LLM Mart Basic

Run ESM protein language models — ESMC for embeddings and representations, ESMFold2 for structure prediction, and ESM3 for generative multimodal protein design across sequence, structure, and function — locally or through the hosted Biohub Platform API (formerly Forge). Use when

Manipulate, annotate, and render phylogenetic trees programmatically with the ETE Toolkit (ete3) — parse and edit Newick/NHX, detect duplication/speciation events, infer orthology and paralogy, query NCBI taxonomy, and export PDF/SVG figures. Use when traversing or reformatting t

Parse and write FCS (Flow Cytometry Standard) files v2.0-3.1 with FlowIO — extract event data as NumPy arrays, read $-keyword metadata and channel/parameter definitions, and convert events to CSV or pandas DataFrame. Use when loading raw .fcs flow-cytometry files, inspecting chan

Run fast one-liner queries to 20+ bioinformatics databases from the gget CLI or Python — gene info (Ensembl), BLAST, AlphaFold structures, Enrichr enrichment, and more. Use for quick interactive lookups of genes, sequences, structures, or pathways — for batch processing or advanc

Analyze and engineer protein glycosylation — scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and reach curated glycoengineering tools (NetOGlyc, GlycoShield, GlycoWorkbench). Use when identifying or designing glycosylation sites, optimizing

Extract and preprocess tiles from whole-slide images (WSI) with histolab — OpenSlide-backed slide loading, tissue detection and masks, Random/Grid/Score tile extraction, and image/morphological filters for H&E preprocessing. Use when the user needs lightweight WSI slide preproces

Manage, annotate, and trace biological data with LaminDB, an open-source FAIR data framework that makes datasets queryable, versioned, and reproducible. Use when registering or querying biological datasets (scRNA-seq, spatial, flow cytometry), validating and curating data against

Design protein sequences around bound ligands, metals, and nucleic acids with LigandMPNN (Dauparas 2023) — inverse folding that conditions on non-protein context, so binding-pocket and metal-site residues are chosen to fit the actual ligand. Use when designing a small-molecule or

Analyze Neuropixels 1.0/2.0 extracellular electrophysiology with SpikeInterface — load SpikeGLX/Open Ephys recordings, preprocess and motion-correct, run Kilosort4 spike sorting, compute quality metrics, apply Allen/IBL curation, and do AI-assisted visual inspection. Use when wor

Runs FASTQ-to-VCF germline and somatic variant calling via the Nextflow nf-core/sarek pipeline pinned to -r 3.10.0 — builds the samplesheet.csv (patient, sex, status, sample, lane, fastq_1, fastq_2), runs bwa-mem/bwa-mem2/dragmap alignment plus GATK4 MarkDuplicates and BQSR again

Run full computational-pathology workflows with PathML — whole-slide-image (WSI) analysis across 160+ slide formats, multiplexed immunofluorescence (CODEX, Vectra, MERFISH), nucleus segmentation/classification (HoVer-Net, HACTNet), tissue- and cell-graph construction, HDF5 datase

Build phylogenetic trees end-to-end from raw sequences — MAFFT multiple sequence alignment, optional TrimAl trimming, IQ-TREE 3 maximum-likelihood inference with model selection and bootstraps, FastTree for large datasets, then visualize with ETE3 or FigTree. Use when reconstruct

Design protein sequences for a fixed backbone with ProteinMPNN (Dauparas 2022) — message-passing inverse folding that outputs sequences predicted to fold to a given structure, with fixed positions, tied/symmetric chains, amino-acid bias, and a soluble-model variant. Use when inve

Run differential gene expression analysis on bulk RNA-seq count matrices with PyDESeq2, the Python port of DESeq2 — size-factor normalization, dispersion estimation, Wald tests, FDR (Benjamini-Hochberg) correction, and volcano/MA plots. Use when identifying differentially express

Build complete mass-spectrometry workflows with pyOpenMS — feature detection, peptide identification, protein quantification, and full LC-MS/MS pipelines across many MS file formats (mzML, mzXML) and algorithms. Use for comprehensive proteomics and MS data processing — for simple

Read and write genomic alignment and variant files in Python with pysam (htslib bindings) — SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences, plus region extraction and per-base coverage/pileup. Use when scripting NGS data-processing pipelines that parse, filt

Runs 16S/ITS amplicon (microbiome) analysis with the QIIME 2 distribution (2026.7; the "amplicon" distribution was renamed "qiime2" in 2026.4) in the correct order: manifest import, cutadapt trim-paired primer removal BEFORE dada2 denoise-paired (trunc-len chosen from the demux q

Generate de-novo protein backbones with RFdiffusion (Watson 2023) — a diffusion model for unconditional monomer generation, motif scaffolding, binder design against a target, and symmetric oligomers. Use when generating a new protein backbone from scratch, scaffolding a functiona

Quantifies bulk RNA-seq transcript abundance with salmon 2.x (the Rust rewrite; selective alignment or --sketch) and kallisto (v0.52.0, kb-python workflow), builds a decoy-aware gentrome index, runs quant with --gcBias -l A, then imports estimates via tximport/tximeta with a tx2g

Run the standard single-cell RNA-seq analysis pipeline with Scanpy on AnnData — QC filtering, normalization, dimensionality reduction (PCA, UMAP, t-SNE), Leiden/Louvain clustering, marker/differential expression, PAGA trajectories, and plotting. Use when analyzing scRNA-seq data

A green PR, a controller reporting success, and not one line of the new code running

Identifies state-changing entry points in smart contracts

Scans Android APKs for Firebase security misconfigurations

Safely analyzes and cleans up local git branches and worktrees, categorizing them as merged, squash-merged, superseded, or active work before deleting anything.

Audit a file, directory, or whole repo for insecure default configuration: fallback secrets, default credentials, fail-open switches, weak crypto, permissive access, debug leakage. Parallel sweeps collect candidates, then a refuting verifier traces each one to the security decision it reaches before it is reported.

Creates Semgrep rules with test-first methodology

This folder gathers the project's 9 slash commands in a single place, plus the sub-procedure files the [Sub-procedure Locations](#sub-procedure-locations) table rosters. **The harness lists every `.md` here as invocable regardless of `user-invocable: false`** (this README is itse

Discover unexpected connections in the LLM Wiki (Memex serendipity).

Export wiki to merged files for Claude.ai Project Knowledge.

Build the LLM Wiki knowledge graph.

Ingest a source document into the LLM Wiki.

Not a slash command — a sub-procedure of [`/wiki-lint`](wiki-lint.md), reached from `contradiction theme --fix`. Invoking it directly runs nothing.

Health-check the LLM Wiki for issues.

Search for latest news related to the LLM Wiki's key topics.

Query the LLM Wiki and synthesize an answer.

Generate a chronological timeline for an entity or concept in the LLM Wiki.

Create, follow, or list associative trails in the LLM Wiki (Memex trail-blazing).

Compute the recent 7-day spend trend (burn rate) from daily sessions and per-session cost.

Quick total cost plus a per-model one-liner from the dashboard pricing engine.

List the top N most expensive Claude Code sessions by inline cost.

Quick Claude Code config audit — counts per surface (user vs project) and totals.

Make any song you can imagine

Leading AI-powered video generation platform that specializes in creating hyper-realistic talking avatars

Hermes Agent is an open-source, self-improving autonomous AI agent developed by Nous Research

Kilo Code is a popular, open-source AI coding agent and "agentic engineering" platform designed to help developers build, refactor, and debug software faster

General-purpose agent in one static Go binary. ReAct loop, ACP server for IDEs, OpenAI-compatible REST API with embedded web UI, Telegram gateway, cron schedule…

Autonomous agent framework with structured memory, safety hooks, and loop management. Built by the agent that runs on it.

TSP自托管、零运维的 A 股「选股 + 监控 + 回测」量化工作台 | 基于 TickFlow 数据源 | LLM能力驱使策略定制+个股分析+复盘 | 自由接入第三方数据源与个性化扩展数据 | 个人开源 ,非TickFlow官方项目

Curated, verified Agent Skills powered by ModelStudio.

Run Claude Code, Codex, Antigravity, Cursor Agent and OpenCode as one runtime — persistent sessions, multi-agent councils, an OpenAI-compatible endpoint, an MCP…

pi had nothing (nothing), so I made something (something) — sorry mariozechner-senpai, I went ahead and lovingly soiled your pure pi for you. opinionated fork o…

A persistent workspace for development work that self-improves and continues beyond one session.

Open-source memory and context for user-aware agents: scoped memory, provenance, retrieval quality, correction, boundaries, evals, and MCP/HTTP access.

📚 A zero-dependency, git-backed micro-lesson library for AI Agents to asynchronously share and search verified debugging experience. Python stdlib only. | http…

Deterministic, local-first memory and guardrails for AI coding agents with no LLM in the hot path.

Deterministic spec-orchestration for local LLMs in the pi coding agent — drives prompts through refine→research→grill→compose→critique, with bundled web/docs/fe…

Native Safari browser automation for AI agents. 97 tools via AppleScript — zero overhead, keeps logins, runs silently in background. Drop-in alternative to Chro…

Agent OS: keep specialist agents in a hub, spin up a temporary orchestrator per task. Local-first, works with any model.

Git for agent memory. Branches, diffs, PRs, and rollback for what your agents know.

Multi-Provider AI Gateway - No personal logs by design. Model autodiscovery, Failover groups, High availability, Android companion app, and more - "Because we h…

Production-grade MCP server for MikroTik RouterOS with secure AI-native network automation.