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

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.

List ConnectWise CPQ quote templates available to copy

Search ConnectWise CPQ quotes by account, status, or date range

Add an internal or external note to a ConnectWise PSA ticket

View agreement status and entitlements for a company in ConnectWise PSA

Close a ConnectWise PSA ticket with resolution notes

Create a new service ticket in ConnectWise PSA

Retrieve detailed ticket information from ConnectWise PSA

Log a time entry against a ConnectWise PSA ticket

Search for configuration items (assets) in ConnectWise PSA

Create a schedule entry/appointment in ConnectWise PSA

Search for tickets in ConnectWise PSA by various criteria

Update fields on an existing ConnectWise PSA ticket

Search recent Crewhu surveys, surfacing detractors and promoters

Run the reliability scorecard for one service, or every connected service if omitted - error-budget burn rate where an SLO is defined, trend reporting otherwise

Generate the current on-call handoff brief - what's paging, what's escalated without an owner, last-shift history, and known-flaky alerts to watch

Draft a blameless postmortem for a given incident (by ID or name), or the most recent significant incident within a time window

List all devices at a Domotz-monitored site

Find a Domotz device by name, IP address, or MAC address

Overview of a Domotz site's network health

Pull full detail for one Checkpoint Harmony Email detection and the message behind it

Unofficial KakaoTalk CLI and native MCP server for macOS — read, watch, and send messages via Accessibility automation.

Local-first AI action assistant for operators: memory, skills, tools, and permission gates to turn work into controlled action.

Agent-driven media library for your cloud drives (Quark 夸克 / 115 / 光鸭 GuangYa / 123网盘 / 天翼 Tianyi)

An open-source desktop AI agent built around Cyrene’s persona and powered by the self-developed Cyrene_Harness framework. It combines immersive character chat w…

在 Android 上运行的 AI 编程 Agent，内置 Linux 终端与代码编辑器，支持 MCP 协议扩展。

TencentDB Agent Memory is a team-level memory hub for AI Agents — turning conversations, docs, and code into four reusable memory assets (Chat Memory, Skill, LL…

Floe — a native iOS/iPadOS AI agent workspace for iPhone and iPad, built for private bring-your-own-key workflows.

Spring Boot AI Agent — an out-of-the-box solution that makes your app converse, remember, think, and act.

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

A tiny Claude Code skill that keeps your prompt cache warm during idle sessions, so your next message reads from cache instead of paying full price.

Monet — Multi-engine mission control for coding agents (Claude Code and Codex today). Browse, search, and drive your agent sessions from a native desktop app.

A DottedSign MCP server that enables AI assistants (Claude, ChatGPT) to manage signing tasks, templates, and document status via natural language.

Курируемый handbook по Claude Code на русском: hooks, skills, CLAUDE.md шаблоны, MCP-серверы, кейсы.

👾 Open Computer Use – Open-Source Alternative to Codex Computer Use

An open-source AI companion that actually remembers you — runs entirely on your own Mac or server. Desktop pet · long-term memory · proactive companionship · mu…

Graphical management tool for Kubernetes on desktop and mobile.

Open-source desktop app for content creation, with an agent runtime and standalone CLI.

Connect Claude and ChatGPT to KDAN PDF — upload, edit, compress, protect, redact, and compare PDFs in chat.

Ekko Studio is a local-first AI workspace for multi-agent chat, coding, and visual workflows, available on desktop and the web.

Open-source native iPhone/iPad client for OpenAI Codex CLI and Claude Code — review diffs, approve actions, steer sessions, and manage Git remotely.