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musharna/README.md

Hi, I'm Jaret 👋

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.

🧬 Genomics MCP servers

  • plant-genomics-mcp PyPI — 50 genomics tools over 23 backends (Ensembl Plants, Phytozome, UniProt, AlphaFold DB, JASPAR, KEGG, …).
  • data-aggregator-mcp PyPI — search and fetch datasets from Zenodo, DataCite, GEO/SRA, PubMed and OpenAIRE through one interface.
  • plantcv-mcp PyPI — PlantCV trait measurements, returned together with the segmentation overlay so you can check them.
  • breedsim-mcp PyPI — breeding-scheme simulation with AlphaSimR. Reports mean, sd and CI across replicates.
  • phylokit-mcp PyPI — phylogenetic inference with IQ-TREE 2, with bootstrap support included.

🛠 Other tools

  • ghostcite PyPI — 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 PyPI — send one question to several LLMs, see all the answers, then let them rebut each other anonymously.
  • jobd PyPI — 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).

🌱 Research

Auxin / ARF genomics · RNA-seq differential expression · long-tail CLIP for orchid ID (5,000+ species).

📫 Find me

musharna.github.io · Hugging Face · ORCID 0009-0003-4055-5238

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  1. data-aggregator-mcp data-aggregator-mcp Public

    Unified research-data acquisition MCP — search & fetch datasets across Zenodo, DataCite, NCBI omics (GEO/SRA/BioProject), and literature (PubMed/OpenAIRE) behind one normalized model.

    Python 2

  2. plant-genomics-mcp plant-genomics-mcp Public

    Plant genomics MCP server — 50 tools across 23 backends (Ensembl Plants, Phytozome, UniProt, AlphaFold DB, PDBe, InterPro, JASPAR, PANTHER, OrthoDB, AraGWAS, NCBI BLAST, Gramene, KEGG, STRING-DB, A…

    Python 5

  3. jobd jobd Public

    Self-hostable GPU-aware job broker for your own machines, with native MCP/agent integration

    Python 4

  4. ghostcite ghostcite Public

    Deterministic, no-LLM CLI that catches ghost citations — when the author/year you cited doesn't match the DOI's CrossRef record (+ retraction flags).

    Python 1

  5. breedsim-mcp breedsim-mcp Public

    MCP server for breeding-scheme simulation (AlphaSimR) — returns distributions, never a single stochastic run

    Python

  6. taxon3d taxon3d Public

    Blind comparison benchmark for AI-generated 3D models of living organisms — plants, fungi and animals — judged against reference photographs. Bradley–Terry rankings with confidence intervals.

    Python