Experiences with a researcher-centric ELN

Badiola, Katrina A.; Bird, Colin; Brocklesby, W.S.; Casson, John C.; Chapman, Richard T.; Coles, Simon J.; Cronshaw, James R.; Fisher, Adam; Frey, Jeremy G.; Gloria, Danmar; Grossel, Martin C.; Hibbert, David Brynn; Knight, Nicola; Mapp, Lucy K.; Marazzi, Luke; Matthews, Brian; Milsted, Andy; Minns, Russell S.; Mueller, Karl T.; Murphy, Kelly A.; Parkinson, T. J.; Quinnell, Rosanne; Robinson, Jan; Robertson, Murray N.; Robins, Michael; Springate, E.; Tizzard, Graham J.; Todd, Matthew H.; Williamson, Alice; Willoughby, Cerys; Yang, Erica; Ylioja, Paul M.

doi:10.1039/c4sc02128b

Cited by 24 publications

(33 citation statements)

References 16 publications

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“…The Creative Commons license covering project content ensures free reuse of all content including for commercial purposes (CC-BY), 50 and uses a free or open source composite technical platform that has recently been reviewed. 51,52 …”

Section: Introductionmentioning

confidence: 99%

Open Source Drug Discovery: Highly Potent Antimalarial Compounds Derived from the Tres Cantos Arylpyrroles

et al. 2016

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The development of new antimalarial compounds remains a pivotal part of the strategy for malaria elimination. Recent large-scale phenotypic screens have provided a wealth of potential starting points for hit-to-lead campaigns. One such public set is explored, employing an open source research mechanism in which all data and ideas were shared in real time, anyone was able to participate, and patents were not sought. One chemical subseries was found to exhibit oral activity but contained a labile ester that could not be replaced without loss of activity, and the original hit exhibited remarkable sensitivity to minor structural change. A second subseries displayed high potency, including activity within gametocyte and liver stage assays, but at the cost of low solubility. As an open source research project, unexplored avenues are clearly identified and may be explored further by the community; new findings may be cumulatively added to the present work.

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Section: Introductionmentioning

confidence: 99%

Open Source Drug Discovery: Highly Potent Antimalarial Compounds Derived from the Tres Cantos Arylpyrroles

et al. 2016

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“…Neverthelessw ew ere able to trial the system and understand where user resist-ance was an issue.W ew ere not at the time able to carry out as ufficient number of experiments to create enough data to experimentw ith data integrationa nd search. As we were doingt his work before SPARQL( SPARQL Protocola nd RDF Query Language) [44] was fully defined,o ur queries would in any event have been limited.…”

Section: The Smart Teap Rojectmentioning

confidence: 99%

“…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] …”

Section: Labtrovementioning

confidence: 99%

The Evolution of Digital Chemistry at Southampton

Bird

Coles

Frey

2015

Molecular Informatics

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In this paper we take a historical view of e‐Science and e‐Research developments within the Chemical Sciences at the University of Southampton, showing the development of several stages of the evolving data ecosystem as Chemistry moves into the digital age of the 21st Century. We cover our research on aspects of the representation of chemical information in the context of the world wide web (WWW) and its semantic enhancement (the Semantic Web) and illustrate this with the example of the representation of quantities and units within the Semantic Web. We explore the changing nature of laboratories as computing power becomes increasing powerful and pervasive and specifically look at the function and role of electronic or digital notebooks. Having focussed on the creation of chemical data and information in context, we finish the paper by following the use and reuse of this data as facilitated by the features provided by digital repositories and their importance in facilitating the exchange of chemical information touching on the issues of open and or intelligent access to the data.

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“…While ELNs are still relatively rare in academic environments with a variety of challenges to overcome [ 3 , 4 ], the advent of computers, and the digital capture of data in particular, has begun to change the way many laboratory scientists record their experiments [ 5 ]. ELNs provide a range of features that can help to improve data management, data retrieval, and collaboration providing positive benefits for teaching, learning, and research [ 6 ].…”

Section: Introductionmentioning

confidence: 99%

Effects of using structured templates for recalling chemistry experiments

2016

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BackgroundThe way that we recall information is dependent upon both the knowledge in our memories and the conditions under which we recall the information. Electronic Laboratory Notebooks can provide a structured interface for the capture of experiment records through the use of forms and templates. These templates can be useful by providing cues to help researchers to remember to record particular aspects of their experiment, but they may also constrain the information that is recorded by encouraging them to record only what is asked for. It is therefore unknown whether using structured templates for capturing experiment records will have positive or negative effects on the quality and usefulness of the records for assessment and future use. In this paper we report on the results of a set of studies investigating the effects of different template designs on the recording of experiments by undergraduate students and academic researchers.ResultsThe results indicate that using structured templates to write up experiments does make a significant difference to the information that is recalled and recorded. These differences have both positive and negative effects, with templates prompting the capture of specific information that is otherwise forgotten, but also apparently losing some of the personal elements of the experiment experience such as observations and explanations. Other unexpected effects were seen with templates that can change the information that is captured, but also interfere with the way an experiment is conducted.ConclusionsOur results showed that using structured templates can improve the completeness of the experiment context information captured but can also cause a loss of personal elements of the experiment experience when compared with allowing the researcher to structure their own record. The results suggest that interfaces for recording information about chemistry experiments, whether paper-based questionnaires or templates in Electronic Laboratory Notebooks, can be an effective way to improve the quality of experiment write-ups, but that care needs to be taken to ensure that the correct cues are provided.Graphical abstractScientists have traditionally recorded their research in paper notebooks, a format that provides great flexibility for capturing information. In contrast, Electronic Laboratory Notebooks frequently make use of forms or structured templates for capturing experiment records. Structured templates can provide cues that can improve record quality by increasing the amount of information captured and encouraging consistency. However, using the wrong cues can lead to a loss of personal elements of the experiment experience and frustrate users. This image shows two participants from one of our studies recording their experiment using a computer-based templateElectronic supplementary materialThe online version of this article (doi:10.1186/s13321-016-0118-6) contains supplementary material, which is available to authorized users.

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Experiences with a researcher-centric ELN

Abstract: Chemical scientists’ experiences with LabTrove.

Cited by 24 publications

References 16 publications

Open Source Drug Discovery: Highly Potent Antimalarial Compounds Derived from the Tres Cantos Arylpyrroles

Open Source Drug Discovery: Highly Potent Antimalarial Compounds Derived from the Tres Cantos Arylpyrroles

The Evolution of Digital Chemistry at Southampton

Effects of using structured templates for recalling chemistry experiments

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