Wendi Bacon

Senior Lecturer at The Open University

Affiliations

ELIXIR Europe avatar ELIXIR EuropeThe Open University avatar OU🖖🏾Single-cell & sPatial Omics Community of practice avatar 🖖🏾SPOC

Former Affiliations

European Bioinformatics Institute avatar EMBL-EBI

Contributions

The following list includes only slides and tutorials where the individual or organisation has been added to the contributor list. This may not include the sum total of their contributions to the training materials (e.g. GTN css or design, tutorial datasets, workflow development, etc.) unless described by a news post.

Editorial Roles

This contributor has taken on additional responsibilities as an editor for the following topics. They are responsible for ensuring that the content is up to date, accurate, and follows GTN best practices.

Tutorials

Slides

FAQs

Video Recordings

Events



GitHub Activity

Issues Reported

153 Merged Pull Requests

See all of the Pull Requests and Commits by Wendi Bacon.

Reviewed 110 PRs

We love our community reviewing each other's work!

News

Hello in many languages
¿Hablas español?: The first curated tutorial in Spanish!
Wendi Bacon avatar Beatriz Serrano-Solano avatar Patricia Carvajal López avatar Alejandra Escobar-Zepeda avatar Saskia Hiltemann avatar Helena Rasche avatar
20 May 2021
¡El primer tutorial en español ya está disponible! Galaxy siempre ha tenido tutoriales traducidos automáticamente mediante Google-Translate, ahora nos estamos embarcando en un nuevo proyecto para estudiar la experiencia de aprendizaje con tutoriales en bioinformática traducidos por humanos. Nuestro objetivo es crear un paquete de tutoriales para el análisis de datos single-cell (célula única) en primera instancia, con el fin de estudiar su uso y utilidad en un taller para hablantes nativos de español. Agradecemos enormemente a las nuevas participantes @gtn:pclo y @gtn:ales-ibt (EMBL-EBI) así como a las miembros existentes de GTN @gtn:beatrizserrano (University of Freiburg), @gtn:shiltemann & @gtn:hexylena (Erasmus-MC), por su arduo trabajo en este proyecto de traducción y mantenimiento y, por supuesto, a @gtn:nomadscientist (The Open University/EBI) como líder de proyecto.
new tutorial español introduction
Pretty dots of different colours combined into two cell cluster plots on the sides. In the middle, a split violin plot showing the expression of unknown genes in blue on one side and the expression of the genes in an opposing sample in orange alongside. Snuck in between these three important plots is a PhD comic of data showing no trend, with the chat box “Hmm… I think there’s a clear trend happening here.”
New Topic: Single Cell Analysis!
Wendi Bacon avatar Mehmet Tekman avatar
18 November 2022
Single-cell analysis now has it’s own topic! These tutorials were previously part of the transcriptomics topic, but due to the amazing efforts by Wendi Bacon, Mehmet Tekmanand others, we now have so many single-cell analysis tutorials that they deserve their own dedicated topic! From introductory slides and practicals, to case study tutorials generating cell clusters and trajectories from raw sequencing files, and even a growing subtopic of smaller tips and tricks for adapting analysis to user needs, the single cell topic either has what you need or is working on it. Come learn or get involved!
new topic single-cell new feature
Heatmap with columns of cell types vs rows of inferred and actual cell type proportions for A and B samples. Cell colours are similar between actual and inferred.
New Tutorial Suite: Deconvolution with MuSiC, from public data to disease interrogation!
Mehmet Tekman avatar Wendi Bacon avatar
29 November 2022
The still new and shiny single-cell analysis topic now boasts a deconvolution tutorial suite! What does deconvolution do you ask? Well, in this context, it infers cell proportions from bulk RNA-seq data. You heard that correctly - instead of expensive new single-cell experiments, you can re-analyse old bulk RNA-seq data and estimate cell proportions. All you need is a reasonably good single cell dataset to use as a reference and you’re good to go! The tutorial suite shows you how to build your reference from publicly available single cell data, and apply analysis to some publicly available bulk RNA-seq data.
new tutorial single-cell transcriptomics
GTN logo with a multi-coloured star and the words Galaxy Training Network
New Feature: Embeddable GTN Tutorial Lists and UseGalaxy Workflow List Widgets
Helena Rasche avatar
5 October 2023
We at the GTN strive to bring you the most fun and fancy features we can in a completely static site! Today we’re addressing the question of Wendi Bacon who needed a solution for keeping her single cell subdomain up-to-date with all the latest happenings in the Single Cell world.
new feature gtn contrributing community
screenshot of the Single Cell Omics subdomain page, with purple mastheader, Single Cell Tools categories along the side, and an updated logo combining the Single Cell Omics connected cells image with the Human Cell Atlas blue embyro logo
Single cell subdomain re-launch: Unified and feedback-driven
Wendi Bacon avatar Pavankumar Videm avatar
12 October 2023
The European Galaxy Days 2023 CoFest combined the forces of administrator, developer and trainer to update and re-launch the single cell Galaxy instance. Where previously there were two subdomains each with their own sets of tools, there is now a unified subdomain with re-categorized tools that makes sense for users.
gtn single-cell
swirled cluster dots surround a circle of people all holding hands, looking towards the bright center (future)
Galaxy Single-cell Community: Year in Review
Mehmet Tekman avatar Wendi Bacon avatar Pavankumar Videm avatar
22 December 2023
🚀Embarking on a cosmic journey, the Galaxy Single-cell Community has clustered together to unveil a constellation of tools, making strides in RNA-stellar discoveries and creating out-of-this-world workflows. With a commitment to battling work duplication across the multiverse, this community is boldly charting a course for global domination, proving that when it comes to bioinformatics, the Galaxy is the limit!✨
gtn communications single-cell
GTN logo with a multi-coloured star and the words Galaxy Training Network
FAIR Data management in single cell analysis
Julia Jakiela avatar Morgan Howells avatar Wendi Bacon avatar
17 January 2024
New single cell section: Changing data formats & preparing objects
single-cell data management data import fair
GTN logo with a multi-coloured star and the words Galaxy Training Network
Simplified GTN News submission via Google Form
Helena Rasche avatar
29 January 2024
Based on user feedback of the difficulties of the GTN news submission process we have significantly simplified and removed the need for manually editing a YAML file by providing a quick and easy Google Form
contributing community
GTN logo with a multi-coloured star and the words Galaxy Training Network
GTN in Discourse
Helena Rasche avatar Jennifer Hillman-Jackson avatar Wendi Bacon avatar Martin Čech avatar
30 January 2024
Howdy teachers and support staff! We are exploring displaying GTN content directly in the Galaxy Help site, furthering the integration between the GTN and the Galaxy community infrastructure. When you paste a GTN Frequently Asked Questions URL into the Galaxy Discourse, it will now be rendered directly in Discourse!
contributing community
GTN logo with a multi-coloured star and the words Galaxy Training Network
From GTN Intern to Tutorial Author to Bioinformatician
Camila Goclowski avatar
13 June 2024
With growing access and interest in sequencing data, Galaxy is a knight in shining armor for wet lab scientists hoping to analyze their own data. With long term intentions of increasing access to bioinformatic analyses, the Galaxy Training Network (GTN) creates a safe space where non-computer-scientists may analyze their own data and even learn to code: an invaluable skill in today’s scientific world. Galaxy introduced me to brand new skills as an undergraduate and ultimately changed the trajectory of my career. Here is my story as a biology undergraduate with no coding experience turned GTN contributor &, eventually, coding bioinformatician: thanks to Galaxy.
single-cell training education trajectory user contributor contributing
A screenshot of the GTN's short introduction to Galaxy tutorial. There are two authors and two editors, but now shown is a new reviewers with 13 individuals, some overlapping with editors and authors.
Credit where it's due: GTN Reviewers in the spotlight
Helena Rasche avatar Wendi Bacon avatar
2 December 2024
We would like to recognise and thank all of the reviewers who have contributed to the GTN tutorials; your efforts are greatly appreciated, and we are grateful for your contributions to the GTN community. Today, we are highlighting your efforts on every single learning material across the GTN.
gtn infrastructure new feature automation contributing community
swirled cluster dots surround a circle of people all holding hands, looking towards the bright center (future)
SPOC CoFest 2024: How did it go?
Wendi Bacon avatar
6 December 2024
First SPOC CoFest
gtn single-cell
A group of people standing along a staircase holding up the Vulcan salute for SPOC: 'Live long and prosper'. They look relatively happy. Taken at 2024 Galaxy Community Conference.
🖖🏾Galaxy SPOC Community: Year in Review
Wendi Bacon avatar Pavankumar Videm avatar
18 December 2024
🚀 2024: A SPOC-tacular Year in Review 🌌
gtn communications single-cell
four graphs showing increases over time: training materials including slides and tutorials; contributors; workflows; and other
GTN's Gift for 2024
Wendi Bacon avatar Helena Rasche avatar
19 December 2024
Community Pages
gtn single-cell new feature new tutorial contributing community
swirled cluster dots surround a circle of people all holding hands, looking towards the bright center (future)
SPOC HDR UK ELIXIR-UK CoFest 2025: How did it go?
Wendi Bacon avatar Morgan Howells avatar
14 February 2025
We held our second 🖖🏾SPOC CoFest, in the great tradition of the excellent CoFests organised in the GTN that welcomed @gtn:nomadscientist and many others into the community.
gtn single-cell
XY plot of actual versus inferred proportions, with coloured dots representing clusters and largely falling in a 1-1 slope
Bioinformatics Projects Pathway for Students: New insights from public data!
Wendi Bacon avatar
3 March 2025
With a huge thanks to ELIXIR-UK’s DaSH Fellowship funding, we are delighted to present our new Learning Pathway, “Bioinformatics Projects: Using deconvolution to get new insights from old bulk RNA-seq”.
gtn single-cell
Three happy looking people on a beach with a ferris wheel in the background. Everyone is wearing glasses and clearly a nerd. The individuals are Helena, Saskia & Wendi
An Ode to Helena - from the 🥓Bacon Brigade
Wendi Bacon avatar Marisa Loach avatar Morgan Howells avatar Julia Jakiela avatar Camila Goclowski avatar
7 March 2025
@gtn:hexylena, as a key member of the phenomenally creative and passionate Galaxy Training Network team alongside @gtn:shiltemann and @gtn:bebatut, pioneered the concept of Training Infrastructure. In a world dominated by clunky virtual learning environments and expensive software, she built an open-source system that could seamlessly support individual users, trainers, and contributors across diverse disciplines and expertise levels.
gtn
Four happy looking people on a stairwell wearing conference lanyards. They look nerdy and delighted, and it's not dissimilar to a family photo of awkward people who genuinely like each other. The individuals are Julia, Wendi, Marisa, and Morgan.
An Ode to the Galaxy Community and all I learned
Wendi Bacon avatar
19 June 2025
This is my ode to the Galaxy Community to say how grateful I have been for your welcome, your energy, and your support. I have learned so very, very much, about bioinformatics; about software development; and most of all, about open-source communities in this complex scientific world.
gtn
A swirl of happy, psychedelic people holding up a Vulcan salute, surrounded by dots in different colours representing cells.
Scaling Up Hands-On Bioinformatics Training with TIAAS – An Open University Perspective
Wendi Bacon avatar
3 July 2025
Back in September 2024, we ran the Open University Bioinformatics Bootcamp—a free, five-day online course introducing students to the core tools and techniques used in single-cell biology. We were genuinely delighted by the level of interest: 120 students signed up, 100 showed up, and around 80 worked through the hands-on tutorials during the week. That’s a fantastic level of engagement, especially for a course that’s entirely optional and doesn’t count towards their degree.
gtn TIAAS
Wendi Bacon avatar

External Links

nomadscientist
wendi.bacon@open.ac.uk
nomadscientist:matrix.org
wendi-bacon-7462aa100
0000-0002-8170-8806
elixir logo for United Kingdom

Favourite Topics

Favourite Formats

Stats for materials contributed to by Wendi Bacon