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standards by end users, even if instrument and soſtware vendors were quick to adopt open, standard format languages, Lemon suggests. ‘Ideally those formats can be applied to existing instrumentation; otherwise it’s going to take a decade or so to get through the instrument replacement cycle before uptake can be considered anywhere near comprehensive. Our clients aren’t going to be able to change their instruments or soſtware just because a new data standard is only being released with new equipment.’ Tere have already been instances of some data
formats naturally being accepted as standards for particular applications,’ comments John Stalker,
STANDARDISATION OF
DATA FORMATS IN THE R&D SECTOR COULD ALSO LEARN A FEW LESSONS FROM THE WEB ITSELF
product manager, Platform for Science at Core Informatics. ‘Te .ab1 file format, for example, originally developed by Applied Biosystems as part of the capillary sequencing platform, became the de facto standard in that that space. Tese were the files stored in NCBI, and all work around analysis tools at the time centred on that input format. In this case, uptake and acceptance of the format as a standard has been organic rather than contrived. Similarly, there is increasing commonality in areas such as next generation sequencing, where much of the data ends up in .bam and .sam files, irrespective of the sequencing instrumentation or methodology used.’ Standardisation of data formats in the R&D
sector could also learn a few lessons from the web itself, Stalker continues. Safari, IE, Chrome and Firefox are all competing web browsing platforms but, nevertheless, all work with the same HTTP and HTML standards. It was necessary to get standards in place very early on in the development of the internet – otherwise it would all have collapsed.’ One alternative to the implementation
of across-the-board standard data formats is to exploit the burgeoning availability of microservices in the cloud, Stalker continues. ‘Tere has been a huge movement towards containerisation of microservices in the cloud. Tere is a burgeoning catalogue of web-based converters and translators that can just be picked up and clicked together to allow the integration of different data formats. As the cloud grows and more tools become available to make the connection of disparate soſtware and data formats more trivial, the need for a standard may become
20 SCIENTIFIC COMPUTING WORLD @scwmagazine l
www.scientific-computing.com
less urgent. Tese containerised microservices are becoming increasingly commoditised, so we can just consume them as a service, in real time. We’ve seen this in the sequencing arena for the last couple of years by purpose-built businesses that string together pipeline analyses; for example, Seven Bridges, DNA Nexus, GeneStack. Soon, consumers will be able to wire up plate readers, LC/mass spec, and a myriad of other data producers in a more cohesive way.’ So what are the ideal attributes of a data
standard? From a technical perspective, it’s all about accessibility for current technologies, as well as being able to embrace new types of analytical instrumentation and methods as they are developed, suggests BSSN Soſtware’s Burkhard Schaefer. ‘A standard must have a natural longevity, and be flexible enough so that it can easily be adopted by new analytical approaches and techniques.’ Data standards will also help to make sure that
data can be retained and easily retrieved, perhaps decades on, he points out. ‘Regulated industries, and particularly the pharma industry, are looking at data retention times of 50 years or more, so having data in a format that can be read without requiring additional soſtware is important. As soon as you put something in binary format, then there’s always a chance the soſtware that can read that format now will become outdated or obsolete.’ Data will oſten outlive the data system that
generated it, Barrington-Light concurs. ‘Tis leaves customers with a serious issue – how can I search and view that data without the original soſtware? If the data was in a standardised format that could be read by any current data system, then the need to retain outdated systems would be removed, and allowing customers to select their next data system based purely on their
business needs and not compatibility with a previous system’s data format.’ Standard formats also spell good news for the
soſtware providers, Schaefer notes. ‘Te more instruments that you can connect to one vendor’s platform, the more valuable and versatile that platform becomes. And an open data standard format will not only make partnering and outsourcing more seamless, it will help to ensure equivalence with respect to data quality, content and reporting.’ At the end of the day, end-users don’t look for
standards; they look for instruments that do a particular job in a particular way, and informatics solutions that will allow them to carry out an application or solve a business problem, Schaefer points out. ‘A data standard only represents a tool that can make something easier to carry out, but it never solves the original problem.’ We need to consider how a standard might
function, continues Schaefer, who is championing the XML-based AnIML data standard, and is also involved with eight other standards organisations, including SiLA. Te primary requirements include ease of adoption – how well does it play with current soſtware tools and instruments. ‘When you design a standard data format, it should, most obviously, fall into place within any existing informatics environment. People already have an infrastructure in place and they want to be able to use the standard without too much new learning, so that their productivity isn’t compromised.’ Cost is another major consideration. ‘You have to ensure that the total cost of ownership will not be prohibitive – just for the sake of getting two systems to talk to one another without the need for an integration tool. And if your data format isn’t an open format, then that cost could be considerable.’ Schaefer also maintains that development of
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