Agilent and AxCell use IBM database technology for faster drug discovery

Somers 21 August 2002Agilent Technologies Inc. and IBM have signed an agreement to bring together complementary technologies to create an informatics system designed to help accelerate drug discovery and development. Through the agreement, the companies will collaborate to make IBM's DiscoveryLink data integration technology compatible with the new Agilent Synapsia Informatics Workbench family of software products. Synapsia is designed to help researchers synthesise and share research knowledge. Another IBM partner, AxCell Biosciences, a subsidiary of Cytogen Corporation, is using IBM DB2 database technology to help its scientists chart the communication pathways within cells that enable proteins to interact and cause or prevent diseases.

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The combined Agilent and IBM technologies will enable researchers to access and perform queries against a broad range of biological and chemical data from diverse sources and in different types of files and formats, including text, images, numeric files, and relational databases.

"The common goal of this collaboration is to offer solutions that will help researchers design better drugs and get them to market faster", stated Chris van Ingen, senior vice president of Agilent's Life Sciences and Chemical Analysis Business. "Researchers need to collaborate throughout the entire discovery process. Agilent and IBM are working together to deliver the critical technologies to help scientists work more productively."

Using DiscoveryLink, researchers can search diverse data sources, such as relational databases including Oracle and Sybase systems, for example, and public bioinformatics and genomics databases. Through its federated approach to data management, DiscoveryLink can perform complex searches quickly and efficiently, and deliver results in a consolidated, consistent format, while leaving the original data and its underlying structure intact.

"Agilent has chosen rock-solid infrastructure technology for data integration to anchor its new informatics solution", stated Dr. Caroline Kovac, general manager, IBM Life Sciences. "This agreement, an important first step in an ongoing collaboration, will bring new efficiencies to lab environments, where there is a continuous flow of new data from experiments and instrumentation. The combined Synapsia and DiscoveryLink offering gives researchers a powerful tool to capture and transform raw data from every research process into valuable knowledge which can be used for scientific discovery."

In turn, AxCell researchers are using IBM DB2 Intelligent Miner to gain new insights into how proteins interact in complex cellular communication networks. Ultimately, this knowledge could help drug makers design more effective and less toxic drugs that can disrupt the communication systems of abnormal proteins without harming healthy cells.

DB2 Intelligent Miner provides powerful mining algorithms that can sift through massive amounts of data and uncover associations, patterns, and trends that can lead to scientific discovery. For example, clustering algorithms enable researchers to segment data with similar patterns, while predictive algorithms can score data by factors such as likelihood of risk or behavioural propensity. DB2 Intelligent Miner also includes time-sequence algorithms that can reveal examples of similar progressions of a disease over a period of time.

"Intelligent Miner's algorithms for clustering and predictive analyses, for example, will help AxCell study sequence-function relationship, and potentially speed up domain and ligand identification for drug discovery. This technology will help give AxCell the competitive edge that comes from having a comprehensive source of information on domain-ligand mediated protein pathways", stated Michael D. Becker, interim chief executive officer of AxCell Biosciences.

AxCell will also augment its new internal data mining system with IBM DiscoveryLink data integration software. AxCell researchers thus can perform simultaneous queries against multiple data sources accessing data in different formats and files, and get results quickly delivered. AxCell's systems biology approach to drug discovery involves the efficient identification of peptide ligands that bind to modular domains on signaling proteins. These peptides are used to identify additional signaling proteins, which share that domain.

Bioinformatic analysis of the ligands and signaling proteins leads to identification of additional peptides and proteins and the pathways in which they are active. This may lead to identification of targets that can be validated in biological models and formatted in high-throughput assays to screen against natural product and small molecule libraries for potential inhibitors or modulators of these validated targets. In addition to deploying DB2 Intelligent Miner Technology and DiscoveryLink, IBM and AxCell expect to explore research collaborations in areas such as visualisation, pattern discovery, and protein folding analysis.

AxCell Biosciences of Newtown, Pennsylvania, is engaged in the research and development of novel biopharmaceutical products using its growing portfolio of functional proteomics solutions and collection of proprietary signal transduction pathway information. Through the systematic and industrialised measurement of protein-to-protein interactions, AxCell is assembling ProChart, a proprietary database of signal transduction pathway information that is relevant in a number of therapeutically important classes of molecules including growth factors, receptors and other potential protein therapeutics or drug targets.

AxCell's database content and functional proteomics tools are available on a non-exclusive basis to biotechnology, pharmaceutical and academic researchers. AxCell is expanding and accelerating its research activities to further elucidate the role of novel proteins and pathways in ProChart, through both external collaborations and internal data mining.


Leslie Versweyveld

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