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.

Create new Svelte components with best practices, proper structure, and optional TypeScript support.

Help debug Svelte and SvelteKit issues by analyzing error messages, stack traces, and common problems.

Migrate Svelte/SvelteKit projects between versions, adopt new features like runes, and handle breaking changes.

Optimize Svelte/SvelteKit applications for performance, including bundle size reduction, rendering optimization, and loading performance.

Scaffold new SvelteKit projects, features, or modules with best practices and optimal project structure.

Migrate Storybook configurations and stories to newer versions, including Svelte CSF v5 and @storybook/sveltekit framework.

Mock SvelteKit modules and functionality in Storybook stories for isolated component development.

Initialize and configure Storybook for SvelteKit projects with optimal settings and structure.

Create comprehensive Storybook stories for Svelte components using modern patterns and best practices.

Diagnose and fix common Storybook issues in SvelteKit projects, including build errors, module problems, and configuration issues.

General-purpose Storybook assistance for SvelteKit projects, including setup guidance, best practices, and common tasks.

Analyze test coverage, identify testing gaps, and provide recommendations for improving test coverage in Svelte/SvelteKit projects.

Troubleshoot and fix failing tests in Svelte/SvelteKit projects, including debugging test issues and resolving common testing problems.

Set up comprehensive testing infrastructure for Svelte/SvelteKit projects, including unit testing, component testing, and E2E testing frameworks.

Create comprehensive tests for Svelte components and SvelteKit routes, including unit tests, component tests, and E2E tests.

Setup automated synchronization workflows

Resolve synchronization conflicts automatically

Sync GitHub issues to Linear workspace

Sync Linear tasks to GitHub issues

Link pull requests to Linear tasks

Offline-first Python AI agent that runs a tiny research business: quotes each job against its own costs, collects via Stripe, fulfils with NVIDIA Nemotron, pays…

DSH 插件 · 注入式优化器 0.8（主线）：你照常说话，它在你发送后,AI接收前把"这一轮到底要什么"理清楚，再把这份理解交给工作 AI(上下文注入) —— 原话不改写，条条带逐字依据。含控制界面（档位/权限/模型/上下文/只读工具）、拦截浮层（思维层+产出层）与真实 token 用量。可明显提升大多数模型的发挥稳…

Reliable AI Skill + MCP toolkit for agent-driven desktop CAD automation.

Curated real-world use cases for Hermes Agent — the self-improving AI agent from Nous Research. Backed by primary sources.

AI Agent 教学仓库 | 系统化 LangChain、RAG、LangGraph、MCP 全栈实战代码 | 万字博客详解 | 开源可运行示例 | 从零构建智能体

从 0 复刻 WorkBuddy-style 桌面 AI 助手 Harness：24 章 Python 教程，覆盖 Agent Loop、工具调用、记忆系统、Sidecar、沙盒审计、DeepSeek/OpenAI 评测轨迹

MCP server and CLI tools for web search and crawling, built on SearXNG and Crawl4AI

Delta MCP is a free app that sits between your AI apps and their MCP servers: one program per task instead of one tool call per step, up to 24.1× fewer tokens i…

Ava turns any Android 5+ device into a voice-first Home Assistant kiosk. Native C++ under the hood, so a 10-year-old tablet still listens, talks, and runs the h…

Roblox Studio macOS Window Capture Fix 2026: Real Screenshot Tool Instead of Magenta Playtest Glitch

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