various minor updates/corrections

Author: afrendeiro

README.md

@@ -2,9 +2,11 @@
 
 # Lab manual
 
-Welcome to the Rendeiro Lab Manual. This manual provides comprehensive information about the lab's culture, procedures, and workflows to ensure a collaborative and efficient research environment.
+Welcome to the Rendeiro Lab Manual.
 
-The manual is hosted in the [`lab-manual`](https://github.com/rendeirolab/lab-manual/tree/main/manual) repository on GitHub. It is written in [Markdown](https://daringfireball.net/projects/markdown/) and can be converted to HTML and PDF using [Pandoc](https://pandoc.org/).
+This manual provides comprehensive information about the lab's culture, procedures, and workflows to ensure a collaborative and efficient research environment.
+
+The manual is hosted in the [`lab-manual`](https://github.com/rendeirolab/lab-manual/) repository on GitHub. It is written in [Markdown](https://daringfireball.net/projects/markdown/) and can be converted to HTML and PDF using [Pandoc](https://pandoc.org/).
 
 This manual is open source and maintained collaboratively. Anyone on GitHub can propose changes.
 
@@ -27,7 +29,7 @@ To contribute:
 2. Submit a pull request with a clear, one-line description of the changes made.
 3. Follow best practices by adding reviewers and referencing related issues, if applicable.
 
-For adding a table of contents to any document, use [mdformat-toc](https://github.com/hukkin/mdformat-toc). Insert `<!-- mdformat-toc start -->` where the table of contents should appear, and run `mdformat <file.md>` on the edited file, or `make format` to format all.
+For adding a table of contents to any document, use [mdformat-toc](https://github.com/hukkin/mdformat-toc). Insert ```<!-- mdformat-toc start -->``` where the table of contents should appear, and run `mdformat <file.md>` on the edited file, or `make format` to format all.
 
 ## Acknowledgements
 

source/getting_started.md

@@ -20,12 +20,14 @@ Onboarding to-dos (responsability of the PI):
 
 1. Ask the new team member for their contact information (optional, but recommended for safety reasons) - [add your own information here](https://cemmat.sharepoint.com/:x:/s/rendeirolab/ETVfBUPmJYpIgl-yDccPCGkBZRMFtOTE9ExejqyvMq6msA?e=lxEuzO);
 1. Add the new team member to lab Microsoft team and mailing list;
-1. Share the lab's resources with the new team member:
+1. Share and introduce the lab's resources to the new team member:
    - the lab manual (this)
    - the lab code of conduct (see [code of conduct](code_of_conduct.md))
-   - the Github account ([here](https://github.com/rendeirolab))
    - lab infrastructure (such as Cytomine, VMs, etc: [infrastructure](infrastructure.md))
-1. Make sure the new team member follow up with the remaining of CeMM onboarding (IT, safety, etc)
+   - Github team ([https://github.com/rendeirolab](https://github.com/rendeirolab))
+   - Weights and Biases team ([https://wandb.ai/rendeiro-group](https://wandb.ai/rendeiro-group))
+   - HuggingFace team ([https://huggingface.co/RendeiroLab](https://huggingface.co/RendeiroLab))
+1. Make sure the new team member follows up with the remaining of CeMM onboarding (IT, safety, etc)
 
 ### CeMM-specific
 

source/offboarding.md

@@ -24,11 +24,9 @@ It is the responsability of the PI to communicate, initiate, and verify the foll
 1. Ask the new team member for their CeMM-independent contact information
 1. Ask the new team member whether they consent to be listed in the lab website as alumni
 1. Remove team member from external organizations:
-   - Github
-   - Weights and Biases
-   - HuggingFace
-   - the lab code of conduct (see [code of conduct](code_of_conduct.md))
-   - the Github account ([here](https://github.com/rendeirolab))
+   - Github ([https://github.com/rendeirolab](https://github.com/rendeirolab))
+   - Weights and Biases ([https://wandb.ai/rendeiro-group](https://wandb.ai/rendeiro-group))
+   - HuggingFace ([https://huggingface.co/RendeiroLab](https://huggingface.co/RendeiroLab))
    - lab infrastructure (such as Cytomine, VMs, etc: [infrastructure](infrastructure.md))
 1. Remove team member accounts from lab-specific infrastructure:
    - Cytomine

source/public_data.md

@@ -44,8 +44,6 @@ Prostate-specific:
 - StarDist
 - DeepCell
 - CellPose
-- Tumor-Infiltrating Lymphocytes Maps from TCGA H&E Whole Slide Pathology Images: https://wiki.cancerimagingarchive.net/pages/vi
-
-.action?pageId=33948919, https://stonybrookmedicine.app.box.com/v/cellreportspaper/folder/42003984813
+- Tumor-Infiltrating Lymphocytes Maps from TCGA H&E Whole Slide Pathology Images: https://wiki.cancerimagingarchive.net/pages/vi.action?pageId=33948919, https://stonybrookmedicine.app.box.com/v/cellreportspaper/folder/42003984813
 
 - NuCLS crowdsourcing approach, dataset, and explainable deep-learning method: https://github.com/PathologyDataScience/NuCLS

source/research.md

@@ -13,7 +13,7 @@
 1. Create a directory for the project in the CeMM cluster at: `/research/groups/lab_rendeiro/projects/`
    1. Create a directory inside called `data` to store raw data.
 1. Create a directory for the project in the CeMM cluster at: `/nobackup/groups/lab_rendeiro/projects/`
-   2\. Create a soft link between `/research/.../data` and `/nobackup/.../data`
+   1. Create a soft link between `/research/.../data` and `/nobackup/.../data`
 1. Create a `cemm_metadata.json` file in `/research/groups/lab_rendeiro/projects/$PROJECT/`
 1. Create a `cemm_metadata.json` file in `/nobackup/groups/lab_rendeiro/projects/$PROJECT/`