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

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.

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.

Analyze git diffs or staged changes and generate conventional commit messages that explain WHY a change was made. Supports auto-detecting type and scope, intelligent file staging, and interactive overrides. Use when asked to "write a commit message", "generate a commit", "describe my changes", "commit this", "summarize my diff", or "/commit".

SOC 2 compliance for Terraform — gap analysis, control implementation, evidence collection, and remediation guidance mapped to SOC 2 Trust Services Criteria.

Generate, review, secure, and test composite GitHub Actions following best practices — full repo scaffold, interview-driven generation, PR creation on existing repos, SHA pinning, secrets-as-inputs, job summaries, and actionlint validation.

Set up and troubleshoot Datadog — Agent deployment on Kubernetes, APM instrumentation, Log Management, Monitors, Dashboards, SLOs, Synthetic tests, and live incident investigation using the Datadog MCP server. Covers Terraform-managed Datadog resources.

Structured platform troubleshooting — classifies the problem layer, collects evidence, forms a root-cause hypothesis, and proposes a fix with validation and rollback steps.

Generate, format, and validate code documentation — docstrings, JSDoc, OpenAPI/Swagger specs, documentation sites, and developer guides.

Measure, benchmark, instrument, and debug DORA metrics (Deployment Frequency, Lead Time for Changes, Change Failure Rate, MTTR) for production engineering teams. Covers GitHub Actions instrumentation, Prometheus recording rules, Grafana dashboards, incident source integration, SaaS tool selection, and anti-pattern detection. Use when asked to "instrument DORA metrics", "benchmark our deployment frequency", "why is my MTTR data missing", or "generate a DORA dashboard".

Deploy and configure Dynatrace — OneAgent Kubernetes Operator, code-level instrumentation, Log Monitoring, custom metrics, SLOs, Dashboards, anomaly detection, Davis AI, and live incident investigation using the Dynatrace MCP server. Covers Terraform-managed Dynatrace resources.

FluxCD entry point — routes to the right workflow based on what you need. Live cluster issue → structured 5-workflow debug trace. Repo health check → 6-phase audit (discovery, validation, API compliance, best practices, security). Helm chart review → helmchart. Starts by asking one question to confirm the right mode.

Design, review, secure, and debug GitHub Actions workflows — reusable workflows, OIDC federation, SHA pinning, token scoping, promotion orchestration, and CI failure diagnosis.

Flux CD and Argo CD — two modes. debug: five structured debug workflows for live clusters (installation, source, HelmRelease, Kustomization, ResourceSet) producing a five-section report. audit: six-phase read-only repo analysis (discovery, validation, API compliance, best practices, security) producing a prioritised Critical/Warning/Info report.

Scaffold, lint, review, security-audit, test, and upgrade-verify Helm charts. Runs an interactive interview to build production-ready charts from scratch. Covers chart structure, values design, schema validation, kubeconform, helm diff, and multi-environment scaffolding. Use when asked to "create a helm chart", "lint my chart", "review my helm chart", "check helm security", "generate values schema", "run helm diff", or "add helm tests".

Design, install, debug, review, plan capacity, audit scaling history, migrate from Cluster Autoscaler, and upgrade Karpenter v1.x on EKS. Covers NodePool, EC2NodeClass, NodeClaim, Spot diversity, disruption strategy, Pod Identity/IRSA, interruption queue, private clusters, AMI rotation, and GitOps integration. Use when asked to "set up Karpenter", "debug why nodes aren't provisioning", "review my NodePool", "what would Karpenter provision for this workload", "why did this node terminate", "migrate from CA", or "upgrade Karpenter".

Design, debug, and review KEDA ScaledObject/ScaledJob autoscaling. Covers all major scalers (Prometheus, SQS, Kafka, Redis, Cron, HTTP Add-on, Azure Service Bus), TriggerAuthentication, scaling lifecycle tuning, GitOps integration, and troubleshooting. Use when asked to "add KEDA autoscaling", "debug why my ScaledObject isn't scaling", "review my KEDA config", or "generate a ScaledObject for <trigger>".

Find, live-validate, map the blast radius of, and revoke leaked secrets with Kingfisher (MongoDB) — across a local repo, Git history, a GitHub/GitLab/Bitbucket org, S3/GCS, Docker images, Slack, Jira, Confluence, Teams, or Postman. Covers local CLI scanning, direct validate/revoke without a scan, baseline management (track only new secrets), kingfisher.yaml policy, CI diff-scan gates, and pre-commit/Husky hooks. Use when asked to "scan for secrets", "is this key still live", "what can this credential reach", "revoke this token", "did we leak a secret", or "block new secrets in CI". Pattern-only secret scan bundled with a CVE pass → /platform-skills:trivy. Secrets-context safety in workflow YAML → /platform-skills:zizmor. Storing/rotating secrets inside the cluster → /platform-skills:secrets.

Cluster baseline scaffolding, RBAC diagnosis and generation, workload hardening, and structured pod/scheduling debug for plain Kubernetes across all distributions.

Generate, test, audit, debug, and migrate Kyverno policies using the new CEL-based policy types (ValidatingPolicy, MutatingPolicy, GeneratingPolicy, ImageValidatingPolicy — all apiVersion policies.kyverno.io/v1). Covers matchConstraints, matchConditions, CEL validations/mutations, generator.Apply(), Audit→Deny promotion, PolicyException, kyverno-cli testing, and migration from legacy ClusterPolicy or PodSecurityPolicy. Use when asked to "write a Kyverno policy", "test a ValidatingPolicy", "audit my cluster for violations", "why is my policy not firing", or "migrate from ClusterPolicy".

Linkerd-specific diagnostics — mTLS verification, proxy injection issues, authorization policy debugging, traffic management, and multi-cluster connectivity problems.

Linux administration and networking diagnostics — DNS, load balancing, VPCs, kernel tuning, and connectivity troubleshooting.

MCP server and client development — scaffold, implement tools/resources/prompts, validate schemas, debug protocol compliance, and deploy with auth and rate limiting.

Okou connects to the tools your team already uses and does the work — across marketing, sales, engineering, and operations, under your control.

An open-source Digital Worker platform for reliable execution, continuous co-evolution, and building Enterprise AI assets.

A curated list of AI Agent evolution, memory systems, multi-agent architectures, and self-improvement projects. | evomap.ai

A governance harness for AI coding.

DeepSeek Harness 手机版：可直接安装的 Android APK，AI 免 Root 操作手机（Shizuku/root 可选），文件编辑只需所有文件访问权限，前台保活 + AI 通知

Local-first, governed AI agent runtime for Python — embed it in your app, or run it as a CLI or ACP server. Permissions, MCP, memory and audit replay built in.

Orbi — the factory that builds and operates AI software factories. GitHub Issues in, releases and runnable system out

Open-source AI agent harness in native Rust — GUI, CLI, headless, and webapp from one binary. Multi-provider, MCP, skills, plugins, agent teams.

The SDK for browser agents. Interact, search, extract, and fetch any site reliably across the web

Agent-native shopping for extreme value: verifiable same-product price evidence, checkout, orders, delivery, and after-sales.

The extensible power-user platform for Google Antigravity. Adds a native In-App Browser, animated Desktop Pets, revamped Gemini UI, and custom BYOK Gemini Pro k…

Open-source, single-binary, self-hosted AI agent — your models and data stay on your machine. A coding agent on par with Claude Code and a personal assistant li…

Your pocket agent. Local-first AI agents on iOS and Android — real workspaces, tool execution with approvals, and your choice of model (DSH · Claude Code · Code…

Bridge between QQ (SnowLuma OneBot v11) and DeepSeek Harness agents: social simulation, safe MCP tools, slang learning and more.

A 7×6 framework for agent architecture. 28 patterns, each placed at a coordinate, runnable Python code with verified engineering slices from Claude Code, Aider,…

针对 AI 自动化渗透 Agent 的新一代反制蜜罐，通过反向代理将API密饵载入真实业务、反向提示词注入等方式反制自动化渗透 Agent，实现多款主流通用Agent的反制上线控制。

Open-source, local-first AI agent for coding and real work. BYOK models, MCP, skills, plugins, workflows, and private knowledge bases.

A free AI-agent toolbox for Android, 一站式安卓AI Agent工具箱

Google Workspace CLI — one command-line tool for Drive, Gmail, Calendar, Sheets, Docs, Chat, Admin, and more. Dynamically built from Google Discovery Service. I…

Independent, unofficial CLI to edit CapCut and JianYing (剪映) projects — subtitles, timing, speed, volume, templates, cut long-form to shorts. No API needed, rea…