iiinova — where your digital self keeps evolving

raw9371 @raw937.bsky.social · 13/08/2026

💥 I built DYNAMITE. 7 gene-calling engines. Phages, viruses, bacteria, archaea, eukaryotes. One command. Pure Rust. No Python. No dependencies circus. Crates crates.io/crates/dynam... GitHub github.com/raw-lab/dynamite 🧬 Genome in. Genes out. #Bioinformatics #Rust #Genomics

crates.io

crates.io: Rust Package Registry

crates.io serves as a central registry for sharing crates, which are packages or libraries written in Rust that you can use to enhance your projects

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raw9371 @raw937.bsky.social · 24/06/2026

Python got bioinformatics started. Rust will scale it. 🦀 Today we released rustyomestats, our first Rust crate for genome assembly statistics. Fast. Memory safe. Built for massive genomic datasets. Crates: lnkd.in/dP88c83F GitHub: lnkd.in/dDw2KNuX Rust is the way. #RustLang #Bioinformatics

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raw9371 @raw937.bsky.social · 24/06/2026

Most high-performance bioinformatics software written 10 years from now will be in Rust. 🦀 Today we released rustyomestats — our first Rust crate ⚡ Genome size 🧬 GC content 📊 N50/L50/U50 🔬 Codon density 🚀 FASTA parsing GitHub: lnkd.in/dDw2KNuX Rust is the way. #RustLang #Bioinformatics

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raw9371 @raw937.bsky.social · 20/06/2026

Regular expressions in perl were rad.

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raw9371 @raw937.bsky.social · 20/06/2026

Perl started it out. Its regular expressions I still teach today - awks was more wild.

raw9371 @raw937.bsky.social · 20/06/2026

Perl was prior to Python. It had great regular expressions - powerful taken from awk. But the syntax was challenging. R then Python took Bioinformatics to the next stage. Rust is its natural evolution

I miss the atomic level perl regular expressions.

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Perl is that a language or something? Haha. Nah man - regular expressions in perl were rad. But, awk's were still more crazy and more powerful

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raw9371 @raw937.bsky.social · 01/05/2026

Its official as of today - I am now an Associate Professor with Tenure at the University of North Carolina at Charlotte Dept of Bioinformatics & Genomics. A promise to my father - 20 years ago this Jan is finally complete. Never give up on your dreams - believe. #tenure

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raw9371 @raw937.bsky.social · 20/04/2026

Bat Immunological Training Education (BITE) outreach at Discovery Place yesterday. We had 171 visitors at our booths today. We will continue to educate the public about diseases and immune responses. At Discovery Place every 3rd Saturday of the month. #microsky #bats #Stem Great job team!

Thank you brother! Exactly 💯 correct! That's why I built it this way! You get analysis of MetaCerberus -> pyGAGE -> Pathview-plus -> think = pubs.

If you’re already doing differential expression in Python: This drops in directly. No exporting. No context switching. That alone saves time!! ALSO outputs feed pathview-plus our pathway tool! pip install pygage pip install pathview-plus #Bioinformatics #rnaseq #computationalbiology

Where this shines: • small RNA-seq studies (n < 5/group) • fast exploratory analysis • pipeline integration (pandas/NumPy workflows) Basically: real-world data!!

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Limitations (important): • ignores gene–gene correlation • pathway size affects variance Not perfect. But the tradeoff → speed + stability is often worth it. But that is corrected in our pathway level tool -> pathview-plus when you feed pyGAGE outputs to it!!

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Hot take: Most people don’t need more advanced enrichment methods! They need ones they’ll actually run. #rnaseq #bioinformatics #computational

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Under the hood: For a gene set S: → compute mean(d_g) → build null by sampling random gene sets of same size → compute Z-score vs that null No permutations. No heavy compute. This is why it’s fast! Its not analysis that takes long - its testing 50 tools that don't run to get some data back!!

8/ It’s not the fanciest method. But it actually works in real pipelines. And now it works natively in Python. #bioinformatics #rnaseq #genomics

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7/ Output: • Z-scores • up/down pathway direction • FDR-corrected significance Fast, interpretable, reproducible! Now and today!!

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6/ pyGAGE avoids that. Gene randomization → stable inference even at low sample size

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5/ That last part matters. Most methods rely on sample permutation. That breaks when n is small (which is most datasets).

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4/ The method is simple and solid: → compute gene-level differential signal → aggregate into pathways → compare to a null via gene randomization

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3/ So I built pygage — a Python implementation of GAGE. No bridges. No friction. Just runs.

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2/ Gene-level stats ≠ biological interpretation. You need pathway-level signals. That’s where gene set enrichment comes in. But most tools are: • slow • fragile with small n • stuck in R

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raw9371 @raw937.bsky.social · 17/04/2026

Most RNA-seq pipelines are doing this wrong. They run differential expression… and stop there. You’re leaving biological signal on the table. I built pygage to fix that 👇 pip install pygage #Bioinformatics #rnaseq #computation #computationalbiology

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🔬 Pathview-plus = powerful pathway visualization for bioinformatics 🚀 Thousands of pathway maps (KEGG + SBGNview) and super easy to use. Install in seconds: pip install pathview-plus GitHub: github.com/raw-lab/path... PyPI: pypi.org/project/path... #Bioinformatics #DataScience #Omics

raw9371 @raw937.bsky.social · 02/04/2026

They should be careful with the word dormancy. Not quite the same things.

raw9371 @raw937.bsky.social · 09/02/2026

Send us a mail. We are always developing it.

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raw9371 @raw937.bsky.social · 09/02/2026

Works well for bacteria as well in mixtures with viruses.

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raw9371 @raw937.bsky.social · 09/02/2026

The first automated computer vision–based software enabling the detection, enumeration, and sizing of virus-like particles from epifluorescence microscopy (EFM) images of environmental samples. Published online in BMC methods today. #giantvirus #phagesky Paper link.springer.com/article/10.1...

link.springer.com

Resolving and quantifying viral-like particles via blind deconvolution - BMC Methods

BMC Methods - Viruses represent the most numerous’biological entities’on Earth; but the direct quantification of viruses within ecosystems is a significant challenge. The classical...

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raw9371 @raw937.bsky.social · 12/12/2025

May the phage be with you!

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raw9371 @raw937.bsky.social · 07/12/2025

Bat Immunological Training Education (BITE) outreach at Discovery Place yesterday. We had 324 visitors at our booths today. We will continue to educate the public about diseases and immune responses. At Discovery Place every 3rd Saturday of the month. #microsky #bats Great job team!

raw9371 @raw937.bsky.social · 02/12/2025

Awesome work. With some phageyness at the end. #phage #phagesky #microsky #evolution

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raw9371 @raw937.bsky.social · 02/12/2025

Wonderful paper, amazing work, wonderful lab, and amazing collaborators!! Well done Morgan!!

raw9371 @raw937.bsky.social · 27/11/2025

We were glad to work on the data! ;-)