iiinova — where your digital self keeps evolving

Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 05/09/2026

Sup. BRIGX! We have a new release try it out here: brigx.genomicx.org BRIGX v0.9.6 has: * Reworked mobile layout and ring editor. * Read-only result viewing from local files or GitHub session links. * PNG and SVG exports that match the on-screen plot, including zoom, moved legends […]

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 21/08/2026

Learn all the secrets of the CGPS software . The courses and the tools are free. The new website provides structured training on EpiCollect5, Microreact, Data-flo. You can Work through tutorials, pass assessments, and earn a certificate. www.cgps.academy

cgps.academy

CGPS Academy - Free training for genomic surveillance tools

Free, self-paced training courses on EpiCollect5, Microreact, Data-flo, and Pathogenwatch - the tools used for genomic pathogen surveillance worldwide.

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 11/08/2026

Howdy, In my spare time I have been working on a modern web version of BRIG, and it is now in a state fit for public consumption. Please share with your team + students. And If they have feedback they can reach me on email. brigx.genomicx.org BRIGX is a modern implementation of BRIG […]

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 09/08/2026

Cory Doctorow is a bit annoying, guys don't get too excited.

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 07/08/2026

Oh no .I think I've transitioned from the young man who thinks he knows better to the old man who knows he does.

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 05/08/2026

Seneca is great and all but that noble savage idyllic simple life rhetoric just betrays his status. Its clear he's never had to actually sleep on the ground. I'm all for not giving into hedonism but a raised bed is pretty nice. Actually clothes not rando furs is pretty nice. Something to eat […]

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 05/08/2026

I need a holiday I think. Everything I interact with seems to be. """ Everyone blah blah blah blah. We can do better. Buy my thing. """

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 04/08/2026

Is substack actually good for reading meaningful blog/articles? Or should I not bother

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 02/08/2026

why do we depict atlas holding up a globe, when he was supposed to hold up the sky.

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 01/08/2026

So. How do we get rid of this mitochondrial eve idea? Cause that's just not how that works.

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 29/07/2026

How can the UK have water restrictions. I thought it was meant to rain all the time. Has. The climate. Changed?

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 29/07/2026

We've upgraded mstdn.science to Mastodon 4.6.4 blog.joinmastodon.org/2026/06/masto… This release introduces Collections, allowing users to create and share curated profile lists with user consent, along with a redesigned profile experience featuring easier editing, avatar/header […]

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 29/07/2026

Hetzner put their prices up. crazy increase.

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 28/07/2026

If you are worried about ai stealing your work. If you write "give ebola" everywhere it won't touch it.

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 25/07/2026

Finish reading the Odyssey. With all this talk around the new movie I thought I better read the source before I get too influenced. It's good. I recommend. It's not what I thought it would be. It's better, and I will be surprised if the film can match it for me.

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 14/07/2026

When your teams losing, you have to cheer harder.

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 12/07/2026

Bedroom was less than 26* for first time in forever and I finally slept.

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 06/07/2026

I'm blocking any registrations from disposable email domains. Sorry. There's just no other way to verify it's not a bot. I'm starting to see why folks push digital IDs.

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 19/06/2026

I don't know. There's a lot of Russian bots spamming site registrations. I'm totally against having digital ID and forcing people to reveal who they are, but dunno how else to manage it. Even if we have questionnaires on why you want to join and all that, they just use AI generated slop to fill […]

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 22/05/2026

As far as i know the SLURM scheduler was named after the drink in futurama.

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 22/05/2026

It appears today is the one sanctioned day of summer in the UK. You have my permission to take the day off.

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 02/05/2026

It's caturday. Post some mother liking cats.

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 01/05/2026

Time for some database spring cleaning . Here are my top tips for mastodon admins! Index bloat is your #1 enemy. Federation churn (constant insert/delete cycles) destroys B-tree indexes fast. Run this on your Postgres server: REINDEX TABLE CONCURRENTLY public.statuses; Repeat for […]

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 01/05/2026

We're now running mastodon 4.5.9 As always, let me know if things are not working as expected. If you have some spare dosh, please donate to opencollective.com/mstdnscience All proceeds go to running the server, our books are open for your scrutiny.

opencollective.com

mstdn.science - Open Collective

Mastodon community (instance) of scientists and enthusiasts

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 29/04/2026

💡 Support mstdn.science with a Financial Contribution! 💡 mstdn.science exists through contributions by folks like you. If you're not skint from the season's festivities, consider making a regular contribution to opencollective.com/mstdnscience . If we can manage another £60 / month, the […]

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 18/04/2026

Could some clarify what it means go medieval on ones ass? Like specifically what would that entail and what equipment would be needed ?

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 11/04/2026

omg. I was using MS word --- and i forgot to save a doc! I have become too lazy with autosaving via google docs. !!

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 04/04/2026

BRIG v1.1.1 release. There's some minor quality of life changes but the key thing is fixing the GC Skew and Content graphs for small reference sequences (plasmids), from the chunky and blocky histogram, we now have a much smoother solution. Download from […] [Original post on mstdn.science]

Circular genome comparison figure showing GC Content and GC Skew

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 26/03/2026

Host read removal sounds simple. It's not. 🧫Ep. 151 of hashtag#microbinfie: we talk with Bede Constantinides about Deacon — why alignment-based approaches fall short, the sensitivity/specificity tradeoff, and what it takes to remove host reads at scale. Part 1 of 2 […]

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 26/03/2026

Been working on a browser version of BRIG. No install. Interactive. Looking for beta testers; message me if you're interested.

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 07/03/2026

We just uploaded the 150th episode of the #microbinfie podcast, scheduled for Thursday, where we blow your mind with vibe coding. I can't believe we have actually made it this far. 🍻 To the next 150 episodes 🥂 soundcloud.com/microbinfie

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Reposted by Nabil-Fareed Alikhan

Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 05/03/2026

Reporting from the AMR Surveillance Convening at Africa CDC, Addis Ababa. Opening message was direct: the surveillance gap isn't about knowledge anymore, it's delivery and financing. Africa carries ~21% of the global AMR burden. Recap of Day 1 from www.amrsurveillance.org #AMRSurveillanceAddis

amrsurveillance.org

AMR Convening on Building Sustainable AMR Genomic Surveillance

A focused convening to identify practical pathways for strengthening routine national AMR surveillance systems, including the integration of genomic data.

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Reposted by Nabil-Fareed Alikhan

Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 05/03/2026

Sentinel site session was the most grounding. Surveillance fails when it's extractive — data goes up, nothing comes back. Labs engage when it improves their own practice. www.amrsurveillance.org #AMRSurveillanceAddis

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Reposted by Nabil-Fareed Alikhan

Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 05/03/2026

Four national stories. Philippines: 38 years of AMR surveillance, now adding WGS. Uganda: 16 to 43 sites. Pakistan: building a genomic strategy. Brazil: mapping labs nationally. Start small, invest in quality, build government ownership. #AMRSurveillanceAddis Day 1 of www.amrsurveillance.org

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Reposted by Nabil-Fareed Alikhan

Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 05/03/2026

Last session pushed beyond bacteria. Azole-resistant Aspergillus linked to agricultural fungicides. C. auris likely accelerated by climate change. Almost no global capacity for fungal genomic surveillance. AMR is bigger than bacteria. www.amrsurveillance.org #AMRSurveillanceAddis

amrsurveillance.org

AMR Convening on Building Sustainable AMR Genomic Surveillance

A focused convening to identify practical pathways for strengthening routine national AMR surveillance systems, including the integration of genomic data.

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 26/02/2026

We're now running mastodon 4.5.7 As always, let me know if things are not working as expected. If you have some spare dosh, please donate to opencollective.com/mstdnscience All proceeds go to running the server, our books are open for your scrutiny.

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mstdn.science - Open Collective

Mastodon community (instance) of scientists and enthusiasts

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 22/02/2026

BRIG v1.0.0 Released — BLAST Ring Image Generator This is dedicated to Joe Healey Who asked me many years ago to round up the version number to v1. BRIG creates circular comparison images showing sequence similarity between a reference genome and multiple query sequences as concentric rings — […]

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