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Welcome to the Genomics-Metadata-Multiplexing (GMM) wiki.

This wiki page contains the following contents:

1. Overview: A brief explanation on the context of this project
2. Sister Repository: The repository to use the merge logic from
3. Future Work: Tasks to be completed by future intakes
4. Essential Wiki Pages: The other must read wiki pages

If needed, please consult the official GMM's WEHI Research Computing Platform and FAQ pages.

Overview

The GMM project at WEHI is tasked with automating processes within the CEL-Seq2 workflow via web applications. CEL-Seq2 is a single-cell RNA sequencing protocol used by researchers at WEHI.

Within the CEL-Seq2 workflow, there exists a step known as cell sorting. WEHI uses Fluorescent Activated Cell Sorting (FACS), an application of flow cytometry, via a machine that both sorts the cells & records flow cytometry metadata in the form of FCS (Flow Cytometry Standard) files. The FCS files are then analysed & processed through an application called FlowJo.

These FCS files are then MANUALLY combined with a Index Primer file/spreadsheet (prepared several days before the FACS process by researchers) to produce an experiment spreadsheet. The experiment spreadsheet & the sorted samples are then used in the next step of the CEL-Seq2 workflow.

The GMM project aims to implement a web application that AUTOMATES the aforementioned merge process between FCS files & the Index Primer file/spreadsheet. This web application is to then be deployed onto WEHI's Milton HPC Ondemand platform via internal R Shiny servers for researchers to use anytime.

For more information on the project's implementation, benefits & future, please visit the Problem Space wiki page.

The current implementation was kickstarted by the 2024 semester 1 intake. The corresponding codebase can be found here.

Sister Repository

Another repository that was concurrently developed alongside the 2023-2024 Summer Intake being: celseq-sample-sheet-generator. This was developed by Marek Cmero, a Senior Research Officer at WEHI.

IMPORTANT: Due to a shift in the GMM project's vision, the FACS merge logic (i.e. operations.py) implemented as part of Marek Cmero's repository, will be used to kickstart the 2024 semester 1 intake's implementation.

For more information, visit the Sister Repository wiki page.

Future Work

• 1. Review and update the CEL-Seq2 workflow diagram
• 2. Fix bugs in Marek Cmero's FACS file merge logic
• 3. Conduct more extensive testing via real FACS files

Essential Wiki Pages

Before contributing to this project please read and understand the following wiki pages:

1. Onboarding Checklist: a collection of resources that WEHI research software engineer interns & contributors MUST familiarise themselves with before contributing to the project
2. Problem Space: Gives a high level overview of the project's purpose, benefits & intended outcome
3. Sister Repository: Information about the web application's features
4. GMM: Contains information about the implementation kickstarted by the 2024 SM1 intake
5. Contributors: A list of people who were or currently involved in the project