure git global variables
+
+
+You can do it just once on each cluster:
+
+```
+/project/def-pbellec/share/data_admin/utils/setup_user_account.sh
+```
+
+## Add a new dataset
+
+Datasets are stored in `~/project/(rrg|def)-pbellec/datasets`
+
+> __IMPORTANT__ When applying to gain access to a dataset, it is important that you involve the lab's management so they can sign data sharing agreement, make sure the use of data is covered by an ethics agreement or other necessary steps. If you want to add a new dataset please contact the lab's data admin (Basile).
+
+## Renewing or terminating your role
+Every year Digital alliance requires you to renew your account. It is important to do so on a timely fashion in order to prevent interruption in access. If you change position within the lab, your current role will be terminated and you will be required to re-apply under a new role. 
+

content/intro.md

@@ -1,35 +1,26 @@
 # SIMEXP
 
-![](images/banner.png)
+![](../images/banner.png)
 
-The laboratory for brain simulation and exploration (SIMEXP) is located in Montreal and affiliated with the [CRIUGM](https://criugm.qc.ca/), [CSS-MTL](https://ciusss-centresudmtl.gouv.qc.ca/) and [Université de Montréal](https://psy.umontreal.ca/accueil/). The main objective of the lab is to train artificial neural networks in order to jointly mimic individual human brain activity and behaviour. To achieve that goal, we lead an intensive effort of individual data collection in neuroimaging (fMRI, MEG), the Courtois project on neuronal modelling ([CNeuroMod](https://cneuromod.ca)). The SIMEXP lab also applies machine learning techniques to identify robust markers of brain disorders in multisite data.
+The laboratory for brain simulation and exploration (SIMEXP) is located in Montreal and affiliated with the [CRIUGM](https://criugm.qc.ca/), [CSS-MTL](https://ciusss-centresudmtl.gouv.qc.ca/) and [Université de Montréal](https://psy.umontreal.ca/accueil/). The main objective of the lab is to train artificial neural networks in order to jointly mimic individual human brain activity and behaviour, notably leading the Courtois project on neuronal modelling ([CNeuroMod](https://cneuromod.ca)). The SIMEXP lab also translates these models to identify markers of brain disorders using neuroimaging data.
 
 ::::{grid}
 
-:::{grid-item-card} CRIUGM
-:margin: 3
-:columns: 12 3 3 3
-:class-body: text-center
-:link: http://www.criugm.qc.ca/en.html
-:img-top: images/logo_criugm_white.png
+```{card} CRIUGM
+:url: http://www.criugm.qc.ca/en.html
+:header: ![](../images/logo_criugm_white.png)
 Research centre of the Montreal Geriatrics Institute
-:::
+```
 
-:::{grid-item-card} UdeM
-:margin: 3
-:columns: 12 3 3 3
-:class-body: text-center
-:link: https://psy.umontreal.ca/accueil/
-:img-top: images/logo_udem.png
+```{card} UdeM
+:url: https://psy.umontreal.ca/accueil/
+:header: ![](../images/logo_udem.png)
 Psychology department, University of Montreal
-:::
+```
 
-:::{grid-item-card} CNeuroMod
-:margin: 3
-:columns: 12 3 3 3
-:class-body: text-center
-:link: https://cneuromod.ca
-:img-top: images/logo_neuromod_black.png
+```{card} CNeuroMod
+:url: https://cneuromod.ca
+:header: ![](../images/logo_neuromod_black.png)
 The Courtois project on neuronal modelling
-:::
+```
 ::::

content/manifesto.md

@@ -2,7 +2,8 @@
 
 Academia means different things to different people. The laboratory for brain simulation and exploration (SIMEXP) is founded on a fairly opinionated, and possibly unusual view of what academia is. This document tries to make the SIMEXP academic values explicit. It does not mean that everybody at SIMEXP shares all of these values, or operates under a particular value at all times. These values are rather guiding principles for many key aspects of the operations of the lab, and form a baseline for expectations.
 
-![Hacking](images/hacking.png)
+![Hacking](../images/hacking.png)
+
 ## The hacker way
 Sharing is a key aspect of all academic communities, but how that sharing works varies widely. Lots of academic collaborations are transactional in nature, with people exchanging one contribution for another. Original founders of free software and the hacker movement operate under very different, simple rules. If you want to learn about something, just ask and you can expect an answer. The day somebody wants to learn something from you, you are expected to help that person. Don’t try to balance out what you get and give to a particular person. By helping others, you’re just building up karma, doing good to your community and the world. A corollary of that collaborative ethos is to strive to openly share as much research material as possible, data, code and ideas. The sharing process is greatly facilitated by adopting tools designed for sharing in your daily research activities (“open by design”).
 
@@ -12,7 +13,7 @@ Some laboratories operate under pretty strict labor division, with technical ass
 ## Automate all the things
 Neural data science requires us to iterate analyses a lot, to explore new ideas, replicate analyses on new datasets, and test the impact of various hyper-parameters. This means that data analysis operations should be automated to the greatest extent possible.  
 
-![Brain art](images/brain_art.jpg)
+![Brain art](../images/brain_art.jpg)
 ## The academic game is not the endgame
 Academia is a highly competitive environment. Some individuals end up focussing their work based on the metrics used to assess them, out of fear of not surviving the game, or simply thinking that it is what the academic community expects them to do. This means that many labs expend considerable energy towards publishing in high impact-factor journals, apply to awards, attend as many conferences as possible, get invited presentations, and sit on many committees, amongst others. The SIMEXP lab does of course support the careers of lab members, whether academic or not, and makes strategic investment of resources towards these metrics. But it is critical to not lose sight that pretty much none of us went into academia to work towards these metrics. The endgame of SIMEXP is to solve problems, namely prognosis of Alzheimer’s disease, and building human-like artificial neural networks. The academic game is a means to these ends. Nothing more. We aim to keep our collective and individual academic boats afloat with bare minimum required efforts, and are committed to not let the academic game ruin the fun and joy we have doing research. We rightfully trust that doing elite research, prioritizing quality over quantity, is all it really takes to strive inside and outside of academia anyway.
 

content/members.md

@@ -4,156 +4,101 @@
 
 ::::{grid}
 
-:::{grid-item-card} Lune Bellec
-:margin: 3
-:columns: 12 6 3 3
-:class-body: text-center
-:link: https://github.com/lunebellec
-:img-top: https://avatars.githubusercontent.com/u/1670887?v=4?s=100
+```{card} Lune Bellec
+:header: ![Lune Bellec](https://avatars.githubusercontent.com/u/1670887?v=4?s=100)
+:url: https://github.com/lunebellec
+
 Professor and laboratory director
-:::
+```
 
-:::{grid-item-card} Julie Boyle
-:margin: 3
-:columns: 12 3 3 3
-:class-body: text-center
-:link: https://twitter.com/juliebo80922597
-:img-top: images/profile_julie_boyle.jpg
+```{card} Julie Boyle
+:header: ![Julie A Boyle](../images/profile_julie_boyle.png)
+:url: https://www.linkedin.com/in/julie-boyle-064b17297/
 Project manager
-:::
+```
 
-:::{grid-item-card} Basile Pinsard
-:margin: 3
-:columns: 12 3 3 3
-:class-body: text-center
-:link: https://github.com/bpinsard
-:img-top: https://avatars.githubusercontent.com/u/1155388?v=4?s=100
+```{card} Basile Pinsard
+:header: ![Basile Pinsard](https://avatars.githubusercontent.com/u/1155388?v=4?s=100)
+:url: https://www.linkedin.com/in/basile-pinsard-94161b8/ 
 Data engineer
-:::
+```
 
-:::{grid-item-card} Marie St-Laurent
-:margin: 3
-:columns: 12 3 3 3
-:class-body: text-center
-:link: https://github.com/MarieStLaurent
-:img-top: https://avatars.githubusercontent.com/u/9339621?v=4
-Data scientist - digital brain phantom trainer
-:::
+```{card} Marie St-Laurent
+:header: ![Marie St-Laurent](https://avatars.githubusercontent.com/u/9339621?v=4)
+:url: https://github.com/MarieStLaurent
+Data scientist - _digital brain phantom trainer_
+```
 ::::
 
 ## Post-doctoral fellows
 
 ::::{grid}
 
-:::{grid-item-card} Hao-Ting Wang
-:margin: 3
-:columns: 12 3 3 3
-:class-body: text-center
-:link: https://wanghaoting.com
-:img-top: images/profile_haoting.jpg
-Post-doctoral fellow - foundation models for fMRI
-:::
-
-:::{grid-item-card} Isil Bilgin
-:margin: 3
-:columns: 12 3 3 3
-:class-body: text-center
-:link: https://github.com/complexbrains
-:img-top: images/profile_isil.jpg
-Post-doctoral fellow - brain-aligned large language models - co-supervision with Dr Leila Wehbe
-:::
-
-:::{grid-item-card} Yann Harel
-:margin: 3
-:columns: 12 3 3 3
-:class-body: text-center
-:link: https://github.com/hyruuk
-:img-top: images/profile_yann.jpg
-Post-doctoral fellow - brain/behaviour correlates of flow in videogames - co-supervision with Dr Karim Jerbi
-:::
-
-
-:::{grid-item-card} Elizabeth DuPre
-:margin: 3
-:columns: 12 3 3 3
-:class-body: text-center
-:link: https://github.com/emdupre
-:img-top: https://avatars.githubusercontent.com/u/15017191?v=4
-Post-doctoral fellow - finding shared functional patterns via alignment techniques
+```{card} Hao-Ting Wang
+:header: ![Hao-Ting Wang](../images/profile_haoting.jpg)
+:url: https://wanghaoting.com
+Post-doctoral fellow - _foundation models for fMRI_
+```
+
+```{card} Isil Bilgin
+:header: ![Isil Bilgin](../images/profile_isil.jpg)
+:url: https://github.com/complexbrains
+Post-doctoral fellow - _brain-aligned large language models_ - co-supervision with Dr Leila Wehbe
+```
+
+```{card} Yann Harel
+:header: ![Yann Harel](../images/profile_yann.jpg)
+:url: https://github.com/hyruuk
+Post-doctoral fellow - _brain/behaviour correlates of flow in videogames_ - co-supervision with Dr Karim Jerbi
+```
+
+
+```{card} Elizabeth DuPre
+:header: ![Elizabeth Dupre](https://avatars.githubusercontent.com/u/15017191?v=4)
+:url: https://github.com/emdupre
+Post-doctoral fellow - _finding shared functional patterns via alignment techniques_
 :::
 ::::
 
 ## PhD students
 ::::{grid}
 
-:::{grid-item-card} Sana Ahmhadi
-:margin: 3
-:columns: 12 3 3 3
-:class-body: text-center
-:link: https://www.linkedin.com/in/sana-ahmadi/
-:img-top: images/profile_sana.jpg
-Phd student - scaling up brain encoding models with high-performance computing - co-supervision with Dr Tristan Glatarad
-:::
-
-:::{grid-item-card} Maëlle Fréteault
-:margin: 3
-:columns: 12 3 3 3
-:class-body: text-center
-:link: https://github.com/maelleF
-:img-top: https://avatars.githubusercontent.com/u/29599311?v=4
-Phd student - personalized auditory brain encoding models - co-supervision with Dr Nicolas Farrugia
-:::
-
-:::{grid-item-card} Maximilien LeClei
-:margin: 3
-:columns: 12 3 3 3
-:class-body: text-center
-:link: https://github.com/MaximilienLC
-:img-top: images/profile_maximilien.jpg
-PhD student - neuroevolution for human alignment in videogames
-:::
-
-:::{grid-item-card} Marie-Ève Picard
-:margin: 3
-:columns: 12 3 3 3
-:class-body: text-center
-:link: https://github.com/me-pic
-:img-top: https://avatars.githubusercontent.com/u/77584086?v=4
-PhD student - physiological correlates of brain/behaviour in videogames - co-supervision with Dr Pierre Rainville
-:::
-
-:::{grid-item-card} Pravish Sainath
-:margin: 3
-:columns: 12 3 3 3
-:class-body: text-center
-:link: https://pravishsainath.wixsite.com/mysite
-:img-top: https://avatars.githubusercontent.com/u/13696562?v=4
-Phd student - brain alignment in memory models - co-supervision with Dr Guillaume Lajoie
-:::
+```{card} Maëlle Freteault
+:header: ![Maelle Freteault](https://avatars.githubusercontent.com/u/29599311?v=4)
+:url: https://github.com/maelleF
+Phd student - _personalized auditory brain encoding models_ - co-supervision with Dr Nicolas Farrugia
+```
+
+```{card} Maximilien LeClei
+:url: https://github.com/MaximilienLC
+:header: ![](../images/profile_maximilien.jpg)
+PhD student - _neuroevolution for human alignment in videogames_
+```
+
+```{card} Marie-Ève Picard
+:url: https://github.com/me-pic
+:header: ![](https://avatars.githubusercontent.com/u/77584086?v=4)
+PhD student - _physiological correlates of brain/behaviour in videogames_ - co-supervision with Dr Pierre Rainville
+```
+
+```{card} Pravish Sainath
+:url: https://pravishsainath.wixsite.com/mysite
+:header: ![](https://avatars.githubusercontent.com/u/13696562?v=4)
+Phd student - _brain alignment in memory models_ - co-supervision with Dr Guillaume Lajoie
+```
 
-:::{grid-item-card} Xanthy Lajoie
-:margin: 3
-:columns: 12 3 3 3
-:class-body: text-center
-:link: https://github.com/Xanthylajoie
-:img-top: images/profile_xanthy.jpg
-Phd student - sex effects on language functional connectivity - co-supervision with Dr Simona Brambati
-:::
 ::::
 
 ## Master's student
 ::::{grid}
-:::{grid-item-card} Hugo Delhaye
-:margin: 3
-:columns: 12 3 3 3
-:class-body: text-center
-:link: https://github.com/HugoDelhaye
-:img-top: images/profile_hugo.jpg
-Master's student in psychology - measuring curiosity in videogames
-:::
+```{card} Hugo Delhaye
+:url: https://github.com/HugoDelhaye
+:header: ![](../images/profile_hugo.jpg)
+Master's student in psychology - _measuring curiosity in videogames_ - co-supervision with Dr Audrey Durand
+```
 ::::
 
-
 ## Alumni
- * **François Paugam**, PhD student - brain/behaviour imitation in videogames - co-supervision with Dr Guillaume Lajoie
- * **Mikkel Schöttner**, PhD student visitor Mitacs internship spring 2024 - graph neural network for brain/phenotype association in HCP
+ * [**François Paugam**](https://www.linkedin.com/in/françois-paugam-b1835910b/), PhD student (2025) - _brain/behaviour imitation in videogames_ - co-supervision with Dr Guillaume Lajoie
+ * [**Sana Ahmhadi**](https://www.linkedin.com/in/sana-ahmadi/), PhD student (2024) - _scaling up brain encoding models with high-performance computing_ - co-supervision with Dr Tristan Glatarad
+ * [**Mikkel Schöttner**](https://www.linkedin.com/in/mikkel-schoettner/), PhD student visitor Mitacs internship (2024) - _graph neural network for brain/phenotype association in HCP_.