Computational Cell Environment: A Problem Solving Environment for integrating diverse biological data

Biologists and bioinformaticists face the ever-increasing challenge of managing large datasets queried from diverse data sources. Genomics and proteomics databases such as the National Center for Biotechnology (NCBI), Kyoto Encyclopedia of Genes and Genomes (KEGG), and the European Molecular Biology Laboratory (EMBL) are becoming the standard biological data department stores that biologists visit on a regular basis to obtain the supplies necessary for conducting their research. However, much of the data that biologists retrieve from these databases needs to be further managed and organized in a meaningful way so that the researcher can focus on the problem that they are trying to investigate and share their data and findings with other researchers. We are working towards developing a problem-solving environment called the Computational Cell Environment (CCE) that provides connectivity to these diverse data stores and provides data retrieval, management, and analysis through all aspects of biological study. In this paper we discuss the system and database design of CCE. We also outline a few problems encountered at various stages of its development and the design decisions taken to resolve them.