Search: "small"

Creates, analyzes, and visualizes complex networks and graphs in Python with NetworkX. Use when working with network/graph data structures, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks (random, scale-free, small-world), reading/writing graph file formats, or drawing network topologies. Common applications include social, biological, transportation, and citation networks.

Selects bounded, graph-informed source slices with Trailmark and delegates focused code analysis or patch-proposal work to a smaller subagent. Use when offloading function-, class-, caller-, callee-, call-path-, entrypoint-, or line-focused code tasks to constrained or locally hosted models without exposing the full repository.

Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis. Sets up protein/small molecule systems, defines force fields, runs energy minimization and production MD, and analyzes trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics.

Processes mass spectrometry data with pyOpenMS. Supports proteomics and metabolomics workflows—feature detection, peptide/protein identification, label-free quantification, adduct/accurate-mass annotation, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. For simple spectral comparison and small-molecule library matching use matchms.

Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API. Use for pKa and macropKa prediction, conformer and tautomer ensembles, docking and analogue docking, protein-ligand cofolding, MSA generation, molecular dynamics, permeability, descriptor workflows, and related small-molecule or protein modeling tasks. Ideal for programmatic batch screening, multi-step chemistry pipelines, and workflows that would otherwise require maintaining local HPC/GPU infrastructure.

Retrieves, versions, and publishes scientific datasets with DataLad and git-annex, and captures computational provenance with datalad run, rerun, and containers-run. Use when cloning or fetching data from OpenNeuro, DANDI, datasets.datalad.org, or any DataLad dataset; when a file in a dataset reads as a broken symlink or a small pointer instead of real data; when an analysis needs a machine-readable record of how each output was produced so it can be re-executed; or when publishing a dataset to siblings such as a GitHub repository plus a storage remote. Also use to decide between DataLad and plain Git for a data-carrying repository.

Featurizes small molecules with Molfeat for QSAR/QSPR, chemical similarity, virtual screening, and molecular ML. Covers ECFP/MACCS fingerprints, RDKit descriptors, pharmacophores, pretrained embeddings, configuration persistence, and molecule-to-label alignment.

Predicts protein-small-molecule binding poses with DiffDock and DiffDock-L from PDB or sequence plus SMILES/SDF/MOL2. Covers batch docking, pose triage, confidence interpretation, and validation. Use for molecular docking and virtual-screening pose generation, not binding-affinity prediction.

Travel MCP server + CLI for AI assistants — flights, hotels, trains, cars, ferries, price alerts. No API keys, single Go binary. 1 smart MCP tool + 66 aliases (98.9% smaller tools/list). Works with Claude, Cursor, Windsurf, Codex.

Check a pull request is small, described, tested, and free of secrets before opening or reviewing it. Use when drafting a PR, reviewing a diff, or verifying a change is ready to share.

Desktop Cowork app for office workers: organize local folders, extract from PDFs/images, generate invoices/contracts/resumes, and build small internal tools.

Saki AI Agent is a desktop AI assistant that runs on your personal computer. Designed to be lightweight and portable, it emphasizes local operation and privacy by utilizing small on-device models for AI capabilities, making it an ideal alternative to platform-based agents like OpenClaw.