Virtualizing the Lab Book

I am a lab-note-freak who loves to write extremely detailed, organized lab notes, so organized that I really want to see the design of a really effective computer-based lab book software system.

With such a system, I’d want to be able to divide my lab work into several categories: Synthesis, Measurement, and other Manipulations. I’d also want to be able to create new categories by selecting and combining from a set of basic operations provided by the software.

Each type of lab work requires a unique form to fill in.Some fields are universal among all types of lab work such as Date, Title, Purpose, Results, Discussion, etc. But some fields depend on the type of lab work you are noting. For example Observations in the progress of a Synthesis lab work are important, but you don’t have any if you are doing NMR (a Measurement lab work) because you cannot see the sample.

With the help of database techniques your software labnotes could be searched, tagged, and, if online, shared! You could search people’s lab notes with “broadening” in Discussion field and “NMR” in Title field, for instance to learn from others’ experiences in the peak-broadening effects of an NMR study. And, of course, the digital chemical noting techniques (Smiles, InChI KEY etc.) connected to search engines could be incorporated into the software, too. I believe this is not very difficult technically speaking.

When I first heard of the online Open Notebook idea I thought it would be like the above-mentioned ideas, but now it seems that the current open notebook instances are essentially mere wikis and blogs. Wikis may be nice if you manually organize them into a labnote database but that’s much more tedious than directly using a database with a user-friendly shell. Blogs can be of some help with their datestamp format. Combined with tags you could make a blog-based lab notebook searchable, but it would still not be as good as specialized software designed for the purpose.

Perhaps I am missing the point of Open Notebook. Maybe it does encompass all my desires. I hope to learn more in the follow-up comments to this post.

— Guest blog post by PhD chemist Andrew Sun who is based in Guangzhou, southern China. You can find Andrew Sun via his Nature Networks blog where he discusses his life in chemistry.

Author: David Bradley

Freelance science journalist, author of Deceived Wisdom. Sharp-shooting photographer and wannabe rock god.

3 thoughts on “Virtualizing the Lab Book”

  1. hi i am a student studying equine science and i need help with my lab book i just wounded if u could email me please to help me

    thanks Beth

  2. It is always fun to say something like “a tool for each purpose and a purpose for each tool” for many a computer program is written that way. At the end of the day (or a career) one finds oneself surrounded by may purposes for which there is no time to create the tool and and many tools for which the purpose has been forgot. It is a hard task to keep it simple.

    I have tried to keep it simple by writing my lab notes in xhtml and text directly. That way I can use my notebooks without the necessity of learning the detailed ways in which the tool created by someone else doesn’t match my purpose. The Cox personal space assigned to me is way too small to contain any substantive work but it will give an indication. The first entry in Whats New, the Notebook Template, has the template used by my programming to generate a new notebook (project).

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