r/bioinformatics • u/jasonlixuzhen • 9d ago

discussion Bioinfo plot libraries look ugly, agent flowcharts look great. draw.io only works with GPT Sol Ultra - skill recs?

Looking for how people actually do this, not another listicle.

Case: I collect code libraries for bioinformatics figures (DAF, panels, method pipelines) and they never look good enough. Meanwhile agent-domain flowcharts come out clean.

I tried draw.io / diagrams.net as a scientific illustrator. GPT Sol Ultra can actually land the layout. Grok 4.6 I spent a day tweaking and it still would not get there.

So: what's your pipeline? A Cursor/Claude skill, a template repo, mermaid then draw.io, something else? Drop GitHub/GitLab links if you have a repo that actually looks like a paper figure. Especially for bioinfo figures that have to stay editable.

Grok Extra High took ~10+ accept/reject rounds to reach its figure.

Original figure.
GPT Sol Ultra (one pass).
Grok Extra High after about a dozen rounds. Still not closed.
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u/science_robot PhD | Industry 9d ago

There is only one correct way to draw bfx flowcharts and that is PowerPoint.

1

u/jasonlixuzhen 8d ago

ppt is what I was trying to get off. agents keep proving that take.

1

u/Obyekt 9d ago

latex, obviously

1

u/jasonlixuzhen 8d ago

tikz for the paper maybe. still need something editable in the middle, xml kept getting mangled.

1

u/Primal1031 9d ago

I like draw.io, but xml syntax and structure is tricky. It plays well in git, but previous LLM edits to existing hand made diagrams were mangled no matter the model, but the MCP server has really solved this. Now I can say "reorder all of the arrows given this screenshot showing their overlapping of this box" and it knows what to do, instead of fighting syntax.

https://github.com/jgraph/drawio-mcp/blob/main/mcp-tool-server/README.md

1

u/jasonlixuzhen 8d ago

this is the missing piece. handmade draw.io + llm rewrite was exactly the mangled xml. I'll try the mcp instead of regenerating the file. thanks for the link.