This Small Business Innovation Research Phase II project will develop an innovative software platform called OpenBio Workbench that will enable researchers in drug discovery to easily access and share mathematical models and model results. Modeling is becoming increasing important, motivated by the FDA's drive to modernize the drug discovery process and the advent of emerging fields such as Systems Biology. A broad adoption of modeling has been limited, however, because the current practice requires programming and computational skills not typically possessed by experimental researchers in biological sciences. In the Phase II project, the tool's capabilities will be augmented by allowing users to calibrate models by including experimental data, adding innovative advanced modeling tools such as model building.
The potential commercial value of this workbench is high as the pharmaceutical industry is investing significantly in mathematical modeling and Systems Biology aiming to overcome both the high costs of drug development and the stagnation in the discovery of new drugs since the 1990's. Further, aging populations in developed countries are going to cause sharp increases in health care costs, while at the same time there are serious budgetary pressures (both from government and private insurers) to keep health care costs under control. Thus, methods that speed up the research cycle and reduce development costs for new drugs and treatments are going to become increasingly important.
Background This SBIR Phase II OpenBio Workbench Project is working towards the development of a breakthrough software platform for scientists and engineers that need to model biological pathways for drug discovery research. The OpenBio Workbench is intended for use in the development of new drugs for many major diseases including cancer, cardiovascular diseases, neurodegenerative diseases such as Alzheimer’s and Parkinson’s, and infectious diseases such as HIV and Hepatitis B. Successful commercialization and application of the OpenBio Workbench will contribute to the development of new drugs with higher efficacy, lower toxicity, and lower costs. This will help to maintain the leadership of our nation’s pharmaceutical industry and improve the lives of patients in need around the world. Mathematical modeling is increasingly attracting attention in the biological and life sciences as a promising technology to improve the R&D performance in drug discovery. However, broad adoption of modeling in drug discovery has been limited to date because it demands programming and computational skills that are uncommon among researchers and bench scientists in the biological and life sciences. Our innovation addresses this limitation through the development of a client-server software application with code-generation technology that will transform models developed from independent and dissimilar sources into the OpenBio Workbench so they can be easily used by a broad spectrum of researchers in the drug discovery research community. Intellectual Merit & Broader Impact of Work Biological pathway modeling is becoming increasing important, motivated by the FDA’s drive to modernize the drug discovery process and the advent of emerging fields, such as Systems Biology. A broad adoption of modeling has been limited, however, because the current practice requires programming and computational skills not typically possessed by experimental researchers in the biological sciences. Our Phase I project addressed this limitation by developing a novel code-generation technology. In Phase II, we worked to make the OpenBio Workbench full-featured, allowing users to adjust models by including experimental data, adding innovative advanced modeling tools such as model building, comparison and merging, and integrating these features into a commercial, maintenance-free beta-quality software tool. Phase IIB R&D will add a new library of mechanistic disease and drug mechanism action models to the OpenBio Workbench. Also developed in this project will be a set of tools that will enable model simulation, calibration, and data analysis. These new features will enable the OpenBio Workbench to be used for drug development and clinical trial R&D. The commercial value of this workbench is high, as the pharmaceutical industry is significantly investing in mathematical modeling and systems biology. They are aiming to overcome the sky-rocketing cost of drug development and the stagnation in the discovery of new drugs since the 1990s. Furthermore, aging populations in developed countries are causing sharp increases in health care costs, while at the same time there are serious budgetary pressures (both from government and private insurers) to keep health care costs under control. Thus, methods that speed up the research process and reduce development costs for new drugs and treatments will become increasingly important. This project is also an excellent platform to foster closer collaboration between model developers, mostly in academia, and experimentalists engaged in drug discovery in industry, and hence will enhance scientific and technological understanding. Outcome of Award After the release of OpenBio Workbench Version 1 in the 3rd quarter of 2010 we have been receiving feedback from industrial and academic users. In Phase II, we successfully developed model transformation methods to support various model formats in OpenBio, including model comparison and merge methods. Due to the current award, OpenBio Workbench has been successfully commercialized, providing both software and service to the pharmaceutical industry through companies such as Pfizer, Vertex, and Merck, and others. In this way, OpenBio Workbench has been able to provide valuable contributions in terms of drug discovery and development research.
