Isaac Larkin

icon indicating a website link https://genemods.wordpress.com/about-us/, http://chitownbio.org/, biomap.io (coming soon)

icon location Chicago icon location Bioengineer working on the Free Genes, OpenEnzyme and OpenCOVID19 projects. Let's make biology easier to engineer!

Results 4 issues of Isaac Larkin

Go implementation of Nonrepetitive Parts Calculator

As discussed Ayaan Hossein's 2020 [first author paper](https://pubmed.ncbi.nlm.nih.gov/32661437/) (a collaboration between Salis and Klavins labs), repeated identical DNA sequences are a significant source of instability in synthetic genetic parts and...

Analyzing sequences for hairpin content, and 'fixing' sequences to remove long hairpins

While designing wetware collections for FreeGenes, I've noticed that a lot of the time Twist will reject a DNA sequence for synthesis because it contains hairpins that are too long...

Quick question about retrieving an SO term name from its corresponding ID code / SO URL

Hi there, I'm starting to do some genetic design with the Synthetic Biology Open Language (SBOL), which employs the SO ontology for annotating the types/'roles' of different genetic parts, like...

Is duplex basecalling currently enabled on Bonito?

I can see from previous issues that duplex basecalling was once enabled, but when I tried running bonito duplex, it said 'duplex' was an invalid command. Is it currently possible...