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strixy16 merged 8 commits into from
Dec 17, 2025
Merged

refactor: stylistic updates and linting configuration update #305

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3101463
feat: update markdownlint configuration and enhance pre-commit setup
jjjermiah Dec 4, 2024
402467c
chore: formatting
jjjermiah Dec 4, 2024
c3d3406
chore: formatting
jjjermiah Dec 4, 2024
63b0220
feat: update markdownlint command to include ignore path and configur…
jjjermiah Dec 4, 2024
3ca258d
Merge remote-tracking branch 'origin/main' into jjjermiah/dev/formatt…
strixy16 Dec 17, 2025
6badd0a
fix: correct pypi dependencies in pixi toml
strixy16 Dec 17, 2025
136efa0
style: add divider lines
strixy16 Dec 17, 2025
9de3437
style: make more consistent with JC page
strixy16 Dec 17, 2025
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1 change: 1 addition & 0 deletions .markdownlint.json
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Expand Up @@ -3,6 +3,7 @@
"no-inline-html": false,
"reference-links-images": false,
"link-fragments": false,
"no-alt-text": false,
"MD007": { "indent": 4 },
"code-block-style": false
}
2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
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Expand Up @@ -8,4 +8,4 @@ repos:
rev: v0.42.0
hooks:
- id: markdownlint
args: ["--ignore-path", ".markdownlintignore"]
args: ["--ignore-path", ".markdownlintignore", "--config", ".markdownlint.json"]
2 changes: 2 additions & 0 deletions docs/General/Meetings/.pages
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@@ -1,3 +1,5 @@
title: Meetings

nav:
- index.md
- lab_meeting.md
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17 changes: 13 additions & 4 deletions docs/General/Meetings/Radiomics_meeting.md
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# Radiomics Meeting
## Time and Room
Radiomics meeting happens every 2 weeks on Tuesday, 2:00 - 3:00pm at PMCRT 11-710.

## When and Where?

**Day**: Tuesdays, bi-weekly

**Time**: 2:00–3:00 PM

**Venue**: PMCRT 11-710.

## Agenda

* Flash updates: 5-10 minutes/person on what they’re working on.
* Q&A for project related challenges.
* Award/presentation updates, if any.
* Data updates: New ORCESTRA announcements for datasets, dataset suggestions, etc.
* Data updates: New ORCESTRA announcements for datasets, dataset suggestions, etc.
* Grant updates.

## Attendees

Attendance is mandatory for Radiomics lab members.

## Resources
The meeting notes need to be filled out for every meeting in the [Radiomics meeting - coverage](https://docs.google.com/document/d/1zlbdjlhEnUrWQExUBrYL56z_FiCE_Dd6nHSAHpGnk5o/edit?usp=sharing) document.

The meeting notes need to be filled out for every meeting in the [Radiomics meeting - coverage](https://docs.google.com/document/d/1zlbdjlhEnUrWQExUBrYL56z_FiCE_Dd6nHSAHpGnk5o/edit?usp=sharing) document.
2 changes: 1 addition & 1 deletion docs/General/Meetings/index.md
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Expand Up @@ -16,4 +16,4 @@ The following meetings are specific to disciplines in the lab and are mandatory
| [PGx team meeting](pgx_meeting.md) | Biweekly | Tuesdays, 2-3 p.m. | #pharmacogenomics |
| [Software Developer team meeting](Software_dev_meeting.md)| Monthly | Mondays, 12-1 p.m. | #software-developer|

We use The Meeting Owl for our meetings so they can be ran hybridly. See the [Meeting Owl Basics](owl_basics.md) page to learn more about how to use it.
We use The Meeting Owl for our meetings so they can be ran hybridly. See the [Meeting Owl Basics](owl_basics.md) page to learn more about how to use it.
37 changes: 20 additions & 17 deletions docs/General/Meetings/journal_club.md
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**Welcome to Journal Club!**

Whether you’re new to the lab or looking for a refresher, this guide will help you navigate **Journal Club (JC)**—our weekly session to explore research papers, exchange ideas, and grow as scientists. Let’s dive in!
Whether you’re new to the lab or looking for a refresher, this guide will help you navigate **Journal Club (JC)** — our bi-weekly session to explore research papers, exchange ideas, and grow as scientists. Let’s dive in!

## When and Where?

**Day**: Wednesdays, usually the first and third week of the month

**Time**: 12:00–1:00 PM

**Location**: PMCRT 11-710

**Format**: Two presenters (30 minutes each)

---

## What Is Journal Club?

Expand All @@ -17,21 +29,12 @@ It’s all about **learning**, **critiquing**, and **getting inspired**.

---

## When and Where?

- **Day**: Wednesdays, usually the first and third week of the month
- **Time**: 12:00–1:00 PM
- **Location**: PMCRT 11-710
- **Format**: Two presenters (30 minutes each)

---

## How Journal Club Works?

- **Presenters**:
- **Option 1**: Each presenter discusses a different paper.
- **Option 2**: Both presenters focus on the same paper, with one highlighting its strengths and the other critiquing its weaknesses.

- **Interactive Elements**:
- **Dumb Questioner**: A participant is randomly chosen to ask a “dumb” question, encouraging open and fun discussions.
- **Audience Poll**: For shared papers, attendees vote on whether the positive or critical perspective was more compelling.
Expand Down Expand Up @@ -62,13 +65,13 @@ It’s all about **learning**, **critiquing**, and **getting inspired**.
If you are planning on presenting remotely, please connect with someone **onsite** to ensure the [Meeting Owl](owl_basics.md) is set up for you.
---

## Audience Role
## Audience Role

Even if you’re not presenting, your participation is essential!
Even if you’re not presenting, your participation is essential!

- **Read the paper** beforehand, if possible.
- **Engage**: Ask questions and share your insights.
- **Be Open**: Every perspective adds value.
- **Read the paper** beforehand, if possible.
- **Engage**: Ask questions and share your insights.
- **Be Open**: Every perspective adds value.

---

Expand All @@ -78,4 +81,4 @@ Even if you’re not presenting, your participation is essential!

---

Journal Club is a great way to stay curious, collaborate, and learn together. We look forward to seeing you there!
Journal Club is a great way to stay curious, collaborate, and learn together. We look forward to seeing you there!
6 changes: 4 additions & 2 deletions docs/General/Meetings/lab_meeting.md
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# Lab Meeting

## Details
## When and Where?

**Time**: Every Tuesday from 10:30 AM to 12:00 PM.
**Day**: Tuesdays

**Time**: 10:30–12:00 PM

**Venue**: PMCRT 4-204.

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18 changes: 8 additions & 10 deletions docs/General/Meetings/project_tracking.md
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# Project Tracking

## For the first 10-15 minutes of every lab meeting, the lab discusses the progress of the projects.
## For the first 10-15 minutes of every lab meeting, the lab discusses the progress of the projects

When it is your turn to present, you **must** include a copy of [this slide](https://docs.google.com/presentation/d/1Gk5uMTpn8XCMvXmoP8AWjW3x-QM0mHfPB1BfteBfqK8/edit#slide=id.g2684830fade_0_0) at the beginning of your slide deck.
When it is your turn to present, you **must** include a copy of [this slide](https://docs.google.com/presentation/d/1Gk5uMTpn8XCMvXmoP8AWjW3x-QM0mHfPB1BfteBfqK8/edit#slide=id.g2684830fade_0_0) at the beginning of your slide deck.
We will be using it to go through the progress of the projects.

We use four different spreadsheets to track updates. Each of them will be linked in their subsection below.
We use four different spreadsheets to track updates. Each of them will be linked in their subsection below.

### To Dos & Deadlines for BHK

If there are any upcoming tasks or deadlines that you need Ben to address, [this spreadsheet](https://docs.google.com/spreadsheets/d/1gnfwpzSho3ePF1WhFLZC8aGuDp9IG-mM6GMHbURjy8A/edit?gid=0#gid=0) is where you add your requests.
The following are the columns in the spreadsheet:

Expand All @@ -18,8 +19,8 @@ The following are the columns in the spreadsheet:
- **Comments**: Add any additional comments that you think are necessary.
- **Relevant links**: Add any relevant links that are necessary for this task.


### Manuscript Progress

If you have any updates on the progress of your manuscript, [this spreadsheet](https://docs.google.com/spreadsheets/d/1dZcNEmIGCdFthwj5cskuATfDTJ-7Mup8D5gO_HrmIPE/edit?usp=sharing) is where you add your updates.
The following are the columns in the spreadsheet:

Expand All @@ -29,9 +30,9 @@ The following are the columns in the spreadsheet:
- **Status**: A drop-down menu where you can select the status of the manuscript. For example, if the manuscript has been submitted, you can select 'Submitted to journal'
- **Comments**: Add any additional comments that you think are necessary. This will include any updates on the progress of the manuscript, such as if there are experiments being done, any review necessary, etc. This will typically be updated during pre-lab meeting overview.


### Grants & Award Applications
Information and updates regarding any grants or awards the lab is applying for can be found in [this spreadsheet](https://docs.google.com/spreadsheets/d/1EuFaUxtk2kPueZwmjTopyRvnFduuSbp5Byf0gEWA7kw/edit?usp=sharing).

Information and updates regarding any grants or awards the lab is applying for can be found in [this spreadsheet](https://docs.google.com/spreadsheets/d/1EuFaUxtk2kPueZwmjTopyRvnFduuSbp5Byf0gEWA7kw/edit?usp=sharing).
The following are the columns in the spreadsheet:

- **Proposed project/idea**: Add a general descriptive title for the project or idea.
Expand All @@ -49,8 +50,8 @@ The following are the columns in the spreadsheet:
- **Link to the Folder**: Add the URL to the folder where the application and relevant files are stored.
- **Comments**: Add any additional comments that you think are necessary.


### Data Access Status

Throughout your time in the lab, you may want to request access to additional datasets. [This spreadsheet](https://docs.google.com/spreadsheets/d/1j4umcD30PE8DM6LPCrkTUeKV3jUgaaPSUBis964FdrQ/edit?usp=sharing) is where you can track the status of your data access requests.
The following are the columns in the spreadsheet:

Expand All @@ -66,6 +67,3 @@ The following are the columns in the spreadsheet:
- **Submission Status**: Add the status of the submission using the drop-down menu; for example, if the request has been approved, you can select 'Approved'.
- **Data Location**: Add the location of the data once the request has been approved; for example, if the data is stored in H4H, GCP, etc.
- **Comments**: Add any additional comments that you think are necessary.



13 changes: 7 additions & 6 deletions docs/General/lab_mission.md
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At BHK Lab, we are on a mission to revolutionize precision oncology by developing cutting-edge computational tools and predictive models. Our goal is to identify new cancer vulnerabilities and improve the delivery of precision medicine to patients.

### Research Focus
## Research Focus

Dive into the world of pharmacogenomics and imaging analysis using the power of machine learning and deep learning. We are all about using innovative approaches to understand cancer better and find new ways to combat it.

### Our Values
## Our Values

- Research Transparency: We believe in open science and transparency in our work.

- Reproducibility: Our research is solid, reproducible, and ready for peer review.

- Reusability: We make sure our tools and models can be easily reused by others to advance cancer research.

### Inclusion, Diversity, Equity, and Accessibility (IDEA)
## Inclusion, Diversity, Equity, and Accessibility (IDEA)

We are committed to making science accessible to everyone. Inclusion, diversity, equity, and accessibility are not just buzzwords for us; they are the guiding principles of our lab.

### Lab Culture
## Lab Culture

Step into our world of collaboration and creativity! We're a diverse team from various disciplines, coming together to tackle one of the biggest challenges in medicine and we thrive on supporting each other's ideas.

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74 changes: 48 additions & 26 deletions docs/onboarding_offboarding/Onboarding/vpn.md
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Expand Up @@ -2,7 +2,7 @@

## Quick introduction: why do we need a VPN?

A Virtual Private Network (VPN) is essential in the workplace to ensure secure and private access to the company network, especially when working remotely or on public Wi-Fi.
A Virtual Private Network (VPN) is essential in the workplace to ensure secure and private access to the company network, especially when working remotely or on public Wi-Fi.

A VPN encrypts internet traffic, protecting sensitive data from potential cyber threats and unauthorized access. This helps maintain confidentiality, ensures data integrity, and supports secure access to internal resources, safeguarding the organization's digital environment.

Expand All @@ -19,53 +19,75 @@ If you are a Windows or Mac user, that's it. The manual is pretty good, simple a
If you are on Ubuntu... There's no downloading link or steps. You get stuck on the very first step. Don't worry, you don't have to open a ticket on Helpdesk and wait for them to respond... The next section will make things easier for you.

## Downloading GlobalProtect software on Ubuntu

After contacting Helpdesk a few times, I finally got an email with the downloading instructions for Ubuntu. Here I leave the email, I think it may be useful.

> Download the installation file from the [link](https://roseshare.rose-hulman.edu/portal/s/162637781701644125980.tgz) or via the curl command:
>
curl https://roseshare.rose-hulman.edu/portal/s/162637781701644125980.tgz --output PanGPLinux-5.3.0-c32.tgz --ciphers 'DEFAULT:!DH'
Download the installation file from the [link](https://roseshare.rose-hulman.edu/portal/s/162637781701644125980.tgz) or via the curl command:

```console
curl https://roseshare.rose-hulman.edu/portal/s/162637781701644125980.tgz --output PanGPLinux-5.3.0-c32.tgz --ciphers 'DEFAULT:!DH'
```

Unzip tar file, by running:

```console
tar -xvf PanGPLinux-5.3.0-c32.tgz
```

Install the program:

On Ubuntu/Debian, this is done through the command:

```console
sudo dpkg –i GlobalProtect_deb-5.3.0.0-32.deb
```

> Unzip tar file, by running: tar -xvf PanGPLinux-5.3.0-c32.tgz
On Redhat/CentOS, this is done through the command:

> Install the program:
```console
sudo yum localinstall GlobalProtect_rpm-5.3.0.0-32.rpm
```

> On Ubuntu/Debian, this is done through the command:
>
sudo dpkg –i GlobalProtect_deb-5.3.0.0-32.deb
To start the program, simply enter in a shell:

> On Redhat/CentOS, this is done through the command:
>
sudo yum localinstall GlobalProtect_rpm-5.3.0.0-32.rpm
```console
globalprotect
```

> To start the program, simply enter in a shell
>
globalprotect

> and then a prompt should display.
and then a prompt should display.

> From the prompt, run
>
connect -portal connect2.uhn.ca
From the prompt, run:

```console
connect -portal connect2.uhn.ca
```

> Login with your email address (username@uhn.ca) as your username and password.
Login with your email address (<username@uhn.ca>) as your username and password.

> Type quit to exit the prompt.
Type quit to exit the prompt.

## That's it - just remember connecting and disconnecting the VPN every time you need it

Now that you have your laptop configured for the VPN, don't forget connecting every time you want to use it, running the following command:

globalprotect
```console
globalprotect
```

And then running in the prompt:

connect -portal connect2.uhn.ca
```console
connect -portal connect2.uhn.ca
```

When you want to disconnect from the VPN, you have to run

globalprotect
```console
globalprotect
```

And then in the prompt:

disconnect
```console
disconnect
```
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