About CERF 6 ELN | Next-Generation Scientific Data Management

Product Overview

What is CERF ELN?

CERF (Collaborative Electronic Research Framework) is a premium electronic lab notebook and scientific document management system designed for commercial biomedical, pharmaceutical, chemical, and histopathology labs that require long-term data integrity, rigorous audit trails, and regulatory compliance.

At its core, CERF is a structured, version-controlled repository for all of the files, data, images, documents, and metadata that your lab generates. Every resource in CERF is tracked, timestamped, signed, and fully searchable — from raw instrument output to finalized SOPs and reports. CERF replaces the patchwork of shared drives, email threads, and disconnected spreadsheets that most labs rely on today.

Designed by scientists for scientists, CERF is more than a Lab Notebook. It functions as a full-featured Enterprise Content Management (ECM) and Scientific Data Management System (SDMS), capable of consolidating the work normally split across LIMS, file-sharing tools, sample management systems, and document repositories. For organizations operating in stringent, regulated, or GxP environments, CERF is a compliant alternative to consumer-grade tools like SharePoint, Dropbox, and OneDrive — bringing all of your data, files, and business documents into a single secure repository that is easy to search, govern, and audit.

Unlike browser-based ELN systems, CERF uses a dedicated Java desktop client application that gives users a rich, responsive interface without dependency on a specific browser version or internet connection. CERF can operate in a completely sealed, air-gapped LAN environment — with no external license servers, no "phone home" calls, and no exposure to cloud-based vulnerabilities.

Lab-Ally provides full IQ/OQ validation support, and CERF is designed to be validated in your specific deployment environment — the only defensible approach under 21 CFR Part 11.

CERF 6 — Resource library showing multiple file types

What's New

CERF 6 — Notable New Features

CERF 6 is a comprehensive upgrade that touches every area of the platform. Here are the headline capabilities introduced in this release.

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Version Diff Tool New

CERF 6 introduces a built-in file comparison (diff) tool that allows users to compare any earlier version of a resource — accessible from the Resource Info window's version history — against the current version. All differences are highlighted, making it simple to track changes over time, review edits before signing, or resolve discrepancies in collaborative workflows. This is a critical capability for regulated environments where the evolution of a document must be fully auditable.

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Image Thumbnails in Tables New

CERF Tables now display re-sizable thumbnail previews of resources within table cells — enabling visual data grids of histology specimens, chemistry structures, experimental images, or any other file type. Tables can receive multiple resources via drag-and-drop, inserting them as rows or columns. Combined with the Table's new internal search tool, this transforms CERF Tables into powerful visual data management interfaces.

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TOTP Multi-Factor Authentication New

CERF 6 introduces optional Time-based One-Time Password (TOTP) multi-factor authentication for the CERF Desktop client and the Automaton tool. Compatible with standard authenticator apps including Google Authenticator, Microsoft Authenticator, and Bitwarden. MFA can be enforced selectively via new Business Policies, giving administrators fine-grained control over authentication requirements.

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Linux Desktop Client New

CERF 6 adds full support for the CERF desktop client application on Debian-based Linux workstations, including Ubuntu 25.10 with GNOME desktop. The Windows installer is now delivered as a modern .MSI package. This expands CERF's reach to the growing number of scientific labs running Linux workstations, particularly in bioinformatics and computational biology environments.

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Modernized UI with Themeable Icons

CERF 6 debuts a thoroughly modernized user interface with updated color schemes and typography throughout. Users and administrators can now choose from multiple light, dark, or custom GUI themes, and can adjust icon sets, icon sizes, and color filters to match organizational preferences or accessibility needs. New keyboard shortcuts (Ctrl+Shift+1/2/3) and a new View menu allow efficient use of screen space.

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Significantly Enhanced Search

Current Versions Only filter — a new top-level checkbox excludes older versions and discarded items from search results, dramatically reducing noise.
CERF Resource cross-reference search — searching for "CERF1202" finds that resource and all resources previously linked to it.
Table content indexing — CERF Table (.sps) files are now fully indexed for search.
Expanded chemical metadata search — improved extraction of molecular weight, formula, CAS number, and other properties from CML files.
Sortable file size column — search results display file size in KB/MB/GB, fully sortable.

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Formal Resource Linking

Users can now formally link any CERF resource to another related resource using the new CERF Resource Link metadata option — making the relationship part of the official versioned record. A new Co-contributor metadata field and search parameter allows attribution of shared authorship. Collections now display a full contributor list, particularly useful for notebook pages that require signatures from multiple contributors.

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Expanded File Format Support

CERF 6 adds viewing, PDF export, and/or search indexing for a broader range of scientific and general file formats, including:

RTF, PSD (Adobe Photoshop), CDXML, JP2, OME-TIFF
Apple iWork formats: .PAGES, .NUMBERS, .KEY
Biological sequence files: FASTA, GFF3, VCF and related text formats
Legacy image formats and technical text/code files

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Performance & Infrastructure

Pre-emptive thumbnail and preview generation on resource check-in delivers dramatically faster on-demand file viewing. The Lucene search library has been upgraded for faster, more accurate indexing. The check-in workflow now cryptographically verifies file hash integrity to prevent man-in-the-middle attack vectors. SMB 2/3 support modernizes links to external network file servers.

Why CERF?

Enduring Strengths of the CERF Platform

Beyond the new features in CERF 6, these are the foundational capabilities that have made CERF the preferred ELN for demanding scientific environments for more than two decades.

Version-Controlled File Management

Every file checked into CERF is automatically versioned. The complete history of every resource — who created it, who modified it, when, and what changed — is retained indefinitely and is fully auditable.

Round-Trip Editing

Check out any file to edit it in its native application — Word, Excel, ChemDraw, ImageJ, or any other tool your scientists use. Check it back in and CERF automatically creates a new version with a complete audit trail.

Digital Signatures & Witnessing

Compliant electronic signatures with date/time stamps, role-based signing workflows, and enforced witnessing. Signature status is visible throughout the system and exportable to CSV for audit review.

Controlled Document Management

A dedicated SOP module manages the full lifecycle of controlled documents — from creation and approval through acknowledgment, expiry notification, and archiving. Users who haven't acknowledged the current SOP version cannot sign relevant notebook pages.

Multi-Parametric Semantic Search

CERF's search engine indexes full-text content, all metadata, extracted file properties, tags, cross-references, and more. Find a specific value buried inside a file from years ago in seconds.

Sample & Entity Management

CERF's SDIMS system allows representation of physical entities — tissue specimens, chemical samples, instruments, cell lines — as structured data cards linked to the experimental records that reference them.

Network File Links

Very large files — multi-gigabyte whole slide images, raw instrument datasets — can be stored on your existing high-capacity storage and richly annotated and indexed within CERF without duplication to the CERF database.

Chemistry & Biology Tools

Supports display and search of chemical structure files, sequence files, biomedical images, image grids, stoichiometric and other tabular calculations and discipline specific metadata and annotations — all within a single compliant repository.

Fast Import of Folder Trees

CERF ingests data quickly and represents it in the same hierarchic schema you created on your computer, automatically extracting metadata from your files and indexing everything for fast, logical search and tracking and making data selectively available to your colleagues.

Automated Data Capture

CERF can automatically ingest data from instruments and off-site partners, and can even capture incoming email and attachments directly into the appropriate notebook or project folder — turning routine data transfer into a hands-off, fully audited workflow.

Database & Backend Flexibility

Choose the database backend that fits your infrastructure: MySQL, Microsoft SQL Server, or Oracle. Data files are always stored in their native format in a secure file store — never "blobbed" into the database — so they can always be recovered in their original form.

One-Click Data Export

Export any data and its metadata as XML or human-readable files in a single click. Your records are never trapped — they remain portable, archivable, and machine-readable for decades to come, regardless of future decisions about the CERF platform.

IT-Friendly Self-Service

CERF is engineered to minimize IT overhead. Researchers can create new notebooks, manage sharing groups, initiate and track signing workflows, and reset their own passwords — tasks that typically require IT intervention on other platforms — freeing IT to focus on infrastructure rather than user support.

Component	CERF 5.3	CERF 6
Java Runtime	Java 8	NEWJava 25 (LTS)
Web Container	Apache Tomcat 9	NEWApache Tomcat 11
Database	MySQL 5.7	NEWMySQL 9
Messaging	ActiveMQ 5.16	NEWActiveMQ 6
Search Engine	Lucene (prior)	NEWLucene (latest)
Network File Access	SMB 1	NEWSMB 2 / 3
Windows Installer	.EXE installer	NEW.MSI package
Linux Client	Not supported	NEWUbuntu 25.10 / Debian
Authentication	Username / password	NEWPassword + optional TOTP MFA
Office Document Export	LibreOffice 7.6	NEWLatest LibreOffice + improved PDF export

Regulatory Compliance

Built for Regulated Environments

CERF's compliance architecture has been rigorously designed and documented for use in GLP, GMP, and GCP environments subject to 21 CFR Part 11. Every capability described on this page operates within a framework of audit trails, access controls, and data integrity verification.

21 CFR Part 11

Electronic records and electronic signatures that fully satisfy the requirements of 21 CFR Part 11, including access controls, audit trails, record integrity, and compliant e-signature workflows.

Audit Trail

Every action in CERF — file check-in, signature, metadata edit, permission change — is timestamped and recorded in an immutable audit log. No original record can be obscured or overwritten.

IQ / OQ Validation

Lab-Ally and qualified validation partners provide Installation Qualification and Operational Qualification documentation and services. CERF is designed to be validated in your specific deployment environment.

GLP / GMP / GxP

CERF supports ALCOA+ data integrity principles: Attributable, Legible, Contemporaneous, Original, and Accurate. Network file links preserve original records. Version history retains all prior states.

Optional Air-Gapped LAN deployment

CERF uses no external license servers and makes no required internet calls. Your server can be in teh cloud, on-premise or in a completely sealed LAN or air-gapped environment — meeting the strictest data security requirements of defense, clinical, and pharmaceutical organizations.

Enhanced Security

CERF 6 adds TOTP MFA, cryptographic hash verification on file check-in, upgraded SMB protocol support, and new Business Policies controlling session timeout, file export permissions, guest user access and more.

Compliant Versioning

CERF 6 keeps all versions forever supports intuitive versioning and version branching of all your notes and files and even includes an advanced text and image diffing tool to help your downstream audience understand exactly what was changed, when and by whom, or help you verify your own changes as you work.

Ultra-Long-Term Confidence

CERF was designed specifically to be a permanent, one stop home for all of your organization's files, data and business documents. The proven sustainable architecture and available perpetual license means you will never have to migrate to another solution and can rely on accurate, perpetually available records for decades to come.

Deployment & Licensing

Flexible to Deploy, Affordable Long-Term

CERF is designed to fit your organization's infrastructure and budget — now and decades from now.

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On-Premises Deployment

Deploy CERF on a physical or virtual server on your own infrastructure. For maximum longevity, an on-premises physical server keeps your data fully under your control, immune to cloud provider changes, and operable indefinitely without external dependencies.

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Cloud Deployment

CERF can be hosted on the cloud provider of your choice — AWS, Azure, GCP, or any VPS provider. Lab-Ally supports deployment on any Linux-based virtual machine. The CERF application has no awareness of whether it's running in a cloud or on-premises environment.

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Perpetual Licensing

CERF is available with a perpetual license — a one-time purchase that gives you permanent access to your CERF system and all your data, regardless of future payments. Annual support contracts are optional: they provide software updates, help desk access, and consulting, but are not required to keep your system running.

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Transparent, Affordable Pricing

CERF is priced as a fraction of comparable enterprise ELN systems — typically $100–400 per user per year under a subscription model. Lab-Ally can also negotiate special terms for long-term or one-time payment arrangements. Contact us for a quote tailored to your lab size and requirements.

Trusted By

Who Uses CERF ELN?

CERF is in production at leading research and commercial organizations around the world, from large pharmaceutical companies to government laboratories to small specialty labs. Its flexibility means it adapts equally well to a bench scientist's daily workflow or to an enterprise that simply needs a secure, governed home for its documents and data.

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Pharmaceutical & Biotech

Researchers at major pharmaceutical companies and biotech firms use CERF for compliant, auditable management of experimental records and regulated study data.

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Government Laboratories

Multiple government labs rely on CERF for secure, on-premises data management in environments where cloud-based tools are not an option.

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Industrial & Petrochemical

One of the world's largest petrochemical companies and a major global food conglomerate use CERF to manage R&D records and protect long-term intellectual property.

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Academic Research

Leading academic research institutions use CERF where rigorous record-keeping and long-term data preservation matter more than short-term convenience.

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Biomedical & Healthcare

Companies operating in the regulated biomedical and healthcare sectors use CERF to support clinical research, histopathology workflows, and quality systems.

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Document & Records Management

Any business needing a secure, on-site document and data repository with strong governance — including financial, legal, and project-driven organizations — can deploy CERF as a compliant alternative to consumer cloud tools.

A New Generation ofScientific Data Management