LabTrove: A Lightweight, Web Based, Laboratory “Blog” as a Route towards a Marked Up Record of Work in a Bioscience Research Laboratory

Abstract

BackgroundThe electronic laboratory notebook (ELN) has the potential to replace the paper notebook with a marked-up digital record that can be searched and shared. However, it is a challenge to achieve these benefits without losing the usability and flexibility of traditional paper notebooks. We investigate a blog-based platform that addresses the issues associated with the development of a flexible system for recording scientific research.Methodology/Principal FindingsWe chose a blog-based approach with the journal characteristics of traditional notebooks in mind, recognizing the potential for linking together procedures, materials, samples, observations, data, and analysis reports. We implemented the LabTrove blog system as a server process written in PHP, using a MySQL database to persist posts and other research objects. We incorporated a metadata framework that is both extensible and flexible while promoting consistency and structure where appropriate. Our experience thus far is that LabTrove is capable of providing a successful electronic laboratory recording system.Conclusions/SignificanceLabTrove implements a one-item one-post system, which enables us to uniquely identify each element of the research record, such as data, samples, and protocols. This unique association between a post and a research element affords advantages for monitoring the use of materials and samples and for inspecting research processes. The combination of the one-item one-post system, consistent metadata, and full-text search provides us with a much more effective record than a paper notebook. The LabTrove approach provides a route towards reconciling the tensions and challenges that lie ahead in working towards the long-term goals for ELNs. LabTrove, an electronic laboratory notebook (ELN) system from the Smart Research Framework, based on a blog-type framework with full access control, facilitates the scientific experimental recording requirements for reproducibility, reuse, repurposing, and redeployment.

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“…It would also be much easier to make the links between the lab book and related data files. Two universities in Sydney are working on a project that, amongst other things, introduces students to ELNs (Milsted, Hale, Frey, & Neylon, 2013). None of the scientists interviewed for this project, however, used an ELN and though while none were vociferously opposed to using one, they had several pragmatic objections to them.…”

The Evolution of Digital Chemistry at Southampton

“…Particularly relevant for this papera re the research themes on chemical information and the Semantic Web [6][7][8][9][10][11][12][13] and the work on Electronic Laboratory Notebooks. [14,15] The e-Science programme was not the only driver for the Southampton Chemical Information group. The EPSRCfunded CombinatorialC hemistryp rojectl ed by Mark Bradley (which funded an ew building at Southampton in 1998), offered huge potential in generating chemical structure and property data.…”

“…That recognition led us to consider am ore informal Web 2.0 approach based on ab log, which resulted in the LabTrove project. [14] LabTrove was followed by blog 3 ,w hich initiatedafully API-driven approach to the ELN blog. The principles developed for blog 3 are being migrated to the LabTrove system and will provide the basis for the future "mobile first"L abTrove-styleE LN.…”

“…This suggested that they would be comfortable with ab log-style approacht hat came with the necessary features for al aboratory notebook and enabled (but did not insist on) the use of metadata. The resultingL abTrove software [14] has now been usedb ys everal research groups, [44] of which we would highlightt he open notebook sciencec onsortia run by Mat To dd. [45,46] …”

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“…They took the "design-by-analogy" research approach in a close collaboration with chemists to develop the "MyteaExperiment" planner [27]. Similarly, LabTrove is a social network system to facilitate the association of the data to the proposed scientific elements at the point of creation (annotation at source) rather than by annotating the data with commentary after the experiment has taken place [34]. The LabTrove application was designed to help researchers to share their experimental plans, thoughts, observations and achievements with the wider online community in a semantically rich and extensible manner.…”