Outsourcing, end-of-life LIMS, and disruptive technologies such as the cloud, are driving changes to the laboratory informatics landscape, as Tom Wilkie discovered at the Paperless Lab Academy in Barcelona Spain, this week.
written by Tom Wilkie, Published online at Scientific Computing World, April 2015.
The laboratory informatics industry is facing unprecedented change, both because the pharmaceutical industry is outsourcing more and more of its activities, and also because many large deployments of Laboratory Information Management Systems (LIMS) are nearing the end of their lives but will not be replaced like-for-like.
According to Patrick Pijanowski, pharma and life-sciences partner at US-based consultancy LabAnswer, pharmaceutical companies and other informatics users are not willing to invest in a new LIMS simply to get an incremental upgrade. What they want is ‘transformational change’, he told the Paperless Lab Academy (PLA) in Barcelona, Spain, on 14 April 2015. What is happening is ‘different from what we have seen before. It’s different from what I’ve seen in 20 years in the business,’ he continued.
Not quite so fully articulated during the sessions at the PLA, but forming a pervasive undercurrent nonetheless, was the issue of disruptive technologies – specifically the cloud and to a lesser extent, big data. The two tended to be bracketed together as if the cloud was seen, albeit implicitly, as the only technology capable of dealing with the challenges presented by big data.
Concerns over data security and the protection of intellectual property and personal information continued to make some delegates uneasy about jumping immediately into the cloud. But, as the PLA progressed, it became clear that, in a world of externalised pharma companies, current technologies and processes are not performing well either.
In contrast, although mobile devices such as tablets and PDAs featured frequently, these appeared to be regarded not as disruptive but rather simply as continuing business more or less as usual.
Pharma outsourcing will force standards on informatics
The implications for informatics of the ‘externalisation’ of the pharmaceutical industry dominated the event. In his keynote address, Pijanowski told the meeting that ‘today, the pharmaceutical industry is outsourcing virtually every function,’ with the result that data integrity and system security were major concerns.
According to Rachel Uphill, pharmaceutical companies are outsourcing not just to contract research organisations (CROs) and contract manufacturing organisations but also to academics, making the need for common data formats and standards all the greater. Uphill is business consultant, early IP and data strategy, to the pharmaceutical giant GSK and is also an advisor to the Allotrope Foundation, which was set up by the pharmaceutical industry some three years ago to build a framework for open data standards.
In the absence of standards the situation today, she said, was one of incomplete, incompatible software; no standard data formats; and inconsistent metadata. It is hard for researchers to mine data for useful information, she pointed out, because the metadata is stored elsewhere and is often captured incompletely, inaccurately, or sometimes not at all due to free-text manual entry.
Allotrope’s goals, she said, were to create re-useable software components; an open document standard; and an open metadata repository. The outcome will be a software toolkit to allow developers to embed a set of standards for analytical data in software utilised throughout the whole of analytical chemistry on different instruments from different vendors.
The project has ambitious deadlines, with the first public release expected in 2016, only three years since software development started and only four years since the Foundation was set up. The hope is that eventually the ADF – the Allotrope Data Format – will be embedded in instrument and informatics vendors’ software. But as a temporary expedient, to promote the usefulness of ADF before 2016, converters are being developed to transform data to ADF as a separate step.
The progress is all the more remarkable since the Allotrope Foundation has to move carefully so as to conform at all times with US anti-trust legislation and avoid any suspicion that the pharmaceutical companies might be coming together in a cartel. Consequently, the secretariat for this highly technical exercise is provided by a team of Washington lawyers, while the technical work is being carried out by the German software company Osthus.
The place to feel the pulse of informatics
The Paperless Lab Academy continues to be possibly the most interesting and thought-provoking event dealing with laboratory informatics. Last year, Scientific Computing World reported not only on how Paperless laboratories do better sciencebut also on the disrupting effect that the cloud might have on traditional LIMS vendors and the impact of process analytic quality control on the traditional QC laboratory. By providing a synoptic overview of the informatics landscape and identifying trends and developments for the future, this year’s meeting of the PLA if anything surpassed the event in Amsterdam last year.
This is the first in a series of reports from the Paperless Lab Academy. The second article Lost knowledge and dead data explores the issues surrounding outsourcing in more detail, while the third discusses Disruptive technologies in informatics.