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pbellec committed May 22, 2024

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6 changes: 3 additions & 3 deletions content/_config.yml
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# Learn more at https://jupyterbook.org/customize/config.html

title: SIMEXP lab
author: SIMEXP lab team
logo: logo.jpg
author: SIMEXP lab team
logo: images/simexp.png

# Force re-execution of notebooks on each build.
# See https://jupyterbook.org/content/execute.html
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# Add GitHub buttons to your book
# See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository
html:
favicon: images/favicon.ico
favicon: images/favicon.png
use_issues_button: true
use_repository_button: true

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format: jb-book
root: intro
chapters:
- file: manifesto
- file: coc
- file: members
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# Code of conduct
The laboratory for brain simulation and exploration (SIMEXP) is dedicated to providing an environment where people are kind and respectful to each other. This could really be the end of that code of conduct, but some forms of harassment and negative behavior are fairly hard to identify at first. Please read carefully through the rest of the document to make sure you avoid them. There is also a section to know what to do and expect if you experience behavior that deviates from this code of conduct.

## Respecting differences
SIMEXP members come from many cultures and backgrounds. We therefore expect lab members to be very respectful of different cultural practices, attitudes, and beliefs. This includes being aware of preferred titles and pronouns, as well as using a respectful tone of voice.

While we do not assume SIMEXP members know the cultural practices of every ethnic and cultural group, we expect members to recognize and respect differences within our community. This means being open to learning from and educating others, as well as educating yourself.

## Harassment
No form of harassment will be tolerated. Harassment includes, but is not limited to:
* Verbal comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, diet (vegetarian, lactose-free, vegan, etc), disability, marital or family status, pregnancy, pregnancy-related conditions, physical appearance, body size, race, age or religion.
* Sexual images in public spaces
* Deliberate intimidation, stalking, or following
* Harassing photography or recording
* Sustained disruption of work
* Inappropriate physical contact
* Unwelcome sexual attention
* Advocating for, or encouraging, any of the above behaviour

## Microaggressions
Incidents can take the form of “microaggressions,” which is a damaging form of harassment. Microaggressions are the everyday slights or insults which communicate negative messages to target individuals, often based upon their marginalized group membership. The [micropedia of microaggression](https://www.themicropedia.org/) is an excellent resource to learn more on the may forms microaggression can take (see some examples in the note below). Over time, microagressions can take a great toll on mental and emotional health, and the target’s feeling of belonging in science and academia.

:::{note}
The following examples can all be labelled micro-aggressions:
* commenting on a woman’s appearance rather than her work;
* only directing questions at male colleagues when there are female experts in the room;
* telling someone of colour that they “speak such good English”;
* forcefully praising meat to an individual with a vegetarian diet;
* praising alcoholic drinks to an individual who do not consume them.
* Exclusion from a group can be a common nonverbal form of microaggression.
* Microaggressions can be couched in the form of a “compliment,” (e.g. “you’re too attractive to be a scientist”).
:::

## Enforcement
Members should seek to pro-actively eliminate behaviors that deviate from our code of conduct. If a member engages in harassing behaviour, the direction of the laboratory and the research center will take any actions necessary to keep the SIMEXP lab a welcoming environment for all. This includes warning the offender, and potentially expulsion from the laboratory. We expect laboratory members to follow these rules at the office and work-related social activities. Members asked to stop any harassing behavior are expected to comply immediately. We think people should follow these rules outside of work too!

## Reporting
If someone makes you or anyone else feel unsafe or unwelcome, please report it as soon as possible in person, or in writing to [Pierre Bellec](mailto:[email protected]) or [Julie Boyle](mailto:[email protected]). It is also possible to make a report with the [direction of CRIUGM](https://criugm.qc.ca/a-propos/notre-equipe/). The direction will follow up with you to understand the problem, and take the necessary actions to resolve it without your direct involvement. Harassment and other code of conduct violations considerably reduce the value of the research environment for everyone, and are taken very seriously. We strive to make the SIMEXP environment rich and joyful for everyone, at all time.
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31 changes: 29 additions & 2 deletions content/intro.md
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# Welcome
# SIMEXP

The laboratory for brain simulation and exploration 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](). 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, most notably as part of the Canadian Consortium on Neurodegeneration in Aging ([CCNA](https://ccna-biomarkers.readthedocs.io/)).
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.

::::{card-carousel} 3

:::{card} CRIUGM
:margin: 3
:class-body: text-center
:link: http://www.criugm.qc.ca/en.html
:img-top: images/logo_criugm_white.png
Research centre of the Montreal Geriatrics Institute
:::

:::{card} UdeM
:margin: 3
:class-body: text-center
:link: https://psy.umontreal.ca/accueil/
:img-top: images/logo_udem.png
Psychology department, University of Montreal
:::

:::{card} CNeuroMod
:margin: 3
:class-body: text-center
:link: https://cneuromod.ca
:img-top: images/logo_neuromod_black.png
The Courtois project on neuronal modelling
:::
::::
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# Manifesto

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.

## 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”).

## The brainhack way
Some laboratories operate under pretty strict labor division, with technical assistants helping researchers implement specific methods. SIMEXP works in data science, and our methods are computational. On one hand, relying on other people to implement computations dramatically limits both your ability to iterate quickly, and your understanding of the methods. On another hand, blind applications of algorithms to neural data without deep understanding of the neuroscience questions is not productive and is, in our typical use cases, a complete waste of time. A core SIMEXP belief is that lab members need to develop both strong computational and neuroscience skills, on top of their own area of expertise. This can be arduous at times, but is key for the type of research we do. It is also a huge asset for employability both inside and outside of academia.

## 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.

## 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.

## Well-being
Finally, there are workplaces that encourage, or even push people to work themselves into the ground. It will happen from time to time to work hard, for a deadline or for the flow. But nothing great happens with chronically overworked people, especially in a creative business. Make sure you take care of yourself. If you feel down or tired, please take as many days off as necessary. Take holidays, it’s great. It is OK to focus on your personal life at times. It is also OK to pass on opportunities, you can’t do it all. Others will come. If you feel overwhelmed, find support. If you see someone being overwhelmed, be patient and supportive. Friends, peers or professionals, there are many ways to find balance. Try to find the mix that works for you, and be proactive at building this support network. You can also join us for Yoga!
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# Lab members
# Members

## Staff

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:class-body: text-center
:link: https://github.com/pbellec
:img-top: https://avatars.githubusercontent.com/u/1670887?v=4?s=100
Lab founder and director
:::

:::{card} Arnaud Boré
:margin: 3
:class-body: text-center
:link: https://github.com/arnaudbore
:img-top: https://avatars.githubusercontent.com/u/2171665?v=4?s=100
Data scientist
Associate professor - scientific director
:::

:::{card} Julie Boyle
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Project manager
:::

::::

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:::{card} Basile Pinsard
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:::
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:::{card} Marie St-Laurent
:margin: 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
:::
::::

## Post-doctoral fellows

::::{card-carousel} 3

:::{card} Hao-Ting Wang
:margin: 3
:class-body: text-center
:link: https://wanghaoting.com
:img-top: images/profile_haoting.jpg
Post-doctoral fellow - foundation models for fMRI
:::

:::{card} Isil Bilgin
:margin: 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
:::

:::{card} Yann Harel
:margin: 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
:::
::::

## PhD students
::::{card-carousel} 3

:::{card} Maëlle Fréteault
:margin: 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
:::

:::{card} Maximilien LeClei
:margin: 3
:class-body: text-center
:link: https://github.com/MaximilienLC
:img-top: images/profile_maximilien.jpg
PhD student - neuroevolution for human alignment in videogames
:::

:::{card} Marie-Ève Picard
:margin: 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
:::
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::::{card-carousel} 3

:::{card} Pravish Sainath
:margin: 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} FranÇois Paugam
:margin: 3
:class-body: text-center
:link: https://github.com/FrancoisPgm
:img-top: images/profile_francois_p.jpg
Phd student - brain/behaviour imitation in videogames - co-supervision with Dr Guillaume Lajoie
:::

:::{card} Xanthy Lajoie
:margin: 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
:::

::::

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