Andrew J. Milsted

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.

MyExperimentalScience, extending the ‘workflow’

Science, especially experimental science, has always depended on the careful capture of plans, actions, raw and processed data and conclusions. With scientific research now so inextricably dependent on computers, the use of an electronic laboratory notebook (ELN) is almost essential. The meticulous notebooks of Michael Faraday and other scientists of his era remain as role models for the recording that is necessary, but they cannot provide the essential support for discussion, sharing, collaboration and formal verification. A blog (a contraction of Web log) can form the basis for implementing an electronic notebook but does not suffice to meet all the needs of an ELN. This paper describes the LabTrove ELN, which is blog based but provides numerous additional features, such as version control, security policies and a flexible metadata scheme, and facilities for interchanging objects with other systems. The MyExperimentalScience project links LabTrove with myExperiment, a repository for workflows in a collaborative environment, thereby making LabTrove templates available for discovery and reuse. Collaboration, sharing and reuse are essential for scientific progress, which depends on individual scientists building on the results already produced by others. Open‐source ELNs such as LabTrove are ideal vehicles to support the growth of Open Notebook Science. Copyright

Data Autodiscovery—The Role of the OPD

The importance of open data and the benefits it can offer have received recognition on the international stage with the signing of the G8 Open Data Charter in June 2013. The charter has an early focus on 14 high value areas, including transport and education, where governments have greater influence. In the UK, we have seen the funding of the Open Data Institute (ODI) with a remit to support small and medium sized enterprises (SMEs) in identifying benefits from using open data, whereas, within HE, open data discussion is in its infancy although is acknowledged as a sector challenge by the Russell Group of universities. There is an evident need for the academic community to influence the adoption of applications using linked open data techniques in data management and service delivery. This article introduces the concept of “data autodiscovery”, highlighting the role of the Organisation Profile Document (OPD) and its contribution to the early success of the UK National Equipment Portal, equipment.data, along with discussing the need for greater dialogue in linked and open data standards development.

eCrystals: A Route for Open Access to Small Molecule Crystal Structure Data.

Recently the funding councils in the UK stated that ‘the data underpinning the published results of publically-funded research should be made available as widely and rapidly as possible’. Thirty years ago a research student would present about five crystal structures as their PhD thesis, however with modern technologies and good crystals this can now be achieved in the timespan of a single morning. This increase in pace of generation further exacerbates a problem in the communication of the results. Additionally, the general route for the publication of a crystal structure report is coupled with and often governed by the underlying chemistry and is therefore subject to the lengthy peer review process and tied to the timing of the publication as a whole. This bottleneck in the dissemination of crystal structure data hinders the potential growth of databases and the data mining studies that are reliant on these collections. Just 500,000 small unit cell crystal structures are available in the CSD, ICSD & CRYSMET databases, while it is estimated that at least twice this number have been determined in research laboratories and are likely to remain unpublished. In addition, publication in the mainstream literature still offers only indirect (and often subscription controlled) access to this data. The work of the eBank-UK project (http://www.ukoln.ac.uk/projects/ebank-uk/) has addressed this problem by establishing an institutional data repository that supports, manages and disseminates metadata relating to the crystal structure data it contains (i.e. all the files generated during a crystal structure determination). This process alters the traditional method of peer review by openly providing crystal structure data where the reader or user may directly check correctness and validity. The repository (http://ecrystals.chem.soton.ac.uk) makes available all the raw, derived and results data from a crystallographic experiment with little further researcher effort after the creation of a normal completed structure in a laboratory archive. Not only does this approach allow rapid release of crystal structure data into the public domain, but it can also provide mechanisms for value added services that allow rapid discovery of the data for further studies and reuse, whilst ownership of the data is retained by the creator. The details of the preparation of data, upload process, files supported and automatic report generation will be presented. Additionally, the process whereby metadata relating to each archive entry is disseminated, using current Digital Libraries technologies, for discovery and reuse by will be summarised. Strategies for the installation of archives at new sites, the construction of harvesting and aggregator services and the interaction with crystallographic data holding bodies, such as IUCr and CCDC, will also be outlined. Additionally links to educational tools, specifically the Schools eMalaria project (http://emalaria.soton.ac.uk), will also be presented.