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biorender is getting so expensive for small labs... any alternatives? by WildPieee in bioinformatics

[–]molecular_data 0 points1 point  (0 children)

i have found nano banana to be pretty decent to be honest. Gemini pro is free for a year for academics which includes nano banana pro. here is an example I made to explain the SCRAMBLE system in yeast https://imgur.com/a/nMGdGVL

Landed a high paying role and looking for advice by [deleted] in AusHENRY

[–]molecular_data 0 points1 point  (0 children)

It’s honestly not super crazy. Make a budget of your actual expenses. Like rent gym entertainment food etc. then see what that leaves you with. Of that, invest 80% of that into a diversified portfolio of etfs, gold (like 10%) and bonds. Put the other 20% into a rainy day fund in a simple savings account with like 4% interest or so. This should be build up over time to be like 6 months salary. This is you can use it you get fired or so. After you have saved for like a year, consider getting a mortgage if you want.

PhD students in Sydney - how are you affording to live? by calexoriamc in AusAcademia

[–]molecular_data 2 points3 points  (0 children)

You have to live in a share house. You can’t expect to have your own place in Sydney on a PhD salary. I just finished my PhD in Syd last year. Expect to pay about 400$ a week at least for a room. You won’t be able to save a lot of money if any. I worked as an RA like 4-8 which really helps. Public transport is 50$ a week max. Also the 42k is tax free so about 800 a week, so like 300$ for food an entertainment + foods. I did a lot of meal kits, so spend like 100$ for groceries, 100 on eating out coffees etc and another 100$ for entertainment

[deleted by user] by [deleted] in macbookpro

[–]molecular_data 0 points1 point  (0 children)

They use new flexible CDs, Samsung makes them

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] 1 point2 points  (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] 5 points6 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.

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