how to use #nextflow "multiMap' to transform a channel if the 'input' of an existing module doesn't fit your needs.
eg: you want
tuple val(meta), path(bam),path(bed)
while the module was designed the following way:
tuple val(meta1), path(bed)
tuple val(meta2), path(bam)
https://gist.github.com/lindenb/fbd76e5887754a7831d95422ea58f499
thanks a lot @mbp for the tip !
The city of #Nijmegen dedicated a #streetart banner to showcase #bioinformatics. Loving it!
If there is any sort of lesson to be learnt from this its that #genomics data will often throw up ‘edge cases’ that will confound your well-reasoned attempt to write some #bioinformatics code to process large datasets.
The fewer assumptions you make about what your data might look like, the better!
Interested in learning about plant genomics? We're offering an opportunity for a few students to join our genomics team and gain hands-on experience in DNA extraction, ONT sequencing, and data analysis. Reach out if you're interested: https://www.pbb.uni-bonn.de
#Genomics #Bioinformatics #PlantScience #OpenScience
@boas_pucker
Whenever I see a DNA logo from a lab, bioinformatics/genomics centre, hackathon, or training course and it’s backwards I sigh a little. I don’t point them out anymore as I usually just receive passive aggression, but what does it say about you that you don’t care? Several big ones in my stream today. If an entomology training centre had a logo with an 8-legged fly it’d be weird right? #bioinformatics #genomics #DNA
💻🧬 Join the Bioconductor project at BioHackathon Europe 2025!
We're excited to be part of BioHackathon Europe 2025 (Berlin, Nov 3–7) with a project focused on improving metadata and interoperability in bioinformatics.
In-person registration closes Tuesday, July 15 - virtual participation stays open!
🔗 Project details: https://github.com/elixir-europe/biohackathon-projects-2025/blob/main/13.md
🔗 All projects: https://biohackathon-europe.org/projects/
Join the discussion in the #edam-collaboration channel on Bioconductor Zulip.
Minigraph to dotplot to image to AI-assited SV detection
Looks like worth trying
https://www.biorxiv.org/content/10.1101/2025.07.06.663386v1.full.pdf
https://github.com/songbowang125/Swave
#bioinformatics #Genomics #pangenome #ShouldTryThis
Join the Bioconductor Developer Forum - R & Rust in Bioinformatics
Curious about combining R and Rust in your bioinformatics workflows?
On 28 July, join us for an online session featuring talks on extendr, Rust-based package development, and real-world use cases in Bioconductor and CRAN.
🗓️ Date: Monday, 28 July 2025
🕔 Time: 17:00–18:00 CEST
📍 Location: Online
🔗 Read the blog post https://blog.bioconductor.org/posts/2025-07-09-developers-forum-july28/
{targets} getting a shoutout in @kgagalova’s talk, even though the focus is on #nextflow #RStats #ReproducibleResearch #Bioinformatics #targets. #Pipelines
Enjoying @kgagalova presenting her ideas for #bioinformatics pipelines and how workflow managers can make your scientific work into #ReproducibleResearch
Pipeline release! nf-core/pairgenomealign v2.2.0 - nf-core/pairgenomealign v2.2.0 – Chagara ponzu!
Please see the changelog: https://github.com/nf-core/pairgenomealign/releases/tag/2.2.0
#comparativegenomics #dotplot #genomics #last #pairwisealignment #synteny #wholegenomealignment #nfcore #openscience #nextflow #bioinformatics
UCSC genome browser: "Unusually Conserved Regions - Ultracons, HARs, etc" https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&position=default&g=unusualcons
The problem is always more complicated, always more nuanced, the second time you look at your #bioinformatics code, and realize an eventuality is unaccounted for
GREmLN: A Cellular Regulatory Network-Aware Transcriptomics Foundation Model
https://www.biorxiv.org/content/10.1101/2025.07.03.663009v1?rss=1
Comments
* really brilliant work: LLM + neural transformer architecture
* a molecular biologist, I long-thought (no time to learn / program) flux-based analysis / ODE models
* this type of modeling is foundational to in silico modeling
* huge proponent of graphs - add LLM, attention heads - brilliant! 😀 👍️ kudos
#BiologicalModeling #FoundationModels #LLM #attention #GraphTheory #bioinformatics
📣 PhD students in #health, #bioinformatics, or #DataScience: this one’s for you!
Join us at Health Data Science Day 2025 on 6 November at the University of Copenhagen for a full day of:
🔍 Cutting-edge talks
🎤 Lightning talks from early-career researchers
📊 Poster sessions
🤝 Networking across disciplines
A great chance to share your work—or get inspired for what’s next.
❗ Deadline is 1st of October
🗓️ Register now: https://lnkd.in/dPGxC4bq
⏰ Reminder: EuroBioC2025 late-breaking poster submissions close this Friday, July 11!
Submit your abstract to present your work in Barcelona, Sept 17–19:
🔗 forms.gle/ewTGdKzB2xyEg58f8
Don’t miss your chance to be part of #EuroBioC2025!
How would you like to apply your passion for #bioinformatics to a real-world research problem?
We co-supervise PhD students in a wide variety of research groups across the University of Melbourne and the Melbourne Biomedical precinct, from oncology to gynaecology to neuroscience.
If you're interested doing a PhD with Melbourne Bioinformatics, get in touch!
https://mdhs.unimelb.edu.au/melbournebioinformatics/teaching/phd-research-projects
Looking for Bioinformatics people to ask about careers and about some of my own sequencing information which I have acquired (accomplished R programmer) #bioinformatics
Stuck on an error message? Just drop it into chatGPT or Claude, and watch the magic unfold.
What a world to live in for learning.
No more excuses. #bioinformatics
Would you be interested in organizing or speaking at meetups, writing blog posts, or promoting the project?
Are you part of any communities or organizations where you could share our project? #annotator #opencravat #bioinformatics #opensource #genomics
