Torsten Seemann
@torstenseemann.bsky.social
Microbial bioinformatics, genomics, software, clinical and public health microbiology
More details at https://tseemann.github.io
More details at https://tseemann.github.io
Pinned
Reposted by Torsten Seemann
🚨Abstract submission & registration for #MicroSeq2025 is OPEN! 🚨Get in quick! The first 50 registrations are FREE for PhD students and ECRs who are current ASM members, thanks to @aussocmic.bsky.social.
Head to our website to register now 👇
www.microseqconference.com/registration...
Head to our website to register now 👇
www.microseqconference.com/registration...
July 21, 2025 at 2:16 AM
🚨Abstract submission & registration for #MicroSeq2025 is OPEN! 🚨Get in quick! The first 50 registrations are FREE for PhD students and ECRs who are current ASM members, thanks to @aussocmic.bsky.social.
Head to our website to register now 👇
www.microseqconference.com/registration...
Head to our website to register now 👇
www.microseqconference.com/registration...
Google Slides has a new "Stock images" option when you "Insert Image" - you get these two options for the search term #bioinfortmics ...
June 25, 2025 at 11:09 PM
Google Slides has a new "Stock images" option when you "Insert Image" - you get these two options for the search term #bioinfortmics ...
Reposted by Torsten Seemann
🚀 Pushed some updates to taxonomy.onecodex.com
- Example queries to help you get started
- Summary section for easier interpretation
- Perf. improvements
- Example queries to help you get started
- Summary section for easier interpretation
- Perf. improvements
Taxonomy Time Machine
Explore and compare the history of the NCBI Taxonomy Database. Instantly browse, search, and reconstruct taxonomic lineages at any point in time. Open source, web-based, and API-accessible.
taxonomy.onecodex.com
May 24, 2025 at 9:38 PM
🚀 Pushed some updates to taxonomy.onecodex.com
- Example queries to help you get started
- Summary section for easier interpretation
- Perf. improvements
- Example queries to help you get started
- Summary section for easier interpretation
- Perf. improvements
Reposted by Torsten Seemann
You might be wondering why we haven't updated outbreak.info for months.
Well, the reason is that GISAID cut our access in January - as they did others. Without telling us.
After a ♾️ back and forth, that is now permanent.
More on that soon - and why GISAID should not be trusted with critical data.
Well, the reason is that GISAID cut our access in January - as they did others. Without telling us.
After a ♾️ back and forth, that is now permanent.
More on that soon - and why GISAID should not be trusted with critical data.
May 28, 2025 at 11:02 PM
You might be wondering why we haven't updated outbreak.info for months.
Well, the reason is that GISAID cut our access in January - as they did others. Without telling us.
After a ♾️ back and forth, that is now permanent.
More on that soon - and why GISAID should not be trusted with critical data.
Well, the reason is that GISAID cut our access in January - as they did others. Without telling us.
After a ♾️ back and forth, that is now permanent.
More on that soon - and why GISAID should not be trusted with critical data.
Reposted by Torsten Seemann
On more than one occasion I've thought of a cool idea for a bioinformatics program only to realize @torstenseemann.bsky.social already wrote it a decade ago.
April 14, 2025 at 4:53 AM
On more than one occasion I've thought of a cool idea for a bioinformatics program only to realize @torstenseemann.bsky.social already wrote it a decade ago.
The 1973 edition of Google Maps. #nostalgia #Melbourne
March 14, 2025 at 3:38 AM
The 1973 edition of Google Maps. #nostalgia #Melbourne
🚀🧬 MY former colleague @micamer.bsky.social who I worked with in the early years of my career has released a BLAST service (GUI + API options) which replicates the NCBI services but with faster response times.
We would love feedback on a new NCBI-BLAST service we are launching today: sky-blast.com
Under the hood it's the same BLAST executable and databases provided by NCBI, with a replica of the NIH's interface - providing an alternative to the US gov service that's less congested, faster & more reliable
Under the hood it's the same BLAST executable and databases provided by NCBI, with a replica of the NIH's interface - providing an alternative to the US gov service that's less congested, faster & more reliable
March 12, 2025 at 1:19 AM
🚀🧬 MY former colleague @micamer.bsky.social who I worked with in the early years of my career has released a BLAST service (GUI + API options) which replicates the NCBI services but with faster response times.
The 10-millionth job run on Galaxy Australia turned out to be my Abricate tool, which itself has been run nearly 500K times. 🤯
If only I had a dollar for every run! 😜
If only I had a dollar for every run! 😜
Which locally-developed bioinformatics tool was used to run Galaxy Australia’s 10 millionth job? It has been used to screen for antimicrobial resistance and virulence genes in 490,507 jobs run on #GalaxyAustralia so far! Clue: @torstenseemann.bsky.social www.biocommons.org.au/news/10m-jobs
Galaxy Australia’s 10 millionth job relied on popular locally-developed tool — Australian BioCommons
The ten millionth job completed on the Galaxy Australia service analysed pathogen samples for known antibiotic resistance genes using the ABRicate tool. You’d be surprised how many time this Australia...
www.biocommons.org.au
March 10, 2025 at 7:59 AM
The 10-millionth job run on Galaxy Australia turned out to be my Abricate tool, which itself has been run nearly 500K times. 🤯
If only I had a dollar for every run! 😜
If only I had a dollar for every run! 😜
While browsing for a new place to rent I came across this bathroom tile design. Makes me want a pixel-art shower one day. Or a valid QR code?
March 10, 2025 at 7:53 AM
While browsing for a new place to rent I came across this bathroom tile design. Makes me want a pixel-art shower one day. Or a valid QR code?
🦘✂️ Thanks to @cziscience.bsky.social , @wytamma.bsky.social and I are writing the next version of the Snippy bacterial variant calling pipeline. We want your input on what features s it will have. Please fill out this (longish) survey to help make Snippy great again!
forms.gle/YJP6WQjsk8KK...
forms.gle/YJP6WQjsk8KK...
Snippy: Microbial Variant Calling Community Survey
Help us drive the next wave of innovation in Single-Nucleotide Polymorphism (SNP) discovery and genome analysis by sharing your valuable experiences and insights. This in-depth survey aims at understa...
forms.gle
March 4, 2025 at 9:04 AM
🦘✂️ Thanks to @cziscience.bsky.social , @wytamma.bsky.social and I are writing the next version of the Snippy bacterial variant calling pipeline. We want your input on what features s it will have. Please fill out this (longish) survey to help make Snippy great again!
forms.gle/YJP6WQjsk8KK...
forms.gle/YJP6WQjsk8KK...
Reposted by Torsten Seemann
Big thanks to @torstenseemann.bsky.social for hosting me at the Centre for Pathogen Genomics. It was lovely to meet everyone and see the awesome binfo work happening in Asia-Pacific!
#Austrakka #Bioinformatics #PublicHealth
#Austrakka #Bioinformatics #PublicHealth
February 28, 2025 at 2:58 AM
Big thanks to @torstenseemann.bsky.social for hosting me at the Centre for Pathogen Genomics. It was lovely to meet everyone and see the awesome binfo work happening in Asia-Pacific!
#Austrakka #Bioinformatics #PublicHealth
#Austrakka #Bioinformatics #PublicHealth
Want to help build capacity public health pathogen bioinformatics in the Asia Pacific region?
🦘 Based in Melbourne Australia with me
✈️ Travel to and work internationally
🧠 Lead strategy, training & infrastructure
Applications close soon!
jobs.unimelb.edu.au/caw/en/job/9...
🦘 Based in Melbourne Australia with me
✈️ Travel to and work internationally
🧠 Lead strategy, training & infrastructure
Applications close soon!
jobs.unimelb.edu.au/caw/en/job/9...
Details : Bioinformatician, International Training & Research : The University of Melbourne
Careers at The University of Melbourne
jobs.unimelb.edu.au
February 5, 2025 at 7:00 AM
Want to help build capacity public health pathogen bioinformatics in the Asia Pacific region?
🦘 Based in Melbourne Australia with me
✈️ Travel to and work internationally
🧠 Lead strategy, training & infrastructure
Applications close soon!
jobs.unimelb.edu.au/caw/en/job/9...
🦘 Based in Melbourne Australia with me
✈️ Travel to and work internationally
🧠 Lead strategy, training & infrastructure
Applications close soon!
jobs.unimelb.edu.au/caw/en/job/9...
Don't know who to follow for the best in microbial bioinformatics?
This is the Starter Pack you need!
bsky.app/starter-pack...
This is the Starter Pack you need!
bsky.app/starter-pack...
January 13, 2025 at 3:08 AM
Don't know who to follow for the best in microbial bioinformatics?
This is the Starter Pack you need!
bsky.app/starter-pack...
This is the Starter Pack you need!
bsky.app/starter-pack...
Really hoping there isn't a Y2.25K bug we missed.
December 29, 2024 at 11:49 PM
Really hoping there isn't a Y2.25K bug we missed.
When blue screens were what made kids dream.
December 8, 2024 at 5:27 AM
When blue screens were what made kids dream.
Reposted by Torsten Seemann
Love this poster on the Mandelbrot Set
December 7, 2024 at 9:14 PM
Love this poster on the Mandelbrot Set
Reposted by Torsten Seemann
🌟 Excited to share my latest preprint with @lachlanjmc.bsky.social on @biorxivpreprint.bsky.social: "Genome size estimation from long read overlaps”! 🚀
Check it out here: doi.org/10.1101/2024...
And find the code here: github.com/mbhall88/lrge
🧵👇
Check it out here: doi.org/10.1101/2024...
And find the code here: github.com/mbhall88/lrge
🧵👇
doi.org
December 3, 2024 at 1:38 AM
🌟 Excited to share my latest preprint with @lachlanjmc.bsky.social on @biorxivpreprint.bsky.social: "Genome size estimation from long read overlaps”! 🚀
Check it out here: doi.org/10.1101/2024...
And find the code here: github.com/mbhall88/lrge
🧵👇
Check it out here: doi.org/10.1101/2024...
And find the code here: github.com/mbhall88/lrge
🧵👇
Reposted by Torsten Seemann
I just made a first release of TNA - new tool to compare 2 bacterial genomes. Is shamelessly inspired by ACT, but should be simpler to use. Drag-n-drop two genomes: it runs BLAST for you and then you can visualize. For Mac, Windows 11, Linux tna.readthedocs.io
TNA documentation — TNA 0.0.1 documentation
tna.readthedocs.io
November 29, 2024 at 11:38 AM
I just made a first release of TNA - new tool to compare 2 bacterial genomes. Is shamelessly inspired by ACT, but should be simpler to use. Drag-n-drop two genomes: it runs BLAST for you and then you can visualize. For Mac, Windows 11, Linux tna.readthedocs.io
I nominate this for #bioinformatiocs tool name of the year. I love it when Aussie home grown software have some "Australiana" in them! 🇦🇺
github.com/AroneyS/binc...
github.com/AroneyS/binc...
GitHub - AroneyS/binchicken: Bin Chicken - recovery of low abundance and taxonomically targeted metagenome assembled genomes (MAGs) through strategic coassembly
Bin Chicken - recovery of low abundance and taxonomically targeted metagenome assembled genomes (MAGs) through strategic coassembly - AroneyS/binchicken
github.com
November 26, 2024 at 11:29 PM
I nominate this for #bioinformatiocs tool name of the year. I love it when Aussie home grown software have some "Australiana" in them! 🇦🇺
github.com/AroneyS/binc...
github.com/AroneyS/binc...
Today I discovered that there is a street near my house named "Nullarbor Pl". I could take my laptop down there and run "nullabor.pl" at Nullarbor Pl. #coincidence
October 8, 2023 at 7:46 AM
Today I discovered that there is a street near my house named "Nullarbor Pl". I could take my laptop down there and run "nullabor.pl" at Nullarbor Pl. #coincidence