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Update email_acknowledgement.md
rowlandm Oct 9, 2025
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2 changes: 1 addition & 1 deletion email_acknowledgement.md
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Expand Up @@ -15,7 +15,7 @@ To make things clearer, I have provided the questions I will be asking in the ca
3. We take Diversity, Equity, and Inclusion seriously. We have a [Code of Conduct that you have to abide](code-of-conduct) by that is in the WEHI RCP Student Internship Handbook on page 10. Have you read it and are you willing to abide by it?
4. Our most successful interns are organised, communicate well and ask lots of questions. How can you demonstrate that you will be organised? What do you use to organise yourself (how do you use your calendar, how do you prioritise, how do you take notes)?
5. Are you willing to have at least 4 touch points per week with your supervisor (project meeting, weekly group email summary, and two other interactions)?
6. How can you demonstrate that you are willing to ask 10+ questions per week in this internship - even if you feel embarrassed or feel uncomfortable?
6. How can you demonstrate that you are willing to ask 10+ questions per week in this internship - even if you feel embarrassed or feel uncomfortable? For example, some interns have asked 23 questions in 15 minutes, 20 questions in 30 minutes, and Rowland can ask 25 questions in 30 minutes.
7. Are you able to work around 6 hours per week if you are an Open Source Contributor, around 8 hours per week if you are from the Faculty of Science at University of Melbourne, or around 24 hours per week if you are from the Faculty of Engineering and IT at the University of Melbourne? [Please note the expectations around the Open Source Contributors as well.](expectations_open_source_contributors)
8. What projects are you interested in and why? You can [read more about them in this summary of projects for Summer 2025/2026.](https://www.canva.com/design/DAG0zIczPN0/MiXn_0tJkDLvWYzn3WIIDA/view?utm_content=DAG0zIczPN0&utm_campaign=designshare&utm_medium=link2&utm_source=uniquelinks&utlId=h6dfc0bd5ba)
9. I will then show you the projects that are currently still available based on your interests.
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1 change: 1 addition & 0 deletions expectations_open_source_contributors.md
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Expand Up @@ -31,5 +31,6 @@ How does an open source contributor differ from the student intern who gets cour
| Must update wiki and documentation as appropriate | encouraged but optional | mandatory |
| Must work on an open source project | mandatory | can work on open source and close source projects |
| Has access to WEHI resources | no | yes |
| Acknowlegement Received | Certificate of Contribution | Certificate of Completion |
| --- | --- | --- |

2 changes: 1 addition & 1 deletion intake_dates.md
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Expand Up @@ -8,7 +8,7 @@ We have three intakes per year - Semester 1 (March to May), Semester 2 (August t
</a>
<div style="clear:both"></div>

## Summer 2025/2026 now available
## Summer 2025/2026 applications have now closed


- **[Engineering and IT](https://eng.unimelb.edu.au/industry/students/internships#key-dates):** start and end dates are tentatively from 17th November 2025 to 27th February 2026 for around 24 hours per week.
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93 changes: 72 additions & 21 deletions intakes/13-Semester-2-2025/index.md
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Expand Up @@ -16,26 +16,74 @@ Please [update and do a pull request for this page via Github here](https://gith

# AIVE

Our objective was ...
### OBJECTIVE
Our team was divided into two groups, each tasked with their own objectives.

What we did as a group was ...
#### Organelle Segmentation
The objective for this group was to contribute to the AIVE project by addressing the intensive manual effort required for organelle segmentation in microscopy images. Identifying the structures of organelles within electron microscopy (EM) images is an important task in the AIVE pipeline which is largely done through manual segmentation- which is time consuming - rather than Machine Learning techniques such as Deep Learning Models due to insufficient investment in the matter. The task included exploring and evaluating the various software tools that can be used to perform segmentation of 3D EM images, thus allowing researchers to determine its viability in the AIVE workflow’s integration requirements. We created documentation regarding the usage of such tools, the results obtained, and observations such as their performance ability and technical capabilities.

How far we got was ...
#### AI Probabilities and AIVE Integration
The second group’s objective was to streamline the AIVE workflow in WEKA. The motivation comes from knowing that in the current workflow, AIVE is a separate step from AI predictions to enhance the results. The goal was to explore WEKA to determine whether adding an extra layer to the model can integrate the AI predictions with the original EM image.
For AIVE integration, one main task was to get the AI segmentation done in WEKA which includes training and evaluating a Random Forest classifier and getting the probability maps per class. The second main task was to preprocess the raw EM image using Fiji/ImageJ which includes applying contrast normalisation and denoising techniques.

## Key links
- Final presentation video
- FInal presentation slides
- Link to individual learning plans
- Link to technical diaries
- Link to Github repos

# BioNix
### WHAT WE DID AS A GROUP
#### Comprehending the AIVE Workflow
As a group, we first reviewed the project background, research paper, and previous interns' work to get a clear understanding of our starting point. After this we began narrowing down the problem space to decide what we would work on, eventually landing on the two objectives mentioned.

Our objective was ...
#### Tasks Undertaken:
- Investigating various segmentation tools: We focused primarily on Empanada and microSam and began by testing the ML models provided by these software tools in their capability to segment FIB-SEM images.
- Develop Scripts for file conversion: Python scripts were written for conversions in relation to .tif format files. Specifically, Zarr to tiff and tiff to NumPy arrays.
- Developed a model runner: A model runner that allows users to run multiple empanada models at the same time was implemented for convenience.
- Setting up and testing workflows for 3D image data: Setup a minimal reproducible pipeline: load → encode→ run models → merge → export
- Documenting technical setups, challenges, and recommendations: All details related to the process, results achieved, and any notable observations as well as insights were recorded in documentation to be referred to.
- Sharing progress and insights in regular group meetings: We had regular group meetings amongst the team members to discuss our progress and to decide the next steps. We conveyed any issues and discoveries that we made during our experience and learned how to employ effective teamwork and communication to achieve results.

What we did as a group was ...
We collaborated actively to identify bottlenecks, benchmark results, and keep documentation up to date for both future interns and project integration.

### FINAL STATUS
#### Organelle Segmentation
By the end of the internship, we had tested and documented the initial analysis of tools for organelle segmentation. We established a reproducible workflow, highlighted tool limitations, and proposed recommendations for further improvements.
While initial tool analysis objectives were achieved, additional development will be needed for full automation and deeper integration with the wider AIVE project
#### AI Probabilities and AIVE Integration
By the end of the internship, we were able to partially reproduce the AIVE core workflow that covers 3 main complex steps including AI segmentation, data preprocessing and voxel multiplication. Unlike AIVE original workflow, we were able to integrate AI segmentation and the voxel multiplication within WEKA by using a mathematical expression tool.

How far we got was ...

## Key links
- [Final presentation video](https://wehieduau-my.sharepoint.com/personal/mosbergen_r_wehi_edu_au/_layouts/15/stream.aspx?id=%2Fpersonal%2Fmosbergen%5Fr%5Fwehi%5Fedu%5Fau%2FDocuments%2FRecordings%2FAIVE%20Weekly%20Project%20Meeting%2D20251007%5F150733%2DMeeting%20Recording%2Emp4&nav=eyJyZWZlcnJhbEluZm8iOnsicmVmZXJyYWxBcHAiOiJTdHJlYW1XZWJBcHAiLCJyZWZlcnJhbFZpZXciOiJTaGFyZURpYWxvZy1MaW5rIiwicmVmZXJyYWxBcHBQbGF0Zm9ybSI6IldlYiIsInJlZmVycmFsTW9kZSI6InZpZXcifX0&referrer=StreamWebApp%2EWeb&referrerScenario=AddressBarCopied%2Eview%2E81ec71a7%2De37d%2D4d53%2Da7ad%2Db07b1cd30418&ga=1)
- [Final presentation slides](https://wehieduau.sharepoint.com/:b:/r/sites/StudentInternGroupatWEHI/Shared%20Documents/AIVE/2025%20Semester%202/AIVE%20-%20Sem%202%202025%20Final%20presentation.pdf?csf=1&web=1&e=gNjPGx)
- [Link to individual learning plans](https://wehieduau.sharepoint.com/:f:/r/sites/StudentInternGroupatWEHI/Shared%20Documents/AIVE/2025%20Semester%202/ILPs?csf=1&web=1&e=qrYrGb)
- [Link to technical diaries](https://wehieduau.sharepoint.com/:f:/r/sites/StudentInternGroupatWEHI/Shared%20Documents/AIVE/2025%20Semester%202/Technical%20Diary?csf=1&web=1&e=bNCcZH)
- [Link to Github repos](https://github.com/MitochondRuna/AIVE-Intro/tree/WEHI-Internship-S2-2025)
- [Semester 2 2025 Folder](https://wehieduau.sharepoint.com/:f:/r/sites/StudentInternGroupatWEHI/Shared%20Documents/AIVE/2025%20Semester%202?csf=1&web=1&e=Iq6CnZ)

# BioNix

##OBJECTIVE
The research project worked to boost bioinformatics workflow reproducibility through its development of BioNix which operates as a Nix package manager extension. BioNix enables scientists to create reproducible environments for complex scientific analyses which can be shared and version controlled. Our main goal was to find the barriers of computational reproducibility and make useful improvements by adding documentation to code and implementing testing and packaging.

##WHAT WE DID AS A GROUP
As a team, we explored the Nix ecosystem, including Bash scripting, Nix, Nixpkgs, and BioNix. The learning process started with a challenging slope because we lacked experience with these tools. We concentrated on:
• Understanding how Nix ensures consistent builds and dependency management.
• Exploring reproducibility challenges in existing bioinformatics workflows.
• Testing and documenting small, reproducible pipelines to demonstrate workflow consistency.
• Trying genome alignment using nixpkgs.
• Improving onboarding materials by creating an “Introduction to BioNix Project” page, which provides guidance on installation, key concepts, and troubleshooting.
• Maintaining detailed technical diaries to record progress, errors, and solutions for future contributors.
We worked collaboratively, shared progress in regular meetings, and updated documentation to support long-term project continuity and accessibility.

##HOW FAR WE GOT
By the end of the project, we achieved several outcomes:
• Developed a foundational understanding of reproducible build systems and workflow management using Nix and BioNix.
• Developed understanding of genome alignment workflows using BWA, samtools, and seqtk within reproducible environments.
• Investigated reproducibility barriers in packaging complex bioinformatics tools, such as Gridss
• Created and published onboarding documentation on GitHub to support new users and interns with minimal programming background.
Although full integration of advanced tools like Gridss into BioNix remains ongoing work, the team established a reproducible foundation, identified technical bottlenecks, and provided documentation that will streamline future development.

##FINAL INSIGHTS
Through this project, we learned how to apply reproducibility principles in real-world bioinformatics contexts.
We moved beyond traditional learning styles to self-directed exploration, iterative testing, and reflective documentation.
Our collective effort resulted in practical contributions to BioNix’s infrastructure and onboarding resources, setting the stage for continued development by future contributors.

## Key links
- Final presentation video
Expand Down Expand Up @@ -94,18 +142,21 @@ How far I got was a **nearly complete system**, with the backend and database fu
- [Link to FastAPI+PSQL Setup Guide](https://wehieduau.sharepoint.com/:b:/r/sites/StudentInternGroupatWEHI/Shared%20Documents/Data%20Commons/Semester%202%202025/Data%20Registry/REDMANE%20FastAPI%20Setup.pdf?csf=1&web=1&e=GejO3b)

# REDMANE Web Dev
Our objective was ...
The objective of our team this semester was to turn the REDMANE Data Registry into a **functional MVP** that could be shown to stakeholders. We aimed to remove hardcoded content, make pages responsive, and connect the frontend to the PostgreSQL database.

What we did as a group was ...
This internship, we completed three core features. **Creating new datasets, a project summary page, and uploading file metadata.** As well as updating the files view page for a dataset to be responsive, and filter between raw / processed / summarised files. The datasets and projects are now also read from the database. These features all interact directly with the database and now allow for basic Create and Read functionality (no Update and Delete just yet) in the demo.

How far we got was ...
This intake we were able to turn what was previously a basic framework for REDMANE, into a functional demo built with core create / upload features, with some advanced features still in progress, paving the way for future development.

## Key links
- Final presentation video
- FInal presentation slides
- Link to individual learning plans
- Link to technical diaries
- Link to Github repos
- [Semester 2 2025 Folder](https://wehieduau.sharepoint.com/sites/StudentInternGroupatWEHI/Shared%20Documents/Forms/AllItems.aspx?csf=1&web=1&e=pDcIAg&CID=96eb9bc2%2D2476%2D442d%2Dbb04%2D3562dbd82c60&FolderCTID=0x0120008FF8F20683AC284798EA496C639CC069&id=%2Fsites%2FStudentInternGroupatWEHI%2FShared%20Documents%2FData%20Commons%2F2025%20Semester%202%20Web%20Dev)
- [Final presentation video](https://wehieduau-my.sharepoint.com/personal/mosbergen_r_wehi_edu_au/_layouts/15/stream.aspx?id=%2Fpersonal%2Fmosbergen%5Fr%5Fwehi%5Fedu%5Fau%2FDocuments%2FRecordings%2FREDMANE%20Web%20Final%20Presentation%2D20251017%5F130758%2DMeeting%20Recording%2Emp4&nav=eyJyZWZlcnJhbEluZm8iOnsicmVmZXJyYWxBcHAiOiJTdHJlYW1XZWJBcHAiLCJyZWZlcnJhbFZpZXciOiJTaGFyZURpYWxvZy1MaW5rIiwicmVmZXJyYWxBcHBQbGF0Zm9ybSI6IldlYiIsInJlZmVycmFsTW9kZSI6InZpZXcifX0&referrer=StreamWebApp%2EWeb&referrerScenario=AddressBarCopied%2Eview%2E5516915a%2Dc2bf%2D4002%2D91b4%2D147cb14d9d9f&ga=1)
- [Final presentation slides](https://wehieduau.sharepoint.com/:p:/r/sites/StudentInternGroupatWEHI/_layouts/15/Doc.aspx?sourcedoc=%7B8B397EA8-4FB4-4765-A4C2-B7F7E689A10A%7D&file=2025_Sem2Presentation.pptx&action=edit&mobileredirect=true)
- [Link to individual learning plans](https://wehieduau.sharepoint.com/sites/StudentInternGroupatWEHI/Shared%20Documents/Forms/AllItems.aspx?id=%2Fsites%2FStudentInternGroupatWEHI%2FShared%20Documents%2FData%20Commons%2F2025%20Semester%202%20Web%20Dev%2FIndividual%20Learning%20Plans&viewid=afd55542%2D8e3a%2D4327%2D95f9%2D63450ae10d2a&csf=1&web=1&e=pDcIAg&CID=96eb9bc2%2D2476%2D442d%2Dbb04%2D3562dbd82c60&FolderCTID=0x0120008FF8F20683AC284798EA496C639CC069)
- [Link to technical diaries](https://wehieduau.sharepoint.com/sites/StudentInternGroupatWEHI/Shared%20Documents/Forms/AllItems.aspx?id=%2Fsites%2FStudentInternGroupatWEHI%2FShared%20Documents%2FData%20Commons%2F2025%20Semester%202%20Web%20Dev%2FTechnical%20Diaries&viewid=afd55542%2D8e3a%2D4327%2D95f9%2D63450ae10d2a&csf=1&web=1&e=pDcIAg&CID=96eb9bc2%2D2476%2D442d%2Dbb04%2D3562dbd82c60&FolderCTID=0x0120008FF8F20683AC284798EA496C639CC069)
- [Link to Github Frontend ReactJS Repo](https://github.com/WEHI-RCPStudentInternship/REDMANE_react.js/tree/13-semester2_2025)
- [Link to Github Backend FastAPI Repo](https://github.com/WEHI-RCPStudentInternship/REDMANE_fastapi/tree/13-2025-Semester-2)
- [Link to Github Database Setup PostgreSQL Repo](https://github.com/WEHI-RCPStudentInternship/REDMANE_fastapi_public_data/tree/sem_2_2025)

# Student Organiser
Our objective was ...
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26 changes: 8 additions & 18 deletions students.md
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Expand Up @@ -10,9 +10,15 @@ We have won a WEHI award - the Kellaway Excellence Education Award in 2024 - for

We have three intakes per year - Semester 1 (March to May), Semester 2 (August to October), and Summer (November to February the next year). The [intake dates currently available and hours per week are here](intake_dates). We have anywhere between 20 and 45 interns in an intake.

<a href="how-to-apply"
### List of student intern projects (subject to availability and eligibility)

Please note that applications for the Summer 2025 / 2026 intake have now closed.

Here are some of the [recurring student intern projects and new projects we are working on](project-wikis).

<a href="https://forms.office.com/Pages/ResponsePage.aspx?id=4nJ8qs_FQEqiKqWFwEygfHucYnIbkjZJm7W73SM5JMBUN1lEOTNXWEI2WjI2OTRDV1E4MjlOSzNQNy4u"
style="color: white; background-color: #2372b9; margin: 0.5em; padding: 0.25em 1em; border-radius: 6px; box-shadow: 3px 3px 3px rgba(0,0,0,0.2); text-decoration: none; float: left; width: 30%; margin-left: 21%; margin-bottom: 24px; text-align: center;">
How to Apply for Summer 25/26
Sign up for Semester 1 2026 updates
</a>
<div style="clear:both"></div>

Expand Down Expand Up @@ -61,22 +67,6 @@ Many of the projects work in the Data Analysis and [Research Software Engineerin
We mainly work with projects that use R and Shiny, Python, Julia, bash, while also making the most out of other technologies such as RStudio, Jupyter notebooks, PowerBI and other applications within the data analytics space.


### List of student intern projects (subject to availability and eligibility)

Here are some of the [recurring student intern projects and new projects we are working on](project-wikis).

<a href="project-wikis"
style="color: white; background-color: #2372b9; margin: 0.5em; padding: 0.25em 1em; border-radius: 6px; box-shadow: 3px 3px 3px rgba(0,0,0,0.2); text-decoration: none; float: left; width: 30%; margin-left: 21%; margin-bottom: 24px; text-align: center;">
View list of projects
</a>
<div style="clear:both"></div>

<a href="intake_dates"
style="color: white; background-color: #2372b9; margin: 0.5em; padding: 0.25em 1em; border-radius: 6px; box-shadow: 3px 3px 3px rgba(0,0,0,0.2); text-decoration: none; float: left; width: 30%; margin-left: 21%; margin-bottom: 24px; text-align: center;">
Intake Dates
</a>
<div style="clear:both"></div>

### List of previous student intern project reports

Here are some of the [previous student intern reports](intakes/).
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