💾 Taking a break? Save your work in Jalview! Alignments, annotations, trees, structures, colours, views and more can be preserved in Jalview, enabling you to begin where you left off. ⬇️ Find out more. 🔗 www.youtube.com/watch?v=xT4g...
Barton Group
@bartongrp.bsky.social
News from Geoff Barton's Computational Biology Research Group. Home of Jalview https://www.jalview.org, JPred and much more! See: https://bit.ly/3YXtgeq for the publications. https://bartongroup.org https://jalview.org Also see: @gjbarton.bsky.social
⚽ As football fever builds, there’s one competition where every nation is poised to win. 📺 Jalview’s YouTube channel has been watched 250,000+ times by scientists, students and bioinformaticians across 150+ countries. 🧬 Why not tune in too? ⬇️ Link below. 🔗 www.youtube.com/@jalviewtrai...
🏊🏼♂️ Dive into molecular structures this summer with Jalview’s integrated 3D viewers. Visualize thousands of protein, DNA and RNA structures with PyMOL, Chimera, ChimeraX and Jmol — whether you're an experienced bioinformatician or just getting started! ▶️ Learn more: www.youtube.com/watch?v=pbms...
🗞️ New preprint: Slivka & Slivka-bio — a lightweight framework for turning command-line tools into web services, developed by Jalview, the Dundee Resource and Genentech. 📜 www.biorxiv.org/content/10.6... ⚡Slivka-bio is set to replace JABAWS in a future release.
Explore the adverse effects of genetic mutations in 2D and 3D views by loading the coding DNA of protein sequences. 1️⃣ Jalview's protein-CDS view: www.youtube.com/watch?v=qFMJ... 2️⃣ Feature mapping: www.youtube.com/watch?v=eK6a... 3️⃣ Genomics file imports: www.youtube.com/watch?v=n_lR...
🔗 JABAWS: hub.docker.com/r/drsasp/jab... 🔗 Jalview Develop: www.jalview.org/development/... 🔗 SLIVKA: www.compbio.dundee.ac.uk/slivka/#cta-...
Protein secondary structure can be inferred using a number of machine learning methods. In our latest training video, we explore how two such methods — AlphaFold and JPred — can be accessed from Jalview to compare and contrast results. ▶️ Watch it here: www.youtube.com/watch?v=x7SH...
💊 Finding druggable protein domains is hard—but AlphaFold's PAE data can help. Jalview lets you import this into alignments, so it can be clustered to understand protein structure better. ➡️ PAE import: youtu.be/jowUEG47F-Q?... ➡️ Domain detection: youtu.be/pQC8LTDCbug?...
Boost your workflow with Jalview’s 'Find' function! ✅ Locate motifs sequentially or en masse ✅ Designate hits as new features ✅ Copy to other alignments ✅ Visualize rapidly using the 'Overview Window' ⏰ Save time and see the big picture. 📖 Read more: www.jalview.org/help/html/fe...
JPred predicts protein secondary structure from multiple sequence alignments—and you can access it directly from Jalview. Supported file formats include: ✅ MSF ✅ FASTA ✅ BLC Add your email to get notified when your job finishes 🪄 ▶️ Learn more in our training video: www.youtube.com/watch?v=EW6b...
➡️ Watch our training video to find out more about structure discovery in Jalview: www.youtube.com/watch?v=ZBDZ...
Using 3D Beacons to access AlphaFold, Protein Data Bank and more in Jalview
YouTube video by Jalview & Dundee Resource Online Training
youtube.com
🌍 Twelve months of hard work - endless possibilities for world science. Watch our video tribute to the Jalview community for making 2025 such an incredible year for all of us! (Sound on 🗣️) Thank you all ❤️
I have to say how happy I am that at least one of the disasters due to Brexit has been undone! Erasmus was always an amazing way to bring talented students to my lab to gain experience, great to see it will be possible again in the future! www.bbc.co.uk/news/live/c4...
Erasmus live updates: Scheme to return for UK students from 2027
British students will be able to spend a year studying at EU universities without paying extra fees, and vice versa for European students.
bbc.co.uk
❄️Thank you so much to all our users and followers worldwide for making 2025 such a memorable year for us! Seasons greetings to all from the Jalview team all the way from wintry Scotland.❄️ We hope to see you in the new year! ❤️
Thanks James! @chromamagic.com All building on the beginnings you helped make!
ChromaMagic@chromamagic.com · last yr.Wow. I was thinking of writing a Jalview / JPred origin story. What an amazing tale of over a quarter century of hard effort you and your team have put in. Sustainable scientific software? ✅ ✅ ✅ I wonder how much direct economic development Dundee has seen through all of your grants?
Oh, an origin story from your perspective would be cool. We could compare notes! Sustaining scientific software long-term is very hard... 35 postdocs/staff (3-20 yrs!) and 16 Ph.D. students all funded on external grants since 2001. I guess they buy stuff locally so help the economy! 😜
ChromaMagic@chromamagic.com · last yr.Wow. I was thinking of writing a Jalview / JPred origin story. What an amazing tale of over a quarter century of hard effort you and your team have put in. Sustainable scientific software? ✅ ✅ ✅ I wonder how much direct economic development Dundee has seen through all of your grants?
Done technical updates (bootstrap 3 to bootstrap 5) and some content revision on our group website. See the link(s) below to learn more about our work and the software/databases we support such as @jalview.bsky.social Jpred and more! www.bartongroup.org www.compbio.dundee.ac.uk/index.html
The Barton Group | Bioinformatics Research | Division of Computational Biology | School of Life Sciences | University of Dundee
The Barton Group is Geoff Barton's Bioinformatics Research Group in the Division of Computational Biology, School of Life Sciences, University of Dundee, UK.
compbio.dundee.ac.uk
How to explore #AlphaFold quality measures interactively for multiply aligned proteins in Jalview! 😀
Jalview@jalview.bsky.social · last yr.📣 Working with AlphaFold's PAE? The latest instalment in our 'Protein Model Quality' series may be of help! Find out how you can visualise the metric with your alignments and 3D structures in Jalview. ▶️ Watch the new training video here: www.youtube.com/watch?v=jowU...
I'll be attending the @iscb.bsky.social #ISMBECCB2025 conference in Liverpool from July 20-24. Who else is coming? Register here and don't miss it. It's going to be great! invt.io/1bxbm6fohph I'll present my PhD work at the @bartongrp.bsky.social on protein-ligand interactions at the 3DSIG panel!
A great way for Javier to finish his time in @bartongrp.bsky.social with our first journal cover! Shame they don’t print them any more! 🤣🤣
Dr Javier Sánchez Utgés@javierutges.bsky.social · last yr.The @narjournal.bsky.social Annual Web Server Issue is now finalised. Congratulations to all other authors for their excellent resources. I am thrilled to share that one of our #LIGYSIS-web paper figures was selected as the cover image for this issue. Check it out here: lnkd.in/dXAb6jwv!
Accessing a wealth of structure data to integrate with your #MSA is possible accessing the #3DBeacons network through #Jalview. Get experimentally determined structures from @pdbeurope.bsky.social as well as predicted structure models from #AlphaFoldDB, @swiss-model.bsky.social and other providers!
Jalview@jalview.bsky.social · last yr.🚀 Structure alert: Discover protein models in Jalview using the 3D Beacons network. Browse thousands of experimental and predicted structures from Protein Data Bank, AlphaFold, SWISS Model and more with the click of a few buttons! ▶️ Watch our instructional video: www.youtube.com/watch?v=ZBDZ...
I am #exhilarated to share that our new paper "LIGYSIS-web: a resource for the analysis of protein-ligand binding sites" is now published in @narjournal.bsky.social! After almost two years of development and more than 600 commits, LIGYSIS-web is out! 📜 : tinyurl.com/utges-LIGYSI...
Two weeks ago, I reached a significant #milestone my career, marking my most substantial #achievement yet. Following four and a half years of dedicated work at the University of #Dundee and a successful #PhD viva defence, I attained the title of Doctor of Philosophy in #Structural #Bioinformatics
Congratulations to Javier @javierutges.bsky.social on his successful PhD viva today! @bartongrp.bsky.social
💡Calling all visualisation enthusiasts - did you know Jalview can help you bring your alignments to life in more ways than one? Experience the beauty of molecular graphics with four 3D viewers - PyMol, UCSF Chimera, JMol and ChimeraX - all accessible from Jalview!
💡Curious about intrinsically disordered regions in your proteins? Jalview's got answers - FOUR of them, infact! Many disease-associated proteins, including those involved in neurodegenerative disorders (e.g., Alzheimer's and Parkinson's) and cancer, contain IDRs.
👩🎓Last month, 60% of our YouTube audience was women. This International Women's Day, we are celebrating all the trailblazing women who watch our training videos online. 💕 Thank you for supporting our educational content! Watch here: www.youtube.com/@jalviewtrai... #IWD2025 #AccelerateAction
