myExperiment and Electronic Laboratory Notebooks for Experimental Laboratory Science
David De Roure and Jeremy Frey, Schools of Electronics and Computer Science and Chemistry, University of Southampton
This extension to the myExperiment VRE project will link the myExperiment system with two existing electronic laboratory notebook (ELN) systems developed in Southampton which are currently in use in several departments in Southampton, Bangor and STFC, with further deployment planned in other institutions. By integrating these ELNs with myExperiment we will embed myExperiment within Southampton and pave the way for longer term takeup in the experimental laboratory science communities, including Chemistry, Physics, Biology and Engineering. This combination of the Web 2.0 VRE and the Web 2.0 laboratory tools is an important step in establishing the Science 2.0 infrastructure for the next generation of researchers in laboratory sciences.
- To widen the myExperiment user community to include laboratory based experimental science (e.g. from Chemistry, Physics, Biology and Engineering laboratories).
- To enhance the drivers to embedding the myExperiment system within institutions by increasing the diversity of the user group and bringing the above communities fully within the scope of myExperiment, thereby increasing the level of institutional buy in and support.
- To link the myExperiment system to laboratory digital infrastructure (including Electronic Laboratory Notebooks) to increase the flow of work and process flows into myExperiment, increasing the number of providers as well as users within the myExperiment community.
- To increase the range of work and process flows that can be used with myExperiment to include those used in the analysis of experimental laboratory data from Chemistry, Physics, Biology and Engineering laboratories (specifically to provide and enhance functionality for Matlab and R users).
This extension project will link the myExperiment system with two existing electronic laboratory notebook systems developed and deployed in Southampton: the Semantic Electronic Notebook from the “Smart Tea” system and the Laboratory Blog Book. These activities have been supported by EPSRC e-Science and JISC ENGAGE funding, with the ENGAGE activity finishing June 2009. The systems are in use in several departments in Southampton, Bangor, STFC and shortly in the University of New South Wales. There are plans for deployment in several other institutions. By integrating these ELNs with myExperiment we will embed myExperiment within University of Southampton and establish the basis for extending this to the broader laboratory science community. In line with the user-centric philosophy of myExperiment, users in Chemical Biology, Physics and Engineering will provide the initial application and user focus within Southampton for the purposes of this extension project.
The extension project will consist of three major activities:
- The integration of process plans and templates from the Semantic ELN and the Lab-Blog systems with myExperiment;
- The integration of MatLab and R workflows used in the analysis of experimental data held in the Lab Blog system to myExperiment;
- The smart integration of the myExperiment, Semantic ELN and Lab Blog systems within the Chemistry domain via the newly developed OREChem ontology and repository system.
The development will continue the user centred approach with agile code development and iterative requirement capture and evaluation that has characterised both the development of myExperiment and the two ELN projects, with continuous evaluation.
- For the Lab Blog systems, the development of more template examples and enhancement of the specification (schemas etc) to enable increased value from sharing;
- Providing easy upload and download to/from MyExperiment of the blog templates;
- User testing of the template sharing, initially within Southampton, then Southampton /STFC then wider audiences;
- Evaluation and enhancement of the current MatLab blogging system to integrate with myExperiment.
- Following the improved specification of the Semantic ELN plans development of the upload/download systems to link the Semantic ELN with myExperiment;
- Development of an R interface in a similar manner to that for Matlab to integrate R. the Blog and myExperiment.
- We will undertake further evaluation and dissemination of the new capabilities of the systems and a code review to ensure the systems are sustainable;
- Discussions with the institution with regard to embedding the Lab Blog/ELN/MyExperiment combination as an institutional Service for selected departments in the physical sciences.
We have identified people to undertake this work. Andrew Milsted who created the Lab Blog system is available to work on the project, as is Kieron Taylor who has experience in using the Blog and writing linking applications that automate the blogging. Both Andrew and Kieron have gained experience with the Blog as a Service via the JISC ENGAGE Project. Andrew and Kieron have experience in collaborating with the myExperiment team via Danius Michaelides, who has been overseeing this liaison as part of his role as a “community champion” in phase 1 of myExperiment and subsequently in eResearch South. Support for work on the Semantic ELN integration will be provided via IT Innovation, specifically Ken Meacham who is currently working on the ELN project enhancement.
Value to the JISC Community
- Enhanced functionality of myExperiment and Laboratory ELNS for the academic community
- Increased institutional uptake and support of these systems
- Pro-active take-up of innovative research practice in related disciplines through use of the infrastructure and adoption of the suite of generic models, frameworks and tools
- Further understanding and experience in Science 2.0 and Open Science.
- Increased research capacity and capability through a highly skilled workforce equipped to succeed in a data-driven science environment, together with additional volunteer effort providing greater capacity to help to curate the growing volume of data.
- Enhanced knowledge transfer through the range of community collaborations.
myExperiment operates an extensive outreach programme and has achieved high visibility in the community as well as academic paper output. This will be applied to the extension project. In addition, Open Science is a strategic theme of eResearch South, the regional consortium led by Oxford and including Reading and STFC, and this provides further outreach and community development support and opportunities. In particular, Mark Baker in Reading is leading the Web 2.0 theme at the e-Science Institute.
IPR and Accessibility Issues
The project will comply with the JISC Funding Agreement. It is expected all outputs will be openly available (with Creative Commons licenses where appropriate), via the myExperiment Web site and Wiki. Intellectual property arrangements are covered by the existing myExperiment VRE. We will address accessibility of Web-based systems.
|Recruitment difficulties||Medium||Low||Staff identified. Existing staff will be re-assigned, summer students enlisted.|
|Loss of a team member||High||Medium||Multiple staff with expertise & skills required.|
|Socio-legal issues||Medium||High||Seek expert legal advice|
|Problems with software||Low||Medium||Work conducted within broad development team.|
|Network & Comms Problems||High||Medium||Provide alternative sites for the Lab Blog at the NGS and commercial hosting site.|