The CoSMo Company, a Lyon, France-based bioinformatics startup, has been selected to participate in a European consortium that aims to build an in silico modeling platform to support research in biology and biotechnology.
The consortium, called New Bioinformatics Methods and Tools for Data-Driven, Predictive Dynamic Modelling in Biotechnological Applications, or BioPreDyn, aims to create a software pipeline that includes computational tools to integrate large quantities of biological data and help biotechnologists design and optimize their production processes.
The three-year, €2.9 million ($3.8 million) project is funded by the European Commission's 7th Framework Program. A kick-off meeting was held earlier this month at the Center for Genomic Regulation in Barcelona. CRG is coordinating the project, which includes eight academic labs and two commercial partners aside from CoSMo.
The project aims to consolidate disparate tools and methods that individual groups have developed internally for systematic data-driven model building, model validation, and analysis. The goal is to develop a standardized platform that can be applied in academic research institutions and commercial biotech settings.
Johannes Jaeger, one of the coordinators of the project at the CRG, explained that the project was launched to create "an integrated suite of robust and solid methods to empower data-driven modeling for systems biology and biotechnology" that will hopefully shorten "the lag time ‘from ideas to the market’".
The group is taking a "holistic approach" that combines expertise from a number of areas, including database development, scientific visualization, statistics, machine learning, mathematical modeling, and biotechnological engineering, it said in a statement.
BioPreDyn will develop tools for integrating and exploiting biological databases, methods for analyzing data and building models, and software that supports the full cycle of dynamic modeling and reverse engineering of biological systems.
Planned applications of the system include large-scale models of metabolism and gene regulation in microorganisms; cellular signaling networks with a focus on the Chinese hamster ovary cell line; inference of developmental gene regulatory networks in Drosophila and Nematostella; and mechanistic and comprehensive modeling of biotechnological production processes based on transgenic microorganisms.
During the three-year project, participants will provide biological and biotechnological use cases that are currently being studied, which will serve as benchmark problems to guide the development process.
The group will also come up with a list of tools that need to be included in the pipeline as well as methods of building and implementing them, Hugues de Bantel, CoSMo's CEO, told BioInform this week.
Once that’s settled, the group will then turn its attention to describing methodologies that will guide the use of the pipeline, de Bantel said.
CoSMo — short for Complex Systems and Modeling — will use its simulation software, which uses a multi-scale approach to represent the individual components of system, to support the modeling processes required by the consortium, he said.
Additionally, the company will work on integrating the tools that are selected for the pipeline into a single framework, he said.
The 11-member group includes researchers from the European Molecular Biology Laboratory; the University of Amsterdam; the Dutch Center for Mathematics and Computer Science; the Telethon Institute of Genetics and Medicine in Italy; University of Manchester; University of Sheffield, and the Spanish National Research Council.
Other commercial partners include Insilico Biotechnology and Fluxome. Both companies are expected to use tools created by the BioPreDyn group to update their own biotech applications.
As part of the project, Insilico will use the toolset to make improvements to its pipeline for microbial biotech applications in the food and healthcare industries, while Fluxome will use the platform to optimize its production processes for dietary supplements.
Ultimately, the consortium plans to make the fruits of its labors — both software and data — open to the public, although the contributions from commercial partners will probably be available through separate licensing agreements, de Bantel said.
Next-Generation Simulation Software
The CoSMo Company opened its doors in June 2010 with the goal of developing a "next-generation simulation platform using a complex system approach," de Bantel told BioInform.
The firm, which spun out of a group of five higher education institutions in France, makes its bread and butter by forming partnerships with commercial and academic groups in which its generic software is used to integrate data from multiple sources into models that are then used to run simulations.
Biologists can use the platform to create integrated models that combine information about cells' internal processes, such as gene expression, with information from cell populations and the geometry of the cell, Eric Boix, the company's chief scientific officer, explained to BioInform.
The company’s software has so far been used in projects studying morphogenesis, HIV epidemiology, and immunoregulation.
In addition to targeting customers in pharmaceutical and biotech markets, the company also peddles its platform in urban planning and sustainability markets, where its software is being used in bioenergy, water distribution, and waste treatment projects.
The company is also pursuing opportunities in business and financial markets, de Bantel said.
Currently, CoSMo doesn’t believe it has any direct competitors within the life sciences; however Boix said some potential contenders are Mathworks' Matlab, which offers systems biology toolkits, as well as open source scripting languages such as C++ that are currently used internally in some labs.
Boix claimed, however, that Matlab's toolkits are difficult to integrate with other research tools and can't capture all the components required to create cellular models for example.
Simulations Plus and GNS Healthcare also offer modeling software that targets pharmaceutical and biotechnology clients.
CoSMo's current headcount stands at about 19 employees, 15 of whom are software developers. It hopes to increase the number of developers it has on staff to 25 in the first quarter of 2012.
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