138 research tools.One local workspace.
An agent-native research operating system. From database queries to grant proposal writing, statistical analysis, and manuscript reformatting — run your entire research lifecycle locally on your laptop.
Other researchers spend 40 hours per week on everything except research.
Research tools have not kept pace with the needs of modern workflows. The administrative overhead of compiling, formatting, and complying takes hours away from actual discovery.
Literature Review Exhaustion
3-4 Days of PubMed Scrolling
Researchers spend up to 40 hours per week doing manual literature searches, deduplicating databases, and formatting bibliographies. In the era of AI-accelerated publishing, keeping up is a full-time administrative burden.
Cloud AI Violates Governance
Legal Departments Block Cloud Tools
Standard web-based LLMs send genomic, clinical, and biobank datasets to third-party cloud servers. Because this creates massive data leak risks, university compliance boards and IRBs ban cloud AI for sensitive datasets.
The Citation Manager Collapse
Mendeley Just Crashed Your Thesis
PhD students and senior researchers know the terror of Word reference plug-ins crashing. Reference field codes get corrupted overnight, requiring days of manual formatting to repair.
An AI workspace built for
how researchers actually work.
Buy Back Your Time
Instead of spending days formatting manuscripts and searching databases, delegate these tasks to background agents. Nexus runs parallel queries, deduplicates hits, and reformats bibliographies while you focus on the science.
Legal Clearance, Shipped Standard
Because Nexus runs entirely locally on your machine, your data never syncs to multi-tenant cloud databases. Fulfills GDPR, HIPAA, and UK Biobank compliance governance criteria by design.
Zero Subscriptions Per Tool
Access specialized engines for NIH/NSF grant proposal writing, KaTeX math blocks, BibTeX citation managers, statistical analysis pipelines, and Opentrons lab automations on day one. No plugins required.
Support the entire
research lifecycle.
Systematic Lit Reviews
Run parallel queries across PubMed, arXiv, Semantic Scholar, and bioRxiv. Nexus uses the PICO framework to deduplicate and filter hits, producing verified PRISMA schematics in minutes.
Grant Proposal Assistant
Pre-loaded with templates for NIH (R01/R21), NSF (broader impacts), DARPA (heilmeyer catechism), and Taiwan NSTC specifications to format compliant documents.
Citation Manager
Ditch crash-prone browser plugins. Nexus manages Reference BibTeX structures natively, syncing with Zotero/Obsidian folders and formatting inline KaTeX references without lags.
Manuscript Reformatting
Instantly adjust draft structures to match targeted journal guidelines. Reformat references, citation styles (e.g. Nature to APA), and adjust abstract word count layout in 8 minutes.
Peer Review Responder
Ingest critiques from Reviewer 2. Nexus strips emotional hostility, extracts actionable modifications, creates a checklist of tasks, and drafts polite responses automatically.
Research Visualizations
Convert Python/R scripts into validated SVG Mermaid workflows, KaTeX math blocks, and publication-ready graphs directly inside your local workspace.
Three steps.
Infinite possibilities.
1// ~/.nexus-agent/config.json2{3 "storage": "local-encrypted",4 "encryption": "AES-256-GCM",5 "vault": "./credentials.enc",6 "cloudSync": false7}
Local-first
by design.
Standard cloud AI tools send your datasets to multi-tenant servers, violating clinical data governance policies. Nexus runs completely locally on your hardware. Fulfills institutional security requirements out of the box.
Why not just use ChatGPT?
ChatGPT is a general-purpose chat interface. Nexus is an agent-native research operating system built for research precision and data security.
| Capability | ChatGPT / Claude | Elicit / Research Rabbit | Mendeley / Zotero | Nexus |
|---|---|---|---|---|
| 100% Local (Data never leaves your machine) | Cloud-only | Cloud-only | Partial | 100% Local |
| University Legal Approval (GDPR/HIPAA) | Blocked | Blocked | Partial | Designed for this |
| Systematic Literature Review Engine | Generic prompt | Partial | No | 700-line PICO engine |
| Grant Writing (NIH/NSF/DARPA Formats) | Generic draft | No | No | Pre-loaded templates |
| Citation Management (No plug-ins) | No | No | Plug-in crashes | Agent-native integration |
| Lab Integrations (Benchling, Opentrons) | No | No | No | 9 native integrations |
| Immutable Session Audit Trail | No | No | No | JSONL Transcripts |
Works with everything
you already use.
200+ pre-built integrations. Connect your entire stack in minutes.
Automate your lab.
While you sleep.
Define scheduled routines, configure local safety parameters, and hook agent outcomes straight to Slack, Discord, or Telegram supergroups.
Cron automation
Schedule literature reviews or dataset pre-processing overnight.
Custom safety rules
Lock down specific directories and forbid destructive shell commands.
Slack & Telegram
Get DMs the exact second your agent finishes a pipeline or escalates permissions.
Extended thinking
Give agents up to 100,000 reasoning tokens for complex research validation.
{"cron": "0 8 * * 1-5","timezone": "America/New_York","actions": [{"type": "prompt","prompt": "Run @literature-review on CRISPR gene therapies in bioRxiv"}]}
Consolidate your stack.
Keep the budget.
Instead of paying for multiple isolated research tool subscriptions, download Nexus. We ship with 138 research skills pre-loaded right on your machine, saving you both budget and context-switching overhead.
Performance you
can measure.
"I used to spend 8 hours doing a literature review. The first time I used Nexus's literature-review skill, the PRISMA diagram was generated automatically. I didn't even know what to do with the time I got back."
Dr. Sarah Chen
Postdoctoral Researcher, Zenith Medical Institute
Recovered 15-20 hours/week
Designed to support research standards at institutions worldwide
One platform.
No subscriptions.
Nexus runs entirely on your local machine. No subscriptions, no tiers, no hidden fees.
Nexus Workspace
Local-first research operating system
- 138 pre-loaded research tools (literature-review, grant-grants, peer-review, citation-management)
- 100% local-first data isolation (GDPR & HIPAA compliant, no data leaves your machine)
- Explore (Safe) Mode with visual diff staging for all file system and tool executions
- Model-agnostic local design: connect standard upstream LLM keys (OpenAI, Anthropic, Gemini, OpenRouter)
- Event-driven automation engine: schedule nightly workflows with 13 custom tool and lifecycle hooks
- Eyes on the Web: controlled Chromium browser automation for data entry, form submissions, and Google Sheets
- Parallel agent workflows: spin up secondary AI instances to process 15+ papers simultaneously
- Immutable session transcripts (JSONL logs) for ultimate research reproducibility and security
- Direct lab integration bridges: Benchling, Opentrons, DNAnexus, protocols.io, and OMERO
- Built-in robust Markdown ELN + TipTap rich text canvas supporting KaTeX formulas and Mermaid SVGs
* Nexus is 100% free to download and use locally. All data resides on your machine. There is no cloud storage or multi-tenant database. The only cloud connectivity is when you choose to connect the client to AI language models. You can either use your own API keys (OpenAI, Anthropic, Gemini, OpenRouter) or connect through our optional local AI gateway at cost, billed exactly at upstream provider rates with zero markup.
Frequently Asked Questions
Everything you need to know about Nexus privacy, setup, and usability in your lab.
Ready to recover
your research time?
Join thousands of scientists recovering 15–20 hours per week from literature reviews, citation formatting, and grant drafting. Keep your research local, private, and yours.
100% Local • Free Local-First Client • No registration required