Product Overview

A Secure Operating System for Your Knowledge Assets

Think of CERF as a secure, access-controlled operating system for your organization's most valuable knowledge assets: experimental data, research records, SOPs, image files, and intellectual property. CERF manages all of it — in one place, with a complete audit trail that meticulously records all activity and keeps your data, documents and access history safe and searchable forever.

Built and supported by Lab-Ally LLC in Columbus, Ohio, CERF has been trusted by pharmaceutical labs, government labs, histopathology facilities, CROs, and GLP/GMP-regulated organizations for nearly 20 years. CERF runs as a client-server system: a central CERF server holds all data and the secure file store; lightweight desktop clients connect from Windows, Mac, or Linux workstations on your network or remotely.

The CERF database is remarkably lightweight — rarely exceeding 10 GB even after years of active use — while the data files themselves are stored in native format in a secure file store. Nothing is compressed into a proprietary container from which recovery could be difficult.

CERF replaces the fragmented, non-compliant tools most labs rely on today — SharePoint, shared drives, email attachments, Dropbox, Google Drive, and paper notebooks — with a single, compliant, centrally managed system that your organization can depend on for decades.

CERF ELN round-trip editing workflow diagram — check out, edit natively, check in with version history

Designed For

Who Is CERF ELN For?

CERF is designed for any organization where data integrity, long-term accessibility, regulatory compliance, intellectual property protection, and data sovereignty matter.

Pharma & Biotech

GLP, GxP, and 21 CFR Part 11 compliant pre-clinical and discovery research environments that need a complete, auditable record of every experiment.

Histopathology Labs

Compliant management of whole slide images, staining protocols, tissue metadata, adjustment histories, and multi-study records in a single searchable system.

Contract Research Organizations

Multi-client, multi-study data isolation with granular sponsor access controls, audit-ready records, and flexible workgroup architecture.

Medical Device Makers

Design history files, verification records, and regulatory submission documentation managed in a system that enforces version control and sign-off workflows.

Academic Research Groups

Flexible collaboration, IP protection, patent support, and principal investigator oversight across careers and projects spanning decades.

Chemistry & Materials Labs

Chemical structure management, automated CML metadata extraction, structural search, and stoichiometric table tools — all within a compliant data repository.

QA / Regulatory Teams

SOP lifecycle management, enforced acknowledgment workflows, training records, and single-click inspection-ready audit exports.

Any Regulated Organization

Replace SharePoint, shared drives, or ad-hoc file systems with a compliant, validated alternative — including financial, legal, and other document-intensive organizations where long-term record integrity matters.

The Problem CERF Solves

Most Labs Are One Audit Away From a Crisis

Most research organizations manage their data across a patchwork of tools that were never designed to work together with regulatory compliance or secure collaboration in mind.

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Fragmented, Non-Compliant Tools

Critical documents lack version control. Shared drives provide no audit trail and poor search options. Expensive customizations designed to add 21 CFR Part 11 compliance to off-the-shelf tools frequently fail validations — leaving labs exposed exactly when it matters most.

CERF enforces compliance automatically — not as an add-on, but as the core architecture of the system.

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Data That's Hard to Find and Impossible to Trust

Years of accumulated data spread across drives, inboxes, and lab notebooks makes retrieval slow and provenance uncertain. When IP ownership is challenged or regulators arrive, the inability to produce a complete, timestamped record of who did what and when is a serious liability.

CERF's immutable, computer-generated audit trail captures every action. Every record, forever.

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Collaboration Without Security

Hybrid organizations with on-site and remote employees find it impossible to collaborate securely. Managers cannot determine who is working on what. Sponsor data bleeds across project boundaries. Access controls are either too loose — or so complex they are simply ignored.

CERF's workgroup architecture supports both open collaboration and strict data isolation, at any scale.

Core Capabilities

Nine Capabilities. One Compliant System.

CERF replaces an entire ecosystem of disconnected tools — ELN, EDMS, LIS, SDMS — with a single, purpose-built platform that enforces compliance automatically.

Electronic Lab Notebook

The daily home for your scientists' experimental work. CERF supports text, tables, image grids, audio recordings, drawings, MS Office documents, and files in any format — all stored with full version history, rich metadata, unique identifiers, and traceable relationships.

Inline file preview — View Word, Excel, PDF, images, chemistry structures, sequence files, and specialist formats directly within a notebook page.
Round-trip editing — Check out any file to your preferred desktop app, edit normally, check back in. Every prior version is permanently preserved.
Notebook templates — Intelligent placeholders ensure a record is structurally complete before it can be signed.
Offline working — Check out files before travel or disconnected work; check back in when reconnected.

Document & File Management

A secure, organized, version-controlled home for every file your organization generates. Drag and drop individual files or entire nested folder trees directly into CERF, with automatic metadata extraction and search indexing.

Universal file support — Stores, indexes, and previews any file type including microscopy images, sequence files, chemistry structures, and instrument data.
Permanent version history — No version of any file is ever deleted in CERF.
Network file links — Link to large files on external SMB volumes without copying them into the system.
CERF Exporter — Export any or all data as native-format files with accompanying XML. Your data is never locked in.

21 CFR Part 11, GLP & ALCOA-PLUS Compliance

Designed from the ground up for 21 CFR Part 11 and ALCOA-PLUS data integrity. Every compliance feature is built into the core system — not added as an afterthought.

Immutable audit trail — Every action captured in a secure, computer-generated, time-stamped audit trail that cannot be modified from within CERF.
True PKI digital signatures — Built-in Public Key Infrastructure (PKI) hashing via the U.S. government's Digital Signature Algorithm (DSA). Every signed record carries a unique cryptographic hash that cannot be transferred or falsified.
Configurable signature workflows — Define multi-tier review chains from Submitter through Peer Reviewer, Manager, and Legal/Regulatory.
GLP-compliant corrections — Built-in Strike Out function keeps original text visible, as required by GLP and ALCOA principles.

SOP & Controlled Document Management

A dedicated Controlled Documents module manages SOPs, protocols, assays, NDAs, and required training documents through their full lifecycle — from creation and approval through distribution, acknowledgment, expiry, renewal, and archiving. This module alone can replace dedicated third-party document management systems.

Enforced acknowledgment — Users who have not acknowledged the current SOP version cannot sign relevant notebook pages.
SOP placeholders — Templates include placeholders that must be filled with the active controlled document before signing.
Expiry management — Configurable warning notifications before documents expire.
Training records — Complete, time-stamped record of every user's acceptance of every SOP version, exportable for audit review.

Advanced Semantic Search

Finding data in CERF is not limited to searching by filename or date. CERF's multi-parametric search engine indexes full-text content of most file types and automatically extracts and indexes file properties, metadata, tags, annotations, and keywords from context-specific controlled vocabularies.

Full-text search — MS Office, PDFs, plain text, sequence files, chemistry structures, scientific data formats, and more.
Metadata & Boolean search — Combine any number of search parameters using AND/OR Boolean logic.
Saved searches — Persistent, reusable queries that function as dynamic smart cohorts.
Find Experts search — Locate colleagues with specific expertise based on their CERF contributions.

Granular Access Control & Workgroup Management

CERF's workgroup architecture supports any combination of open collaboration and tight data isolation — from a single user's file cabinet to multi-site organizations with dozens of projects and client-specific data boundaries.

Nine access roles — Read Only, Annotator, Editor, Notebook Editor, Manager, and more — enforced down to the individual record.
Hierarchical delegation — Administrators delegate workgroup management to project leads without sacrificing security.
Session security — Single-session login, account lockout, configurable session timeout, and optional TOTP MFA.
Full cross-platform support — Windows, Mac, and Ubuntu Linux users collaborate seamlessly within the same system.

Automated Data Capture

The CERF Automaton monitors designated locations on your network and automatically ingests files into CERF as they are generated — establishing an unbroken chain of custody for instrument data from the moment of creation.

Code-free configuration — Set up ingestion jobs for any file type, from any instrument, folder, or network source, using a simple configuration interface.
Email-to-CERF — Any user can send files and email attachments directly into CERF via email, attributed to the correct user with automatic metadata extraction.

CERF Table — Scientific Data Grids

CERF Tables (.sps files) are native CERF spreadsheet objects for structured, tabular scientific data. They are edited, versioned, and searched entirely within CERF — not tied to external spreadsheet applications.

Image thumbnails — Display resizable image thumbnails inline within table cells, enabling annotated grids of histology specimens, chemistry structures, or any image collection.
Drag-fill rows or columns — Drop CERF resources into tables as rows or columns with automatic linking.
Internal search — Built-in table search tool available in both view and edit mode.
Row locking — GLP-relevant: lock finalized rows after peer review to prevent modification.

Flexible Deployment & Long-Term Architecture

CERF runs as a client-server system with three deployment models. Data files are stored in native format in a secure file store — not compressed into a proprietary container. CERF is built exclusively on open-source, industry-standard components selected for technological longevity.

Cloud, on-premise, or sealed LAN — Deploy where your security and compliance requirements dictate.
Database-agnostic — Compatible with MySQL (included), Microsoft SQL Server, or Oracle.
Perpetual licensing available — Your system operates indefinitely, even on a sealed LAN, regardless of your ongoing vendor relationship.
Regular updates included — All CERF software updates (typically two per year) are included in the standard support package.

What's New

New in CERF 6

CERF 6 is the most significant release in the product's history. Nearly all core components and libraries have been updated, bringing major improvements to speed, stability, security, and user experience alongside important new capabilities.

See the full CERF 6 feature guide →

Modernized UI — Customizable light and dark themes, modern and classic icon sets, adjustable font sizes.

TOTP Multi-Factor Auth — Optional MFA via Google Authenticator, Microsoft Authenticator, or Bitwarden.

Built-in Diff Tool — Compare any two versions of a resource to immediately see all differences in content and metadata.

Linux Desktop Client — Full support for CERF client on Debian-based Linux workstations (Ubuntu 25.10).

Image Thumbnails in Tables — Display annotated grids of resources such as images and chemical structures.

Enhanced Chemistry Metadata — Auto-extracted melting point, molecular weight, CAS numbers, and PubChem IDs from CML files.

Expanded File Formats — OME-TIFF, JP2, PSD, RTF, Apple iWork (.pages, .numbers, .key), CDXML, and more.

Resource-Specific Metadata — Re-designate any resource as a Tissue Sample, Cell Type, or other category to unlock appropriate metadata fields.

Updated Core Stack — Java 25, Tomcat 11, MySQL 9, ActiveMQ 6, and latest Lucene with improved build and installer technologies.

Architecture & Sustainability

Built to Last Decades, Not Years

CERF's architecture reflects a deliberate commitment to data longevity and organizational independence that most ELN vendors cannot match.

Native File Storage

Data files are stored in their original native format in a secure file store — not compressed into a proprietary database from which they may be difficult or impossible to extract.

Lightweight, Scalable Database

The referential SQL database rarely exceeds 10 GB even after years of active use, and does not slow down as data accumulates. Compatible with MySQL, Microsoft SQL Server, or Oracle.

Open-Source Components Only

CERF is built exclusively on open-source, industry-standard components selected for technological longevity. No component depends on proprietary or externally hosted services.

Perpetual Licensing Option

On-premise deployments are available with a perpetual license. Your system continues to operate indefinitely — even on a sealed LAN with no internet access — regardless of changes in your vendor relationship.

Regular, Included Updates

All CERF software updates (typically two per year) are included in the standard support package and involve no significant service interruption.

Proven Long-Term Sustainability

CERF has operated continuously for nearly 20 years. While other technologies rapidly become obsolete, CERF's stable, open-standards architecture has remained a reliable long-term home for scientific data through multiple generations of computing.

Deployment Options

Flexible to Deploy — On Your Terms

CERF supports three deployment models. Choose based on your security requirements, IT resources, and regulatory environment.

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Cloud

Deploy on any cloud provider of your choice — AWS, Azure, GCP, or any VPS. Alternatively, Lab-Ally can host and manage a private AWS instance for you with no IT burden on your team.

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On-Premise

Install CERF on your own physical or virtual server for maximum control over your data and infrastructure. The CERF server requires minimal ongoing IT maintenance and can run on modest hardware.

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Sealed LAN

For the most stringent security environments, CERF can operate on a completely air-gapped local area network with no internet connectivity whatsoever — meeting the requirements of defense, clinical, and pharmaceutical organizations.

Licensing

Available as an annual subscription or, for on-premise deployments, a perpetual license. Named-user seats belong to your organization permanently. If a user leaves, the vacated seat becomes available to someone else.

Pricing

CERF is priced at a fraction of comparable enterprise ELN systems — typically $100–400 per user per year under a subscription model. Special terms for one-time payment arrangements are available on request.

Free Trial

Access a free trial server at demo.cerfnotebook.com or contact Lab-Ally to arrange a hosted trial in your own environment.

Deployment & Support

Lab-Ally Was Founded by Scientists

Our implementation and support team brings deep familiarity with research workflows, regulatory requirements, and the practical challenges of deploying data management systems in active laboratory environments.

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Full Deployment Assistance

Server configuration, workgroup setup, SOP workflow design, and user onboarding for organizations of any size — from a single-PI lab to a multi-site enterprise.

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IQ/OQ Validation Support

Installation Qualification and Operational Qualification documentation and services in partnership with qualified third-party validation specialists. Validated in your specific environment — the correct approach under 21 CFR Part 11.

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Cross-Platform Flexibility

CERF excels in mixed environments: Mac, Windows, and Linux users collaborating on-site or remotely, with fine-grained workgroup controls that reflect your actual organizational structure.

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Comprehensive Training

Administrator and end-user training including live webcast sessions and formal user certification materials. Your team becomes confident and self-sufficient quickly.

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Responsive Human Support

Email, phone, and scheduled appointments. A live human being answers your support questions — not a chatbot or a ticketing queue that takes days to resolve a simple issue.

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Free Trial Server Access

Try CERF before you commit. Access a fully functional trial server at demo.cerfnotebook.com, or contact us to arrange a live guided demonstration at a time that suits you.

What Is CERF ELN?