Omix Navigator
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In bioscience, thousands of new biological datasets and resources are published on an annual basis. Integration of these diverse data types such as disease, genomic, proteomic or transcriptomic datasets is extremely time and resource consuming. Omics-specific tools are efficient in focusing on one data type but cannot help the users to work on the necessary, multi-scale level and combine different omics datasets.
New software being developed at The Genome Analysis Centre (TGAC), following a recent funding boost, aims to solve the issue of data integration. To learn more about the funding provided by Norwich Research Park Translational Fund and the Omix Navigator Project we spoke to Project Lead, Tamás Korcsmáros.
JR: A number of projects at TGAC have recently received funding from the Norwich Research Park Translational Fund. Could you tell us about your particular project and why this funding is so important?
TK: Between 2010 and 2013 the development of Navigator was funded by a total of £110,000 from a Hungarian innovation grant and an EU Regional Development Fund grant. The project was carried out by the Hungary-based BioNav Ltd., led by Tamas Korcsmaros, current TGAC Computational Biology Fellow. The developed software meets the market needs as it provides: 1) a highly user-friendly, customizable interface with high compatibility with other tools, 2) a simple way to handle complex and various biomedical datasets; 3) tools to point out novel drug targets and to support network pharmacology needs; 4) a way to integrate biomedical datasets and network approaches to current cheminformatics and pharmacoinformatics pipelines.
TGAC and BioNav recently signed an agreement to give the exclusive licence of OmiX Navigator to TGAC. This allows the further improvements of OmiX Navigator. In the past few years, TGAC has developed several specific and gap-filling algorithms and approaches that alone have limited business potential. They were published under GPL3 licence providing that all codes should be shared with the users and they are too specific. Combining the general visualisation, data integration and workflow management framework of Navigator with TGAC developed software to meet the needs of research institutes and SMEs would be a perfect match that could not be achieved separately. The funding from the Norwich Research Park Translational Fund gives the proper funding to carry out this project.
JR: How will the bespoke Omix Navigator you are developing reduce the time taken to integrate, transform and cleanse data?
TK: Thousands of new biological datasets and resources are published on an annual basis. Evaluation of these systematic results is difficult as many of the datasets are stored in different formats. Roughly 70% of any data-driven project now involves simply managing data—integrating, transforming, and cleansing it—before any actual analysis can begin. Integration of diverse data types (e.g., disease, genomic, proteomic or transcriptomic datasets) is a very time and resource consuming process that makes the collected data much less useful. Omics-specific tools are efficient to focus on one data type but cannot help the users to work on the necessary, multi-scale level and combine different omics dataset.
The features of the Navigator framework is that it is an “all-in-one” solution. It contains:
• integrated molecular, cellular and medical databases
• a highly interactive data visualization mode (providing visualization of molecule structures, networks, analytical results together in a customizable “virtual sandbox”)
• an intuitive workflow-designer platform allowing informative and interactive overview of a complex analysis and easy import of algorithms as well as the export and import function of protocols
• standardized file formats with high compatibility
Navigator was developed as a cloud based solution, thus it is customizable, safe and extendable.
JR: With a release date set for early 2016 could you tell us who your new software will primarily be aimed at?
TK: Our comprehensive market research indicated that the primary target market will be academic researchers involved in systems biology research and other data-heavy projects, CROs (contact research organisations) and other small and medium-sized enterprise (SME) life sciences companies involved with clinical studies. Research groups are already spending money on similar software solutions to (1) gain visualized insight to advanced computational analysis without professional computational help; (2) predict the most promising experiments and, by this, decrease the cost of wet lab work; (3) investigate complex questions not possible with traditional approaches. Based on secondary research and focus groups interviews, consisting of a representative cohort including bioinformaticians and doctors; we have established that large pharmaceutical companies normally have their own in-house systems. Whereas life science SMEs and CROs are in need of an effective and customisable data management and visualisation infrastructure.
JR: How will this novel software benefit researchers working with metadata?
TK: Whilst the market leader software solutions for metadata analysis are functional, they are mostly only for interpreting experimental and clinical results. However, OmiX Navigator besides providing the main features of the market leaders, avoids long data integration development cycles and excess data replication. OmiX Navigator will have many specific advantages over current available software solutions. These include:
• flexible data visualisation architecture
• integrated molecular, cellular and medical databases
• an interface for various ‘omics datasets
• a highly interactive data visualization mode
• an intuitive workflow-designer platform
• standardized file formats with high compatibility to other programs
• a way to integrate genomics, transcriptomics, proteomics and biomedical datasets with network approaches to support current cheminformatics and pharmacoinformatics pipelines
Tamás Korcsmáros was speaking to Jack Rudd, Editor for Technology Networks
New software being developed at The Genome Analysis Centre (TGAC), following a recent funding boost, aims to solve the issue of data integration. To learn more about the funding provided by Norwich Research Park Translational Fund and the Omix Navigator Project we spoke to Project Lead, Tamás Korcsmáros.
JR: A number of projects at TGAC have recently received funding from the Norwich Research Park Translational Fund. Could you tell us about your particular project and why this funding is so important?
TK: Between 2010 and 2013 the development of Navigator was funded by a total of £110,000 from a Hungarian innovation grant and an EU Regional Development Fund grant. The project was carried out by the Hungary-based BioNav Ltd., led by Tamas Korcsmaros, current TGAC Computational Biology Fellow. The developed software meets the market needs as it provides: 1) a highly user-friendly, customizable interface with high compatibility with other tools, 2) a simple way to handle complex and various biomedical datasets; 3) tools to point out novel drug targets and to support network pharmacology needs; 4) a way to integrate biomedical datasets and network approaches to current cheminformatics and pharmacoinformatics pipelines.
TGAC and BioNav recently signed an agreement to give the exclusive licence of OmiX Navigator to TGAC. This allows the further improvements of OmiX Navigator. In the past few years, TGAC has developed several specific and gap-filling algorithms and approaches that alone have limited business potential. They were published under GPL3 licence providing that all codes should be shared with the users and they are too specific. Combining the general visualisation, data integration and workflow management framework of Navigator with TGAC developed software to meet the needs of research institutes and SMEs would be a perfect match that could not be achieved separately. The funding from the Norwich Research Park Translational Fund gives the proper funding to carry out this project.
JR: How will the bespoke Omix Navigator you are developing reduce the time taken to integrate, transform and cleanse data?
TK: Thousands of new biological datasets and resources are published on an annual basis. Evaluation of these systematic results is difficult as many of the datasets are stored in different formats. Roughly 70% of any data-driven project now involves simply managing data—integrating, transforming, and cleansing it—before any actual analysis can begin. Integration of diverse data types (e.g., disease, genomic, proteomic or transcriptomic datasets) is a very time and resource consuming process that makes the collected data much less useful. Omics-specific tools are efficient to focus on one data type but cannot help the users to work on the necessary, multi-scale level and combine different omics dataset.
The features of the Navigator framework is that it is an “all-in-one” solution. It contains:
• integrated molecular, cellular and medical databases
• a highly interactive data visualization mode (providing visualization of molecule structures, networks, analytical results together in a customizable “virtual sandbox”)
• an intuitive workflow-designer platform allowing informative and interactive overview of a complex analysis and easy import of algorithms as well as the export and import function of protocols
• standardized file formats with high compatibility
Navigator was developed as a cloud based solution, thus it is customizable, safe and extendable.
JR: With a release date set for early 2016 could you tell us who your new software will primarily be aimed at?
TK: Our comprehensive market research indicated that the primary target market will be academic researchers involved in systems biology research and other data-heavy projects, CROs (contact research organisations) and other small and medium-sized enterprise (SME) life sciences companies involved with clinical studies. Research groups are already spending money on similar software solutions to (1) gain visualized insight to advanced computational analysis without professional computational help; (2) predict the most promising experiments and, by this, decrease the cost of wet lab work; (3) investigate complex questions not possible with traditional approaches. Based on secondary research and focus groups interviews, consisting of a representative cohort including bioinformaticians and doctors; we have established that large pharmaceutical companies normally have their own in-house systems. Whereas life science SMEs and CROs are in need of an effective and customisable data management and visualisation infrastructure.
JR: How will this novel software benefit researchers working with metadata?
TK: Whilst the market leader software solutions for metadata analysis are functional, they are mostly only for interpreting experimental and clinical results. However, OmiX Navigator besides providing the main features of the market leaders, avoids long data integration development cycles and excess data replication. OmiX Navigator will have many specific advantages over current available software solutions. These include:
• flexible data visualisation architecture
• integrated molecular, cellular and medical databases
• an interface for various ‘omics datasets
• a highly interactive data visualization mode
• an intuitive workflow-designer platform
• standardized file formats with high compatibility to other programs
• a way to integrate genomics, transcriptomics, proteomics and biomedical datasets with network approaches to support current cheminformatics and pharmacoinformatics pipelines
Tamás Korcsmáros was speaking to Jack Rudd, Editor for Technology Networks
