iiinova — where your digital self keeps evolving

Geoff Barton @gjbarton.bsky.social · 25/09/2026

Great to see the enthusiasm at this introductory course!

Reposted by Geoff Barton

Jalview @jalview.bsky.social · 18/09/2026

📂 Who says iPhones have all the folding fun? If your alignment is wider than your screen, try Jalview’s ‘Wrap’ feature! Fold long alignments neatly into your window — then add scales on the left, right or top to create polished figures for papers, seminars & tutorials. ⬇️ www.jalview.org/download/

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Jalview @jalview.bsky.social · 15/09/2026

👓 Visualising sequence alignments in 3D? Jalview enables multiple structures to be visualised with Chimera, ChimeraX, PyMOL and Jmol — helping scientists and educators bring biology to life. 📺 Explore the editor's functionality: www.youtube.com/watch?v=pbms... www.youtube.com/watch?v=yRBL...

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Geoff Barton @gjbarton.bsky.social · 11/09/2026

One of the smaller but useful features of Jalview!

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Jalview @jalview.bsky.social · 07/09/2026

📣 Calling all sequence sleuths! 📣 Our latest training video investigates how colouring by conservation in Jalview can be used to deduce the locations of intermolecular interactions like salt bridges in a protein family. 📺: www.youtube.com/watch?v=1O34...

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Jalview @jalview.bsky.social · 20/08/2026

✂️ Editing sequence alignments in Jalview is flexible and reversible. Move sequences ↕️, create groups 👥, insert gaps ➖, using both mouse or keyboard. Edits can also be undone! 🎥 Learn how: www.youtube.com/watch?v=FXGI...

Keyboard with finger hovering over the section containing the up, down and left and right keys.

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Jalview @jalview.bsky.social · 05/08/2026

Batches of protein sequences can be submitted to the JPred server for protein secondary structure prediction, with the option to receive a copy of the results via email. 🔗 www.youtube.com/watch?v=yLga... 🔗 www.compbio.dundee.ac.uk/jpred/help.s... 📜 academic.oup.com/nar/article/...

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Geoff Barton @gjbarton.bsky.social · 02/08/2026

This is a feature I use a lot to help focus in on the parts of an alignment that are most relevant to my question. Incredibly helpful when combined with tree calculations to find the most interesting parts of huge sequence sets!

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Reposted by Geoff Barton

Jalview @jalview.bsky.social · 23/07/2026

📬 Protein and nucleotide structures can be imported into Jalview, mapped on to MSA sequences and visualised in 3D. Our latest training video summarises some of the structure import options available to users. ▶️ Watch it here: www.youtube.com/watch?v=xFUu...

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Geoff Barton @gjbarton.bsky.social · 16/07/2026

Another neat feature in Jalview that helps working with large alignments.

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Reposted by Geoff Barton

Jalview @jalview.bsky.social · 10/07/2026

💾 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...

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Jalview @jalview.bsky.social · 01/07/2026

⚽ 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...

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Jalview @jalview.bsky.social · 23/06/2026

🏊🏼‍♂️ 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...

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Jalview @jalview.bsky.social · 10/06/2026

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...

An alignment of ferredoxin proteins in Jalview with associated coding DNA sequences shown above in the split-screen view. Binding sites imported from UniProt are highlighted in pink in all views, including the associated AlphaFold structure displayed on the right in ChimeraX.

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Jalview @jalview.bsky.social · 27/05/2026

🔗 JABAWS: hub.docker.com/r/drsasp/jab... 🔗 Jalview Develop: www.jalview.org/development/... 🔗 SLIVKA: www.compbio.dundee.ac.uk/slivka/#cta-...

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Geoff Barton @gjbarton.bsky.social · 21/05/2026

Protein secondary structure prediction by AlphaFold and Jpred combined in Jalview. Enjoy!

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Geoff Barton @gjbarton.bsky.social · 18/05/2026

Structural domain analysis it alphafold and Jalview

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Geoff Barton @gjbarton.bsky.social · 12/05/2026

Ah yes. That’s true. One of my adults did his PhD there!

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Geoff Barton @gjbarton.bsky.social · 12/05/2026

Probably just too many great grants in the pile… the only consolation (?) is you know the proposal is good! Which countries are better for science funding now?

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Geoff Barton @gjbarton.bsky.social · 12/05/2026

🤣🤣 congratulations! I remember that moment vividly!

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Geoff Barton @gjbarton.bsky.social · 12/05/2026

Sorry to hear that…. It is never fun getting a rejection after all the strong signals you got. 😢

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Jalview @jalview.bsky.social · 06/05/2026

🧮 Are you making the most of Jalview’s annotation rows? These visual layers add context for interpreting biological structure & function: conservation, alignment quality, consensus, secondary structure, AlphaFold's pLDDT & PAE. ➡️ Group/user-specific annotations can also be created.

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Jalview @jalview.bsky.social · 01/05/2026

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...

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Jalview @jalview.bsky.social · 24/04/2026

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...

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Geoff Barton @gjbarton.bsky.social · 21/04/2026

It’s blossom time of year again in sunny Dundee Scotland UK!

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Reposted by Geoff Barton

Jalview @jalview.bsky.social · 17/04/2026

Did you know Jalview can bring your alignments to life in 3D? Experience the beauty of molecular graphics with PyMol, UCSF Chimera, ChimeraX and JMol in the editor. ▶️ Watch our NEW training video for more insights: www.youtube.com/watch?v=pbms...

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Reposted by Geoff Barton

Jalview @jalview.bsky.social · 15/04/2026

💡AlphaFold's pLDDT scores can be visualised in Jalview as annotation tracks at the bottom - useful when comparing regions of high confidence across predicted protein structures in alignments. ▶️ For a guided tour of AlphaFold metrics in Jalview, watch: www.youtube.com/watch?v=WVCM...

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Jalview @jalview.bsky.social · 09/04/2026

➡️ Watch our training video to find out more about structure discovery in Jalview: www.youtube.com/watch?v=ZBDZ...

youtube.com

Using 3D Beacons to access AlphaFold, Protein Data Bank and more in Jalview

YouTube video by Jalview & Dundee Resource Online Training

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Jalview @jalview.bsky.social · 09/04/2026

🔎 Browse extensive libraries of protein structures in Jalview using the 3D Beacons Network. Once imported, these can be colored, superimposed and viewed in 3D in conjunction with alignments. 👓 Synced views provide precision and clarity, allowing you to hone in on regions of importance.

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Geoff Barton @gjbarton.bsky.social · 18/03/2026

I’ll bear that in mind, but as someone who has perfected falling asleep in seminars ( even the interesting ones!) it will have to be an amazing story! 🤣

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Geoff Barton @gjbarton.bsky.social · 18/03/2026

Hahaha! I use “Sliced Bread” on BBC sounds and other shows…. As a change from books… I’ll branch out and try your suggestions. 👍

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Geoff Barton @gjbarton.bsky.social · 18/03/2026

99/100 times I wake up more than an hour later, go back to the bookmark and realise I fell asleep within a few minutes. I repeat this through the night. Music doesn’t work for me but maybe that or white noise can help others? 2/2

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Geoff Barton @gjbarton.bsky.social · 18/03/2026

I had the same experience when I got my Garmin. I relaxed more about sleep patterns. Getting back to sleep was always a problem though. My solution is to listen to an audiobook. I bookmark then set a timer for 60 minutes. 1/2

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Geoff Barton @gjbarton.bsky.social · 10/03/2026

I was very sad to hear this morning that Phil Bourne had passed away on 8th March. I've known Phil for many years but we had a great collaboration in the early days of the RCSB-PDB when he led the San Diego part of the consortium and I was in charge of the European project at EMBL-EBI. RIP Phil.

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Geoff Barton @gjbarton.bsky.social · 02/03/2026

My favourite index at the moment is the Field Weighted Citation Index which does a better job than h-index, particularly for early career folk, since h is so biased by field and age. Neither h nor FWCI do what your metric does of course!

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Geoff Barton @gjbarton.bsky.social · 02/03/2026

yes, probably preprints and also other outputs that have a DOI? I'm not sure what openalex.org include but we do have a lot of software releases with doi from zenodo and will have mostly the same set of authors. Great idea!

openalex.org

OpenAlex

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Geoff Barton @gjbarton.bsky.social · 02/03/2026

Nice idea! I tried it for me "Geoffrey Barton" and Got 77 but I think it is perhaps double counting some outputs?

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Geoff Barton @gjbarton.bsky.social · 01/03/2026

New awards? Crikey! The USA is abandoning science. Very sad to see.

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Geoff Barton @gjbarton.bsky.social · 23/02/2026

The annual crocuses on campus at #dundee university #scotland photo!

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Jalview @jalview.bsky.social · 05/02/2026

🌍 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 ❤️

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 09/01/2026

🎉 Happy #new #year to everyone! 📢 No better way to kickstart 2026 than by sharing our latest work, now available on #Open #Biology by @royalsociety.org. The title is "Mutations within the predicted fragment-binding region of FAM83G/SACK1G abolish ints interaction with the Ser/Thr kinase CK1α".

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Jalview @jalview.bsky.social · 17/12/2025

❄️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! ❤️

Jalview team members Geoff, Jim, Khadija, Renia and Ben posing for a festive photo in the School of Life Sciences, University of Dundee!

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Geoff Barton @gjbarton.bsky.social · 17/12/2025

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...

bbc.co.uk

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.

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Jalview @jalview.bsky.social · 04/12/2025

💡Beacon of hope! Did you know Jalview allows you to access thousands of experimental and predicted protein structures programmatically through the 3D Beacons network? 🔽Find out how on our YouTube channel: www.youtube.com/watch?v=ZBDZ...

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Geoff Barton @gjbarton.bsky.social · 22/11/2025

One of those November sunsets at Dundee Scotland today 😀

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Geoff Barton @gjbarton.bsky.social · 06/10/2025

Yes, core funded research institutes do this (EMBL, CRUK, MRC-LMB, MaxPlanck etc) but it is rare for universities to.

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