Library
Papers, tools and agents I have actually used or read, with what I think of them. Each one has a page with the longer version.
7 of 7
- paperAgentic genomics: from pipeline automation to autonomous validation
A good first read on what agentic genomics means. Its argument is that the bottleneck has moved from building pipelines to validating what agents produce. It is a review, so it will not tell you how any one system performs on your data.
- toolAgentomics
The claim to check is that it beat human expert solutions on a number of benchmark datasets. Performance on benchmarks does not always carry over to messier data, so I would want to see how it does on a new dataset before relying on it. Most interesting to people who build models from biomedical data and want an automated baseline.
- agentAutoBA
Minimal user input is the appeal and also the risk. Someone still has to check the plan and the output, and that checking is the validation problem the Cell Genomics review puts at the centre.
- agentBio-Copilot
The interesting part is that human-agent interaction is built into the design. A person sits inside the analysis loop. Worth a look if you want an agent to help with large omics analyses without handing over the whole thing.
- agentCellAtria
An agentic framework from AstraZeneca that ingests and standardises single-cell RNA-seq data, with a chat interface in front of a pipeline called CellExpress. Worth a look if you work with single-cell data and want to see how an agent can handle the ingestion and standardisation step.
- agentClawBio skill library
I contribute to this project, so weigh my view accordingly. It gives agents bioinformatics-specific skills to work from. The local-first design is the thing to check if your data is sensitive.
- toolPRIDICT 2.0
My own pegRNA pipeline uses it. A predicted score is a prediction to test, and it does not replace checking designs at the bench.