Science plugins

Search USGS and EMSC seismic data — real-time feeds, event queries, and earthquake counts via MCP. STDIO or Streamable HTTP.

35 skills · 1 MCP server

Look up elevation worldwide, profile route ascent/descent, grid areas, check terrain line of sight via MCP. STDIO or Streamable HTTP.

35 skills · 1 MCP server

Skills, commands and review agents for computational research. Domain-neutral: adversarial code and statistics review, run verification (catching jobs that exit 0 having silently dropped work), figure provenance, container builds, runtime/resource studies, scatter-gather design, and journal-club paper analysis. Genomics specialisations on top: Snakemake and nf-core pipeline authoring, IGV screenshots, cohort overviews, chimeric-read validation, and a catalogue of empirically confirmed silent-failure modes across DSS, parallel R, small-n cross-validation, Clair3 and Severus.

13 skills · 10 commands · 3 agents

Single-cell and single-nucleus RNA-seq: QC, integration, annotation and downstream analysis.

19 skills

Pooled CRISPR screens with a single-cell readout (Perturb-seq): escaping cells, per-perturbation differential expression and effect sizes.

19 skills

DNA variant analysis from VCF files: normalization, callset QC, result tables, research triage and variant databases.

19 skills

Run 300+ Tamarind Bio protein and molecular-science tools through the authenticated MCP server — structure prediction, design, docking, and analysis.

17 skills · 1 MCP server

Run Tamarind Bio biology tools from your agent through the Tamarind CLI.

16 skills

Skills for the path from a bioinformatics question to a decision: grilling, a plan with controls, checks, a report checked by a supervisor in a fresh context, a deck, and a signed release.

15 skills

Install, configure, run and analyse calphy free-energy calculations (fe, ts, tscale, pscale, alchemy, composition_scaling, melting_temperature) with LAMMPS.

10 skills

Molecular dynamics for agents: inspect a trajectory, render a frame or a video, and run LAMMPS or OpenMM jobs on hosted GPUs through the MDEngine MCP server.

8 skills · 2 MCP servers

REINVENT4 molecular design as MCP tools — sampling, transfer learning, and staged RL with interactive scoring-function design — plus skills for validation, job status, analysis, and custom scoring components. Requires a locally built GPU Docker container (see README).

7 skills · 1 MCP server

A Codex adapter for the agent-portable Galaxy Analysis Harness.

1 skill · 7 commands

EGPT-Evidence — the missing corpus. Query the egpt community's evidence app: the primary sources of Einstein, von Neumann, Ulam, Shannon and Rota that the published record left out, a verbatim quotation corpus with SHA-256s, the Lean 4 proofs, the debate record and the patent. Answers cite by record id; nothing is quoted that the collection does not hold.

6 skills · 1 agent · 1 MCP server

Denario multi-agent research assistant over MCP: drive the end-to-end pipeline (setup -> idea -> literature -> methods -> results -> evaluate/iterate -> paper -> classify/publish) through the denario MCP tools, configure per-role/multi-provider models and the VLM image-reviewer via params.yaml, and run/resume the cmbagent_lg analysis engine (plan/execute/restart). Bundles both MCP servers via env-var-configured registration.

4 skills · 2 MCP servers

Gods World — talk to Maxi, build physically realistic simulations for it to learn from, and see what it dreams about.

2 skills · 3 agents · 1 MCP server

Run FragPipe headless on your own computer, track the run, and read the results.

1 skill · 5 commands

FRQTL Lab — adopt the FRQTL builder or experiment-designer role and run visual physics experiments with the published @descix/frqtl-web / @descix/frqtl-node. Personas, method, and recipes are served live by the egpt-frqtl app over the DeSciX MCP connector; this plugin is the thin adopter.

2 skills · 2 agents · 1 MCP server

Build, check and test WorldViz SightLab (Vizard) experiments from a research brief. Carries one skill per SightLab generation; SightLab 2 today.

1 skill · 3 commands

Build PySB rule-based kinetic models by being interviewed about your biology, in biology rather than in code. Ships three skills: environment setup, a two-tier model-building interview, and a diagnostic workflow.

3 skills

Set up runs, diagnose failures and explore results of the smORF-Bullpen pipeline

3 skills

Operator and plugin-development skills for ABI. Documentation-only; no analysis plugins, tools, databases, or runtime resources are installed.

2 skills · 1 MCP server

Use Galaxy data, tools and workflows from desktop AI assistants.

1 skill · 1 MCP server

DeSciX — the DEcentralized SCIence eXchange — is a platform for supporting and contributing to open-source innovation. DeSciX gives open source an economic model, using the blockchain to track and reward intellectual property contributions. Daita = Data + AI: a blockchain-based tracking and value mechanism so that creators and contributors benefit from the economics of intellectual property rights. Install, run /descix-setup, then ask any community's knowledge base and get answers you can verify against the sources.

1 skill · 1 MCP server

Find published results for DNA, RNA, protein and cell models in the Rewire benchmark graph, and reproduce or run benchmarks locally with rewirebench.

1 skill · 1 MCP server

Drive Geenee, the Aiden Lab's genome workspace (igv genome browser, Juicebox Hi-C contact maps, Spacewalk 3D chromatin), by chatting: search ENCODE/4DN, load maps, tracks and ensembles, navigate loci, and share views.

1 skill · 1 MCP server

Run solid_gemc (SoLID experiment) simulations from plain language: an orchestrator skill drives the full loop through bin/solid-gemc-run (init, run, analyze), on Claude Code and Codex CLI. JLabCE 2.5 container pulled via wget; solid_gemc cloned + built per workspace; ROOT analysis in the container (host uproot optional).

1 skill

Place, price, track, and verify Full Circle Labs sequencing orders from Claude Code — with a code-enforced billing-confirmation gate and pre-flight balance checks.

1 skill

Safety hooks for genomics work. Blocks writes to immutable raw data, cross-species and cross-build genome mixing, untagged genomic outputs, and destructive shell commands; warns on hardcoded contig lists, invalid YAML, and absolute paths in scripts.

hooks

Site configuration for a SLURM HPC cluster: reference-genome registry, container image registry, Snakemake/Nextflow executor profiles, language plot defaults, and measured MSKCC cluster operational knowledge. Fork this one and swap in your own site.

1 skill