adding new commits to revert

.github/workflows/deploy.yml

@@ -0,0 +1,30 @@
+name: Deploy MkDocs site to GitHub Pages
+
+on:
+  push:
+    branches:
+      - main  # deploy whenever main branch is updated
+
+permissions:
+  contents: write  # allows pushing to gh-pages branch
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+
+      - name: Install dependencies
+        run: |
+          pip install mkdocs  # or your theme/plugins
+
+      - name: Deploy to GitHub Pages
+        run: |
+          mkdocs gh-deploy --force

docs/Policies/hours_remote_vacation.md

@@ -1,6 +1,6 @@
 # Working hours, remote work, and vacation
 
-As our work is predominantly theoretical/computational, we have a lot of flexibility around when and where we work. Please set your hours based on how you work best. I'm generally in lab ~930-~6. 
+As our work is predominantly theoretical/computational, we have a lot of flexibility around when and where we work. Please set your hours based on how you work best. I'm generally in lab ~930-~6. As our work is predominantly theoretical/computational, we have a lot of flexibility around when and where we work. Please set your hours based on how you work best. That being said, part of our job is being a contributing member to the lab community, and in my experience the spontaneous interactions we have here are some of the most impactful for the quality of our research. I'm generally in lab ~930-~6, and I try to be as available as possible during that time.
 
 If it fits you, I would encourage you to plan one day a week where you work from home (or elsewhere out of office). This shift in perspective can be helpful for your work and I encourage you to take advantage of this time to think freely and critically about your project and current approaches. I do ask that you plan to attend lab meetings in person -- in my experience, remote attendance encourages people to listen (at best), rather than participate, in lab meetings. Also, I ask that you plan to be physically in lab 3-4 days a week. Of course, this can vary week to week and exceptions will be made to fit people’s circumstances.
 

docs/README.md

@@ -1,6 +1,5 @@
 # Lab-Handbook
-The lab handbook of the Levenstein Lab for NeuroAI and Dynamics at Yale University
-
+The lab handbook of the Levenstein Lab for NeuroAI and Dynamics at Yale University. Please note that this is an in-development and "living document", which means that it will evolve as needed to fit the lab as it grows and develops. Furthermore, it means that as a lab member, you're encouraged to contribute and discuss its contents with Dan and in the #lab-handbook channel on slack.  
 
 **About the lab**
 
@@ -16,27 +15,3 @@ In addition to our work on sleep, the lab works broadly at the interface of theo
 So you want to join the lab? - prospective members start here
 
 [Onboarding](https://github.com/LevensteinLab/Lab-Handbook/blob/main/onboarding.md) - new members start here
-
-
-**Table of Contents**
-
-- `README.md`: Landing page.
-- `contact.md`: Names, positions, emails for current lab members.
-- `meetings.md`: Specified schedule for regular meetings 
-- `onboarding.md`: Relevant information for your first day through your first couple of weeks. 
-- `Resources and How-Tos`
-    - `adobe.md`: Instructions on how to get access to Adobe suite tools (e.g. for figures)
-    - `basic_github.md`: Some helpful pointers on how to use git for version control and also how to make contributions to this repository.
-    - `gen_ai.md`: Tips on how to use generative AI tools responsibly and ethically.
-    - `hpc.md`: How to get access to the Misha HPC cluster.
-    - `mailing_lists.md`: Helpful mailing lists to engage in the WTI research community (journal clubs etc.)
-    - `mental_health.md`: Resources and support options for managing mental health
-    - `printers.md`: Tutorial on how to connect to lab printer, as well as links to drivers & docs
-    - `recommended_reading.md`: Links to relevant publications on topics of interest to the lab (e.g. sleep, memory consolidation, neuroAI)
-    - `science_general.md1`: How to do good science (in general).
-    - `travel.md`: Information on how to arrange travel with Yale.
-- `Lab policies, practices, and expectations`
-    - `code_software.md`: Link to helpful resources on good coding conventions
-    - `health_wellness.md`: Tips on how to manage work-life balance and health while doing research
-    - `hours_remote_vacation.md`: Policies on remote work, working hours, vacations, and holidays
-

docs/Resources/hpc.md

@@ -2,7 +2,7 @@
 
 As part of computational research, we will need to dispatch jobs to high-performance computing (HPC) clusters. Access to these clusters gives us stronger power for computationally-intensive tasks like training models. Running the same process on your local machine may take *much* more time.
 
-To get started visit this page for [some info](https://docs.ycrc.yale.edu/clusters/misha/#access-the-cluster) about the HPC prepared by the Yale Center for Research Computing (YCRC) specifically for the Wu Tsai Institute.
+To get started visit this page for [some info](https://docs.ycrc.yale.edu/clusters/misha/#access-the-cluster) about the HPC prepared by the Yale Center for Research Computing (YCRC) specifically for the Wu Tsai Institute. To use the cluster off-campus, you will need to use a VPN, please see the `vpn.md` file for instructions.
 
 ### Instructions
 1. Fill out the [form](https://docs.google.com/forms/d/e/1FAIpQLSfLghL1gSHRkIQj73zPzvLCJ0sojm9aUHZLQGBD_auD054gqA/viewform?usp=send_form) to access the cluster, noting Dan as the PI from which to get access. You should get access in ~48 hours. 

docs/Resources/recommended_reading.md

@@ -27,6 +27,10 @@
 - https://www.nature.com/articles/s41583-023-00705-w
 - https://www.nature.com/articles/s41593-019-0520-2
 
+**Replay in brains and ANNs**
+- https://www.cell.com/trends/neurosciences/abstract/S0166-2236(21)00144-2
+- https://direct.mit.edu/neco/article-abstract/33/11/2908/107071/Replay-in-Deep-Learning-Current-Approaches-and
+
 **hippocampus**
 
 - https://pmc.ncbi.nlm.nih.gov/articles/PMC4648295/

docs/Resources/vpn.md

@@ -0,0 +1,3 @@
+Some of Yale's internal tools, such as the cluster, are only available on the Yale network. If you are off campus, you will need to use a VPN. For Windows and Mac OS X, download the Cisco AnyConnect VPN Client from the [ITS Software Library](https://yale.onthehub.com/WebStore/ProductSearchOfferingList.aspx?srch=cisco). See [this guide]([url](https://docs.ycrc.yale.edu/clusters-at-yale/access/vpn/)) for Linux and for the full instructions, which will be briefly outlined below.
+
+Once you have installed the Cisco software, type in the server address: `access.yale.edu` and click connect. This should open an authentication tab in your browser, where you will be able to log in using your Yale net ID and password.

docs/onboarding.md

@@ -17,7 +17,7 @@
         - Yale Central ID Center, 57 Lock St (**M-F, 8am-4pm**), walk-in visits accepted but appointments are encouraged.
         - Medical School ID Center, 333 Cedar St (**M-Th, 8am-12pm**) for walk-ins
     - Get 100 College/WTI card access (note: it will take about 24 hours for your card to gain access)
-        - Note that a Yale ID card does NOT automatically provide access to 100 College/WTI. You must request access seaparately; this is done through Dan and/or Jenn.
+        - Note that a Yale ID card does NOT automatically provide access to 100 College/WTI. You must request access seaparately; ideally email the WTI facilities manager, [Matt Milano](mailto:matthew.milano@yale.edu).
 - Familiarize yourself with campus, and how to get to 100 College Institute
     - Multiple areas of campus (Old Campus, Science Hill, etc)
     - The Wu Tsai Institute is located on the 11th floor at 100 College Street. The building is owned by Alexion Pharmaceuticals (owned by AstraZeneca)