Merge branch 'main' into mtran/add-tidyverse-page

.gitignore

@@ -11,3 +11,5 @@ site
 __pycache__
 
 **/__pycache__/*
+
+**/.idea

docs/General/Meetings/Radiomics_meeting.md

@@ -0,0 +1,16 @@
+# Radiomics Meeting
+## Time and Room
+Radiomics meeting happens every 2 weeks on Tuesday, 2:00 - 3:00pm at 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.  
+* 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.

docs/General/Meetings/journal_club.md

@@ -0,0 +1,73 @@
+# 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!  
+
+## **What Is Journal Club?**
+
+Journal Club is a weekly session designed to:
+
+- **Discuss**: Explore research papers relevant to our lab or scientific interests.
+- **Analyze**: Evaluate the strengths and weaknesses of each study.
+- **Collaborate**: Share insights on how the paper could impact or inspire our work.
+- **Apply**: Optionally consider incorporating the findings or methods into your projects.
+
+It’s all about **learning**, **critiquing**, and **getting inspired**.
+
+---
+
+## **When and Where?**
+
+- **Day**: Wednesdays  
+- **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.
+
+---
+
+## **How to Present at Journal Club?**
+
+1. **Choose a paper**:
+    - Select a paper that interests you or aligns with the lab’s focus.
+    - Ensure its relevance and potential impact on ongoing projects.
+
+2. **Prepare your slides**:
+    - **Introduction**: Why did you choose this paper?  
+    - **Methods**: How was the study conducted?  
+    - **Results**:  What are the key findings?  
+    - **Key Takeaways**: What are the main insights from the study?  
+    - **Your Perspective**: What worked well? What could be improved?  
+
+3. **Share the paper**:
+    - *(Optional)* Upload the paper to Slack at least two days before the meeting for participants to review.
+
+---
+
+## **Audience Role**  
+
+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.  
+
+---
+
+## **Resources**
+
+- After presenting, upload your slides to the **[JC Slides List](https://docs.google.com/spreadsheets/d/17j4Pzs24Vkem04yUdMgydnpDWQEGwLaPxVF7j7PFapE/edit?gid=0)** to maintain a shared record for future reference.
+
+ ---
+
+Journal Club is a great way to stay curious, collaborate, and learn together. We look forward to seeing you there! 

docs/General/Meetings/lab_meeting.md

@@ -0,0 +1,39 @@
+# Lab Meeting
+
+## Details
+
+**Time**: Every Tuesday from 10:30 AM to 12:00 PM.
+
+**Venue**: PMCRT 4-204.
+
+**Presenter(s)**: One.
+
+## Status Updates
+
+Every lab meeting begins with a 15-20 minute status update. See [pre lab meeting catchup slides](https://docs.google.com/presentation/d/1Gk5uMTpn8XCMvXmoP8AWjW3x-QM0mHfPB1BfteBfqK8/edit#slide=id.g2684830fade_0_0) for a list of status update materials.
+
+## Meeting Objectives
+
+During lab meetings, you may present the research idea and feasibility, preliminary analyses, progress of your work, or any topics that require feedback from the lab.
+
+You will be sent an email notifying you of the date of presentation as per the lab schedule. If you want to (re)schedule a lab meeting, please contact the lab coordinator after finding a person to switch your presentation with.
+
+### Slides
+
+It is best to follow a standard slide format:
+
+* Agenda
+* Introduction
+* Methods
+* Results
+* Challenges
+* Key Takeaway/Learning
+* Future Directions
+
+!!! tip
+
+    Feel free to use the BHK lab-wide templates for the slide deck:
+
+    * [BHKLab External Presentation Template](https://docs.google.com/presentation/d/1B-iTfzHvVSOD9fW80NZz14ct6HENHWOgTxU8C673TmY/edit#slide=id.g855186e73f_0_44)
+
+    * [BHKLab Internal Presentation Template](https://docs.google.com/presentation/d/1GRdR3ExBVbXwgmjkHBp82i3x_mdQZPzJNHsEz1LiYWk/edit#slide=id.p)

docs/General/Meetings/owl_basics.md

@@ -0,0 +1,17 @@
+# Lab Owl meeting Basics
+
+The Owl is a device that works as video and audio input for all meetings conducted in the BHK lab. It is pivotal to include the Owl in all lab meetings to bridge the gap between the users tuning in remote to the users on site.
+
+## How to find/obtain the Owl
+
+1. Go to Jermiah's work station (W-16).
+2. Grab the key located on the bottom side of Jermiah's desk.
+3. Using the key open the top drawer of the filing cabinet under Jermiah's workstation and grab the key labelled "Owl key".
+4. Use this new key to open the bottom drawer of the filing cabinet directly to the right of the lab/GPU server and pull out the green Owl duffle bag.
+
+## How to use the Owl
+
+The Owl has two major setup components. The Owl must be connected to an electrical outlet and also be connected to your computer via a USB connection.
+If you have a Mac laptop you may need to use an adapter to allow direct USB connection. Once the Owl is connected to power and your computer you may set it down in a spot that will
+be able to easily see/hear everyone participating in the meeting physically. If you're hosting the meeting you also want to verify that the Owl is being used as the
+audio and video input to the call.

docs/General/Meetings/project_tracking.md

@@ -0,0 +1,71 @@
+# Project Tracking
+
+## 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. 
+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. 
+
+### 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:
+
+- **Task**: Add a general descriptive title for the task.
+- **Deadline**: Add the deadline for this task.
+- **BHK review deadline**: Add the deadline for when you need Ben to review the task.
+- **Lab Members**: The lab members involved in this task. (If it's just yourself, only write your name. If it's multiple people, write all their names.)
+- **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:
+
+- **Lead Author (Mandatory)**: Add the name of the lead author of the manuscript. There can be multiple names if there are multiple lead authors working on this manuscript.
+- **Paper (Mandatory)**: Add the title of the manuscript.
+- **URL to the Folder (Mandatory)**: Add the URL to the folder where the manuscript and relevant files, such as figures, are stored.
+- **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). 
+The following are the columns in the spreadsheet:
+
+- **Proposed project/idea**: Add a general descriptive title for the project or idea.
+- **Name of the funding agency**: Add the name of the funding agency you are applying to.
+- **Link to funding call**: Add the URL to the funding call.
+- **Year of Submission**: Add the year you are submitting the application.
+- **Application Type**: Add the type of application you are submitting. For example, if you are submitting a grant, select 'Grant' from the drop-down menu.
+- **Applicants**: Add the names of the applicants involved in this application. (If it's just yourself, only write your name. If it's multiple people, write all their names.)
+- **Name of PI**: Add the name of the PI for this application.
+- **Name of Co-PIs**: Add the names of the Co-PIs for this application.
+- **Deadline for Abstract**: Add the deadline for the abstract submission.
+- **Deadline for LOI**: Add the deadline for the Letter of Intent submission.
+- **Deadline for Full Application**: Add the deadline for the full application submission.
+- **Status by Action**: Add the current status of the application using the drop-down menu.
+- **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:
+
+- **Dataset Name**: Add the name of the dataset you are requesting access to.
+- **Request Link**: Add the URL to the request form or page, or where you can find more information on how to request access.
+- **Data Type**: Add the type of data you are requesting access to; for example: RNA-seq, clinical data, etc.
+- **Lab Project**: Add the lab project that this dataset is relevant to.
+- **Model Type**: Add the type of model this data is using; for example: mouse model, cell line, patient data, etc.
+- **Processed Data**: Add whether the data is raw or processed.
+- **Name of Requestor**: Add the name of the person requesting access to the data.
+- **Lab Personnel in Charge**: Add the name of the lab personnel in charge of this data request.
+- **Priority**: Add the priority level of this data request.
+- **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.
+
+
+

docs/General/Presentations/database.md

@@ -0,0 +1,38 @@
+# Presentations Database
+
+This page contains links to previously created presentations and is intended to support the creation of future presentations.
+
+## 2024 Presentations
+
+**Radiomics and Pharmacogenomics: From Research To Clinic** ([Slide Deck](https://docs.google.com/presentation/d/1opViHXEd1PjO7glqesinhdQfJUf4_HUQ6F-uol_hCrA/edit#slide=id.gc3323ced22_0_0))
+
+   *Joint Symposium in Cancer Biology and Ecosystem, October 2024*
+
+**Pharmacogenomics Data Analysis** ([Slide Decks](https://drive.google.com/drive/folders/1TO5YAc3wJpZWoMdR1EISqGa5CWyb53rm?usp=drive_link))
+
+   *Canadian Bioinformatics Workshop, October 2024*
+
+**An Open Science Approach to Computational Pharmacogenomics** ([Slide Deck](https://docs.google.com/presentation/d/1mR4wYLbbRcaz6ZVBCZyXhtMnvn-XDBcuL1L_PB_TmeQ/edit?usp=sharing))
+
+   *RECOMB/ISCB Regulatory & Systems Genomics/DREAM conference, October 2024*
+
+**An Open Science Approach to Drug Response Prediction in Sarcoma** ([Slide Deck](https://docs.google.com/presentation/d/15n0wnM5_33EJBr5580JchIyt_bZB6BeRwEtpJVe2RHI/edit#slide=id.gc3323ced22_0_0))
+
+   *2024 NLMSF-SPAGN International LMS Research Roundtable, September 2024*
+
+**Development of Chromatin Accessibility Liquid Biopsy Biomarkers for Breast Cancer Drug Response Prediction**
+([Slide Deck](https://docs.google.com/presentation/d/16fTvMb6qgN3fL1nlzBLlS8HnQdWB1XBTWpckxBjFAcc/edit?usp=sharing))
+
+   *2024 Collaborative Breast Research Internal Award, June 2024*
+
+**Hallmarks of Drug Response Models: A Qualitative Framework to Evaluate Multivariable Predictive Biomarkers** ([Slide Deck](https://docs.google.com/presentation/d/12_qdW8u5jGVSvAJ22-kaorGUlcPN6C44-HTWMG4Lh-w/edit#slide=id.p1))
+
+   *AACR Annual Meeting - San Diego, April 2024*
+
+**AI for Clinical Trials** ([Slide Deck](https://docs.google.com/presentation/d/18R2ZfBfW_gfx0Yti3GB5J46vKVGOh5HIfiN-iTQ_hk4/edit#slide=id.gc3323ced22_0_0))
+
+   *Amplitude, April 2024*
+
+## Previous Presentations
+
+For presentations from 2023 and before, please visit the [BHKLab website](https://bhklab.ca/#presentations)

docs/General/Presentations/index.md

@@ -1,7 +1,41 @@
 # Presentation Standards
 
-TODO: #35 Add Presentation Standards
+## Talk Standards
+
+### Key Slides
+
+- **Title slide**: Include your name, date, affiliation, event/conference, and contact information (e.g. email). Optional: include the BHK Lab logo and others (e.g. UHN, University of Toronto, etc)
+- **Acknowledgements slide**: Include names of lab members (or can reference 'BHK Lab') and other collaborators along with your institutional affilications/funding sources (e.g. UHN, CIHR, NSERC)
+
+### Other slides
+
+- All slides should include slide numbers
+- Slide headings should be short (1-2 lines max) and descriptive
+- Use visuals whenever possible (feel free to take from existing presentations in the [database](database.md))
 
 ## Poster Standards
 
-## Talk Standards
+### Components
+
+- **Heading**: Include title, author(s) name, supervisor name (if student poster) across the top border
+- **Abstract** (optional): Brief paragraph (~250 words) outlining purpose, methods, results, and conclusions
+- **Introduction**: Background information pertinent to your project to help audience understand motivation. Outline the goal, objective(s), and hypothesis(es) of your research.
+- **Materials and Methods**: Brief outline of materials and methods used in your work, listed clearly and logically.
+- **Results**: Present data in photographic, graphical, or tabular form. Include descriptive figure titles and avoid lengthy captions. Be sure to not include abbreviations not explained in the text.
+- **Discussion**: Address results and describe relevance to objective(s) and hypothesis(es).
+- **Conclusions**: Stated clearly and concisely, addressing project objectives and stating overall significance.
+- **References**: All references (publications)
+- **Acknowledgements**: Any key lab members, collaborators, and funding sources.
+
+### Text Sizing
+
+Size of lettering must be large enough to be legible from approximately 2m. Use a clear and simple font between 18 point and 30 point in size. We recommend the following for Arial:
+
+- 18 point: best viewed at 1m (for figure titles, legends, acknowledgements, etc)
+- 24 point: best viewed at 2m (for main text)
+- 30 point: best viewed at 3m (for section headings)
+
+### Suggestions
+
+- Avoid overloading with text, use bullet points where possible
+- Whenever appropriate, use clear diagrams, figures, and tables (e.g. materials and methods)

docs/General/Presentations/tools.md

@@ -1,10 +1,38 @@
 # Presentation Tools
 
-TODO: Add descriptions of presentation tools
-
-- Google Sheets
-- Templates
-- Miro
-- Flaticon
-- Biorender
-- Slido
+This page describes standards, tools, and resources for creating presentations for the lab.
+
+**Google Sheets**
+
+All external presentations (conferences, workshops, external working groups), should be created on Google Sheets directly by or shared to the `[email protected]` account.
+
+Internal presentations, such as journal clubs, should also be created on Google Sheets. *Link Lab Meeting and Journal Club pages here.
+
+
+**Templates**
+
+Several slide templates have already been developed for the lab: 
+
+- [BHKLab Internal Presentations Template](https://docs.google.com/presentation/d/1GRdR3ExBVbXwgmjkHBp82i3x_mdQZPzJNHsEz1LiYWk/edit)
+- [BHKLab External Presentations Template](https://docs.google.com/presentation/d/1B-iTfzHvVSOD9fW80NZz14ct6HENHWOgTxU8C673TmY/edit)
+
+
+
+**Miro**
+
+[Miro](https://miro.com/login/) is a collaborative white board platform that enables simple diagram and multi-figure panel creation for presentations and/or manuscripts. For diagrams that will be used and updated by others in the lab, please request a Miro Board be created via the BHK Lab Miro account.
+
+
+**Images and Icons**
+
+The following are open-source biological imaging databases and platforms. The BHK Lab holds a premium Flaticon account. If Biorender and/or BioArt are used, please remember to add them to the acknowledgements.
+
+- [Flaticon](https://www.flaticon.com/)
+- [Biorender](https://www.biorender.com/)
+- [BioArt](https://bioart.niaid.nih.gov/)
+
+
+
+**Slido**
+
+[Slido](https://www.slido.com/) is an interactive polling platform that can be easily integrated into Google Sheets. We recommend using this platform to improve engagement in presentations, particularly workshops or other relevant use cases.

docs/General/index.md

@@ -17,7 +17,7 @@ you to check out our **[Contributing Section][contributing-to-the-lab-handbook]*
 
 Whether you're looking to [report an issue][submitting-issues],
 [add new content][adding-content], or
-[suggest an enhancement](#submitting-issues), the [Contributing Section](#contributing-to-the-lab-handbook) has all
+[suggest an enhancement][submitting-issues], the [Contributing Section][contributing-to-the-lab-handbook] has all
 the resources you need to get started. Your contributions help make this
 handbook a valuable tool for the entire lab community!