LLM Mart Basic

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

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

Fourteen posts of being wrong in production, compressed to checkboxes

Healthy nodes, a quiet network, 300 restarts in three days, and a latency budget measured in milliseconds

Discovery worked. Ping worked. Every TCP connection timed out, and later the tunnel only worked when someone had a terminal open.

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.

Update the Hivemind plugin to the latest version

credo - Disable credo for this directory (silence onboarding and the [credo] line here, reversible)

credo - Enable credo for this directory (opt in; overrides a previous decline)

credo - Explain something in depth (what/why/example/consequences)

credo - Migrate an existing repo into the .credo/ structure

credo - Pin the target repo for credo's project layer (hub-aware), or show the resolved target

credo - Interactive guide to available topics and workflows

credo - Clear this session's default role (back to no role; the agent does everything)

credo - Set this session's default role to plan/clarify (owns clarifying 1_clarify items, no commits/push)

credo - Set this session's default role to task/build (owns implementing GO items incl. commits/push per dogma)

credo - Promote an accepted sandbox artifact from .credo/sandbox-tmp/ to .credo/sandbox/

credo - Set the session mode to active (intensive live collaboration, no keep-alive)

credo - Set the session mode to autonomous (work approved GO items unattended, hook-enforced keep-alive ON)

credo - Initialize session with main agent workflow instructions

credo - Set the session mode to passive (user available for clarifications only, no keep-alive)

credo - Set up Claude Code with recommended workflows and plugins

dogma - Find and fix AI-typical patterns in code (reactive cleanup)

dogma - Sync documentation across README files and wiki articles

dogma - Interactively collect and apply CLAUDE rules to the project

dogma - Add ignore patterns to multiple locations at once

AI agent orchestration kit for Windows, Linux/MacOS with Codex skills, hooks, routing rules and profiles for Claude, OpenCode, Cursor, Gemini and Windsurf.

Skills & reviewer agents for AI-first climate science — built and used by a PhD atmospheric scientist

出行路书工作流 skill：联网实查 + 多源交叉验证，产出可核验、能执行的旅行攻略。覆盖吃住行游拍避全维度，附美食情报卡、基准骨架与校验工具，支持一键部署在线版。

Self-hosted AI code reviewer with indexed PR reviews, walkthroughs, vulnerability scanning, dependency graphs, custom rules, and a learning loop.

🧬 Extend EvoScientist with Installable Skill & Knowledge Packs

Give the agent a machine. Just not yours. Each AI coding agent gets its own isolated machine with root, Docker, and systemd - active defense detects and stops t…

Automatic memory consolidation for OpenClaw agents — like sleep for your AI. Powered by MyClaw.ai

🗂 The essential checklist for modern web development, for humans and AI agents

Distribb CLI, Claude, Codex, Hermes, OpenClaw skill for AI-powered SEO. Write content with your own AI, publish through Distribb's backlink network.

Open-source AI browser agent — type plain-language commands and Bah operates the web for you. Works with cloud AI (DeepSeek, Mistral, NVIDIA) or local Ollama mo…

DeepSeek Harness Desktop (dsh-desktop). EAC: Embracing All Creation (揽尽万象). Bundled Node.js runtime with full dsh-CLI kernel, one-click startup, 10 built-in UI…

Use your ChatGPT / Codex subscription with DeepSeek Harness via OAuth, with model access, usage quotas, search, and image generation — no API key or Codex CLI r…

Local-first A-share research workbench for DeepSeek Harness: market dashboards, watchlists, valuation, four investor agents, versioned reports, and continuous p…

Open-source video pipeline (clipper, AI video & more) — scout trends, clip long videos, generate captioned shorts, design motion graphics. Local-first, BYOK. AG…

Desktop app for the pi coding agent: streaming timeline, Git review with hunk staging, session tree, native UI for pi extensions. Windows · macOS · Linux. pi 编程…

Zero-dependency browser video editor that AI agents can drive — JSON timeline, MCP + REST, live-reloading UI

Personal Context Manager for Claude Code. Your life in walnuts.

Fast way to switch between Claude Code configuration profiles

AutoClip｜一个链接，一键出片。开源 AI 视频剪辑桌面工具，将播客、访谈、课程等长视频自动剪成短视频，生成字幕、封面和发布文案，适配抖音、小红书、TikTok、Reels 与 YouTube Shorts。Open-source AI video clipping & content repurposing.