# Biocompile documentation

> How to use Biocompile, the research workspace for life-science R&D teams: projects, the assistant, files and data, skills, and organization security, explained task by task.

Every page below is Markdown; the same page for people is at the same address without `.md`. All pages in one file: https://www.biocompile.com/llms-full.txt. Site overview: https://www.biocompile.com/llms.txt.

## Get started

What Biocompile is and how to reach a first answer from your own files.

- [What is Biocompile? AI research workspace for life sciences](https://www.biocompile.com/docs/introduction.md): Biocompile is an AI research workspace for life-science R&D where you ask your lab files and the literature, run Python and R analyses and keep decisions.
- [Quick start: your first answer from your own lab data](https://www.biocompile.com/docs/quick-start.md): Create a Biocompile project, ask the AI research assistant about a plate-reader CSV, check the Python code behind the answer and keep the result on the project.

## Projects and assistant

Keep a line of research on a project, ask questions, run analyses and turn results into project records.

- [Research projects: hypotheses, evidence and decisions](https://www.biocompile.com/docs/projects.md): Organize a line of research as a Biocompile project, with hypotheses and the evidence for and against them, experiments, plans, reports and contributions.
- [Electronic lab notebook: experiments, protocols and e-signatures](https://www.biocompile.com/docs/electronic-lab-notebook.md): Record experiments, reuse versioned protocols and collect e-signatures in Biocompile's electronic lab notebook, with every approval step kept in the audit log.
- [AI research assistant: ask your files and the literature](https://www.biocompile.com/docs/ai-research-assistant.md): Biocompile's AI research assistant searches PubMed and bioRxiv, reads your CSV, FASTA and PDF files, runs Python and R code and proposes project changes.
- [Agent profiles: persona, skills and memory for the assistant](https://www.biocompile.com/docs/agent-profiles.md): Biocompile agent profiles set how the assistant behaves, which skills and executables it may use, and which memories it keeps between conversations.
- [Research reports: save cited findings and build on them](https://www.biocompile.com/docs/research-reports.md): Write conclusion reports on a Biocompile project in Markdown, link the literature, hypotheses and experiments they cite, and give them a report template.
- [Literature and database search: papers, patents and sequence records](https://www.biocompile.com/docs/literature-and-database-search.md): Biocompile's assistant searches OpenAlex, Semantic Scholar, patents and the web, queries NCBI, Ensembl and ENA, and stores papers you can read and cite.
- [Agent Skills: scientific workflows for the AI assistant](https://www.biocompile.com/docs/skills.md): Agent Skills give the Biocompile assistant written guides for PubMed, UniProt, Ensembl, PDB, BLAST and RNA-seq work, and let your organization add its own.
- [Why AI models decline biology questions, and what to do](https://www.biocompile.com/docs/model-declines.md): Why an AI model in Biocompile may decline a question about pathogens or toxins, how to rephrase it as a safe scientific task, and when another model fits.

## Files and data

Bring files in, preview them and work with tables and workbooks.

- [Knowledge Atlas: upload, preview and edit lab files](https://www.biocompile.com/docs/knowledge-atlas.md): Upload lab files to Biocompile's Knowledge Atlas, preview FASTA, FASTQ, VCF, CSV, Excel and PDF in the browser, and edit tables and workbooks online.

## Organizations and security

Control which models, tools and destinations your organization may use.

- [Organization security: AI models, tools and EU processing](https://www.biocompile.com/docs/organization-security.md): Choose which AI models, research tools and outside services your Biocompile organization may use, keep AI processing in the EU and preview every policy change.
- [Organization members: invitations, roles and teams](https://www.biocompile.com/docs/organization-members.md): Invite colleagues to your Biocompile organization by email, set Owner, Admin or Member roles, restrict email domains, manage teams and transfer ownership.

## Get access to Biocompile

Biocompile is used in the browser at https://app.biocompile.com. It is free to start and no payment method is required: sign up at https://app.biocompile.com/signup?mc_cta=docs-md&mc_path=/docs/index.md. If your team already uses Biocompile, ask an organization admin to invite you. Research teams that want hands-on setup can apply for the founder-led pilot at https://www.biocompile.com/pilot/. Questions: https://www.biocompile.com/contact/.