PhD student in Genetics, Bioinformatics & Computational Biology at Virginia Tech (Wright lab, co-advised by David Haak). I work on plant genomics and plant computer vision, and I build the MCP servers and CLI tools I use to do that research with LLMs.
- PhD work: auxin / ARF genomics and RNA-seq differential expression.
- orchid-clip: a BioCLIP 2 fine-tune for orchid identification. The demo reports a genus and names a species only when it is confident. Write-up.
- orchid-hybrid-visualizer: predicted appearances of 27 Cattleya hybrids. Across 1,002 registered hybrids, a real hybrid's image embedding sits near its parents' midpoint, and further off the line between them when the parents look more different. Demo.
- Undergraduate research (Case lab, Kent State): leaf measurement and whole-plant silhouettes from Lobelia herbarium specimens. Write-up.
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, released only after you have seen the segmentation overlay they come from (batch mode reuses a recipe checked that way).
- breedsim-mcp
— breeding-scheme simulation with AlphaSimR. Reports mean, sd and CI across replicates.
- phylokit-mcp
— phylogenetic inference with IQ-TREE 3 (through piqtree), with bootstrap support included.
- taxon3d — blind comparison benchmark for AI-generated 3D models of organisms, judged against reference photographs.
- ghostcite
— checks author/year against the DOI's CrossRef record and flags retractions. No LLM in the core check. 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 job broker for your own machines: one FastAPI + SQLite service plus a worker on each host. Routes by GPU/tool tags and exposes the queue over MCP.
musharna.github.io · Hugging Face · ORCID 0009-0003-4055-5238