timothymeyers/discovery-tools

Agents, skills, and starter kits for Microsoft Discovery — the AI for Science platform.
This repo is a catalog. It is simultaneously:
an Agent Skills source — every skill under
skills/ is individually installable into ~50 agent hosts with gh skill install
a Copilot CLI plugin marketplace — copilot plugin marketplace add timothymeyers/discovery-tools
a Claude Code plugin marketplace — /plugin marketplace add timothymeyers/discovery-tools
Everything works from a single physical copy of each skill: the plugin root is the repo
root, so skills/ satisfies both the Agent Skills distribution convention and the plugin
component layout. No symlinks, no duplication, no build step.
## Catalog
### Skills
Every skill declares a scientific category and subfield, both in its
metadata: block and as a leading cue in its description, so installing users
and agents can tell at a glance whether it is relevant to their domain.
#### Life sciences
| Skill | Ver | Subfield | Also relevant to | What it does |
| alphafold-structure-provenance | 1 | Structural and computational biology | Biophysics (diffusion values computed from structures) | Taxon-scoped UniProt lookup plus version-aware AlphaFold DB retrieval. Keeps pLDDT/PAE triage separate from assembly flags and records which structure version a derived quantity came from. |
| biochemical-identifier-crosswalk | 1 | Biochemistry / bioinformatics | Chemistry (formula, charge and mass balance checks) | Reconciles reactions, compounds, proteins, and taxa across Rhea, ChEBI, MetaNetX, and UniProt without collapsing ambiguity. Verifies mass and charge balance. |
| biocyc-network-context | 1 | Systems biology / metabolic networks | Genomics (gene-reaction links) | Bounded BioCyc/EcoCyc/CyanoCyc traversal: reaction → enzyme/complex → gene → pathway. Preserves isoenzymes, expands complexes, distinguishes a missing frame from a gated one. |
| brenda-enzyme-data | 1 | Enzymology | — | Extracts and canonicalizes enzyme kinetics from a caller-supplied licensed BRENDA bulk JSON. Never bundles, downloads, or accepts the license for any dump. |
| sabio-rk-kinetics | 1 | Enzymology / biochemical kinetics | Physical sciences (chemical kinetics) | Ingests SABIO-RK kinetic laws with organism/genus/EC query tiering and taxid-ancestry fallback. Never conflates a confirmed-empty result with a transport or auth failure. |
#### Cross-domain
| Skill | Ver | Subfield | Also relevant to | What it does |
| build-research-paper | 2 | Scientific writing and publication | — | Builds publication-quality, arxiv-ready PDFs from LaTeX or Markdown + figures via tectonic or pandoc. Ships templates, a scaffolder, and referee-revision scaffolding. |
| discovery-add-agents | 1.16.0 | Research platform engineering | — | Adds agents from the public microsoft/discovery repo, then deploys to one target: local Copilot .agent.md companions, a Discovery project + Azure, or promoting a local agent up. |
| discovery-clarify-project | 1 | Research methodology and experiment design | — | Pre-flights a Discovery project before any task runs: reads purpose, outcomes, and task list, then asks up to 5 course-correcting clarifying questions. Clarifies only — never starts the work. |