Maria Nattestad πŸ§¬πŸ’»

Maria Nattestad πŸ§¬πŸ’»

@omgenomics.com

Co-founder OMGenomics Labs. Creator of Circa https://circa.omgenomics.com, Ribbon, YouTube.com/omgenomics. Worked on DeepVariant+DeepConsensus at Google.

2.4K followers94 following25 posts

Maria Nattestad πŸ§¬πŸ’» reposted

Robert Aboukhalil
@robert.bio

How do you spot amplified cancer genes in noisy sequencing data? Find out in my latest interactive article with @etalevich.bsky.social, where you get to run CNVkit (Python) and DNAcopy (R) in your browser on real data to see how CNV calling works under the hood. ➑️ sandbox.bio/concepts/cnv

sandbox.bioGenomic copy numberLearn how copy number variants are called from sequencing data, then segment real HER2-amplified breast cancer data in your browser with CNVkit.
Maria Nattestad πŸ§¬πŸ’»
@omgenomics.com

Okay I'm sorry if you're all getting tired of it, but here's yet another I-built-this-with-AI post. It is my first time really vibe-coding something, but it's for a good cause: updating my old academic software Assemblytics that I had nearly shut down multiple times due to server issues.

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Maria Nattestad πŸ§¬πŸ’»
@omgenomics.com

And I spent like a day just polishing things and another day getting it up on PyPI and Bioconda. But I would have never had the energy to start (let alone finish) this project without a modern AI agent to do the heavy lifting.

Maria Nattestad πŸ§¬πŸ’»
@omgenomics.com

Okay I'm sorry if you're all getting tired of it, but here's yet another I-built-this-with-AI post. It is my first time really vibe-coding something, but it's for a good cause: updating my old academic software Assemblytics that I had nearly shut down multiple times due to server issues.

Maria Nattestad πŸ§¬πŸ’»
@omgenomics.com

Now it doesn't need a server anymore! I used AI to rewrite all the R scripts and that one Perl script into Python, now you can `pip install assemblytics`! And then I told the AI to use Pyodide to turn it into a web app, and it just did it. It worked right away, but of course I did a lot of testing.

Maria Nattestad πŸ§¬πŸ’» reposted

Robert Aboukhalil
@robert.bio

Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.

Maria Nattestad πŸ§¬πŸ’» reposted

Robert Aboukhalil
@robert.bio

We always tell people to create a portfolio to showcase their work, so today we're releasing a template to get you started: github.com/omgenomics/p... It's made for scientists & engineers who want a living resume that showcases projects, work timeline, and blog posts that demonstrate your expertise

Maria Nattestad πŸ§¬πŸ’» reposted

Mike Schatz
@mikeschatz.bsky.social

Friends are looking for jobs. Collaborators are dropping off papers. Funds are being pulled away. But let’s just pretend everything is normal.

Maria Nattestad πŸ§¬πŸ’»
@omgenomics.com

I'm working on a little feature for Circa. It's been over a month since I really coded with all the other startup things like marketing and "strategic thinking" taking up my brain space, so it's really nice just to sit down and code a little algorithm and some SVG paths for overlap-avoiding text.

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Maria Nattestad πŸ§¬πŸ’»
@omgenomics.com

I'm working on a little feature for Circa. It's been over a month since I really coded with all the other startup things like marketing and "strategic thinking" taking up my brain space, so it's really nice just to sit down and code a little algorithm and some SVG paths for overlap-avoiding text.

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Maria Nattestad πŸ§¬πŸ’»
@omgenomics.com

Ooh fun, it's making an interesting pattern when there are too many data points. I think it's because the little pins wrap around so far that they connect to the other side of the circle. It's pretty. Reminds me of the spirograph toy from when I was a kid.

Maria Nattestad πŸ§¬πŸ’»
@omgenomics.com

I'm working on a little feature for Circa. It's been over a month since I really coded with all the other startup things like marketing and "strategic thinking" taking up my brain space, so it's really nice just to sit down and code a little algorithm and some SVG paths for overlap-avoiding text.

Maria Nattestad πŸ§¬πŸ’» reposted

Robert Aboukhalil
@robert.bio

I made a little swiss army knife tool for quickly inspecting FASTA/FASTQ sequences, including GC content, codon analysis, reverse complement, and file format conversions: πŸ–₯️ 🧬 42basepairs.com/tools/sequen...

42basepairs.comSequence Analysis - 42basepairsBioinformatics sequence analysis on FASTA and FASTQ files, including reverse complement, GC content calculations, codon usage analysis, and converting your files to FASTA, FASTQ, or SAM format

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