Wayne

@pawjast You can use this link and it will start the MyBinder session with the copy in my gist automatically (patience may be needed): mybinder.org/v2/gh/fomighte…

@Fomightez Awesome, thanks. I'll test it out tomorrow!

One thing I've been meaning to learn for close to 2 years now is making animations using @matplotlib. But to make them properly. And it's finally happening. How do you actually start learning something you've been procrastinating on for so long? The same way you eat an elephant - one bite at a time. I've found the smallest thing I can animate - a dot! 🔴 And I've built a short animation of a dot moving about. The cool thing about this exercise is that it taught me a few things already. I tried to animate the dot using both: ▪ `ax.plot` ▪ `ax.scatter` And this highlighted some differences in how to update the data in order to make the dot move. Also displaying an animation inside Jupyter Notebook also took some researching as it didn't work out of the box for me. I think I understand the animation making mechanism a bit now. And it's cool as now I can think of other types of animations and how to technically code them as moving dot about is one thing. But making a line appear, change shape, disappear. Or making rectangle change shape (creating own version of "bar chart" run), or generally plotting multiple artists that do various things at the same time is going to be an interesting challenge. I'll keep you posted. And now behold, my moving dot animation! 🎥 🍿 ▶

@pawjast For modern Jupyter, you are looking for `%matplotlib ipympl`. See #basic-example" target="_blank" rel="nofollow noopener">matplotlib.org/ipympl/#basic-… for more about that backend. Updated in gist.github.com/fomightez/a40f… that will work in sessions launched from github.com/fomightez/anim…

The code for this breath taking animation can be found below. Let me know if you spot any obvious errors, rookie mistakes etc. github.com/pawjast/code_a…

@nooriefyi @jtpio You may be interested in py.cafe . Example app: py.cafe/app/maartenbre… The documentation goes through a step-by-step at py.cafe/docs/apps/stre…

@jtpio does this work for streamlit too?

Deploy your Jupyter Notebook as a static web app! 🚀 I recently built a small app with ipywidgets in a notebook and recorded the process of deploying it to GitHub Pages using Voici. 🛠️ Watch the full video here: youtu.be/H4Zt1vHWbJc

I'm excited to get Binder / JupyterHub launch button functionality back into Jupyter Book 2! Gets a little better every day! github.com/jupyter-book/m…

Project Jupyter is thrilled to share the news about the Jupyter Foundation! #jupyter #jupyterfoundation #opensource

@bicknell_l @ppgardne There was an earlier mention that, at least for RNU4-2, it was this 'whole' exome approach not being whole. My impression from the statement at x.com/nickywhiffin/s… was that it wasn't covered in the exome sequencing despite being in a conserved exon.

@ppgardne I don't think missed - even if covered on an exome, I think it can be harder to prioritise variants if there are gene paralogues (so presume functional redundancy), and in smaller cohorts maybe only one patient with a variant. These findings show the power of massive RD datasets!

Is anyone digging further into why these highly conserved ncRNA variants were missed for so long?

This is super cool: a full Python app and LLM running in the browser at @py_cafe

@jtpio The better launch link would be mybinder.org/v2/gh/jupyterl… so tutorial presented. However, `/usr/share/dict/` is empty in launched session so that notebook fails to generate to generate a thousand more files in the notebook tree.

Just published a new version of the Quick Open extension for JupyterLab and Jupyter Notebook 🎉 jupyterlab-quickopen lets you quickly open files in JupyterLab and Jupyter Notebook⚡️ ➡️ Install with: pip install jupyterlab-quickopen ➡️ Try on Binder: mybinder.org/v2/gh/jupyterl…

How does the human #ribosome machinery select an open reading frame on mRNA for translation? Check out our #cryoEM work @NatureSMB: rdcu.be/dUbMg Thanks to all involved - most of all first author @V_Petrychenko and our collaborators from the Rodnina lab @mpi_nat. 1/5

First structure of a H/ACA snoRNP acting in ribosome synthesis. In a great collaboration with the Hurt lab, we provide a detailed structural and biochemical view of the snR30 snoRNP guiding local 18S rRNA subdomain folding. 👇👇👇

We're thrilled to share an update about our continued collaboration with @developmentseed on the @NASA Visualization, Exploration and Data Analysis (VEDA) platform! See how we've made it easier for researchers to explore large geospatial datasets 🌍 2i2c.org/blog/2024/veda…

🥳 Exciting news! You can now experiment with free-threaded Python! 🐍 This major change to CPython allows running multiple threads in parallel for better performance on modern CPUs. Check out Quansight Labs' blog to learn more and get started! 👀 buff.ly/3LIRwdV #python

The Animation Lab is hiring! We're looking for a software developer for an exciting new project creating intuitive tools for molecular animation. Experience with Python req'd and Blender preferred. Please forward to any interested folks! employment.utah.edu/salt-lake-city…

I am excited to share this story led by Yujing Cheng and Siwen Wang (not on X) in @CellCellPress which describes a new function for a small nucleolar RNA (snoRNA) in senescence and ribosome biogenesis. Read on for a brief 🧵1/ cell.com/cell/fulltext/…

YeastMine is closing July 15 due to ongoing funding cuts. For more info: community.alliancegenome.org/t/yeastmine-sh… #yeast

Did you see the bridge RNA papers yesterday? Bacterial transposons promote programmable, RNA-guided DNA recombination. Remarkably, we found that the recombinase was co-opted in archaea and eukaryotes for widspread RNA-guided RNA modification, an essential function in humans!

"In this first map of pseudouridine modifications for C. elegans, we find that they largely reside in coding sequences and that the number of genes with this modification increases with age."

It was a pleasure presenting at my first @Sca_DS.AI #SummerSchool! I spoke about #LLMs for #BioImageAnalysis, including best-practices for prompt-engineering, LLM fine-tuning, RAGs and benchmarking. 🔬💻🚀🔓 Slides #openaccess: zenodo.org/records/125180…

🎉 Great news for the #GIS and #Jupyter communities! The @ESA is funding a project by @QuantStack and @simula_research to bring collaborative editing to GIS workflows in JupyterLab. Let's explore new ways of working with geospatial data! 🚀 blog.jupyter.org/jupytergis-d63…

Here is another fun one over on @py_cafe ☕️ Protein residue coloring in ipymolstar is now super fast with the latest PDBeMolstar version. Makes for very responsive protein viewer apps! And supports dark mode 😎