June 26, 2023:
I completed some more reading on biopython - I'm going to using that on the back end as I finish up wiring in an API call to Ensembl for our genome chart. I'll package up a phenotype query to the API, get back a list of related sites, then map to genome and sequence displays with visual interaction. I hope to have everything working in a few weeks, and made public here not long after. Then back to the language model research.
Onward!
June 18, 2023:
Finally cracked the animation on the full-genome circos chart, it looks good! I did a bit of refactor, then gathered the lessons learned and moved on to a sequence chart. I have the basics set up already, but this one's going to have a lot more happening on the server side, so it will take a while. I'm still mulling whether it's worth the time investment to scrap this template website for one that has public access to the back end, so that I can show off those charts and tie this worklog to the one in workbench. Either way, time to get back to the books.
Oh, forgot to mention - last week I set up the basics of a paper-tracking tool in workbench as well. It's not there yet, but over the next couple weeks I hope to get enough done so that I can wire up an API call to OpenAI for conversational access to saved research data.
June 13, 2023:
Circos charting coming well - I've got a couple variants working nicely, but still need to finalize the selection animations. Both feed via API from the django back end (dummy data for now) and allow zooming in to look at more detail for a particular part of the sequence. Most of the "hard" work is done - the rest looks mostly like implementation details. Depending on how the next few weeks go, I may be replacing this site with a react one, the better to show live demos, update this page to feed from my live work-in-progress log, etc.
June 4, 2023:
I put down the books for a day to start playing with circos charts: after playing with a couple off the shelf packages I decided to start coding up one myself to get to know d3 better. I've got the basics in place, but still need to connect it to the back end and start feeding in real data. Once that's done I'll add animation, some APIs to fetch data on the fly at the right resolution, and build the thing out into a proper browser. What a neat tool!
May 27, 2023:
Currently supplementing So Simple.. with Walter Isaacson's Code Breaker. It's a fast read so far, and a very nice bit of human depth to the study. It's fascinating to think all these tools we're working with are in fact very new, and their inventors are quite active in the field! What a fascinating time to be alive.
May 14, 2023:
Currently I'm five chapters in to Raghuveer Parthasarathy's So Simple a Beginning. After an initial push through the first part of Rocha and Ferreira's's Bioinformatics Algorithims, this is a good reminder of the physicality of our genetic material. We in the software world are blessed in that we can (generally) safely ignore the exact strength of a magnetic field in a particular spot in physical memory - a ribosome's reading material for protein construction is not so lucky.
I'm getting strong Goedel, Escher,Bach vibes from this book so far. An interesting reminder of how hard these problems can be.