Genedata Profiler

Organizing and managing data is key to effective patient profiling. Built on nearly two decades of experience in omic data architecture gained from chip, micro-array, NGS and other omic data such as mass spectrometry, Genedata Profiler offers:

  • A technology-agnostic infrastructure able to federate all your omic data together with any relevant clinical data in a scalable, open, interoperable and compliance-ready manner;

  • The infrastructure to ensure that all the stakeholders in your research ecosystem are able to securely access, use and generate scientific information from rich multi-omic data.

Security and privacy of patient data is critical. Genedata Profiler has been designed to meet the technical requirements for compliance by providing:

  • Study-centric, comprehensive role-based permissions;

  • Three layered security model;

  • Complete chain of custody of data and results;

  • Audit trails and reasons for change;

  • Method lifecycle management;

  • Electronic signatures;

  • Sophisticated reporting infrastructure.

These features ensure that your organization can validate any Genedata Profiler system in accordance with applicable regulations such as GxP, 21 CFR Part 11, HIPAA etc.

Security

Key to the robust security for your research provided by Genedata Profiler is a three-layered security model. The model allows secure access to genotypic and phenotypic information across the whole enterprise while balancing the administrative burden of security. The layered design couples high throughput omics analysis capabilities with the necessary controls required for handling sensitive patient data. The model uses a:

  • Study layer—provides the role based permissions for the study;
  • Operational layer—provides the role-based permissions required to operate the software;
  • Physical layer—translates the operating system and file system permissions into the other layers;
  • Hardware abstraction layer—eases integration and interoperability with a wide variety of physical data sources e.g. files, databases, FTP sites, web resources, Amazon S3 and high performance file systems (HPFS).

The majority of our customers are global organizations and research consortia with distributed research groups in multiple locations and countries. Genedata Profiler was designed with collaboration in mind.

  • Data, processing pipelines and analytical tools can be located where most appropriate and efficient for effective work.
  • Comprehensive role-based access controls allow researchers to collaborate securely both internally and externally.
  • Powerful annotation and search capabilities coupled to the chain of custody of data gives visibility to data, eliminates data handovers and reduces duplicate work.
  • Method lifecycle management permits processing pipelines to be standardized throughout your organization and scales analysis to non-expert bioinformaticians.

Scalability and performance has been a critical element in the widespread adoption of Genedata Profiler since its inception. Core to this scalability is a unique combination of:

  • A flexible, extensible and robust data architecture scalable to millions of genomes and associated clinical data annotations;
  • Processing pipelines that incorporate best practice algorithms optimized by Genedata computational experts, coupled with support for major high performance computing platforms (HPC);
  • Ability to massively parallelize genomic computing operations using our native grid scheduling service on a per sample or per chromosome basis and take advantage of on-demand and elastic compute resources;
  • Federation and linking of data that brings computing power to the data “in place”, reducing copying, moving or importing potentially huge volumes of data;
  • Comprehensive role-based access control and method standardization to scale processing, analysis and scientific insights to all stakeholders in an organization, rather than relying solely on often over-burdened expert resources (e.g. bioinformaticians);
  • Complete flexibility in deployment, whether on your premises, cloud, private cloud, hosted by Genedata or a hybrid solution, ensures the optimum balance of cost, performance, scalability and security.

Consistently generating high quality data regardless of researcher location, expertise or role is key to building robust scientific outcomes and ensuring compliance. Features of Genedata Profiler such as chain of custody, method life cycle management and comprehensive audit trails ensure that you can:

  • Completely reproduce an analysis from raw data to results with exactly the same processing workflow, parameters, data sets, reference genomes and statistical results;
  • Inspect and trace back the data at any point from raw data to results, including quality metrics, intermediate processing steps, statistics, curation, references and ontologies;
  • Know exactly who operated on the data, when, with what methods and where;
  • Standardize and harmonize methods throughout an organization, so everyone uses agreed approved methods;
  • Generate comprehensive data quality metrics to build trust and confidence in data;
    Allow only individuals with appropriate permissions to change anything, and log those changes.

Omic data offers great promise for precision medicine, which requires effective and efficient data analysis to rapidly generate scientific insights. Such insights are dependent on the various stakeholders having the right tools.

  • With comprehensive statistical, data-mining and visualization capabilities, Genedata Profiler empowers your researchers to get to scientific insights fast, whether the data is in-house or public domain, or managed by in-house data warehouses such as tranSMART.
  • Comprehensive interpretation of data through built-in integrations with popular public data sources such as GEO and ArrayExpress and commercial tools such as Ingenuity Pathway Analysis.
  • Best-in-class algorithms, cutting-edge statistical analyses and machine learning approaches enable deep insight into complex data.
  • In house, third party and public algorithms as well as R-scripts are easily integrated into Genedata Profiler via an open shell API, enabling you to leverage this investment while benefiting from Genedata’s open, interoperable and compliance-ready platform.
  • Linkage of final results with processed and raw data facilitates validation and ensures quality while promoting a deep understanding of data.
  • Flexible reporting capabilities drive communication of results for effective decision making.
  • Genedata software has been the tool of choice for uncovering scientific insights in complex omic data as part of many research consortia such as EpiFemCare, NewGeneris and CVgenes@target.

The end-to-end automation capabilities of Genedata Profiler enable:

  • One-click processing of data from raw data to results using standard workflows with the ability to investigate the data at any step in the workflow for quality or scientific insights;

  • Unparalleled scalability and performance on data sets of all sizes and complexity—with processing times reduced to hours instead of days, and working on hundreds of samples in parallel, Genedata Profiler automatically uses your high performance computing resources only as required;

  • Automated generation of comprehensive quality reports and metrics.

Genedata Profiler is designed to be interoperable, making maximum use of your data and existing systems to facilitate global collaboration.

  • Technologically agnostic, Genedata Profiler federates and harmonizes data from in-house and external databases, file systems, websites and public data sources.
  • Powerful APIs allow permission-based read/write of data and integration with existing and third party systems while maintaining compliance and chain of custody of data.
  • An open shell API allows easy integration of existing in-house or third party algorithms and scripts into the Genedata Profiler infrastructure. This powerful approach automatically gives these algorithms complete access to the enterprise security, scalability and compliance resources, including HPC support without writing a single line of code.