LLM Mart Basic

Predict biomolecular complexes with Chai-1, an open AlphaFold3-style model that folds multi-entity assemblies (proteins, ligands, nucleic acids) from a single typed FASTA — strong on antibody–antigen and protein–ligand complexes, with optional MSA and restraint inputs. Use when p

Build and analyze genome-scale constraint-based metabolic models with COBRApy — flux balance analysis (FBA), flux variability analysis (FVA), gene and reaction knockouts, flux sampling, and SBML model I/O. Use when simulating metabolic networks, predicting growth or knockout phen

Process and visualize deep-sequencing coverage with the deepTools CLI — convert BAM to bigWig (bamCoverage), build log2 ratio tracks (bamCompare), run QC (multiBamSummary correlation, PCA, plotFingerprint), apply the ATAC-seq Tn5 shift (alignmentSieve --ATACshift), and make TSS/p

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

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

Discover testnet↔mainnet subnet lineage from repo configs and open a PR for review (pass --dry-run to report only)

Triage raw inbox notes into reviewed repository destinations without deleting their sources.

Audit and rewrite content to remove AI writing patterns

Log a completed piece of content to content/log.md after the user confirms it was published.

Validate a dream artifact, review each proposal, and apply only individually accepted changes.

Run a curator pass against the validated memory directory and produce a proposal artifact.

End a session — log what happened, update state and the decision log, propose memory updates, and check for uncommitted or unpushed work

Find relevant context files by topic. Use when you need to load files for a topic without a slash command, or when a task spans multiple domains.

Inventory and migrate selected Gemini CLI workflows with dry-run review and parity checks.

Find repeated workflows in selected Gemini CLI sessions and draft portable skills after review.

Scan multi-session drift and offer individually reviewed fixes only after explicit approval.

Scan orphaned worktrees and stale branches, then offer explicit approval-gated cleanup.

Guided onboarding or import for durable workspace context

Start a session — load state files, flag staleness, and give a briefing on current priorities, deadlines, and blockers

Create a morning heartbeat from repository state and update the local heartbeat log.

Mid-session checkpoint — append progress to today's session log and update state files if a priority shifted, without ending the session

Maintainer-only. Find every file that would newly ship to adopters, classify each one against the written distribution-boundary categories, default to withhold on no clean match, and ask the maintainer only where the taxonomy does not settle it. Drives the release CLI, which refuses to produce a manifest until every shipping file has an answer.

Audit memory, wiki, and auto-loaded files for duplication, conflicting instructions, and stale content. The default path researches, then asks you a single Apply / Discuss / Decline question; on Apply it applies the report, files any out-of-scope problem as a tech-debt issue, then commits, opens a PR, and merges it on a main-branch run like /update-deps. Pass --apply to re-run the apply-and-publish stage against the most recent report.

Fix the tech-debt backlog, a single issue or a recommended related batch, highest severity then oldest first, on a fresh isolated branch through the audit gate, closing the issue(s) on merge. Pass `list` to see the ordered backlog, `why <issue-number>` to explain the recommendation, or a bare `<issue-number>` to fix that issue directly.

Health-check and auto-heal this project's Claude integration, triage, heal, verify, and report an F-to-A+ grade.

LLM-powered toolkit for skill analysis, AI interviews, resume scoring, and job structuring. Automates professional skill taxonomy and interview processes with a…

【三年面试五年模拟】AIGC/LLM/AI Agent算法工程师面试资源平台。涵盖AIGC、LLM大模型、AI Agent、具身智能、传统深度学习、计算机视觉、自然语言处理、自动驾驶、机器学习、强化学习、大数据挖掘、世界模型、元宇宙、AGI等AI行业面试笔试干货经验与核心跨周期知识。

Easiest and laziest way for building multi-agent LLMs applications.

Drive Claude Code or OpenAI Codex from your phone — resume sessions, stream output, approve tool permissions remotely. End-to-end encrypted, zero-knowledge rela…

MCP server for autonomous agent economies: wallets, signed RTC micropayments, bounty discovery, BoTTube video publishing, and Beacon agent-to-agent messaging. G…

Free, open-source alternative to Microsoft Office with built-in AI agents — Word (.docx), Excel (.xlsx), PowerPoint (.pptx), PDF and Markdown editing for macOS,…

NSE BSE Indian Stock Market Data MCP server — search, screen & analyze all 8,200+ NSE/BSE stocks with 34 tools: live quotes, financials, technicals, 326-ratio s…

全流程 智能招投标 Agent：标书生成 · 招投标解读 · 标书检查 · 标书文档ai排版 · 商机发现 一键完成。 21 项合规检查 · 多模型切换 · RAG 知识库 · OCR 抽取。 从招标公告到可交付 docx 文档，全流程 AI 自动化。

Benzi is AI-native code intelligence infrastructure. Claude Code greps; Cursor embeds; Aider maps signatures; Benzi resolves — and answers in O(1). Every langua…

From ticket to reviewed pull request. Free and open-source, on your machine.

Get web data for AI agents and LLMs - fast, efficient, and reliable with Rust

Open-source, license-free MCP server for RTL waveform debug: reads FST waveforms (VCD/FSDB auto-convert) plus a SystemVerilog netlist, with 34 tools covering dr…

Open-source, desktop-grade AI agent that gets real work done — data analysis, slides, docs, video & web research. Built on OpenClaw; runs tools on your real des…

Parallel, isolated dev environments for humans and AI coding agents. Real containers. Real databases. Zero collisions.

OpenCode goal plugin for Codex-style goal mode, /goal slash commands, persistent objectives, and AI coding agent focus.

Battle-tested skill library for AI agents. Save 98% of API costs with ready-to-use code for crypto, PDFs, search, web scraping & more. No trial-and-error, no ex…

Deep Code 是专为 deepseek-v4 模型优化的终端 AI 编码助手，支持深度思考、推理强度控制以及 Agent Skills。

China Unicom's Yuanjing Wanwu Agent Platform is an enterprise-grade, multi-tenant AI agent development platform. It helps users build applications such as intel…

⚡ CloakBrowser MCP server for AI agents: Playwright-powered browsing, clean tool forwarding, Docker support, and multi-session HTTP transport.

MCP-NixOS - Model Context Protocol Server for NixOS resources