Periodic Reporting for period 3 - DD-DeCaF (Bioinformatics Services for Data-Driven Design of Cell Factories and Communities)
Reporting period: 2019-03-01 to 2020-02-29
Omics data is currently rapidly accumulating in public domain and proprietary databases and has the potential to accelerate development of biotechnology-based products significantly. However, omics data is not leveraged effectively in the biotechnology industry due to lack of tools to rapidly access public and private data and to design cellular manipulations or interventions based on the data. With this project we aim to make a broad spectrum of omics data useful to the biotechnology industry covering application areas ranging from industrial biotechnology to human health. Our approach is based on using omics data to develop, parameterize and constrain large-scale models of biological systems. We will develop novel approaches for omics data analysis using models to enable 1) Identification of novel enzymes and pathways by mining genomic data collected from environments such as oceans and soils, 2) Data-driven design of cell factories for the production of chemicals and proteins, and 3) Analysis and design of microbial communities relevant to human health, industrial biotechnology and agriculture.
All research efforts will be integrated in an interactive web-based DD-DeCaF platform that will be available for academic research and teaching as well as industrial product development communities. The DD-DeCaF platform will incorporate tools to analyze and visualize diverse omics datasets, and to use these datasets for designing cell factories and communities. This platform can be leveraged by biotechnology SMEs to increase their competitiveness through economizing resources and reducing time-to-market within their respective focus areas. The platform will be composed of standardized and interoperable components that service-oriented bioinformatics SMEs involved in the project can reuse in their own products. Two end-user companies will be involved in practical testing of the platform built within the project using proprietary omics data generated at the companies. These companies are involved in production of nutrition-related products (vitamins and other dietary supplements) in a renewable fashion and the project is expected to accelerate the development of new products within the companies.
On the technological side (WP7, WP8) the project focuses on building software packages, reusable software services, and visual user interfaces to exploit the models an algorithms developed in WP2-WP6. During this reporting period the project has delivered a comprehensive software library for cell factory design that can be used as a foundation to develop user friendly software tools within the project (Cameo), software service APIs that allow manipulating and simulating models, and a prototype implementation of a web-based platform for cell factory design and pathway based data and simulation result visualization (http://app.dd-decaf.eu). This platform includes facilities for uploading and storing data relevant for cell factory design, tools for integrating data with models and tools for performing advanced computations using the models. The prototype platform is under constant testing by the end user partners (WP9) who are providing valuable input for further development.