ELN to LIMSBeta
Cypher AI: from ELN entry to LIMS records, without retyping
Write the experiment once, in the ELN. The agent reads the entry, proposes the samples, plates and materials it describes, and writes them to the LIMS when you approve.
Syncing ELN entries to the LIMS is in Beta. The ELN is on every plan, including Free. The LIMS comes with Pro and Enterprise.
Compare NADPH depletion rates of eight BVMO variants (V1–V8) on the plate 3 substrate.
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
| 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.
The problem
Why does lab data get entered twice in most systems?
Because the experiment and the sample records usually live in different tools. A scientist writes up the plate in an ELN or on paper, then enters the same sample names, volumes and well positions again in a LIMS or a spreadsheet.
Each copy is a chance for the two to disagree. A volume corrected in the entry stays wrong in the inventory, and a reading in a spreadsheet can't point to the tube it came from. In Cypher AI the ELN and the LIMS share records, so the samples written into an entry become LIMS records, and each reading traces back to the sample it came from.
If your samples live in spreadsheets today, start with our guide on when to move from spreadsheets to a LIMS.
How it worksAI-assistedBeta
How does syncing the LIMS from a notebook work?
It hands the entry to the agent, which proposes one plan covering every record the entry describes. You approve the plan, or send it back with a note.
ELN entry
Enzyme screen, plate 3- Eight clarified lysates, V1 to V8
- Plate layout: three wells per lysate
- 50 µL of diluted lysate per well
Confirm plan · 1 change
Create 1 96-well plate with 24 samples- New container
- Plate 3
- Positions
- A1 to H3
- Inputs
- 8 lysates
RejectApprove
LIMS records
Plate 3, CTR-20260922-0007Each well traces back to its lysate. The plate and samples link to the entry.
- Start from the entryIn the ELN, choose File → Sync LIMS from Notebook. The agent opens with the request filled in, and you send it.
- The agent understands the entryIt works out what the entry describes and what's already in the LIMS, and asks you when something is unclear instead of guessing.
- You check one planA Confirm plan card lists every change: new plates and tubes, samples and their wells, materials, and the workflows, with the volume drawn from each source.
- Approve, or send it backApprove applies the whole plan. Reject it with a note, and the agent revises the plan and asks again.
What it creates
Which LIMS records can the agent create from an ELN entry?
Any of the record types the Cypher AI LIMS keeps, from what a material is to the readings on a plate. When you approve the plan, each new record gets its LIMS ID, such as SPL-20260922-0101 for a sample saved on September 22, 2026. Labels, lineage and results all point to that ID, so nobody has to make one up or type it.
| Record | What it holds | What the ELN entry says | What the agent does in the LIMS |
|---|---|---|---|
| Material | What a thing is: DNA, RNA, protein, cell, reagent or chemical. Reused across experiments. | "BVMO V3 expression plasmid" | Creates a DNA material, or links the one already in the LIMS. |
| Sample | An amount of a material, with its volume, location and metadata. | "V3 lysate, 1.2 mL" | Creates a sample of that material and tracks its volume. |
| Container | A tube, a rack, or a plate of 6 to 384 wells, with each sample in its position. | "Plate 3, columns 1 to 3" | Creates a 96-well plate and places 24 samples in their wells. |
| Workflow | The lab work done to samples, such as transfers, aliquots and dilutions, recorded as steps that keep the lineage. | "50 µL per well" | Records a workflow that draws 50 µL from each lysate and links each well to its source. |
| Readings | Measurements on wells, with their units, from an instrument file. | Plate reader export attached | Puts each reading on its well, with units. |
Samples and containers carry whatever metadata the assay needs, such as condition, timepoint or replicate, as named fields. Nothing has to be designed up front.
Other ways in
What else turns ELN content into LIMS records?
Syncing covers a whole entry. These routes work from the same entry, one piece at a time.
Under your control
Does the agent change records without asking?
No. In Ask mode, the default, every LIMS change waits for your approval. Each person can switch their agent to Auto, which applies LIMS changes straight away.
- One card shows the whole plan. New records, the volume drawn from each source, and the positions on each plate, before anything is saved.
- Warnings come before the save. For example, if every sample would land in one container when you meant one tube each, the card says so.
- The ELN entry stays yours. The agent drafts text for you to copy into the entry. The records it writes are LIMS records.
- Changes are logged. The LIMS logs who changed each record and when, and workflows the agent writes are recorded as the agent's, with the model it used.
- Complex entries can take a second pass. When several inputs pool into one output, check the plan closely. If it's wrong, reject it with a note and the agent revises it.
After the sync
What does using LIMS records make possible?
Results trace back to the source. Each sample page shows its lineage, its readings, its change history and the ELN entries it appears in.
Analyses rerun on the next plate. Because the readings sit on the right wells, an analysis widget can read the plate directly and run again on plate 4 with no reformatting.
Orders start from the same samples. A Marketplace order records the project, the ELN entry and the LIMS samples it was created from.
New entries can point back to them. Drop an existing sample, material or request into any ELN entry by its ID, or add a workflow to show where its samples came from.
Get started
How do you start syncing ELN entries to the LIMS?
First steps
- Write an entryCreate a free account and record your next experiment in the ELN. Free includes 15 AI messages a month.
- Turn on Pro for the teamThe LIMS comes with Pro. Startups can apply to the Startup Program for 90 days free.
- Sync your first entryChoose File → Sync LIMS from Notebook and approve the plan. Book a free 15-minute onboarding call if you want a walkthrough.
Need it in your own cloud account? Cypher AI Enterprise is a dedicated deployment, set up with you.
FAQ
Questions about ELN to LIMS in Cypher AI.
What is AI sample management in an ELN?
It means the ELN's agent turns what you write about samples into structured LIMS records, so nobody re-enters them. In Cypher AI, the agent reads an ELN entry, proposes the materials, samples, plates, workflows and readings it describes, and saves them to the LIMS when you approve.
Can I undo records the agent created from an ELN entry?
Yes, for samples. Deleting a sample in the Cypher AI LIMS is a soft delete, so the agent can restore it later. Deleting and restoring both need your approval, like any other LIMS change.
Which Cypher AI plan includes syncing ELN entries to the LIMS?
The ELN is on every Cypher AI plan, including Free. Turning entries into LIMS records needs the LIMS, which comes with Pro at $100 per user a month and with Enterprise, from $25K per year.
Does syncing an ELN entry duplicate samples that already exist?
The agent checks which materials, containers and samples the entry mentions are already in the LIMS before it proposes anything, and proposes new records only for what's missing. The plan marks which containers are new and which already exist.
What happens if the ELN entry is unclear?
The agent asks before it proposes anything it can't tell from the entry, such as which stock a sample was drawn from. If the plan still isn't right, reject it with a note and the agent revises it.
Can I see which ELN entry a sample came from?
Yes. Records the agent creates from an entry are linked to it, and each sample, material and request page lists its entries under Linked Notebooks.
How is this different from an ELN with a sample inventory?
An inventory lists what is in the freezer. The Cypher AI LIMS also records the work: which sample was drawn from which, how much was used, and what each well read. Because the ELN and LIMS share records, the entry, the samples and the results point to each other.