IT Innovation Contest

A team-based contest for creative IT solutions

A Paperless Electronic Lab Notebook for UCSF

Proposal Status: 

DESCRIPTION OF THE PROJECT. A laboratory notebook is the single most important record of research accomplishments.  For the investigator, keeping an accurate and detailed record of all experiments is essential to document new discoveries and to allow the experiments to be reproduced by others. The lab notebook is used as a crucial legal document to protect intellectual property. As such maintaining a proper paper record is a requirement for all UCSF lab personnel.  However, for a number of reasons outlined below, paper records are rapidly becoming an antiquated format and many institutions are adopting electronic lab notebooks (ELNs).

The vision.  Recent technological advances such as the iPad and related devices promise to promote efficiency, compliance, and security to lab notebooks. We have a future vision where a digital tablet is the mainstay laboratory notebook.  Before that can happen, laboratories need to adopt the routine practice of keeping digital data appropriately archived.  This includes the legally compliant laboratory accreditation criteria found in the ISO 17025 and Title 21 CFR Part 11 standards.

UCSF data are not presently secure.  UCSF is a cutting-edge research institution housing thousands of scientists and has a responsibility to ensure its research data are compliant, secure, and in a format that would foster collaboration across its many labs.  Currently, UCSF lab notebooks are not kept in a standardized format and are subject to data loss by natural disaster, or equally nefarious, falsification.

DELIVERABLE. A secure and user-friendly ELN web application that can be accessed anywhere and anytime, on desktop computers and mobile devices.

Existing solutions.  Over 50 commercial vendors offer ELN services, with expensive contracts. Our solution uses open-source software to develop an ELN that can be shared freely within the UC community. Importantly, it takes advantage of an existing Drupal framework that is central to the UCSF web roadmap. 

Our goal.  In this project, we propose to take an important step and create the first UCSF electronic lab notebook.  The proposed ELN will also offer a fast, user-friendly, and secure ELN web application that facilitates knowledge management and improves collaboration.  Off-site backup and versioning is already part of the existing UCSF:Acquia Drupal contract.



  • Creates a paperless “green” work environment, although labs can print ELN entries for paper notebooks
  • Convenience – easy to use and improves productivity; pull-down SOPs, and relational database structures
  • Direct importation of data which have already been captured elsewhere, such as images, tables, and text
  • Configurable universal formats allows easy searching and interpretation of records; bar-coding possible
  • Space and cost savings – no bulky filing cabinets and no ongoing storage and handling fees
  • Ensures business continuity and data protection in the case of natural disasters like earthquake or fire
  • Improves accessibility – can be accessed anytime and anywhere with desktop, laptop, and mobile devices
  • Facilitate knowledge management and improve collaboration - share information between UCSF labs easily
  • Improves data tracking by saving data with all revisions
  • Improves intellectual property protection by integrating legally compliant laboratory accreditation criteria






Lewis Lanier

Chair, Micro & Immunology

Project Coordination/Adviser/Tester

Michael McManus

Assoc Professor, Diabetes Center

Project Coordination/Adviser/Web Admin/Tester

Khang Nguyen

Programmer/Analyst, Micro & Immunology

Web Admin/Programmer/Tester

Peter Werba

Programmer/Analyst, CMP

GUI designer/Programmer/Tester


ESTIMATED TIME DEVOTED BY EACH TEAM MEMBER. Nguyen, 30 hours; Werba, 25 hours; McManus; 20 hours, Lanier, 10 hours.


Surprising that in this day and age that paper lab notebooks are still standard. For all the reasons mentioned, an electronic alternative is needed at UCSF. Leveraging open source tools and the existing UCSF Drupal environment are key to ensuring widespread adoption and keeping costs down. HIPAA compliant security is a must.

There are some free, open source solutions out there that you may be interested in looking at. In radiation oncology we implemented an elog for each of our treatment machines over a year ago for use by physicists/engineers/therapists. We generally use these for recording details of routine testing and calibration of the machines in place of paper log books, as well as errors encountered by the therapists in daily use. We are using the following open-source elog originally designed for high energy physics experiments:

Hi Lisa, Our ELN solution also uses free open source system. We are taking advantage of the existing Drupal/Acquia UCSF hosting. Regards, Khang

Thanks, Enrique. Yes, we will make it meet the HIPAA policy.

Are there any ELN data formats that are useful to support — either to import existing content, or to prevent lock-in and allow interoperability with the other 50+ ELN vendors?

Hi Anirvan, Our ELN system allows users to import existing content, however, we don't intend to design our system to interact with the other 50+ ELN vendors. We don't have enough info about the systems that the other 50+ vendors are using and are not sure when those online vendors will disappear. Regards, Khang


I wrote an open source electronic lab notebook that fits ALL of the points you are listing :

  • paperless : OK
  • convenient with RDBMS : OK
  • import external data : OK
  • bar-coding possible : OK
  • no fees, of course it's free and open source : OK
  • easy to backup : OK
  • can be accessed anywhere, anytime : OK, it's on a server
  • improve collaboration : OK
  • data tracking : OK (revisions implemented)
  • intellectual property : OK (timestamping of experiments (pdf export) compliant with European standard ETSI TS 102 023 and certified RGS (French General Security Specifications)

Please visite the demo too :



Commenting is closed.