# OpenScience documentation

> Guides for installation, model access, Ace pricing, scientific research, and customization.

Full text: https://www.openscience.sh/docs/llms-full.txt

## Start here

- [OpenScience](https://www.openscience.sh/docs): A workbench for literature, data, code, experiments, and scientific writing.
- [Quickstart](https://www.openscience.sh/docs/quickstart): Install OpenScience, choose model access, and complete your first research task.
- [What OpenScience can do](https://www.openscience.sh/docs/capabilities): Explore every major user workflow, its inputs, outputs, and setup.
- [Source and file types](https://www.openscience.sh/docs/source-types): Choose the right way to bring papers, tables, code, images, and scientific data into a project.
- [Installation and updates](https://www.openscience.sh/docs/installation): Install the desktop app or CLI, check your version, and keep your work when updating.

## Your workspace

- [Workspace](https://www.openscience.sh/docs/workspace): Find your projects, follow a conversation, and review the files OpenScience produces.
- [Projects and source folders](https://www.openscience.sh/docs/projects): Create a workspace, connect existing material, and keep related research organized.
- [Sessions and terminal runs](https://www.openscience.sh/docs/sessions): Start, continue, export, and import a research conversation.
- [Files and storage](https://www.openscience.sh/docs/files): Keep inputs, working files, and final results organized and recoverable.
- [Saved Results](https://www.openscience.sh/docs/results): Retain a completed output, download its exact file, and manage saved research results.

## Models and account

- [Account and workspaces](https://www.openscience.sh/docs/account): Complete sign-in, distinguish project folders from funding workspaces, and manage device access.
- [Models and providers](https://www.openscience.sh/docs/models): Choose Ace, connect your own provider access, and select a model for each task.
- [Ace and your account](https://www.openscience.sh/docs/ace): Set up managed access, choose a funding workspace, and manage your Wallet.
- [Ace model directory](https://www.openscience.sh/docs/ace-models): Browse the reviewed managed model identities and token limits shipped with this documentation version.
- [Pricing and usage](https://www.openscience.sh/docs/pricing): What the workbench costs, how Ace uses your Wallet, and how to control spending.
- [Usage reports and CSV exports](https://www.openscience.sh/docs/usage): Filter activity by source, model, and date, and distinguish Wallet charges from local estimates.
- [Local models](https://www.openscience.sh/docs/local-models): Connect Ollama, LM Studio, or an endpoint on infrastructure you manage.
- [Custom providers](https://www.openscience.sh/docs/custom-providers): Connect a compatible model service that is not in the provider picker.

## Plan and continue

- [Research controls](https://www.openscience.sh/docs/agents): Plan a task, choose research effort, and decide when OpenScience should ask you.
- [Planning and persistent goals](https://www.openscience.sh/docs/planning): Turn a broad research objective into a plan, bounded experiments, and reviewable progress.
- [Context, checkpoints, and handoffs](https://www.openscience.sh/docs/context): Keep long investigations understandable and recoverable as a conversation grows.
- [Share and hand off research](https://www.openscience.sh/docs/team-workflows): Package files, instructions, and results so another person can continue the work.

## Personalize and get help

- [Appearance, notifications, and updates](https://www.openscience.sh/docs/preferences): Set up the workspace for how you read, monitor work, and keep the app current.
- [Privacy and data](https://www.openscience.sh/docs/privacy): Understand local storage, model and tool requests, session trace sharing, and deletion controls.
- [Keyboard shortcuts](https://www.openscience.sh/docs/keyboard-shortcuts): Navigate projects, compose requests, and reach workspace actions from the keyboard.
- [Troubleshooting](https://www.openscience.sh/docs/troubleshooting): Resolve installation, model access, account, file, and research-tool problems.
- [Frequently asked questions](https://www.openscience.sh/docs/faq): Short answers about accounts, pricing, local models, projects, and research results.

## Research and evidence

- [Workflow cookbook](https://www.openscience.sh/docs/workflow-examples): Start with a complete request and know what a useful result should contain.
- [Literature reviews](https://www.openscience.sh/docs/literature-review): Search with a clear scope, compare evidence, and save a review you can check.
- [Research search](https://www.openscience.sh/docs/research-search): Find web and scholarly material, apply source filters, and inspect what a search actually returned.
- [Searching scientific databases](https://www.openscience.sh/docs/database-workflows): Discover a database, query its records, fetch supported files, and retain source identifiers.
- [Reading and extracting documents](https://www.openscience.sh/docs/documents): Work through papers, protocols, PDFs, and reports with checkable source references.

## Analyze and experiment

- [Data analysis](https://www.openscience.sh/docs/data-analysis): Inspect inputs, agree on an analysis, and save code and results together.
- [Code, repositories, and the terminal](https://www.openscience.sh/docs/code): Explore research code, make reviewable changes, and run project commands.
- [Statistical analysis](https://www.openscience.sh/docs/statistics): Build a transparent analysis from the study design through uncertainty and sensitivity checks.
- [Python and R analysis](https://www.openscience.sh/docs/python-r): Run calculations, retain working variables, inspect plots, and turn an interactive analysis into reusable code.
- [Machine learning experiments](https://www.openscience.sh/docs/machine-learning): Build baselines, compare models, and preserve an evaluation that can be repeated.
- [Genomics and sequence analysis](https://www.openscience.sh/docs/genomics): Work from reference records through read, variant, annotation, and single-cell inspection.
- [Molecular and structural research](https://www.openscience.sh/docs/molecular-research): Inspect molecules and structures, calculate properties, and prepare supported scientific workflows.
- [Reproduce a result](https://www.openscience.sh/docs/reproduction): Turn a paper or repository into a bounded experiment with explicit success criteria.
- [Experiment plans and evidence](https://www.openscience.sh/docs/experiment-tracking): Keep the objective, planned checks, trial outcomes, and lessons tied to concrete research outputs.

## Communicate results

- [Scientific figures and visualization](https://www.openscience.sh/docs/figures): Turn data into clear plots with inspectable code, captions, and export checks.
- [Figures and writing](https://www.openscience.sh/docs/writing): Turn checked analysis into figures, methods, and research documents.
- [Generate and edit images](https://www.openscience.sh/docs/image-generation): Create illustrations and revise existing images while keeping the outputs in your project.

## Run substantial work

- [Compute](https://www.openscience.sh/docs/compute): Prepare analysis tools and connect your own resources for larger experiments.
- [Compute jobs and output recovery](https://www.openscience.sh/docs/jobs): Plan a run, launch it on an available target, follow status, and retrieve its outputs.
- [Remote compute and GPU accounts](https://www.openscience.sh/docs/remote-compute): Connect your own Modal account or SSH host and understand other compute-account connections.
- [Autoresearch](https://www.openscience.sh/docs/autoresearch): Let a study hill-climb a metric over many runs while you watch: tracked metrics, a baseline, ideas ranked by expected value, and a ledger of what was kept.

## Find a tool

- [Explore tools](https://www.openscience.sh/docs/explore-tools): Browse research tools, scientific software, databases, and connected services, with setup and usage guides.
- [Built-in research tools](https://www.openscience.sh/docs/built-in-tools): See the operations available to the agent and learn how to request useful, checkable work.
- [Scientific tool catalog](https://www.openscience.sh/docs/tool-catalog): Every scientific catalog entry, with a purpose, documentation link, and setup or availability details.
- [Scientific tools](https://www.openscience.sh/docs/scientific-tools): Check which analysis tools can run and what setup they need.

## Data and viewers

- [Scientific databases](https://www.openscience.sh/docs/databases): Find the scientific records and literature sources available to the agent.
- [Tables and datasets](https://www.openscience.sh/docs/tables): Inspect columns, filter and sort rows, explore distributions, and export a useful subset.
- [Scientific viewers](https://www.openscience.sh/docs/scientific-viewers): Explore structures, sequences, genomic files, and scientific datasets in the workspace.

## Connect and extend

- [Connectors and MCP](https://www.openscience.sh/docs/connectors): Add external tools and services to your research workflow.
- [Service credentials](https://www.openscience.sh/docs/service-credentials): Connect your own research services and distinguish saved access from a working integration.
- [Create a custom tool](https://www.openscience.sh/docs/custom-tools): Add a small typed operation that the agent can call from a project.

## Use skills

- [Skills](https://www.openscience.sh/docs/skills): Use reusable research procedures and add your own.
- [Skill directory](https://www.openscience.sh/docs/skill-library): Browse the research procedures included with this documentation version.
- [Skill recipes](https://www.openscience.sh/docs/skill-workflows): Choose a reusable procedure, provide the right input, and ask for a concrete deliverable.

## Project setup

- [Project instructions](https://www.openscience.sh/docs/instructions): Teach OpenScience the conventions, methods, and limits of a project.
- [Configuration](https://www.openscience.sh/docs/configuration): Save repeatable model, instruction, skill, and tool settings.
- [Slash commands](https://www.openscience.sh/docs/slash-commands): Use conversation controls and define reusable project requests.
- [Permissions and control](https://www.openscience.sh/docs/permissions): Choose when the agent asks and review consequential actions before they happen.

## CLI and integrations

- [CLI reference](https://www.openscience.sh/docs/commands): Commands for setup, research, models, accounts, sessions, and extensions.
- [Automation and JSON output](https://www.openscience.sh/docs/automation): Run repeatable terminal tasks and consume their results programmatically.
- [Runtime SDK and API](https://www.openscience.sh/docs/api): Build a scientific assistant against the same runtime used by the OpenScience workbench.
- [Headless server hosting](https://www.openscience.sh/docs/server-hosting): Connect to, own, and build an OpenScience runtime without the browser workbench.
- [Plugins, SDK, and editors](https://www.openscience.sh/docs/extensions): Extend OpenScience or connect it to your own application.