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LabTrove: a lightweight, web based, laboratory “blog” as a route towards a marked up record of work in a bioscience research laboratory

LabTrove: a lightweight, web based, laboratory “blog” as a route towards a marked up record of work in a bioscience research laboratory
LabTrove: a lightweight, web based, laboratory “blog” as a route towards a marked up record of work in a bioscience research laboratory
Background

The 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 Findings

We 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/Significance

LabTrove 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.
1932-6203
e67460-[18pp]
Smalheiser, Neil R.
b3ee0d9a-1b20-4716-b722-6ecfb76762aa
Milsted, Andrew J.
c21008b0-99a9-4980-8957-cca95e774a76
Hale, Jennifer R.
751f2ebe-5573-42e0-a176-0135cd696859
Frey, Jeremy G.
ba60c559-c4af-44f1-87e6-ce69819bf23f
Neylon, Cameron
697f067b-db25-4c41-9618-28f4b74f73aa
Smalheiser, Neil R.
b3ee0d9a-1b20-4716-b722-6ecfb76762aa
Milsted, Andrew J.
c21008b0-99a9-4980-8957-cca95e774a76
Hale, Jennifer R.
751f2ebe-5573-42e0-a176-0135cd696859
Frey, Jeremy G.
ba60c559-c4af-44f1-87e6-ce69819bf23f
Neylon, Cameron
697f067b-db25-4c41-9618-28f4b74f73aa

Smalheiser, Neil R., Milsted, Andrew J., Hale, Jennifer R., Frey, Jeremy G. and Neylon, Cameron (2013) LabTrove: a lightweight, web based, laboratory “blog” as a route towards a marked up record of work in a bioscience research laboratory PLoS ONE, 8, (7), e67460-[18pp]. (doi:10.1371/journal.pone.0067460).

Record type: Article

Abstract

Background

The 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 Findings

We 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/Significance

LabTrove 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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More information

Published date: 23 July 2013
Organisations: Computational Systems Chemistry

Identifiers

Local EPrints ID: 355078
URI: http://eprints.soton.ac.uk/id/eprint/355078
ISSN: 1932-6203
PURE UUID: 36e6bc44-b7a9-4fb8-85ab-bb452f80c163
ORCID for Andrew J. Milsted: ORCID iD orcid.org/0000-0003-4693-8785
ORCID for Jeremy G. Frey: ORCID iD orcid.org/0000-0003-0842-4302

Catalogue record

Date deposited: 13 Aug 2013 09:12
Last modified: 18 Jul 2017 03:50

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Contributors

Author: Neil R. Smalheiser
Author: Andrew J. Milsted ORCID iD
Author: Jennifer R. Hale
Author: Jeremy G. Frey ORCID iD
Author: Cameron Neylon

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