How to make your discovery scientists twice as productive


Discovery scientists waste 50% of their time on preparing omics data – but not for much longer. Genestack has responded to this frustration with two new modules for its biodata platform. CEO Misha Kapushesky is to talk about how a modular approach can overcome the obstacles at the Bio-IT World Conference and Expo 2018.

Frustrated that their discovery scientists spend more time looking for and preparing relevant omics data than analysing it, Genestack’s pharmaceutical clients challenged the company to solve this industry problem. The result is two new modules for its biodata platform, which will both be previewed at Bio-IT World Conference 2018. The omics data manager module allows biologists to interrogate and visualise transcriptomics data at scale, and the expression data miner module supports users to collaborate on omics studies to speed up research and enable data re-use and meta-analysis.

Misha Kapushesky, PhD, CEO of the Cambridge-based bioinformatics software company, explains that by incorporating the two new modules into its omics data management offering, scientists will be more productive and need less support from bioinformaticians: “Biologists tell us it’s hard to find relevant data, as they have to log on to different servers and databases. Without a single point of truth you can have different versions of the data from different sources with no way of telling what is correct. It is also hard to write analytical tools to work with data in different formats.”

“They estimate that more than fifty percent of their valuable time – which should be spent on data mining and analysis – is being wasted.”

The expression data miner module accelerates not only the workflow, but also new target discovery, by enabling biologists to look across multiple sources of transcriptomic data to better understand gene function. A custom interface enables biologists to interrogate and visualise data without support of a bioinformatician, for example viewing the highest expressed gene or most specific gene for any organ or organ system. The module also makes it easier to work with multiple genes and tissues/cell lines/cell types in one flexible, super-fast interface.

The omics data manager module provides a collaborative environment for capturing and organising study and sample-level metadata along with required sequencing procedures, produced raw data and secondary analyses. The result is a single point of truth for all omics metadata, including sequencing and analysis requirements. Metadata is cleaned up with validation rules and ontologies. Results are easy to find and use in meta-analyses.

Genestack’s platform has a rich metadata system, which enables both proprietary and public data and metadata to be captured, described consistently and stored securely in a centralised location ready to be used for studies.

Imad I. Yassin, Genestack’s VP of Sales and Marketing adds: “Genestack is one of the strongest players in the market when it comes to the management and analysis of omics data. Our clients like that the platform is open and agile, so people can work in a way that suits their organisational culture. “

“We are not prescriptive. Certain visualisation capabilities are included but if your team wants to use another tool such as Tableau or Spotfire, it doesn’t matter – the platform can facilitate that; it is completely agnostic.”

“Then in the back end, when you think about pipelining, you may want to use open source packages, or other existing pipelines you have such as those coded in Common Workflow Language or set up on a commercial cloud such as DNAnexus. The metadata editing and indexing in Genestack will make it easier to work with this data and make it available via APIs and visualisation.”

Genestack’s mission is to help scientists make decisions. Its omics data management platform, with its new modules, is set to free discovery scientists and bioinformaticians to concentrate on the challenges that will bring greatest value to their organisations.

Genestack CEO, Dr Misha Kapushesky, will be discussing how creating a collaborative ecosystem of multi-vendor systems can offer the best solution for discovery science, in the Pharmaceutical R&D Informatics Track of the Bio-IT World Conference and Expo 2018 on Wednesday 16 May at 2.55pm. Genestack is also on stand 436 and the new modules will be available to trial in Summer 2018.


More information about the two modules is available here:

Omics Data Manager

Expression Data Manager

To read more information, click here.

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