Nabil-Fareed Alikhan

@[email protected]
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1.3K Posts
Admin for @mstdn.science. #bioinformatician. Interested in #microbiology and #genomics.
Websitehttp://happykhan.com
Twitterhttps://twitter.com/happy_khan
GitHubhttps://github.com/happykhan
Nabil-Fareed AlikhanMar 12
Bye bye research fish
Nabil-Fareed AlikhanMar 7

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 🥂

https://soundcloud.com/microbinfie

Micro Binfie Podcast

Microbial Bioinformatics is a rapidly changing field marrying computer science and microbiology. Join us as we share some tips and tricks we’ve learnt over the years. If you’re student just getting to

SoundCloud
Nabil-Fareed AlikhanMar 5
Centre for Genomic Pathogen SurveillanceMar 5
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

AMR Convening on Building Sust...
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.

Nabil-Fareed AlikhanMar 5
Centre for Genomic Pathogen SurveillanceMar 3
Nearly 90% of AMR pathogen genomes come from high-income countries.109 participants from 52 countries meeting in Addis Ababa to close this gap. www.amrsurveillance.org #AMR #HealthEquity #Genomics #AMRSurveillanceAddis

AMR Convening on Building Sust...
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.

Nabil-Fareed AlikhanMar 5
Centre for Genomic Pathogen SurveillanceMar 5
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
Nabil-Fareed AlikhanMar 5
Centre for Genomic Pathogen SurveillanceMar 5
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
Nabil-Fareed AlikhanMar 5
Centre for Genomic Pathogen SurveillanceMar 5
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

AMR Convening on Building Sust...
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.

Nabil-Fareed AlikhanFeb 26

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 https://opencollective.com/mstdnscience

All proceeds go to running the server, our books are open for your scrutiny.

mstdn.science - Open Collective

Mastodon community (instance) of scientists and enthusiasts

Show threadNabil-Fareed AlikhanFeb 22

What's new in v1.0.0:

- Native macOS (DMG) and Windows (MSI) installers — no Java setup required
- BLAST+ bundled inside the installers, works out of the box
- New command-line interface (brig-cli) for scripted and server-side usage
- Modernised build with Maven, CI/CD via GitHub Actions
- Documentation site at happykhan.github.io/BRIG
- Bug fixes for various bugs people have pointed out to me, and that I remembered.

Nabil-Fareed AlikhanFeb 22

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 —
a staple visualisation in microbial genomics.

Download from: https://github.com/happykhan/BRIG/releases/tag/v1.0.0

Or sourceforge: https://sourceforge.net/projects/brig/files/v1.0.0/

Release v1.0.0 · happykhan/BRIG

BRIG v1.0.0 First official release of BRIG (BLAST Ring Image Generator) with a modernised build and native installers. Highlights Maven build — migrated from legacy Ant scripts to a Maven-based bu...

GitHub