CRUK Manchester Institute - Case Study Part II: Dotmatics ELN – a software evolution

The Cancer Research UK Manchester Institute is a leading cancer research institute within The University of Manchester, core funded by Cancer Research UK. In 2009, the Drug Discovery Unit (DDU) of the Institute began building a laboratory, expert team and informatics infrastructure from the ground up. At the time, its current Head of Chemistry, Dr Allan Jordan, met with Dotmatics, the scientific informatics solutions provider, to discuss possible options for the future of its informatics implementation.

It was essential that the chosen informatics solution fit the team’s workflows and provide all the necessary functionality, but as a charity-funded laboratory it was also essential that the solution was cost effective. Dotmatics put forward a proposal: to work closely to collaborate on further development of the Dotmatics ELN. Thus, the Dotmatics team alongside Dr Jordan’s Manchester Institute team and the CRUK Drug Discovery Unit in Glasgow (Beatson Institue), worked together to design a next-generation ELN that was flexible and easy to adopt by users.

Being part of that software evolution offered a number of advantages – including the opportunity to provide input on the features developed. In 2009, Dr Jordan and his team worked with Dotmatics to create a list of requirements that would enable the ELN to fit their workflows, but also to have a broad appeal by solving common research problems. Based on these discussions, Dotmatics provided an iteration of the package which the team implemented across the lab. From Spring 2010 until now, the ELN has continued to evolve and has been in continuous use while new functionalities have been added.

Dr Allan Jordan, Head of Chemistry at The Cancer Research UK Manchester Institute explained ‘We’re a charity-funded enterprise and the fact that a company like Dotmatics gave us the possibility to customise an ELN so that it closely fitted our specific needs – and at a price we could afford – was attractive.’

When the Institute first began recruiting new staff members, discussions were already underway with Dotmatics which meant that the incoming team knew from the very beginning that, as far as practicable, they were joining a predominantly electronic organisation. Other than the analytical equipment, the lab is pretty much paper free and it was made very clear at interview that people would be expected to conform to that environment and workflow.

One of the biggest challenges an organisation can face is the problems that result from the absence of a central repository for data. A common practice is for data from complex biological experiments – pharmacokinetic experiments, for example – to be captured on Excel spreadsheets and then saved in scientist’s personal drives or desktops. This can lead to many issues, as Dr Jordan explained: ‘My previous experiences highlighted that trying to discover why a compound hadn’t gone through and been nominated as a development candidate, despite looking very good in the early assays, was incredibly difficult, especially if the scientist involved had left the company. Writing papers and writing patents also faced stumbling blocks because much of the critical information was soft intelligence that was buried in an individual’s mind.’

‘We didn’t want that to happen to us and so everything had to be captured, audited and transparent to the entire team.’ He added that ‘transparency is particularly critical because people who aren’t necessarily part of the direct team will look at the data in a different way and therefore be able to offer new interpretations and draw different conclusions. Having an informatics platform that provides a very open, yet secure, environment aids that idea generation and flow, and in the past few years packages like the Dotmatics Suite have evolved to the point where they encompass most of the drug discovery process.’

The current project within the DDU is to integrate the system with pieces of equipment and experiments that traditionally would not be captured into an ELN or database system. The team is using different statistical tools and scripting packages to effectively pre-analyse the data and present it to Dotmatics interface in a form the software can analyse as if it were a biochemical screen. Dotmatics can then process the data and bring it into the database, and it’s all done in a way that ensures there’s no bias on the part of the end user. It’s a defined data processing system that pulls together a number of packages, including Dotmatics, and transforms raw data in a completely reproducible manner.

‘The support we’ve received from Dotmatics and its wider user community has been very valuable,’ commented Dr Jordan. ‘We’re a small team of just 30 people and we have no internal informatics department, team of programmers or dedicated scientist whose responsibility it is to manage our database and ensure everything is robust, repeatable and viewable. Because we lack that intrinsic expertise, being able to ask other users within similar organisations questions about how they have integrated their ELN with compound acquisition, for example, has been vital.

‘What we’ve learned from this experience of co-developing and implementing an evolving ELN is that although the package is highly configurable, and although an end user can get it up and running, we found it helpful to allocate some initial budget for someone with more relevant and direct expertise,’ continued Dr Jordan. ‘Not having that knowledge at the outset, we weren’t aware we needed to think about how we would structure the data in a way that made the integration easier downstream, so the advice I’d offer is that having that initial implementation be as right as possible will be beneficial later on.’