Our latest paper now accessible in preprint: how we used a #visualanalytics approach to dig deeper into the #microbiome of hairy root disease in tomato doi.org/10.21203/rs.... #topologicaldataanalysis #TDA #topicmodelling #latentdirichletallocation

A nice intro to #marimo, the #jupyter alternative codecut.ai/marimo-a-mod... #python #datascience

‘Big pharma’ kraakt complexe biologie dankzij Belgische software van Aspect Analytics www.tijd.be/ondernemen/f...

Dear interwebs. We're trying to find out how many scientific papers use a specific visual, e.g. upset or circos. Any ideas on how to identify these? A search for the term doesn't work because it is not always named. Also: a simple picture search seems too limited. Any ideas appreciated with a beer.

Thank you to all the organisers and participants for joining us at @ebi.embl.org for this week's data visualisation for biology course. Sign up for updates on 'Introduction to multi-omics data integration and visualisation' 2026 course: www.ebi.ac.uk/training/eve... @janaerts.bsky.social #dataviz

In preparation for a #dataviz course at the @training.ebi.embl.org later this month, I've created a cheatsheet for creating custom SVG images in #marimo #python. If anyone finds errors: let me know! aida-lab.be/assets/marim...

Being dependent on US services has become a clear liability. The head prosecutor of the International Criminal Court has lost access to his email (apnews.com/article/icc-...). Can #kuleuven move towards open source / EU software? cc @tinebaelmans.bsky.social #kuleuven #ict

Our latest paper is out: peerj.com/articles/cs-.... We added functionality to the #HDBSCAN clustering algorithm to also detect branches hdbscan.readthedocs.io/en/latest/ho... #eda #datavis #clustering

Eigenvalues of a parameterized 4×4 matrix Each point corresponds to a non-real eigenvalue of a matrix of the form: [[0, 0, -1, -1], [1, -1, 0, 0], [0, 1, A, 0], [1, 0, -1, B]] where A and B are independently drawn from a continuous uniform distribution on (−3, 3). #mathart #Mathematics #p5js

SpatialRNA: a Python package for easy application of Graph Neural Network models on single-molecule spatial transcriptomics dataset www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/pyg-team/pyt...

For a #dataviz course I'm looking for scientific images in #SVG that could be improved by different colour schemes, removing unnecessary elements, better fonts, titles, etc. The students in the course can then use #inkscape to improve those images. If you know of good examples, let me know!

If you're a biologist interested in data visualisation, check out the vizbi conference www.linkedin.com/events/vizbi... #omics

We are excited to introduce Mercury, the first commercial-grade diffusion large language model (dLLM)! dLLMs push the frontier of intelligence and speed with parallel, coarse-to-fine text generation.

On how to use #mistral #llm to talk to your #zotero library: www.youtube.com/watch?v=x34I...

Google's AI co-scientist and similar tools may disrupt scientific research even more than AI is already doing. We'll still have to see how it pans out, but we'll need to be prepared. Also: not everyone will have the same access to these tools! storage.googleapis.com/coscientist_...

Just released a first version of my #graph #anywidget at pypi.org/project/grap... for displaying (and brushing) force-directed node-link diagrams in #marimo. With a little help from @manzt.sh

📊 & 🧪 Join the #DataViz for #LifeScience course at EMBL-EBI! Organised by Jan Aerts/Ryo Sakai, this year with my Keynote! :) --> Application due March 9th www.ebi.ac.uk/training/eve...

If you would like to gain knowledge and practical experience in how to use data visualisation tools to gain insights into complex biological data, apply for this course by 9 March: www.ebi.ac.uk/training/eve... Some financial assistance is available - see course website for more info. #dataviz 🧪

Very interesting paper: "A Grammar of Hypotheses for Visualization, Data, and Analysis", by Remco Chang's group arxiv.org/abs/2204.14267 This will definitely go into my #dataviz course, and can anchor several of the discussions we have with collaborators.

Are you a biologist interested in data visualisation to help you explore complex data or create effective visuals? If so, make sure to register for the course that we're organising at the EBI in June www.ebi.ac.uk/training/eve... #biovis #viz #dataviz

A generalised paradigm for composable visualisations in python #dataviz I'll definitely be checking this out. genomebiology.biomedcentral.com/articles/10....

Interesting paper by van den Brandt (TU/e): "Understanding Visualization Authoring Techniques for Genomics Data in the Context of Personas and Tasks" ieeexplore.ieee.org/stamp/stamp.... #omics #dataviz #biovis

Just realized BlueSky allows sharing valuable stuff cause it doesn't punish links. 🤩 Let's start with "What are embeddings" by @vickiboykis.com The book is a great summary of embeddings, from history to modern approaches. The best part: it's free. Link: vickiboykis.com/what_are_emb...

Look who's here @pnas.org ✔️ @science.org ✔️ @naturecellbiology.bsky.social ✔️ @natrevgenet.bsky.social ✔️ @naturebiotech.bsky.social ✔️ @naturemicrobiol.bsky.social ✔️ @naturechemistry.bsky.social ✔️ @genesdev.bsky.social ✔️ @cellchembiol.bsky.social ✔️ @genomeresearch.bsky.social ✔️ @jcellbiol.bsky.social ✔️

@mithridates.bsky.social You may know this: what graph algorithms are available for #surrealdb? I'm talking about centrality measures (betweenness centrality, degree centrality, ...), shortest path, minimal spanning tree, etc?

First post on Bluesky, let’s share some websites offering many free illustrations for scientific figures 🖼️ 🧪 🌍 : scidraw.io bioart.niaid.nih.gov www.phylopic.org More well known but very nice though: www.freepik.com

This #surrealdb tutorial has some chunky bacon vibes: surrealdb.com/learn/book/w... (Check out _why's poignant guide to #ruby here: www.rubyinside.com/media/poigna...)

If you're handling complex data, have a look at #surrealdb It brings together relational, document, graph, key/value databases, but with querying similar to #SQL www.youtube.com/watch?v=W0Iz...

“The majority has spoken, and researchers are moving en masse” to Bluesky, says @shaine.bsky.social. Couldn't help myself and had to write about science twitter, X, bluesky and "the migration"... www.science.org/content/arti... 🧪

Amazing to see the influx of new users here 🤩🧬🖥️🧪 I've gotten 100s of requests to be added to my bioinfo starter pack. If your recent ~20 posts are -- (1) bioinfo-relevant, (2) original, not just reposts, (3) snark/politics-free, (4) free from breakfast/bird photos -- ask again, I'd love to add you!

[Recent History] LSTMVis (2017) has been one of my first projects in the VIS+ML field. It tries to help identify meaningful state change patterns in RNN hidden states and map them to NLP concepts. #NLP #XAI #VIS lstmvis.vizhub.ai vimeo.com/172145096

If you hate statistics like I do, then you'll love my free lectures. Putting science before statistics, 20 lectures from basics of inference & causal modeling to multilevel models & dynamic state space models. It's all free, made with love and sympathy. 🧪 #stats www.youtube.com/playlist?lis...

I like this quote: "Visualizations act as a campfire around which we gather to tell stories." (Al Shalloway) True for research and for outreach/communication.

This high resolution model (1.5km) 3D model of Carbon Dioxide shows its sources of emissions and its transport across the globe. Full details and credits here: svs.gsfc.nasa.gov/5196/

Was reminded by @matthewbjane.bsky.social on the other site of some fancy ideas I've implemented for presenting ordinal data, here's one for paired ordinal data (@chelseaparlett.bsky.social was originally asking about it on the other site years back).

Great resource! But check that it's sandbox.bio instead of sandbox.io (cc @chrismiller.science )

Was looking up information on colourblind-safe colour schemes, and bumped (again) into this great write up by the ever-inspiring Martin Krzywinski on visualising biological data mk.bcgsc.ca/biovis2012/k... It's from 2012 but still equally relevant #biovis #dataviz #genomics #plots

Interactive canvases can be nicely built with Svelte renderless components. Here’s another example: stackblitz.com/edit/svelte-...

I've noticed a lot of new followers recently — thanks to the Vis Researcher starter pack! If you're interested in visualization research, you might find vispubs.com useful. It's a site I created to make it easier to access visualization publications and related resources.

Recipe for life: 500 genes, 21 amino acids, 4 nucleotides... now @jamessaenz.bsky.social shows: And only 2 lipids! 🧪

I teach a class on data science here at Illinois and during the seminar I host a competition for the class called "The Hunt for the Worst Data Visualization." This was my most popular post on Xitter, so reproducing some of the best submissions from previous years here:

What is the difference between weather and climate. This #dataviz shows the "Central England" average temperature for periods ranging from 1 day (weather) to 30 years (climate). This shows the climate signal emerging. Note the varying y axis that covers the range of the data.

I have 3 MSc thesis students working on #biodiversity data in Belgium/Europe. This is some inspiration! @naturalis.bsky.social

In three weeks, I‘ll be teaching Svelte with D3 for interactive data visualization in Utrecht. And yes, we’ll of course use Svelte 5! ➡️ graphichunters.nl/interactive-... @graphichunters.bsky.social @sveltesociety.dev

🚨out now! 🚨 From zero to figure hero - A checklist for designing scientific #datavisualization Come if you want to improve your/review #figures, stay to learn the science of #sciencecommunication 😇 #womenintech #WomeninSTEM for #PhD #Postdoc #Academics in 🧪 and 📊 . osf.io/preprints/os...

UPDATE: The NIH just released an icon collection, entirely in public domain and growing: bioart.niaid.nih.gov PS with equipment, I know many look for their PCR cycler or microscopes...

First there was FriendFeed where we met as life scientists, and shared interesting research. Then that disappeared and many of us moved to twitter. Now I only see vitriol there, so moving to other places _again_. Is Bsky useful? I'm also on mastodon @[email protected]. #omics #dataviz