PhD student in Genetics, Bioinformatics & Computational Biology at Virginia Tech. Most of what I build is MCP servers and CLI tools for plant genomics and for doing research with LLMs.
To try one: uvx plant-genomics-mcp starts a server, and each repo's README has the one-line config for Claude Code or any other MCP client.
- plant-genomics-mcp
— 50 genomics tools over 23 backends (Ensembl Plants, Phytozome, UniProt, AlphaFold DB, JASPAR, KEGG, …).
- data-aggregator-mcp
— search and fetch datasets from Zenodo, DataCite, GEO/SRA, PubMed and OpenAIRE through one interface.
- plantcv-mcp
— PlantCV trait measurements, returned together with the segmentation overlay so you can check them.
- breedsim-mcp
— breeding-scheme simulation with AlphaSimR. Reports mean, sd and CI across replicates.
- phylokit-mcp
— phylogenetic inference with IQ-TREE 2, with bootstrap support included.
- ghostcite
— checks author/year against the DOI's CrossRef record and flags retractions. No LLM involved. Runs as a pre-commit hook or GitHub Action.
- llm-panel
— send one question to several LLMs, see all the answers, then let them rebut each other anonymously.
- jobd
— a small job broker for your own machines. Routes by GPU/tool tags and exposes the queue over MCP.
Also: ldraw-mcp (LEGO renders for vision models) · tmodloader-mcp (drive tModLoader from an agent).
Auxin / ARF genomics · RNA-seq differential expression · long-tail CLIP for orchid ID (5,000+ species).
musharna.github.io · Hugging Face · ORCID 0009-0003-4055-5238
