The Southampton E-lab blog notebook – Part 1 Aims
This is the starting point for a description of the development work being done in the School of Chemistry at the University of Southampton on a blog-based electronic laboratory notebook for biochemistry/molecular biology. Ultimately the aim is for this document to form the first draft of a paper describing the system.
First things first, acknowledgements:
All the system development work is being done in the group of Professor Jeremy Frey, largely by Andrew Milstead a PhD student. The contribution of my group, mainly through the work of another PhD student, Jenny Hale, is to break the system, complain and generally make Andrew’s life difficult. Through various iterations this has lead us to propose a system that seems to fulfill a number of our criteria. A working prototype is being used ‘in anger’ in the laboratory. This work is partially funded by the UK biological research council (BBSRC) through an e-science development grant and partially by the engineering and physical sciences research council (EPSRC) through a Platform grant held by Jeremy.
Directed evolution is a process whereby a library is generated by introducing random changes to a gene that encodes a protein and that library is then screened to identify protein variants with enhanced or desired function. The libraries can be large and the experimental process usually goes through multiple cycles, with variants selected in one cycle being used as a starting point for the next. Our ultimate aim is to capture the data from these experiments in such a way that allows us to identify the path a sample has taken through the whole experiment. These experiments can generate a lot of data, most of which is usually thrown away. By capturing the data we aim to enable significantly more detailed analysis of the experiment with the ultimate goal of optimising the directed evolution process in a rational way.
The purpose of and aims of an electronic laboratory notebook
Our aim in developing an electronic laboratory notebook system (ELN) is essentially two fold. The first is to collect the day to day workings and records of a research worker, or workers, in electronic form. This will allow searching through text, easy archival and backups, and provides a route towards making raw data available. This can be achieved by essentially any free form recording system including scanning a paper notebook and placing pdfs on the web.
Our second aim is to collect information on samples, protocols, and experimental data and link this together in a form that can be processed by a machine. Such a system would allow questions to be asked like ‘which PCR reactions used primer X’, or ‘who was the last person to use the gel running buffer?’. Ultimately such a system could also assist in archival of samples provide the basis of a database recording all materials, samples, and protocols used in the lab. However, recording all the relevant data would be an immense amount of work. A system that could capture and relate every element of an experiment would be unwieldy and probably unworkable in the context of an academic research laboratory.
Thus our target is to develop a system that captures as much of the ‘metadata’ from a laboratory procedure as possible, without imposing an undue burden on the research worker. Ideally such a system should be flexible, to allow any process, or modfication to a process to be captured. It must therefore allow free text. It should be easy to use and not place restrictions on the ability of users to carry out their experiments in the way they want. If it does require a ‘correct’ workflow to operate optimally, the system must encourage users to use that workflow by providing added value or ease of use. And the system should not break if a user pursues an ‘incorrect workflow. Finally, it must allow the uploading of any type of file that might be relevant. If a file type is not recognised some form of placeholder should be provided to show the file is there an allow download.
So our criteria for a successful system can be set out as follows:
- The system must allow free text entry (free description)
- It must allow the capture of metadata that describe, type, category, quality or any other aspect of a material, sample or protocol (flexible metadata)
- It should allow an inexperienced user to record their experiments without any undue extra burden above and beyond that required for best practise in using a paper notebook (ease of use)
- If a specific workflow is required for optimal performance the system should encourage this workflow but it should not break if the workflow is not followed (robustness)
- It must allow the upload and download of arbitrary file types (arbitrary uploads)
Part 2 will look at the underlying structure we have adopted to develop an ELN system.