LLM Mart Basic

Predict protein 3D structures with AlphaFold2 via ColabFold — MMseqs2-accelerated MSAs, monomer and AlphaFold2-Multimer complex folding, and confidence-based validation (pLDDT, pTM/ipTM, PAE). Use when folding a protein sequence or complex from FASTA, generating a predicted struc

Build, slice, concatenate, read, and write AnnData annotated data matrices (obs, var, X, layers, obsm, uns) — the scverse data STRUCTURE, not an analysis pipeline. Use when creating or wrangling .h5ad/zarr files, managing cell and gene annotations, concatenating batches, or handl

Infer gene regulatory networks (GRNs) from expression matrices using arboreto's scalable GRNBoost2 and GENIE3 tree-ensemble algorithms with Dask-distributed computation. Use when analyzing bulk or single-cell RNA-seq transcriptomics to map transcription-factor-to-target-gene regu

Manipulate biological sequences, parse FASTA/GenBank/PDB files, run phylogenetics, and access NCBI/PubMed programmatically via Biopython (Bio.SeqIO, Bio.Entrez, Bio.PDB, Bio.Blast). Use when scripting custom bioinformatics pipelines, batch-processing sequence files, automating BL

Query 40+ bioinformatics web services through one consistent Python API with bioservices (UniProt, KEGG, ChEMBL, Reactome, Ensembl, NCBI and more). Use when a workflow must hit multiple databases together, map identifiers across services, or run cross-database analyses — for quic

Runs NCBI BLAST+ 2.17.0 sequence searches from the command line: makeblastdb (with -parse_seqids), blastn/blastp/blastx/tblastn with tabular -outfmt 6/7 for parsing, correct -task choice (megablast vs blastn vs blastn-short), -taxids/-negative_taxids taxonomic scoping, and -mt_mo

Co-fold biomolecular complexes with Boltz-2, an open AlphaFold3-style model — predict protein + ligand (SMILES/CCD), protein + nucleic-acid, and multi-chain structures in one pass, with binding-affinity prediction. Use when folding a protein together with a small-molecule ligand,

Predict genome-wide functional genomics tracks from DNA sequence with Borzoi (Linder 2025) — a sequence-to-function model outputting RNA-seq, CAGE, ATAC, and ChIP coverage across long context, used to score non-coding and regulatory variant effects. Use when predicting functional

Query the CZ CELLxGENE Census (200M+ cells) programmatically via cellxgene-census and TileDB-SOMA, slicing expression by tissue, disease, or cell type and returning AnnData. Use when pulling reference single-cell RNA-seq data from the largest curated public atlas, running populat

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

Every VM came back. The cluster did not. Declarative systems converge on config, and the datapath isn't config.

A surprising share of AI-in-the-terminal failures aren't the AI. They're zsh, and a version of bash from 2006.

A Claude Code plugin turns standalone project configuration into a namespaced, installable extension that teams and communities can update as one unit.

None of the safety came from the model. It came from six boring habits.

Skills package instructions and references. Subagents run work in a separate context and return results. They solve different problems and can be composed deliberately.

Six hours in, one step left, everything green, and the incident that didn't happen

CLAUDE.md carries persistent project context. Skills load reusable procedures when relevant. Separating stable facts from task-specific workflows keeps both easier to maintain.

Twenty minutes recovering secrets that never existed, and the one sentence from a human that ended it

An API request routing a model's tool call through an approval gate to a remote MCP server

31 config keys, two audits, and why the first one was wrong in both directions

The official MCP Registry stores standardized server metadata rather than package code. Publishers verify a namespace, describe installation or remote access, and submit immutable versions.

Everyone looks at the Dockerfile. The file that actually leaked the key was the project file.

Remote MCP authorization uses established OAuth standards, but secure integration still requires issuer validation, least-privilege scopes, protected token handling, and server-side enforcement.

"Copy it over and switch the reference" is two steps, and the outage lives in the one nobody checks

stdio fits local processes and prototypes. Streamable HTTP fits hosted services and shared integrations. The right choice follows where the capability runs and who must reach it.

The most important rule wasn't about what I could change. It was about what I was allowed to display.

Tools perform operations, resources expose readable context, and prompts provide reusable templates. Choosing the correct primitive makes an MCP server easier to understand and govern.

Use MCP Inspector to connect to local or remote servers, inspect capabilities, call tools, read resources, test prompts, and diagnose failures before release.

Build an MCP server in TypeScript with focused tools, validated schemas, local and remote transports, Inspector tests, and production security controls.

An MCP server exposes tools, resources, or prompts through a standard protocol so an AI application can discover and use external capabilities.

How my sources developed over time

Show which pages an answer used

Add relation types where they matter

The weekly review

Implement an approved plan or issue in its own worktree, run the gate, open the pull request.

Close a finished session: sweep for unfinished work, land and hand off, file the follow-ups, tell the sessions that depend on this one, then archive.

Write the repository handoff file for the next session, and record any durable learning.

Merge an approved pull request, clean up its worktree and branch, then check whether a release is due.

Turn a topic or issue into a plan the reviewer approves in the native plan pane.

Answer a research question with parallel read-only gatherers and one synthesized digest.

Review the branch's diff in two fresh contexts — scope against the spec, then quality — and report findings only.

Transform a vague prompt into precise, structured AI instructions

AI assistant in Telegram that remembers everything and helps you run your life. Self-hosted in one command.

知更 — 本地 AI 的上下文与记忆层。Mac 上用语音输入、情境代回并调度 Codex / Claude Code；iOS 正在成为随身记忆终端和本地 Agent 遥控器。Local-first · BYOK.

Agent skill that turns Claude Code / Codex into a motion-design studio for voiceover-driven explainer videos — word-level voiceover sync, 78 motion recipe cards…

CoCo Super Intelligence is the orchestration layer that turns Claude Code, Cursor, or Codex into an engineering department: a routed advisory board, 185 skills,…

Deploy AI agent teams at scale without compromise

大师.skill — 输入行业，自动调研 6 轨[行业大佬 / 工具地图 / 工作流 / 知识正典 / 信息源 / 术语标准] → 提炼为可运行的行业 Master OS skill；装到任意 Claude Code / OpenClaw / Codex / Hermes agent 即让其进入「这一行的资深人」模式。…

Notion MCP server for Claude, Cursor, ChatGPT & Claude Desktop. Connect AI agents to Notion via Model Context Protocol — pages, databases, blocks, comments, fil…

Hook-based token compressor for 5 AI CLI hosts (Claude Code, Copilot CLI, OpenCode, Gemini CLI, Codex CLI). Up to 95% bash compression, signature-mode for code…

Model-neutral agent desktop/runtime for private, enterprise, and OpenAI-compatible / Anthropic-compatible model API. Tested on DeepSeek, Qwen, Kimi, GLM models.…

AI agent skill for end-to-end hotel search and booking—compare live rates across leading OTAs and hotel suppliers, verify availability, book stays, and manage r…

More than just Karpathy’s LLM Wiki, 100% local with Ollama. Drop Markdown notes → AI extracts concepts → your Obsidian wiki auto-links and grows. Zero sharing.…

Claude Code Guide - Setup, Commands, workflows, agents, skills & tips-n-tricks from beginner to power user!

A magical tool that changes how you use Agents. Install once — every Agent automatically discovers and uses all your MCP tools, and saves your tokens along the…

Open-source 24/7 Cowork app for OpenClaw, Hermes, Claude Code, Codex, OpenCode and 20+ more CLI Agent | Customize your assistants | Team them up｜Star if you lik…

AgenticX is a unified, production-ready multi-agent platform — Python SDK + CLI (agx) + Studio server + Machi desktop app. Features Meta-Agent orchestration, 15…

Query, provision and operate Cloud, SaaS, API and Model Context Protocol (MCP) resources through a unified SQL-based framework for humans and AI agents.

Open-source AI job search: scan job portals, evaluate listings into a structured A-H report with a global 1-5 score, tailor your CV, track applications — runs l…

A self-healing scraper for hostile sites: broken selectors repair themselves, browser rendering kicks in when needed, and a coherent identity layer (Chrome TLS…

Lightweight AI-native workflow builder for individuals and small teams — describe your idea in natural language, get a runnable workflow on a visual canvas, pub…

Minimal AI coding agent (~1,000 lines of Python) inspired by Claude Code. Works with any LLM. Think NanoGPT for coding agents. Formerly NanoCoder.