scitex.ai | uv pip install scitex[all]
(Demo) Automated Research with SciTeX MCP Server in 40 min. Literature Search → Analysis → Graphing → Manuscript → Revision Letter
| Component | Description | Repository |
|---|---|---|
| SciTeX-Python | Modular Python toolkit for scientific research with 200+ MCP tools | scitex-python |
| SciTeX-Hub (Live at scitex.ai) | Django-based, self-hostable browser application for scientific research | scitex-hub |
┌──────────────────────────┐
L5 — umbrella │ scitex (re-export) │
└────────────┬─────────────┘
▼
┌──────────────────────────────────────────────────────────────┐
│ L4 — observers / UX (depend ↓, never ↑) │
│ scitex-clew scitex-audit scitex-notification scitex-audio│
└────────────────────────────┬─────────────────────────────────┘
▼
┌──────────────────────────────────────────────────────────────┐
│ L3 — workflow producers (apps + orchestrators) │
│ scitex-app · -browser · -genai · -ml · -notebook · -repro · │
│ -scholar · -seizure-metrics · -session · -todo · -ui · -web │
│ · -writer · socialia │
└────────────────────────────┬─────────────────────────────────┘
▼
┌──────────────────────────────────────────────────────────────┐
│ L2 — domain producers (peer ⇄ peer optional) │
│ figrecipe ⇄ scitex-stats · scitex-plt · -pd · -nn · -dsp · │
│ -cv · -linalg · -math · -tex · -msword · -benchmark · │
│ -capture · -events · -git · -hpc · -template │
└────────────────────────────┬─────────────────────────────────┘
▼
┌──────────────────────────────────────────────────────────────┐
│ L1 — IO + data leaves (no peer deps) │
│ scitex-io · -db · -dataset · -ssh │
│ crossref-local · openalex-local │
└────────────────────────────┬─────────────────────────────────┘
▼
┌──────────────────────────────────────────────────────────────┐
│ L0 — tooling leaves (no peer deps; used by all) │
│ scitex-types · -path · -str · -dict · -logging · -etc · │
│ -compat · -dev · -config · -core · -context · -datetime · │
│ -decorators · -gen · -gists · -introspect · -os · -parallel │
│ · -repl · -resource · -sh │
└──────────────────────────────────────────────────────────────┘
Orthogonal (orchestration / platform — not in the cascade):
scitex-hub scitex-orochi scitex-agent-container
scitex-container newb
All 68 active packages — single table with layer + dependency view
Sourced from scitex_dev._ecosystem._registry.ECOSYSTEM
| Package | scitex Module | Layer | Depends on (scitex-* runtime) | Description |
|---|---|---|---|---|
| scitex | — (umbrella) | L5 | re-exports the full ecosystem (≈40 peers) | A comprehensive Python library for scientific computing and data analysis |
| scitex-audio | scitex.audio |
L4 | dev | Text-to-Speech with multiple backends for scientific workflows |
| scitex-clew | scitex.clew |
L4 | — | Verifiable knowledge graph for scientific experiments |
| scitex-notification | scitex.notification, scitex.notify |
L4 | dev | Multi-backend notification system for SciTeX |
| scitex-app | scitex.app |
L3 | — | SciTeX App SDK — write-once interface for local + cloud apps |
| scitex-browser | scitex.browser |
L3 | config, logging | Browser automation for scholarly paper access |
| scitex-genai | scitex.genai |
L3 | dev, io, str | Modality-organised generative-AI provider abstraction (LLM, agents, image/audio/video stubs) |
| scitex-ml | scitex.ml |
L3 | context, dev, io, logging, plt, repro, str, types | Machine learning, classification, and training utilities |
| scitex-notebook | scitex.notebook |
L3 | clew | Jupyter notebook verification, compilation, and DAG-based conversion |
| scitex-repro | scitex.repro |
L3 | — | Reproducibility utilities (random state, timestamps, hashing) |
| scitex-scholar | scitex.scholar |
L3 | browser, io, logging, session | Scientific paper search, enrichment, download, and management |
| scitex-seizure-metrics | scitex.seizure_metrics |
L3 | — | Standardised evaluation metrics for epileptic seizure detection and forecasting |
| scitex-session | scitex.session |
L3 | dict, io, logging, plt, repro, str | @session decorator + lifecycle (auto-CLI, output dir tree, RandomStateManager) |
| scitex-todo | scitex.todo |
L3 | — | Canonical YAML task store with pluggable adapters (mermaid dependency graphs) |
| scitex-ui | scitex.ui |
L3 | — | Shared frontend UI components for the SciTeX ecosystem |
| scitex-web | scitex.web |
L3 | dev | Web scraping (URLs, images), PubMed search, URL summarization helpers |
| scitex-writer | scitex.writer |
L3 | dev, ui | LaTeX manuscript compilation with automatic versioning and diff generation |
| socialia | scitex.social |
L3 | config, dev | Unified social media management (posting, analytics, and insights) |
| figrecipe | scitex.fig, scitex.diagram, scitex.plt |
L2 | app, config, dev | Reproducible matplotlib wrapper with mm-precision layouts and 47 plot types |
| scitex-benchmark | scitex.benchmark |
L2 | — | Performance benchmarking, runtime monitoring, and profiling helpers |
| scitex-capture | scitex.capture |
L2 | — | Session-based screen capture (screenshots, multi-frame GIFs, grid overlays, monitor info) |
| scitex-cv | scitex.cv |
L2 | — | cv2/Pillow image-processing (load/save, resize/rotate/crop, blur/sharpen/edge, drawing) |
| scitex-dsp | scitex.dsp |
L2 | decorators, gen, nn | Digital signal processing (PAC, Hilbert, Wavelet, filters, demo signals) |
| scitex-events | scitex.events |
L2 | config | General-purpose async event bus (file-backed, JSON Lines) |
| scitex-git | scitex.git |
L2 | — | Git + GitHub Actions utilities (clone, branch, commit, retry, gh secrets) |
| scitex-hpc | scitex.hpc |
L2 | config, ssh | Generic SLURM dispatch (srun, sbatch, sync, poll, fetch) |
| scitex-linalg | scitex.linalg, scitex.torch |
L2 | dev | Linear-algebra helpers (distance, geometric median, cosine, nannorm) |
| scitex-math | scitex.math |
L2 | — | Mathematical utilities (parity helpers, etc.) |
| scitex-msword | scitex.msword |
L2 | — | .docx reader/writer with journal-style profiles (MDPI, IEEE, Springer, Elsevier, RESNA, IOP) |
| scitex-nn | scitex.nn |
L2 | config, decorators, gen | Neural network building blocks (BNet, Hilbert, PAC, Wavelet, filters) |
| scitex-pd | scitex.pd |
L2 | types | Pandas helpers (force_df, melt_cols, find_pval, mv, slice, sort, round) |
| scitex-plt | scitex.plt |
L2 | figrecipe | SciTeX plotting module (alias for figrecipe) |
| scitex-stats | scitex.stats |
L2 | config, dev, logging | Publication-ready statistical testing with 23 tests, effect sizes, power analysis, MCP server |
| scitex-template | scitex.template |
L2 | config, dev | Project template cloner + code snippet library (six templates vendored, shallow-cloned on demand) |
| scitex-tex | scitex.tex |
L2 | dev | LaTeX helpers — export to .tex, render preview images, vector formatting |
| crossref-local | scitex.scholar.crossref |
L1 | config, dev | Local CrossRef database with 167M+ works and full-text search |
| openalex-local | scitex.scholar.openalex |
L1 | — | Local OpenAlex database with 284M+ works, abstracts, and semantic search |
| scitex-dataset | scitex.dataset |
L1 | config, dev | Multi-domain dataset fetcher (OpenNeuro, DANDI, PhysioNet, GEO, ChEMBL, ClinicalTrials) |
| scitex-db | scitex.db |
L1 | core | Database utilities for scientific computing with SQLite3 and PostgreSQL |
| scitex-io | scitex.io |
L1 | dev, logging | Universal scientific data I/O with plugin registry (30+ formats) |
| scitex-ssh | scitex.ssh, scitex.tunnel |
L1 | — | SSH primitives (exec/copy/attach/tunnel) with per-host allowlist |
| scitex-compat | scitex.compat |
L0 | — | Backward compatibility shims and deprecation wrappers |
| scitex-config | scitex.config |
L0 | — | Config + path management (direct → yaml → env → default cascade; per-package state-dir resolver) |
| scitex-context | scitex.context |
L0 | — | Execution-context detection (script vs Jupyter vs IPython) + stdout/stderr suppression |
| scitex-datetime | scitex.datetime |
L0 | dev | Datetime helpers (linspace, normalize_timestamp, format helpers) |
| scitex-decorators | scitex.decorators |
L0 | compat, config, dev | Decorator library — numpy/torch/pandas/xarray type converters, caching, batching, deprecation |
| scitex-dev | scitex.dev |
L0 | newb, config, logging | Shared developer utilities and AST linter (absorbs scitex-linter) |
| scitex-dict | scitex.dict |
L0 | dev | Dictionary utilities (DotDict, safe_merge) |
| scitex-etc | scitex.etc, scitex.media |
L0 | — | Cross-cutting utilities (interactive keyboard input, parameter-grid iteration, regex, media display) |
| scitex-gists | scitex.gists |
L0 | — | SigmaPlot macro conversion utilities for matplotlib |
| scitex-introspect | scitex.introspect |
L0 | — | IPython-style introspection (signatures, docstrings, members, source, call graphs, class hierarchy) |
| scitex-logging | scitex.logging, scitex.errors |
L0 | — | Logging utilities |
| scitex-os | scitex.os |
L0 | — | Host check + safe file move |
| scitex-parallel | scitex.parallel |
L0 | — | Thread/process pool parallel execution utilities |
| scitex-path | scitex.path |
L0 | — | Scientific project path utilities (find, split, symlink, versioning) |
| scitex-repl | scitex.repl |
L0 | — | Interactive REPL helpers (embed, less, paste) |
| scitex-resource | scitex.resource |
L0 | dev | System resource info, processor usage logging, RAM limit |
| scitex-sh | scitex.sh |
L0 | — | Safe subprocess wrapper (list-only, no shell injection) with stream/timeout support |
| scitex-str | scitex.str |
L0 | dev, dict, logging | Text processing (LaTeX formatting, colored output, string parsing, plot text helpers) |
| scitex-types | scitex.types |
L0 | dev | Scientific type definitions (ArrayLike, ColorLike) and validation |
| newb | — | Orthogonal | — | "A fresh AI agent tries to use your package" — pytest-style; if it succeeds, your docs work |
| scitex-agent-container | scitex.agent_container |
Orthogonal | config, container, logging, ssh | Declarative YAML framework for managing AI coding agent instances |
| scitex-container | scitex.container |
Orthogonal | config, dev | Unified container management for Apptainer and Docker |
| scitex-hub | scitex.cloud, scitex.module, scitex.project |
Orthogonal | app, config, dev, session, writer | SciTeX Hub — deployment and management CLI |
| scitex-orochi | scitex.orochi |
Orthogonal | config, resource | Agent communication hub |
| Title | Code |
|---|---|
| A deep learning model for the detection of various dementia and MCI pathologies based on resting-state electroencephalography data | eeg-dementia-classification |
| Towards threshold invariance in defining hippocampal ripples | Code, pip |
| Hippocampal neural fluctuations during working memory | ripple-wm-code |
| gPAC: GPU-accelerated phase-amplitude coupling analysis (341x faster than TensorPAC) | gPAC |
| Intestelligence: A pharmacological neural network using intestine data | intestelligence |
| Category | Package | Description |
|---|---|---|
| AI | emacs-claude-code | Claude Code integration (SciTeX-Engine) |
| emacs-llm | LLM chat client in Elisp | |
| genai | LLM chat interface with streaming and conversation history | |
| emacs-whisper-live | Real-time speech transcription with Whisper | |
| emacs-mcp-server | MCP server for Emacs | |
| Dev | elisp-test | Testing framework for Elisp |
| elisp-linter | Linter for Elisp | |
| emacs-python-import-manager | Python import management | |
| emacs-python-config | Python environment configuration | |
| UI | emacs-tab-manager | Tab management |
| emacs-buffer-navigation | Buffer navigation | |
| emacs-recentf-project | Project-aware recent files | |
| emacs-spinner | Spinner animations | |
| Tools | emacs-header-footer-manager | Header/footer management |
| emacs-slack | Slack integration | |
| emacs-message | Toggle print/message | |
| emacs-gif-screencast | GIF screencast & capture | |
| emacs-password-manager | GPG-encrypted password manager |
| Resource | Description |
|---|---|
| agents | Sync MCP servers, skills, and instructions across AI coding tools |
| automated-research-demo | Demo: AI-driven autonomous research from data to manuscript |
| .dotfiles-public | Linux configuration |
| ai-ielts.app | IELTS speaking/writing practice |
| Programming advice (EN) / (JA) | Tips for younger self |
ywatanabe@scitex.ai