Electronic Lab Notebook
Cypher AI ELN
A living record of every experiment: searchable and audit-ready.
The ELN is on every plan, including Free.
format_color_fillfunctions=ROUND(FORECAST.LINEAR(C8,$B$2:$B$7,$C$2:$C$7),0)titledownloaddeleteProtein (Bradford)
Coomassie reagent, 5 min at room temperature, read at 595 nm. Lysates diluted 1:20 in 50 mM Tris-HCl, pH 7.5.
| Sample | BSA (µg/mL) | A595 | Protein (µg/mL) |
| Std 1 | 0 | 0.412 | |
| Std 2 | 125 | 0.519 | |
| Std 3 | 250 | 0.614 | |
| Std 4 | 500 | 0.801 | |
| Std 5 | 750 | 0.968 | |
| Std 6 | 1000 | 1.117 | |
| V1 lysate | 0.702 | 386 | |
| V2 lysate | 0.688 | 366 | |
| V3 lysate | 0.731 | 427 | |
| V4 lysate | 0.664 | 332 | |
| V5 lysate | 0.623 | 274 | |
| V6 lysate | 0.695 | 376 | |
| V7 lysate | 0.719 | 410 | |
| V8 lysate | 0.676 | 349 | |
| R² | 0.9969 |
What you get
What every notebook entry includes with Cypher AI.
Cypher AI ELN keeps the whole experiment in one place, connected to your samples, protocols and the agent.
The problem
Most lab records are split across paper, Word files and spreadsheets.
See it workCore
Notes, tables, protocols and samples in one entry.
One entry, an enzyme screen of eight BVMO variants, in the app's own screens. None of these tabs uses the agent.
Objective
Compare NADPH depletion rates of eight BVMO variants (V1–V8) on the plate 3 substrate.
Samples
Clarified lysates, expressed in BL21(DE3) on Sep 21: scienceV1 lysate scienceV2 lysate scienceV3 lysate scienceV4 lysate scienceV5 lysate scienceV6 lysate scienceV7 lysate scienceV8 lysate
Plate layout
/96
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | |
| A | V1 | V1 | V1 | |||||||||
| B | V2 | V2 | V2 | |||||||||
| C | V3 | V3 | V3 | |||||||||
| D | V4 | V4 | V4 | |||||||||
| E | V5 | V5 | V5 | |||||||||
| F | V6 | V6 | V6 | |||||||||
| G | V7 | V7 | V7 | |||||||||
| H | V8 | V8 | V8 |
format_color_fillswap_horizview_columnfit_screentext_decreasetext_increasefunctions=SUM(B2:B7)=ROUND(FORECAST.LINEAR(C8,$B$2:$B$7,$C$2:$C$7),0)=ROUND(RSQ(B2:B7,C2:C7),4)titledownloaddeleteProtein (Bradford)
Coomassie reagent, 5 min at room temperature, read at 595 nm. Lysates diluted 1:20 in 50 mM Tris-HCl, pH 7.5.
| Sample | BSA (µg/mL) | A595 | Protein (µg/mL) |
| Std 1 | 0 | 0.412 | |
| Std 2 | 125 | 0.519 | |
| Std 3 | 250 | 0.614 | |
| Std 4 | 500 | 0.801 | |
| Std 5 | 750 | 0.968 | |
| Std 6 | 1000 | 1.117 | |
| V1 lysate | 0.702 | 386 | |
| V2 lysate | 0.688 | 366 | |
| V3 lysate | 0.731 | 427 | |
| V4 lysate | 0.664 | 332 | |
| V5 lysate | 0.623 | 274 | |
| V6 lysate | 0.695 | 376 | |
| V7 lysate | 0.719 | 410 | |
| V8 lysate | 0.676 | 349 | |
| R² | 0.9969 |
Objective
Compare NADPH depletion rates of eight BVMO variants (V1–V8) on the plate 3 substrate.
Samples
Clarified lysates, expressed in BL21(DE3) on Sep 21: scienceV1 lysate scienceV2 lysate scienceV3 lysate scienceV4 lysate scienceV5 lysate scienceV6 lysate scienceV7 lysate scienceV8 lysate
Assay
NADPH depletion assay (340 nm)
Initial-rate assay for NADPH-dependent monooxygenases, 200 µL per well.
Consumables
- NADPH (200 µM final) - made fresh, kept on ice
- Substrate, 50 mM in DMSO (1 mM final)
- 96-well plate, clear flat bottom
Equipment
- Plate reader (absorbance) - 340 nm, 30 °C
Steps
- Pre-warm: Set the reader to 30 °C and warm the master mix.
- play_arrowaccess_time10m 0srestart_altsettingsclosepauseaccess_time10m 0spausesettingsclosepauseaccess_time9m 59spausesettingsclosepauseaccess_time9m 58spausesettingsclosepauseaccess_time9m 57spausesettingsclosepauseaccess_time9m 56spausesettingsclosepauseaccess_time9m 55spausesettingsclosepauseaccess_time9m 54spausesettingsclosepauseaccess_time9m 53spausesettingsclosepauseaccess_time9m 52spausesettingsclosepauseaccess_time9m 51spausesettingsclose
- Dilute lysates: Dilute each lysate 1:1000 in 50 mM Tris-HCl, pH 7.5.
- ⚠️ Warning: Use diluted lysate within 30 min; keep it on ice until then.
- Start and read: Add 150 µL master mix and 50 µL diluted lysate per well. Read A340 every 30 s for 20 min.
- play_arrowaccess_time20m 0srestart_altsettingsclose
Insert Protocol
close| Name | Description | Version | Created By | Created | |
|---|---|---|---|---|---|
| NADPH depletion assay (340 nm) | Initial-rate assay for NADPH-dependent monooxygenases, 200 µL per well | v3 | Michael Taylor | Aug 14, 2026 | |
| Bradford protein assay | Coomassie microplate assay with BSA standards | v2 | Jamie Cho | Jun 3, 2026 | |
| BL21(DE3) expression, 0.5 mM IPTG | Starter culture, induction at OD600 0.6, harvest | v5 | Yaoyu Yang | May 19, 2026 | |
| Lysate clarification by sonication | 10 s on, 20 s off on ice; spin 20 min at 16,000 × g | v1 | Michael Taylor | Sep 2, 2026 |
Objective
Compare NADPH depletion rates of eight BVMO variants (V1–V8) on the plate 3 substrate.
Samples
Clarified lysates, expressed in BL21(DE3) on Sep 21: /Insert sample SPL-0412ProtocolWidgetAI ChatEmbed FileLink to FileBullet ListSPL-0412, SPL-0413, SPL-0414, SPL-0415, SPL-0416, SPL-0417, SPL-0418, SPL-0419
Clarified lysates, expressed in BL21(DE3) on Sep 21: scienceV1 lysate, SPL-0413, SPL-0414, SPL-0415, SPL-0416, SPL-0417, SPL-0418, SPL-0419
Clarified lysates, expressed in BL21(DE3) on Sep 21: scienceV1 lysate, scienceV2 lysate, SPL-0414, SPL-0415, SPL-0416, SPL-0417, SPL-0418, SPL-0419
Clarified lysates, expressed in BL21(DE3) on Sep 21: scienceV1 lysate, scienceV2 lysate, scienceV3 lysate, SPL-0415, SPL-0416, SPL-0417, SPL-0418, SPL-0419
Clarified lysates, expressed in BL21(DE3) on Sep 21: scienceV1 lysate, scienceV2 lysate, scienceV3 lysate, scienceV4 lysate, SPL-0416, SPL-0417, SPL-0418, SPL-0419
Clarified lysates, expressed in BL21(DE3) on Sep 21: scienceV1 lysate, scienceV2 lysate, scienceV3 lysate, scienceV4 lysate, scienceV5 lysate, SPL-0417, SPL-0418, SPL-0419
Clarified lysates, expressed in BL21(DE3) on Sep 21: scienceV1 lysate, scienceV2 lysate, scienceV3 lysate, scienceV4 lysate, scienceV5 lysate, scienceV6 lysate, SPL-0418, SPL-0419
Clarified lysates, expressed in BL21(DE3) on Sep 21: scienceV1 lysate, scienceV2 lysate, scienceV3 lysate, scienceV4 lysate, scienceV5 lysate, scienceV6 lysate, scienceV7 lysate, SPL-0419
Clarified lysates, expressed in BL21(DE3) on Sep 21: scienceV1 lysate, scienceV2 lysate, scienceV3 lysate, scienceV4 lysate, scienceV5 lysate, scienceV6 lysate, scienceV7 lysate, scienceV8 lysate
Clarified lysates, expressed in BL21(DE3) on Sep 21: scienceV1 lysate (SPL-0412), scienceV2 lysate (SPL-0413), scienceV3 lysate (SPL-0414), scienceV4 lysate (SPL-0415), scienceV5 lysate (SPL-0416), scienceV6 lysate (SPL-0417), scienceV7 lysate (SPL-0418), scienceV8 lysate (SPL-0419)
Plate layout
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | |
| A | V1 | V1 | V1 | |||||||||
| B | V2 | V2 | V2 | |||||||||
| C | V3 | V3 | V3 | |||||||||
| D | V4 | V4 | V4 | |||||||||
| E | V5 | V5 | V5 | |||||||||
| F | V6 | V6 | V6 | |||||||||
| G | V7 | V7 | V7 | |||||||||
| H | V8 | V8 | V8 |
Objective
Compare NADPH depletion rates of eight BVMO variants (V1–V8) on the plate 3 substrate.
Samples
Clarified lysates, expressed in BL21(DE3) on Sep 21: scienceV1 lysate scienceV2 lysate scienceV3 lysate scienceV4 lysate scienceV5 lysate scienceV6 lysate scienceV7 lysate scienceV8 lysate
Initial rates
Slopes of A340 over the first 5 min, one well each, 30 °C. Mean and SD are table formulas.
| Variant | Rep 1 | Rep 2 | Rep 3 | Mean | SD |
| V1 | 21.6 | 21.1 | 22.3 | 21.7 | 0.6 |
| V2 | 18.9 | 19.4 | 18.2 | 18.8 | 0.6 |
| V3 | 41.2 | 40.6 | 42.1 | 41.3 | 0.75 |
| V4 | 16.3 | 15.8 | 16.9 | 16.3 | 0.55 |
| V5 | 7.9 | 5.1 | 8.2 | 7.1 | 1.71 |
| V6 | 20.1 | 20.8 | 19.6 | 20.2 | 0.6 |
| V7 | 38.9 | 37.8 | 39.2 | 38.6 | 0.74 |
| V8 | 14.4 | 13.9 | 14.8 | 14.4 | 0.45 |
Request Review to Complete Notebook Entry
Objective
Compare NADPH depletion rates of eight BVMO variants (V1–V8) on the plate 3 substrate.
Samples
Clarified lysates, expressed in BL21(DE3) on Sep 21: scienceV1 lysate scienceV2 lysate scienceV3 lysate scienceV4 lysate scienceV5 lysate scienceV6 lysate scienceV7 lysate scienceV8 lysate
Initial rates
Slopes of A340 over the first 5 min, one well each, 30 °C. Mean and SD are table formulas.
| Variant | Rep 1 | Rep 2 | Rep 3 | Mean | SD |
| V1 | 21.6 | 21.1 | 22.3 | 21.7 | 0.6 |
| V2 | 18.9 | 19.4 | 18.2 | 18.8 | 0.6 |
| V3 | 41.2 | 40.6 | 42.1 | 41.3 | 0.75 |
| V4 | 16.3 | 15.8 | 16.9 | 16.3 | 0.55 |
| V5 | 7.9 | 5.1 | 8.2 | 7.1 | 1.71 |
| V6 | 20.1 | 20.8 | 19.6 | 20.2 | 0.6 |
| V7 | 38.9 | 37.8 | 39.2 | 38.6 | 0.74 |
| V8 | 14.4 | 13.9 | 14.8 | 14.4 | 0.45 |
Review Signature Request
- Pages as tabs, with a table of contents
- Formulas in any notes table
- Protocols copied in, timers included
- Samples linked to LIMS
Workflow
From plan to signed record.
The same entry, from plan to sign-off, as four steps.
- Plan the experimentStart from a protocol or a template, and link the samples you'll use.
- Run and captureFill in tables, attach instrument files and ask the chat to run the analysis.
- Review and signSend the entry for sign-off when the work is done.
- ReuseFind it later by what you wrote, or save it as the template for the next run.
The entryCore
One entry holds the plan, the numbers and the samples.
Samples link to LIMS, protocols come in with their timers, and the agent reads the whole entry before it proposes a change.
Objective
Compare NADPH depletion rates of eight BVMO variants (V1–V8) on the plate 3 substrate.
Samples
Clarified lysates, expressed in BL21(DE3) on Sep 21: 3scienceV1 lysate scienceV2 lysate scienceV3 lysate scienceV4 lysate scienceV5 lysate scienceV6 lysate scienceV7 lysate scienceV8 lysate
NADPH depletion assay (340 nm)
Initial-rate assay for NADPH-dependent monooxygenases, 200 µL per well.
Steps
- Pre-warm: Set the reader to 30 °C and warm the master mix.
- 4play_arrowaccess_time10m 0srestart_altsettingsclose
- Start and read: Add 150 µL master mix and 50 µL diluted lysate per well. Read A340 every 30 s for 20 min.
Here's the plan for the new plate. Nothing is written until you approve.
Enzyme screen plate 396-well-plate24A1, A2, A3 … H3 (24 wells)50 µL- Pages along the bottom.Split an entry into pages such as Setup, Protein and Rates. Headings build a table of contents.
- Insert what the work needs.Files, protocols, widgets, tables, plate layouts, structures, inline Python and timers.
- Samples link to LIMS.Type / before a sample ID such as SPL-0414 to link it to the sample record.
- Protocols in the page.A saved protocol lands with its steps, warnings and timers for this run.
- The agent works across all of it.The chat reads the entry, turns it into LIMS records, and shows you the plan to approve first.
Start the next run from a template.
Save an entry as a template with the files, protocols, widgets and dashboards it needs. Templates keep earlier versions you can restore.
Save as Template
Search the text inside every entry.
Search every entry by name, description, project, author or the text inside its notes. Each match shows where the words were found.
What an entry links to
- LIMS recordsSamples, containers, materials and workflows
- ProtocolsThe current version, copied into the page
- WidgetsYour team's analysis tools, run from the page
- FilesFrom your computer, Google Drive, S3 or Egnyte, with previews
Everything about the experiment stays in one record.
Review and sign-offCore
Sign-off, built into the entry.
With required signatures on, an entry completes only when its reviewers approve.
- Who asked, and why.The request shows who sent it, when, and the note they left for reviewers.
- Every reviewer's answer.Each reviewer sees the others' decisions. The entry completes only when every reviewer has approved.
- A written reason each time.A reviewer can't approve or reject without a comment, and the comment stays on the entry.
- Approve or reject.An approval counts toward completion. A rejection sends the entry back to In Progress, unlocked, once every reviewer has answered.
Review Signature Request
Set once by a team admin.
Turn on required signatures and choose how many reviewers must approve, from one to ten. The rule applies to every entry in the team, and an entry in review is locked.
Compliance Settings
Signatures are kept on the entry.
On a completed entry, the Collaborators list shows each reviewer marked Approved, with the comment they signed with.
Export the audit trail as a PDF. Beta
The PDF lists each signature request with every reviewer's decision, then every recorded change: who made it, when and what changed, including formula edits.
Status: completed
Report Generated: 9/22/2026, 5:02:11 PM
Status: APPROVED
Requested By: Michael Taylor (michael.taylor@example.org)
Requested At: 9/22/2026, 4:12:40 PM
Comment: Rates and Bradford for plate 3 are in. V5 rep 2 is low; see the note on Rates.
Reviewers:
1. Yaoyu Yang
Status: APPROVED
Signed At: 9/22/2026, 4:26:51 PM
Comment: Bradford curve and dilutions look right.
2. Jamie Cho
Status: APPROVED
Signed At: 9/22/2026, 4:31:08 PM
Completed At: 9/22/2026, 4:31:08 PM
By: Michael Taylor (michael.taylor@example.org)
Table formulas: added 9
Formulas added:
D8: =ROUND(FORECAST.LINEAR(C8,$B$2:$B$7,$C$2:$C$7),0) => 386By: Michael Taylor (michael.taylor@example.org)
Added text to notes
Notes tab: Rates
Text added:
"V5 rep 2 re-read at 3:40 PM: 5.1 mAU/min, unchanged."
Sign-off happens inside the record.
Part 11–style e-signature workflows and audit trails. Compliance depends on your validated process; talk to us about your assessment.
With the agentAI-assisted
The agent works from the entry you're in.
The notebook chat reads every page of the entry and any files you select. It answers in the chat, runs analyses, and asks before it writes to LIMS.
Initial rates
Slopes of A340 over the first 5 min, one well each, 30 °C. Mean and SD are table formulas.
| Variant | Rep 1 | Rep 2 | Rep 3 | Mean | SD |
| V1 | 21.6 | 21.1 | 22.3 | 21.7 | 0.6 |
| V2 | 18.9 | 19.4 | 18.2 | 18.8 | 0.6 |
| V3 | 41.2 | 40.6 | 42.1 | 41.3 | 0.75 |
| V4 | 16.3 | 15.8 | 16.9 | 16.3 | 0.55 |
| V5 | 7.9 | 5.1 | 8.2 | 7.1 | 1.71 |
| V6 | 20.1 | 20.8 | 19.6 | 20.2 | 0.6 |
| V7 | 38.9 | 37.8 | 39.2 | 38.6 | 0.74 |
| V8 | 14.4 | 13.9 | 14.8 | 14.4 | 0.45 |
Hello! I'm your Cypher Notebook Agent. I specialize in helping with experiment design, protocol optimization, scientific methodology, and research strategy. How can I assist you today?
Cypher is thinking...closeCancelFrom the Initial rates table: V3 (41.3 mAU/min, 1.9× V1) and V7 (38.6, 1.8×) are the only variants above 1.5×.
One replicate looks off. V5 rep 2 reads 5.1 against 7.9 and 8.2, which is why V5's SD (1.71) is about three times the others. It may be worth re-reading that well before you request review.
Cypher is thinking...closeCancelHere's a draft you can paste into Results:
Of eight BVMO variants screened on the plate 3 substrate, V3 and V7 depleted NADPH fastest (41.3 and 38.6 mAU/min, 1.9× and 1.8× V1). V5 was slowest (7.1 mAU/min), and one of its three wells should be re-read before these rates are used.
Initial rates
Slopes of A340 over the first 5 min, one well each, 30 °C. Mean and SD are table formulas.
| Variant | Rep 1 | Rep 2 | Rep 3 | Mean | SD |
| V1 | 21.6 | 21.1 | 22.3 | 21.7 | 0.6 |
| V2 | 18.9 | 19.4 | 18.2 | 18.8 | 0.6 |
| V3 | 41.2 | 40.6 | 42.1 | 41.3 | 0.75 |
| V4 | 16.3 | 15.8 | 16.9 | 16.3 | 0.55 |
| V5 | 7.9 | 5.1 | 8.2 | 7.1 | 1.71 |
| V6 | 20.1 | 20.8 | 19.6 | 20.2 | 0.6 |
| V7 | 38.9 | 37.8 | 39.2 | 38.6 | 0.74 |
| V8 | 14.4 | 13.9 | 14.8 | 14.4 | 0.45 |
Hello! I'm your Cypher Notebook Agent. I specialize in helping with experiment design, protocol optimization, scientific methodology, and research strategy. How can I assist you today?
6sFitted A340 over 0–5 min in all 24 wells. V3 and V7 are fastest; V5 is slowest, and its rep 2 fit is the weakest (R² 0.94). Per-well rates are in initial_rates.csv.
| Variant | Rate (mAU/min) | R² (0–5 min) |
|---|---|---|
| V3 | 41.3 | 0.998 |
| V7 | 38.6 | 0.998 |
| V5 | 7.1 | 0.981 |
Objective
Compare NADPH depletion rates of eight BVMO variants (V1–V8) on the plate 3 substrate.
Samples
Clarified lysates, expressed in BL21(DE3) on Sep 21: scienceV1 lysate scienceV2 lysate scienceV3 lysate scienceV4 lysate scienceV5 lysate scienceV6 lysate scienceV7 lysate scienceV8 lysate
Plate layout
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | |
| A | V1 | V1 | V1 | |||||||||
| B | V2 | V2 | V2 | |||||||||
| C | V3 | V3 | V3 | |||||||||
| D | V4 | V4 | V4 | |||||||||
| E | V5 | V5 | V5 | |||||||||
| F | V6 | V6 | V6 | |||||||||
| G | V7 | V7 | V7 | |||||||||
| H | V8 | V8 | V8 |
Hello! I'm your Cypher Notebook Agent. I specialize in helping with experiment design, protocol optimization, scientific methodology, and research strategy. How can I assist you today?
Cypher is thinking...closeCancelHere's the plan for the new plate. Nothing is written until you approve.
Enzyme screen plate 396-well-plate24A1, A2, A3 … H3 (24 wells)50 µL2sDone. "Enzyme screen plate 3" is in LIMS with 24 samples in A1–H3, 50 µL each.
- Reads every notes page, and the files you select
- Drafts text in the chat for you to copy in
- LIMS writes wait for Approve unless you switch to Auto
Also in the ELN
More ELN features.
Two ways in
Start on your own, or bring the whole lab.
Start free. Upgrade when the team joins.
- Free: the ELN, 15 AI messages a month, unlimited public projects
- Pro, $50 per user a month: unlimited AI messages
- Pro adds team features, more compute and 100 GB of storage
Your own deployment, set up with you.
- A dedicated deployment in your cloud account
- Data residency, SSO and custom data integrations
- A forward-deployed engineer and priority support
First steps
- Create a free accountSign up and open your first project. No setup or admin configuration needed to start writing.
- Write your first experimentCreate an experiment record, attach a file or two, and ask the AI agent to help structure the write-up.
- Invite your teamAdd collaborators when you're ready, and turn on signatures if your work needs a review trail.
Startups, academic and core labs: contact us for special pricing. Full plans are on the pricing page.
FAQ
Questions about the ELN.
What is the Cypher AI ELN?
The Cypher AI ELN is an electronic lab notebook where each entry holds one experiment: the plan, notes, tables with spreadsheet formulas, protocols, linked samples and files. It runs on the same platform as LIMS, analysis tools and AI agent, so entries connect to the samples and data behind them.
Is the Cypher ELN free?
Yes. The Cypher AI ELN is included on every plan, including the Free plan at $0 with 15 AI messages a month. It works on its own, and when a team adds the LIMS access on Pro, entries can link to its samples and containers.
Does the Cypher ELN support 21 CFR Part 11 workflows?
Cypher supports Part 11–style workflows: required electronic signatures, entries that lock during review, and a record of every change with who made it and when. Whether a process meets Part 11 depends on your own validation, so talk to Cypher about your assessment.
How does the AI agent work in the Cypher ELN?
The ELN's AI chat reads the entry you are in and the files you select. It drafts text, summarizes results and runs analyses, and drafts appear in the chat for you to copy into the entry. It can also turn an entry into LIMS samples and containers.
Can Cypher ELN entries link to samples?
Yes. On Pro and Enterprise, a Cypher ELN entry can link to LIMS samples and containers by their IDs. The agent can also read an entry and propose the samples it describes, which wait for your approval unless you switch the chat to Auto.
What happens to a Cypher ELN entry during review?
The entry locks. Its title, description and notes can't change while it is in review, though owners can still manage access, add files and comment. It stays locked after approval, and setting it back to In Progress reopens it and cancels the earlier approvals.
How do teams reuse past experiments in the Cypher ELN?
Teams save any entry as a template, so a new experiment starts with the same structure, notes and prompts. The ELN also searches the text of every entry, by name, description, project or author.