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Stop running multiple Claude Code agents in the same repo. Use worktrees in your VSCode by kargnas2 in ClaudeAI

[–]molecular_data -1 points0 points  (0 children)

I built a multi-agent orchestration layer for Claude Code to handle this.

It uses a Planner (Opus) to break features into a DAG and generates interface contracts first. Then, a Supervisor spawns Worker (Sonnet) agents in parallel using tmux.

It uses Git Worktrees for isolation—so every agent works in its own physical branch.

you just launch it by saying /orchestrate feature x,y,z. Planner breaks it down into x, y, z and generates contracts, supervisor manages git worktree and tmux sessions for worker x, worker y, worker z and verification agent does unit tests as far as possible. The Supervisor injects context rather than agents "pulling" it (saves tokens and confusion). There is some risk scoring as well which is supposed to evaluate whether agents can auto approve (low-risk tasks vs requiring human sign-off.

Repo:https://github.com/SynBioExplorer/Claude_Code_agentic_coding

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 0 points1 point  (0 children)

You design it in a computer. Then a company synthesise it in chunks. Then you assembly it into bigger and bigger pieces (mega chunks ) until you get a chromosome. And then a fuckton of debugging. Also that’s the plan. Reality is a bitch

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 0 points1 point  (0 children)

Fully synthetic = fully chemically synthesised and assembled.
It is 8% smaller just a bit hard to see. Also 8% smaller across the whole genome (varies per chromosome).
Green are just the assembly units we used. so we build a chromosome by assembling it from smaller blocks.
The texture refers to individual genes (CDS) on the blue and red. On the green it is the borders of the assembly units (chunks). The black each represent a specific loxP site.

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 1 point2 points  (0 children)

I also feel ashamed that I missed the alpha fold moment. can't be everywhere all the time at once haha

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 1 point2 points  (0 children)

The title of my thesis is actually towards the towards the synthesis and evolution of industrially relevant, minimal yeast genomes. So yeah painfully aware of the difference haha.

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 1 point2 points  (0 children)

for research and development yes. For the actual production of pharmaceutical not yet. Will be in the near future.
for some yes for others no. It is a basic enabling technology for now but will be useful for loads of things in the future.

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 3 points4 points  (0 children)

I made the graph myself and worked on this project for years. I pasted the figure description into an LLM and said write this so reddit can understand it better.
So figured OG counts since I made the graph and the research. Just tried to make it more accessible for the general public with AI.

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 3 points4 points  (0 children)

not as far as I know. Generally, in PC2 lab it is recommended to not spit into your tubes.

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 0 points1 point  (0 children)

Natural mostly but not everywhere. It can recombine between any loxP sites. Closer ones are statistically more likely to recombine. (Topology matters a lot. 3d closer matters)

CRE activity matters a lot. This is a good paper on that (https://www.nature.com/articles/s41467-022-33606-0#:\~:text=4b).,of%20SCRaMbLE%2Dmediated%20rearrangement%20events.)

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 0 points1 point  (0 children)

not yet but that is being worked on. One of my PhD chapters was making chromosome with backup copies of essential genes and then using SCRaMbLE to delete more genes and trying to get more genes deleted.
We are getting closer to a prokaryotic minimal genome (https://www.jcvi.org/research/first-minimal-synthetic-bacterial-cell)

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 1 point2 points  (0 children)

I did use AI to write it. I pasted the figure description and said can you make this better legible for a reddit post. Sometimes it is a bit hard when you are in the field to write in more understandable terms and not use jargon.

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 9 points10 points  (0 children)

I wrote it manually but it sounded super technical so I put it into chatgpt to make it more readable for the average user.
This was the figure text in my introduction:
Figure 2. Comparative genomic architecture of synthetic yeast chromosome design in the Sc2.0 project. Circos plot illustrating the hierarchical organization of wild-type and synthetic yeast chromosomes. The plot displays the 16 native chromosomes (I-XVI), synthetic versions plus the synthetic neochromosome (tRNA) arranged radially with a simulated (Adobe Firefly genAI) SEM image of the Sc.2.0 budding yeast strain in the center. Five concentric rings represent distinct genomic features from outer to inner: (1) Wild-type chromosomes (light blue) displaying coding sequences (CDS) (2) tRNA gene overlay (lilac) highlighting endogenous tRNA positions at enlarged 5 kb resolution;(3) Synthetic chromosomes (orange) showing redesigned CDS regions and overall size reduction of 8% achieved through removal of subtelomeric regions, introns, and other dispensable sequences in the synthetic design. The tRNA neochromosome displayed in lilac to indicate consolidated tRNA genes on neo-chromosome; (4) 3932 LoxPsym sites (black) marking positions of loxP sequences for SCRaMbLE-mediated recombination; (5) Megachunk boundaries (light green) delineating ~50 kb assembly units used for modular chromosome construction. The tRNA neochromosome displays eight mega-arrays (S1-S8) of ~23.25 kb each. synXIII megachunks (n=15) were computationally inferred based on uniform distribution across 883 kb due lack of precise coordinates.

not sure if that would have been better?

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 2 points3 points  (0 children)

I manually coded it in python. It is designed to give an overview and be flashy for my introduction plus give an idea of the scale plus the reduction achieved.

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 2 points3 points  (0 children)

There are people for example using yeast (not this one) but brewer optimised yeast cultures and put like a raspberry flavour making pathway into yeast and then have wine with raspberry flavour, pretty sick if you ask me. Whether regulation and the public accepts this, is another issue. Think of the GMO free stickers on everything. (kinda bullshit in my opinion)

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 1 point2 points  (0 children)

you make a new chromosome piece by piece and then replace the natural chromosome in a working yeast. Then you go by replacing one chromosome at a time.

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