BLACKSBURG, May 18, 2002 - Researchers from Virginia Bioinformatics Institute led key discussions at the first of a series of bioinformatics workshops held in collaboration with the College of William and Mary and INCOGEN. Supported by a Commonwealth Technology Research Fund Industry Inducement Award, this series of semi-annual workshops brings bioinformatics researchers from the three institutions together to collaborate on developing the latest tools and technologies for bioinformatics and computational biology, including software development.
Kicking off the workshop for VBI, Dr. J Dana Eckart, lead software architect for the PathPort project, illustrated modular and scalable bioinformatics software architecture under development at VBI. By connecting multiple web services and developing a software architecture that allows independent software visualization components to work together, this bioinformatics platform will allow for faster and more effective data integration and visualization.
Christine Lee, a VBI software engineer working on the project, said at the workshop, “This open, scalable bioinformatics tool will greatly accelerate informatics processing. The application interface is designed to be ‘transferable,’ or independent of data type. This makes it adaptable to any discipline or sector with a need to organize and extract useful knowledge from large volumes of data.”
A mathematician specializing in the study of networks, Dr. Reinhard Laubenbacher provided an overview of VBI’s mathematical approach to understanding gene regulatory networks. Applying theories previously used to understand patterns in large-scale traffic models and the spread of pathogens, Dr. Laubenbacher will mathematically model parts of the gene regulatory network of yeast. The modeling technique will also be applicable to other species – including humans – to help understand gene functions, the sequence in which genes are turned on or off in a living organism, and the effect of a particular gene or gene complex on other function in a biological system.
To allow researchers to achieve complex biochemical network simulations, Dr. Stefan Hoops described the development of COPASI, a novel computerized simulator that will be used to visualize biochemical networks in action. A VBI research team led by Dr. Pedro Mendes –including Hoops—in collaboration with European Media Labs designing both this high performance computing platform and the simulation software. This architecture, scalable to computer sizes from a desktop PC to a supercomputer, will allow researchers to visualize and understand the relationships of hundreds of thousands of data interacting in very large and complex biochemical networks. The first of its kind, COPASI will greatly accelerate our understanding of gene function and the biochemistry of biological functions on a systems level.
“The advent of the genomic age—with its resulting plethora of data—compels us to create bioinformatics platforms that will allow researchers to visualize complicated biological processes, which are based on complex biochemical networks. COPASI will allow data visualization in pathways - and hence biological discovery – on an unprecedented scale,” said Hoops.
Also at the workshop, researchers from INCOGEN (the Institute for Computational Genomics) and the College of William and Mary talked about the latest research and developments at their respective Institutes. INCOGEN Director of Software Development Krista Miller illustrated the company’s development of a novel software framework. This software will allow researchers lacking programming expertise to integrate existing data resources, including the vast amounts of genomic data publicly available. The framework can also be used to integrate medical records and retail sales information. INCOGEN also previewed bioinformatics software now commercially available, which is designed to optimize analysis and mining of genomic data. Researchers from William and Mary, Dr. Gregory Smith and Dariya Malyarenko, lead discussions in computational models in cellular processes and the use of MALSI and SELDI (mass spectrometry applications used extensively in research), respectively.
Dr. Allan Dickerman, representing VBI on a panel discussing the next decade of bioinformatics research and the future of bioinformatics companies summed up the progress in this frontier area of research. He said, “The input of interdisciplinary research will be essential to solve the large, complex problems posed by biological systems. Bioinformatics, as a catalyzing discipline, will deliver cutting-edge applications and statistical approaches needed to understand life on the molecular level. This goal will be nurtured faster and further with collaborations such as this. VBI is excited to play a role.” The next CTRF workshop for this collaboration will be hosted by VBI in Blacksburg in the fall.
Please address any inquiries to:
Education and Outreach
Virginia Bioinformatics Institute
Blacksburg, VA 24061-0477
tel: 540.231.1259 / fax: 540.231.2606
May 17, 2002