MyExperimentalScience, extending the ‘workflow’

Frey, Jeremy G.; Milsted, Andrew J.; Michaelides, Danius T.; Roure, David De

doi:10.1002/cpe.2922

Cited by 8 publications

(5 citation statements)

References 14 publications

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“…As such, they are potentially very useful objects to share between researchers working with similar procedures and protocols. We have implemented a link [37] with myExperiment [29] so that we can export the XML description, together with authorship details and a representative image of the template, from the LabTrove e-Notebook to myExperiment. From there, other users can be share the template or import it and use it in their own LabTrove notebook.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2013

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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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Section: Discussionmentioning

confidence: 99%

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

et al. 2013

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“…130 The MyExperimentalScience project is an interesting integration of ELN and workflow that links LabTrove with myExperiment, thereby making LabTrove templates, which are preformed posts that are in effect represent single steps in a workflow, available for discovery and reuse. 131 The Semantic Web…”

Section: Collaboration and Sharingmentioning

confidence: 99%

Laboratory notebooks in the digital era: the role of ELNs in record keeping for chemistry and other sciences

2013

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Egyptian evidence of scientific records dates back almost 50 centuries. In more recent times da Vinci and Faraday provide role models for scrupulous recording of ideas, observations, and conclusions. Their medium was paper, but despite the quality of their notebooks, we cannot turn the clock back. Our primary purpose is to review the influences of the digital era on scientific record keeping. We examine the foundations of the emerging opportunities for preserving and curating electronic records focussing on electronic laboratory notebooks (ELNs), with an emphasis on their characteristics and usability.

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“…Some academic laboratories have developed surrogate ELNs by adapting software that were originally not intended for data recording. Examples include the use of Evernote, Googledocs, Microsoft OneNote, and web blogs as ELNs [ 13 – 16 ]. In addition, the following studies on inclusion of ELN in teaching laboratories have been reported in the literature: An ELN based on the Sakai software was used in an inquiry-based biochemistry teaching laboratory course [ 17 ], and the Pebblepad ePortfolio system was used as ELN in a biochemistry and molecular biology lab course [ 18 ].…”

Section: Introductionmentioning

confidence: 99%

Implementation and use of cloud-based electronic lab notebook in a bioprocess engineering teaching laboratory

2017

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BackgroundElectronic lab notebooks (ELNs) are better equipped than paper lab notebooks (PLNs) to handle present-day life science and engineering experiments that generate large data sets and require high levels of data integrity. But limited training and a lack of workforce with ELN knowledge have restricted the use of ELN in academic and industry research laboratories which still rely on cumbersome PLNs for recordkeeping. We used LabArchives, a cloud-based ELN in our bioprocess engineering lab course to train students in electronic record keeping, good documentation practices (GDPs), and data integrity.ResultsImplementation of ELN in the bioprocess engineering lab course, an analysis of user experiences, and our development actions to improve ELN training are presented here. ELN improved pedagogy and learning outcomes of the lab course through stream lined workflow, quick data recording and archiving, and enhanced data sharing and collaboration. It also enabled superior data integrity, simplified information exchange, and allowed real-time and remote monitoring of experiments. Several attributes related to positive user experiences of ELN improved between the two subsequent years in which ELN was offered. Student responses also indicate that ELN is better than PLN for compliance.ConclusionsWe demonstrated that ELN can be successfully implemented in a lab course with significant benefits to pedagogy, GDP training, and data integrity. The methods and processes presented here for ELN implementation can be adapted to many types of laboratory experiments.

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MyExperimentalScience, extending the ‘workflow’

Cited by 8 publications

References 14 publications

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

Laboratory notebooks in the digital era: the role of ELNs in record keeping for chemistry and other sciences

Implementation and use of cloud-based electronic lab notebook in a bioprocess engineering teaching laboratory

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