LLM Mart Basic

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

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

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.

One-screen inventory of skills, agents, commands, MCP servers, and hooks counts.

List the file-based memory store grouped by project (auto-memory) plus the CLAUDE.md files.

Show current Claude Code spend versus a budget number

Quick month-end spend projection from the daily trend

List the most expensive sessions pushing your spend up

Print the Agent Monitor dashboard URL and how to start/open it

Check Agent Monitor reachability and print UP/DOWN with latency

One-line Agent Monitor health + counts summary from /api/stats

Quick connectivity + health probe of the Agent Monitor dashboard.

Export Agent Monitor data (sessions/events/analytics/costs/all) as json/csv/md.

Show the latest N ingested events with timestamp, event_type, and tool_name.

List current cost and token outlier sessions via z-score

Compare two sessions side-by-side with cost and workflow deltas

Surface the top 3 data-backed insights about your Claude Code usage right now

Read-only inventory of CCAM alerts, webhook targets, and remote sources

CCAM platform status across hooks, config, updates, and MCP prerequisites

One-screen focus snapshot — avg turn duration, thinking-block usage, and longest sessions.

Quick daily standup from today's Claude Code sessions — grouped by project, with cost and errors.

Suggest the next action from your most recent in-progress sessions and recent errors.

List the most recent APIError events with their session and a summary

A systematic AI Agent development tutorial covering LLM agents, RAG, tool use, memory systems, multi-agent systems, LangChain, LangGraph, MCP, and agentic RL.｜从…

Convert Files / Folders / GitHub Repos Into AI / LLM-ready Files

Open-source, local-first conversational AI video editor with a professional multi-track timeline, Agent Skills, MCP integration, and Remotion rendering.

Maintainer-governed agent for evidence-backed open-source contribution proposals

A Claude Code skill by Hao (駱君昊) that learns your Facebook voice and auto-posts to FB / IG / Threads / X with a 14-day content calendar. Mega-viral validated: 8…

Local-first AI agent workspace for coding, writing, design, research, and automation — one runtime for desktop GUI and TUI.

Open-source AI Agent platform for teams. Your agents don't just chat — they read files, run code, call APIs, and deliver results.

Give your AI agent eyes for PDFs — structured text, tables, OCR, visual evidence, and page-level citations via MCP. Native Rust, local-first.

Real-world AI penetration testing engineer for authorized assessments — built-in cloud module covering AWS/Azure/GCP + Aliyun/Tencent/Huawei clouds. Built on Cl…

OpenGUI is an Android GUI agent framework for phone-use AI that can see, plan, and operate real mobile apps through the GUI.

Tinybot is a lightweight personal AI Agent that is constantly evolving

Goink 桌面 AI 小说创作助手，对话式写作 + 自动状态追踪 + 本地语义搜索。跨平台开箱即用。AI Agent Novel Generator.

Pluggable DeepSeek-colored TUI for DeepSeek Harness

Entity-level git merge driver. Resolves false conflicts git invents when independent agents edit the same file. ~95% reduction vs. line-based merge.

Percho: Minimalist desktop GUI for the Pi coding agent — the same engine as the Pi CLI, in a clean visual interface. Multi-session chat, visual tool approvals,…

Run Claude Code, Codex & Gemini in parallel on Windows & macOS — git worktree fan-out with atomic hunk adoption, approval gates, reboot-surviving sessions

A hierarchical memory framework for personalized presentation agents. Try it at memslides.com.

Real-time multimodal desktop agent evolving toward a persistent AI OS interface (0.1 α).

clawdcursor compiles whatever's on screen into one UI map — accessibility tree and OCR fused into stable, addressable elements, with a screenshot only when need…

Repeatable agentic engineering. The workflow layer that turns AI coding agents into a disciplined factory: durable specs, fresh-context workers, adversarial cro…