Plant Tissue Culture Constantly Reveals Surprising Cellular Tricks
Coolest part of plant tissue culture is that no matter how much experience you have, you will always learn something new about the strange things plant bits do when given some molecular encouragement.
Meet Gravy: Your Snarky Claude Code Buddy Debugger
This lil brat is growing on me. Have you hatched your Claude Code buddy yet? Type in /buddy and see which one you get. Mine is a snarky dragon named Gravy. Low key kinda helpful. Caught some nuanced bugs in...
AI-Ready Handoff Docs Enable Vibecoded App Forking
I came up with this handoff document I think would be helpful so others can vibefork my vibecoded apps. This is a thorough documentation of how I got here using Claude Code, written specifically for other Ai agents to follow...
Rust Prototype Brings Terminal Transcriptome Browser to Life
Almost done with a prototype Rust port of my Scriptoscope python app for transcriptome browsing, all in-terminal. Inspired by @Psy_Fer_'s ask to read from the holy books of Rust. https://t.co/OPr8rjFKj6
Optimizing Transcriptome Workflow with C Timing Tests
Now time to vibe some more. Working on some tests to see where I can speed up some steps to streamline the transcriptome workflow I'm envisioning. Asking the bot to do some wall-clock timings in C to peep a few...
Savoring a Lazy Weekend of Sleep and Stillness
I slept like 12hrs and was the first time in months I got a proper weekend with zero to do. Gonna roll around some more and enjoy the nothing. Bliss.
C Regex Boosts Transcript Loading Speed Over Biopython
Music to my ears. Finally squashed a slowdown by focusing on a C regex instead of the slower biopython bits. Took a lot of back and forths to find a solution but thats a substantial speed difference. This becomes substantial...
BLAST Integration Progressing; Tackling Self‑hits and API Slowdown
Internally pinged NCBI BLAST working nicely. Need to add a "this transcript" flag for any self-referencing BLAST hit, but all in all things are shaping up. Now to dig into some slowdowns and see where to optimize and where we're...
Direct GenBank Transcriptome Downloads Enable DIY Tool Creation
Can now download transcriptome data directly into my app from GenBank with kinda decent search functionality. Strangely exciting to start cobbling some tools I always dreamed of having but never had the will to learn to code well. Making useful...
Paid for Claude Max, Built Essential Tools Fast
Treating myself to a month of Claude Max to build some tools needed asap. Expensive, but worth it. https://t.co/eHLGUy5GLE
Annotate Second Methionine when CDS Begins with MM
Question: If a transcript has a CDS that starts with two methionines, what's the general rule for sequence annotation? Should I make it so if two METs in a row at the beginning, annotate the closest MET to rest of sequence...
Vibecoding Streamlines Transcriptome to Pfam to NCBI Workflow
Amazing how far you can push vibecoding if you know what you need and the general theory behind the tool chains needed to get your result. I can now load a transcriptome dataset, find the pfam associated with that transcript,...
From Black‑White TV to 4K: Mom Witnesses Artemis
My mom was a little kid when Apollo launched, and she saw it live on a tiny black and white TV in her village. Now she gets to see us return to the Moon with Artemis in glorious 4K. Wish...
New Transcriptome Browser Streamlines BLAST DB Creation
Another feature adding to my terminal plasmid editor is a transcriptome browser. Helps you quickly build blast databases from a heap of transcripts in a single fasta file. Gonna add HMM/Pfam detection and Pfam search. I really love this current...
Terminal Plasmid Editor Blends Beauty with Functionality
Vibing some more on my in-terminal plasmid editor. Drafting a parts bin that's aesthetically pleasing but also functional. TUI's are wonderful. https://t.co/yu8WUSLgwA
Advocating for Team Growth Fuels My Biotech Fulfillment
Managing people in biotech has been such a rewarding experience, but mostly taught me how much I value advocating for the people I manage. I love helping folks realize their potential and its been such wildly fulfilling watching my munchkins...
Evolution Enables Shape‑Shifting Within a Single Lifetime
Just so amazing evolution found a way to change shape in a single lifespan. Some of the cell types run a few laps around the cocoon too.
Repeated Callus Filtering Yields Red Pigment Without
Now THAT is some strong RUBY expression. Filtering transgenic callus a heap of times really pays off. Chasing the red hue without any herbicide or antibiotic pressure. Just hormones to induce callus and careful scalpel work. Some German Chammomile for...
Free Lens Wipes vs Velveteen: Seeking Effective Alternatives
I bet this is one of those lens wipes you get for free with any screen protector kit, lol. I know proper velveteen is a thing, but also wonder what alternatives work just as well. https://t.co/0BaGNWaBYV
Seeking Enzymes that Decolorize Anthocyanins Like Carotenoid Cleavers
Are there enzymes that cleave anthocyanins into colorless bits? I know there are carotenoid cleavage enzymes that can bite various parts of the saturated chain, but never heard of anthocyaninases... https://t.co/rUHXDWkWvc
Keyboard Shortcuts Let You Reposition Plasmid Origins Instantly
I love this so much lololol You can use the arrow keys to circularly permute the plasmid to shift the reference origin as you please, you can use . and , to adjust the circularity of the...
Vibecoding Peaks Between PCRs, Meeting at 9
Vibecoding between PCR's has hit an all time high. See you at 9pm, Claude. https://t.co/8mJv5GJIut
New Terminal Plasmid Editor Simplifies Golden Braid Domestication
Making good progress on my vibecoded mutagenesis tool. Now it makes golden braid part domestication easy too. I may disappoint Patrick and just make a plasmid editor that works inside your terminal with external GUI libraries necessary aside from Textual...
Bungie's Stylish ARG Delivers Addictive, Sweaty Gameplay
Probably one of the most stylish games I have ever played. The design aesthetic ooozes into every nook and crannie of this game. It's a very sweaty game but the loop is so addictive and I just can't get over...
Choosing a Second Life Account over NSF Extension
We could have had a few more years of the NSF, but we decided Creepy Mark needed a Second Life account... https://t.co/ZCYreLM6q8
Spacewalk Safety Tech Stuns While Working on Laptop
Doin some laptop work and watching the latest ISS space walk. Amazing how much tech goes into the safety of it. https://t.co/2vpLaqhNEd
Kindness: The Secret Longevity Prescription
Kindness is a powerful longevity drug. There is a steep mental cost to undue negativity and cruelty; if left untreated will manifest in very physical stress. If you wish to live long, live with kindness and love as pillars of your...
US Travelers Should Secure UK ETA Amid Uncertain Politics
Yay, booked my UK visa for any subsequent trips now until 2028, in case the geopolitiking of the US decides to piss off an old ally. Always good to be extra sure and on-record. If you plan on visiting the...
Testing Ubiquitin Promoter for Stable Petunia Transformation
Alright, Alice 24-0001 petunia bits co-culturing with Agribacterium strain Gv3101 carrying a PcUBI4::RUBY::THSP construct. Testing out this ubiquitin promoter for stable transformation to avoid silencing. These will bake at 30°C until Monday and then transfered to selection. 🤞 https://t.co/SO1EKELMgU
Testing Parsley Promoter RUBY in Stable Petunia Transformation
Okee, two more cultivars to sterilize and transform and I'm done for the day. Let's rile up the agro and get this done. Also among the stuff I need to test for work, I'm going to see if this parsley...
Parsley Uniquitin Promoter Matches 35S at 72
Great signal at the 72hr mark which is peak RUBY accumulation. Parsley uniquitin promoter as reliable as 35s for my projects. Glory be. Here's the expired patent: https://t.co/njN84BkHho https://t.co/kDfx1RoenJ
Sterile PES Filters Prove Effective for Algae Work
YES. My dumb idea of using sterile PES filters and/or their parchment slip covers for algae work seems to be workinggg. Gonna try to genegun these and tranafer the filter onto selective media once a recovery period passes. Was looking...
War Spending Dwarfs Research Funding, Reveals Misplaced Priorities
We can bankroll another nation's warpath and burn $11B in a week but things like cancer research, food security, and fightin disease takes the back seat. Fascinating. Imagine what we could do with an added NSF budget worth just 30%...
Your Choices Define the Game, Not the End
Carve your path in life. We all go into the same box at the end of the game, so its how you choose to play that matters.
Black Stripe Marks Successful Agroinfiltration, Red
More agroinfiltration tests. Black sharpie stripe indicates injecred bloom. Right lobe is positive control. Should turn red in the next 72hrs. https://t.co/2lRTbwAjhq
Precise Wording Matters: Avoid Overclaiming “All Molecules”
This is a far better tweet about the work. Note no claim of "all molecules". This may be pedantic, but words have meaning and if the difference between a quantum leap in virtual cell vs incremental progress rests on words...
Swapped 3D‑printed Arm for Metal, Automating Plate Dispensing
I got tired of futzing with the huggingface printable arm so I ordered a metal one from china. Gonna make it dispense into well plates via a peristaltic and later a universal pipettor module holding my old Gilsons or cheapo...
Ubiquitin Gene PCR Works, Other Primers Unreliable
I used the extracted gDNA from tonight's prep to try and PCR a larger chunk of petunia genome hunting for one of its ubiquitin genes. I'm using a published genome as reference but its not my cultivar so need to...
End‑to‑end Lab Validation: Essential for ML Biology
"Valodated end to end in the lab" is music to my ears. THIS is how you do ML for biology. Show validation or gtfo.
Consumer Biotech Undervalued, Ripe for Cyberpunk Trends
Consumer biotech is perpetually slept on because it doesnt have the returns of pharma. Thats like saying don't build wooden chairs; carpentry is reserved only for yachts. Make. Good. Products. People. Want.
Treatable, Not Curable: Biotech Must Rise Now
"Treatable, not curable" should be a call to arms for any cancer biotech that isn't a grift to step up. Life is so cruel more often than not, but humans are tenacious and unstoppable.
Startups Must Verify CRISPR Patent Freedom Before Launch
Anyone who uses CRISPR systems outside of non-profit and research purposes is subject to the patents that claim those processes as theirs. A lot of startups forget to do due diligence on that and think its fair game. Have you...
Respecting the Meticulous Skill Behind Biolab Hardware Design
Started my day with a peer review duty for Hardware X. Another cool build landed on my desk and it's delightful to see folks really take the minutiae and nuance of designing a tool seriously. People often make wild assumptions...
Tricot Snapdragon Mutant Reveals Triple Leaf Pattern Mechanism
Some fun observations: Ive been growing this tricot mutant of my snapdragon line. Note the triple leaf pattern. I cut off the apical meristem and the new lateral buds formed normal dicot branches. So cool to explore the mechanism of this lil...
User Feedback Beats Accolades: PCR Primer Guide Shared
Nothing means more to a toolbuilder than knowing their tools and tutorials are helpful to someone. I'll take a comment like this over a million accolades and degrees worth of institutional validation any day. PCR Primer Design Guide here if...
Affordable Duckweed Lines & Stellar Service From Rutgers
I had such a fantastic experience with the Duckweed archivists at the Rutgers Duckweed Stock Cooperative. Many of their lines are open for commercial entities too for just $170+ship. Got some great duckweed for rapid prototyping in and customer service...
Successfully Cloned Infernal Arabinose Promoter Despite Synonymous Mutation
Infernal arabinose inducible promoter finally cloned. Two of the positive colonies had the same point mutation, but luckily it was synonymous and the affected Tyrosine is still intact. Cloning promoters into modular part libraries is always a pain even with...
Cloning Error Deletes Lac Operator and T5 Promoter
Man, not my lucky day with cloning. A positive control plasmid had one of its lac operators and the -10 element of the T5 promoter removed during cloning. Gonna screen a few more. https://t.co/O09jf6Qf7F
Project Updates: Prototype Chassis Needed, Sucrose Transformation Progress
So first thing will be to recap the progress of both projects and make a gameplan. I have a draft prototype of the 24well reader but needs chassis work to fit the plate just right, hinge, magnetic assembly, etc. Sucrose needs...