laboratory informatics
a foundation on top of which you can build applications. It underpins the other products that we have to offer, including laboratory information management system (LIMS), electronic laboratory notebook (ELN), and SDMS capabilities.’
No more closed systems Core Informatics’ vision for supporting the effective use of complex and huge biological datasets is to move away from ‘closed, black box systems’ that are difficult to get data into and out of, Stalker continues: ‘We are just about to launch version 5.2 of our PFS environment. Tis will include a new API built on the OASIS-standard open data protocol, OData for building RESTful APIs. It’s really nice and simple to program. We are actively looking for similarly user-friendly and open solutions for our expanding family of APIs.’ Core is working with the industry to
develop user-friendly apps for the PFS, says Stalker. ‘As an example, we have built a plugin for the Geneious solution from Biomatters, which effectively allows our platform to operate as a document repository. Using the plugin you can query against and annotate your sequences directly and then bring them back into PFS without having to worry about importing and exporting to and from the LIMS and Geneious. It’s all done seamlessly through the API, and this is where our platform technology really shines, as it’s easy to add these integrations. We have additional partnerships ongoing to develop plugins or apps that will directly link the functionality within our PFS with other bioinformatics platforms and tools.’ Core Informatics is effectively fostering
unique framework for bioinformatics data management, and can integrate disparate data sources and instrumentation. ‘When you model your data in our system, that data becomes exposed in our application programming interfaces (APIs), scientific data management system (SDMS), and other areas, so that you can immediately start coding against it and integrating with other systems and tools,’ Stalker comments. PFS is a cloud-hosted platform as a
service (PaaS), which contrasts with single- point soſtware as a service (SaaS) solutions. ‘Whereas SaaS are offered as individual pieces of soſtware, our platform represents
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what Stalker describes as an ecosystem of developers, and a community that can collaborate to build solutions on top of the PFS infrastructure. ‘Everyone is trying to move away from standalone analysis tools that companies have to buy licenses for and install in house. We want these capabilities offered as a service, on demand. Tis is what we are developing within the Platform for Science environment.’
Sifting through the public repository It’s not just in-house research that is creating vast quantities of biological data. Expanding capabilities in mulitple biological disciplines have resulted in huge volumes of experimental and analytical data sitting in the public domain. Te commercial sector is looking to exploit this repository to help
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inform and direct their own disease and drug research and development, notes Jaqui Hodgkinson, VP product development biology and preclinical products at Elsevier R&D Solutions. ‘Te failure rate in drug discovery is very
high, and there is a lot that we can learn from viewing published data contextually alongside in house and collaborative research,’ Hodgkinson notes. ‘However, there are few tools that can filter through millions of published works according to precise search parameters. We have developed Pathway Studio as an open and flexible platform that gives customers the ability to search, mine and model data in exactly this way.’
CORE INFORMATICS IS EFFECTIVELY FOSTERING AN ECOSYSTEM OF DEVELOPERS
Pathway Studio is founded on a
proprietary natural language-processing text-mining tool that can rapidly search through potentially hundreds of thousands of full text articles in just a few hours to search for any gene, protein, biological concept or pathway, disease or drug response/interaction of interest. Te soſtware allows users to build maps of interacting pathways, as well as map, analyse and visualise complex disease mechanisms, gene networks and drug response profiles. ‘Users can search for key concepts within
relevant data sets, perhaps for gene and protein interactions, or inhibitory activities of drugs on gene expression, using simple search terms. Powerful statistical tools also allow users to import and analyse their own experimental data to help identify possible cause and effect on biological pathways, and to model the effects of gene expression and protein-protein interactions on disease,’ Hodgkinson explains. ‘You could, for example, use microarrays to compare analytical samples from sick and healthy individuals, and then import the resulting data into the platform to identify major differences between the datasets, and the networks that are involved.’
Supporting biomarker and target discovery Pathway Studio can provide new insights into the molecular basis of disease, and supports target and biomarker discovery programs and the pathway analysis of clinical and experimental data, Hodgkinson
AUGUST/SEPTEMBER 2016 17
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