R & D Summary

    CyNote - Cyber Laboratory Notebook for Biologists and Bioinformaticists

A research project today has been littered with numerous digital documents in the forms of  images and discussion emails to name a few. It is not uncommon to encounter hundreds of digital documents pertaining to research work within a month of active biological research and management of these data generate a new set of problems for biologists:

• Data generated can be too voluminous to print (as in the case of microarray results)

• Multiple, similar images which may be difficult to keep track (often cross-referencing to actual experimental conditions written in the physical notebooks)

• Multimedia data such as videos, time-lapsed microscopy, are impossible to print.

• Authenticity of digital data for intellectual property filings.

• Issues of data management from ad hoc uses of external databases such as PubMed.

Currently, there is no standard means and practices for electronic research record-keeping; thus, many institutional policies still require crucial digital documents (images, emails etc) to be printed, affixed in physical notebooks, dated and counter-signed (witnessing of entries by an independent person). The main reason is that

"Computer files do not provide sufficient evidence of invention. The reason for having invention records such as a notebook is to be able to prove the earliest date of invention. Since computer records can be updated and changed at will, and their dates are subject to tampering, they cannot serve as evidence that their content was created at a particular time. With a bound notebook, it is clear that the work occurred in a particular sequence and was witnessed by others. Also, scientific experiments can be conducted on the ink and paper in a notebook to prove their age." (Adapted from School of Engineering & Science, Stevens Institute of Technology)

However, this is not foolproof as loss of physical notebooks through theft and misplacement is not unheard of.

It should also be noted that some factors can reduce the value or credibility of your laboratory notebook:

• illegible entries are totally worthless;

• unsigned or undated pages are almost totally worthless;

• notebook pages which have not been witnessed are almost as bad as unsigned and undated pages;

• a long delay between the signing of the page by the inventor and the witness raises questions;

• consecutive notebook pages which are not dated in chronological order raise questions;

• missing notebook pages raise questions;

• erasures and deletions raise questions -- instead, any later discovered mistakes should be corrected and explained on the next available blank page, referencing the page with the mistake.

CyNote aims to be a electronic research record management system that conforms to record-keeping standards of physical notebooks based on 3 principles:

1. Notebooks can be setup for encryption and routine backup on secured data centres (such as Amazon S3)

2. Date-time stamping of notebooks are performed by remote systems (immediate date-time stamp upon upload)

3. Page edits are generally disallowed (in conformance to US FDA 21 CFR Part 11's Rules on Electronic Records). However, if page edits are forcefully done, it will be tracked and date-time stamped using source code management systems (such as Subversion)

At the same time, research tools can be developed as plugins into CyNote and records can be tracked immediately; thus, saving the effort in transposing data across systems.

In my case, I am developing CyNote as a teaching tool for my bioinformatics classes where I can incorporate some common bioinformatics and data analysis functions into it, as well as a laboratory data management tool for myself and my students.

Annotated Publications from this project

Ng, YY and Ling, MHT. 2010. Electronic Laboratory Notebook on Web2Py Framework. Accepted.

This paper presents CyNote version 1.4 as a prototype of an electronic laboratory notebook that is built on Web2py framework. CyNote uses a blog-style structure (entries and comments) as laboratory notebook and had implemented a number of bioinformatics and statistical analysis functions. At the same time, this paper evaluates CyNote against US FDA 21 CFR Part 11.