Samuel Lampa
@smllmp.bsky.social
Clinical Microbiology #Bioinformatics @ Karolinska Hospital | PhD alum http://pharmb.io | Author of scipipe.org | Looking to get more into genomic algorithms & systems understanding of microbes+hosts, TEs etc
Married to Emebet. Dad. Sinner saved by grace.
Married to Emebet. Dad. Sinner saved by grace.
I might be biased (as they mention scipipe.org), but a recommended related paper:
www.nature.com/articles/s41... #sciworkflows
www.nature.com/articles/s41... #sciworkflows
November 13, 2025 at 8:45 PM
I might be biased (as they mention scipipe.org), but a recommended related paper:
www.nature.com/articles/s41... #sciworkflows
www.nature.com/articles/s41... #sciworkflows
Reposted by Samuel Lampa
The last episode of the three part debate is out today! Check it out on the platform of your choice
🤩 Don't forget to give us stars and reviews to help spread the podcast to new listeners!
🤩 Don't forget to give us stars and reviews to help spread the podcast to new listeners!
🍏 We just finished a three part debate on @nextflow.io! Please don't hate me for volunteering on the cons side of the debate! Subscribe to #microbinfie on the podcast app of your choice or go here m.soundcloud.com/microbinfie/...
146 - NextFlow debate 1
Play 146 - NextFlow debate 1 by Micro Binfie Podcast on desktop and mobile. Play over 320 million tracks for free on SoundCloud.
m.soundcloud.com
November 13, 2025 at 5:17 PM
The last episode of the three part debate is out today! Check it out on the platform of your choice
🤩 Don't forget to give us stars and reviews to help spread the podcast to new listeners!
🤩 Don't forget to give us stars and reviews to help spread the podcast to new listeners!
⚠️Important bugfix release, 0.5.1 of SciCommander (tool to track shell commands in a reproducible way), fixing the scanning of output files and audit files in subdirectories!
github.com/samuell/scic...
github.com/samuell/scic...
Release 0.5.1: Fix handling of outputs in sub-folders · samuell/scicommander
This is a bugfix release that fixes #21 and makes sure that output paths in subfolders of the main directory are correctly handled.
Thanks to @GuilloteauQ for reporting it!
Changes
Fixes #21
Adds ...
github.com
November 13, 2025 at 6:20 PM
⚠️Important bugfix release, 0.5.1 of SciCommander (tool to track shell commands in a reproducible way), fixing the scanning of output files and audit files in subdirectories!
github.com/samuell/scic...
github.com/samuell/scic...
Reposted by Samuel Lampa
Metagenomics colleagues!
I'm looking for studies where both Illumina and ONT sequencing were performed on the same samples from soil, human, ruminent, and other sample types for comparison. Bonus if those studies include PacBio data.
Please help and share!
I'm looking for studies where both Illumina and ONT sequencing were performed on the same samples from soil, human, ruminent, and other sample types for comparison. Bonus if those studies include PacBio data.
Please help and share!
November 11, 2025 at 8:21 PM
Metagenomics colleagues!
I'm looking for studies where both Illumina and ONT sequencing were performed on the same samples from soil, human, ruminent, and other sample types for comparison. Bonus if those studies include PacBio data.
Please help and share!
I'm looking for studies where both Illumina and ONT sequencing were performed on the same samples from soil, human, ruminent, and other sample types for comparison. Bonus if those studies include PacBio data.
Please help and share!
Reposted by Samuel Lampa
📢 Just released 0.5.0 of SciCommander, a tool to automatically track provenance information about shell commands, into HTML reports with the full provenance graph for every output. This version brings much improved usability and better looks.
github.com/samuell/scic...
#provenance #bioinformatics
github.com/samuell/scic...
#provenance #bioinformatics
November 6, 2025 at 8:27 PM
📢 Just released 0.5.0 of SciCommander, a tool to automatically track provenance information about shell commands, into HTML reports with the full provenance graph for every output. This version brings much improved usability and better looks.
github.com/samuell/scic...
#provenance #bioinformatics
github.com/samuell/scic...
#provenance #bioinformatics
Reposted by Samuel Lampa
1/ Everyone’s chasing AI.
But in bioinformatics, solid foundations still win.
Here’s why mastering the basics matters more than ever. 🧵
But in bioinformatics, solid foundations still win.
Here’s why mastering the basics matters more than ever. 🧵
November 9, 2025 at 2:45 PM
1/ Everyone’s chasing AI.
But in bioinformatics, solid foundations still win.
Here’s why mastering the basics matters more than ever. 🧵
But in bioinformatics, solid foundations still win.
Here’s why mastering the basics matters more than ever. 🧵
This has been a fantastic course, very well done @valentinapeona.bsky.social and @ritarebollo.bsky.social ! 🙌
Looking forward to continue diving into the field 😊
Looking forward to continue diving into the field 😊
This week we're running the Transposable Elements course with @valentinapeona.bsky.social and @ritarebollo.bsky.social
www.physalia-courses.org/courses-work...
#TE25 #Bioinformatics #Genomics
www.physalia-courses.org/courses-work...
#TE25 #Bioinformatics #Genomics
November 7, 2025 at 3:50 PM
This has been a fantastic course, very well done @valentinapeona.bsky.social and @ritarebollo.bsky.social ! 🙌
Looking forward to continue diving into the field 😊
Looking forward to continue diving into the field 😊
Reposted by Samuel Lampa
This week we're running the Transposable Elements course with @valentinapeona.bsky.social and @ritarebollo.bsky.social
www.physalia-courses.org/courses-work...
#TE25 #Bioinformatics #Genomics
www.physalia-courses.org/courses-work...
#TE25 #Bioinformatics #Genomics
November 4, 2025 at 3:04 PM
This week we're running the Transposable Elements course with @valentinapeona.bsky.social and @ritarebollo.bsky.social
www.physalia-courses.org/courses-work...
#TE25 #Bioinformatics #Genomics
www.physalia-courses.org/courses-work...
#TE25 #Bioinformatics #Genomics
📢 Just released 0.5.0 of SciCommander, a tool to automatically track provenance information about shell commands, into HTML reports with the full provenance graph for every output. This version brings much improved usability and better looks.
github.com/samuell/scic...
#provenance #bioinformatics
github.com/samuell/scic...
#provenance #bioinformatics
November 6, 2025 at 8:27 PM
📢 Just released 0.5.0 of SciCommander, a tool to automatically track provenance information about shell commands, into HTML reports with the full provenance graph for every output. This version brings much improved usability and better looks.
github.com/samuell/scic...
#provenance #bioinformatics
github.com/samuell/scic...
#provenance #bioinformatics
Reposted by Samuel Lampa
At @embo.org #EMBOMobileGenome and want to connect with other TE researchers and follow the latest goings on?
Use #TEworldwide and #TEsky in your posts to be featured in the TEworldwide feed, which you can also find here:
bsky.app/profile/did:...
Use #TEworldwide and #TEsky in your posts to be featured in the TEworldwide feed, which you can also find here:
bsky.app/profile/did:...
November 5, 2025 at 5:14 AM
At @embo.org #EMBOMobileGenome and want to connect with other TE researchers and follow the latest goings on?
Use #TEworldwide and #TEsky in your posts to be featured in the TEworldwide feed, which you can also find here:
bsky.app/profile/did:...
Use #TEworldwide and #TEsky in your posts to be featured in the TEworldwide feed, which you can also find here:
bsky.app/profile/did:...
November 6, 2025 at 11:12 AM
Reposted by Samuel Lampa
Time to kick off #EMBOMobileGenome for 2025! A great selection of speakers and posters on the agenda!
#TEWorldwide #TESky
#TEWorldwide #TESky
November 4, 2025 at 12:32 PM
Time to kick off #EMBOMobileGenome for 2025! A great selection of speakers and posters on the agenda!
#TEWorldwide #TESky
#TEWorldwide #TESky
Reposted by Samuel Lampa
@tobybarilbio.bsky.social and I are very excited to release MycoMobilome! A very extensive effort to discover, QC and annotate TEs across the fungal kingdom.
👉 Ready-to-use for your own genome with a simple tutorial!
👉 Metadata about TEs discovered in your genome!
👉 Contribute and get recognition!
👉 Ready-to-use for your own genome with a simple tutorial!
👉 Metadata about TEs discovered in your genome!
👉 Contribute and get recognition!
1/ Ever needed to annotate TEs in a fungal genome, but didn't know where to start?
We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!
www.biorxiv.org/content/10.1...
We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!
www.biorxiv.org/content/10.1...
October 29, 2025 at 4:32 PM
@tobybarilbio.bsky.social and I are very excited to release MycoMobilome! A very extensive effort to discover, QC and annotate TEs across the fungal kingdom.
👉 Ready-to-use for your own genome with a simple tutorial!
👉 Metadata about TEs discovered in your genome!
👉 Contribute and get recognition!
👉 Ready-to-use for your own genome with a simple tutorial!
👉 Metadata about TEs discovered in your genome!
👉 Contribute and get recognition!
Reposted by Samuel Lampa
A horrific mass murder is unfolding in Sudan, where no one can see it. The RSF are murdering civilians in El Fasher, having finally defeated the Sudanese army forces holding out in the city. The BBC has managed to speak to some who escaped
www.youtube.com/watch?v=i7fC...
www.youtube.com/watch?v=i7fC...
Sudanese survivors of el-Fasher siege tell the BBC about RSF brutality | BBC News
YouTube video by BBC News
www.youtube.com
November 1, 2025 at 7:14 AM
A horrific mass murder is unfolding in Sudan, where no one can see it. The RSF are murdering civilians in El Fasher, having finally defeated the Sudanese army forces holding out in the city. The BBC has managed to speak to some who escaped
www.youtube.com/watch?v=i7fC...
www.youtube.com/watch?v=i7fC...
Reposted by Samuel Lampa
Make sure to register ASAP!
bsky.app/profile/jlst...
bsky.app/profile/jlst...
Come join the Workshop on Phylogenomics in Cesky Krumlov, Czechia, from January 25 through February 7, 2026!
Applications close November 15!
#phylogenetics #evolution #genomics #ai
evomics.org/apply-worksh...
Applications close November 15!
#phylogenetics #evolution #genomics #ai
evomics.org/apply-worksh...
Apply: Workshop on Phylogenomics 2026 - Evolution and Genomics
Application for the 2026 Workshop on Phylogenomics Use this form to apply for the 2026 Workshop on Phylogenomics being held in Cesky Krumlov, Czechia from 25th January through 7th February, ...
evomics.org
October 30, 2025 at 6:50 PM
Make sure to register ASAP!
bsky.app/profile/jlst...
bsky.app/profile/jlst...
Reposted by Samuel Lampa
Used EMBL-EBI data resources to find, analyse, or archive your data? 🧬
Now’s your turn: tell us how you’ve used them + why they matter.
It takes 15 mins and helps keep these services open and free for all.
👉 tinyurl.com/bdf73zpp
Closes 16 July
#opendata #FAIRdata
Now’s your turn: tell us how you’ve used them + why they matter.
It takes 15 mins and helps keep these services open and free for all.
👉 tinyurl.com/bdf73zpp
Closes 16 July
#opendata #FAIRdata
June 17, 2025 at 8:00 PM
Used EMBL-EBI data resources to find, analyse, or archive your data? 🧬
Now’s your turn: tell us how you’ve used them + why they matter.
It takes 15 mins and helps keep these services open and free for all.
👉 tinyurl.com/bdf73zpp
Closes 16 July
#opendata #FAIRdata
Now’s your turn: tell us how you’ve used them + why they matter.
It takes 15 mins and helps keep these services open and free for all.
👉 tinyurl.com/bdf73zpp
Closes 16 July
#opendata #FAIRdata
The @scikit-learn.org docs are such a nice overview of the common types of learning in classical machine learning! A great visual overview and guide for newcomers.
scikit-learn.org
scikit-learn.org
October 25, 2025 at 10:32 PM
The @scikit-learn.org docs are such a nice overview of the common types of learning in classical machine learning! A great visual overview and guide for newcomers.
scikit-learn.org
scikit-learn.org
I did all of those!
October 25, 2025 at 7:38 PM
I did all of those!
Reposted by Samuel Lampa
Version 3 of the Snakemake rolling paper is now pulbished on @f1000publishing.bsky.social: f1000research.com/articles/10-...
We have updated the presented features and the design patterns.
#sciworkflows #reproducibility
We have updated the presented features and the design patterns.
#sciworkflows #reproducibility
F1000Research Article: Sustainable data analysis with Snakemake.
Read the latest article version by Felix Mölder, Kim Philipp Jablonski, Brice Letcher, Michael B. Hall, Peter C. van Dyken, Christopher H. Tomkins-Tinch, Vanessa Sochat, Jan Forster, Filipe G. Vi...
f1000research.com
September 23, 2025 at 10:18 AM
Version 3 of the Snakemake rolling paper is now pulbished on @f1000publishing.bsky.social: f1000research.com/articles/10-...
We have updated the presented features and the design patterns.
#sciworkflows #reproducibility
We have updated the presented features and the design patterns.
#sciworkflows #reproducibility
Always nice when someone has not only cited you, but also actually read your paper 😊 Hat tip to the authors! 👍
doi.org/10.1016/j.co... #sciworkflows
doi.org/10.1016/j.co... #sciworkflows
October 24, 2025 at 10:10 PM
Always nice when someone has not only cited you, but also actually read your paper 😊 Hat tip to the authors! 👍
doi.org/10.1016/j.co... #sciworkflows
doi.org/10.1016/j.co... #sciworkflows
Reposted by Samuel Lampa
The next five videos from our #IMMEM XIV poster presentations are available now on our YouTube channel and cover topics like #microbiome, transmission and more. #IDSky
https://youtube.com/playlist?list=PLBG53xT7PX7v-C3XcKHnKeVP1NxsrLqBU&si=tpFqDe_obR6LZLtx
https://youtube.com/playlist?list=PLBG53xT7PX7v-C3XcKHnKeVP1NxsrLqBU&si=tpFqDe_obR6LZLtx
IMMEM XIV Poster presentations
Explore the different post presentations that were recorded as part of the 14th edition of the International Meeting on Microbial Epidemiological Markers (IM...
youtube.com
October 22, 2025 at 12:50 PM
The next five videos from our #IMMEM XIV poster presentations are available now on our YouTube channel and cover topics like #microbiome, transmission and more. #IDSky
https://youtube.com/playlist?list=PLBG53xT7PX7v-C3XcKHnKeVP1NxsrLqBU&si=tpFqDe_obR6LZLtx
https://youtube.com/playlist?list=PLBG53xT7PX7v-C3XcKHnKeVP1NxsrLqBU&si=tpFqDe_obR6LZLtx
I'm baffled as to why so many presenters are sounding like they are reading a script ...😒Why are we listening to you live if we could have just read the script ourselves? 😏
October 22, 2025 at 9:15 AM
I'm baffled as to why so many presenters are sounding like they are reading a script ...😒Why are we listening to you live if we could have just read the script ourselves? 😏
Reposted by Samuel Lampa
Almost there! Starting tomorrow morning (Paris time), the webinar on Bacterial strain Taxonomy for Genomic Surveillance organized within the ECDC sponsored GenEpi-BioTrain programme; registration is free; see more here: research.pasteur.fr/en/event/bac...
Bacterial strain Taxonomy for Genomic Surveillance - GenEpi-BioTrain Webinar - Research
This workshop aims to provide participants with a comprehensive understanding of bacterial classification and nomenclature approaches used in genomic surveillance. Participants will gain insight into ...
research.pasteur.fr
October 21, 2025 at 1:47 PM
Almost there! Starting tomorrow morning (Paris time), the webinar on Bacterial strain Taxonomy for Genomic Surveillance organized within the ECDC sponsored GenEpi-BioTrain programme; registration is free; see more here: research.pasteur.fr/en/event/bac...
Reposted by Samuel Lampa
Interesting paper on bacteriophage genomics and bioinformatics
'Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world' by @sebwielgoss.bsky.social and colleagues
academic.oup.com/bib/article/...
'Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world' by @sebwielgoss.bsky.social and colleagues
academic.oup.com/bib/article/...
Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world
Abstract. The increasing interest in finding new viruses within (meta)genomic datasets has fueled the development of computational tools for virus detectio
academic.oup.com
October 21, 2025 at 1:45 PM
Interesting paper on bacteriophage genomics and bioinformatics
'Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world' by @sebwielgoss.bsky.social and colleagues
academic.oup.com/bib/article/...
'Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world' by @sebwielgoss.bsky.social and colleagues
academic.oup.com/bib/article/...
Reposted by Samuel Lampa
Our Metabuli taxonomic classifier is now available as an app compatible with Windows, Linux, and macOS. It features an interactive visualization developed by @sunjaelee.bsky.social, along with improvements to Metabuli by @jbeom.bsky.social.
📄 academic.oup.com/bioinformati...
📄 academic.oup.com/bioinformati...
October 16, 2025 at 1:01 PM
Our Metabuli taxonomic classifier is now available as an app compatible with Windows, Linux, and macOS. It features an interactive visualization developed by @sunjaelee.bsky.social, along with improvements to Metabuli by @jbeom.bsky.social.
📄 academic.oup.com/bioinformati...
📄 academic.oup.com/bioinformati...