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Managing Data on the Go


By Robert M. Frederickson

Nov. 15, 2006 | Data management continues to be a challenge for researchers, from those involved in pharmaceutical drug discovery to more basic researchers working out signaling pathways in model organisms. The ability to integrate new findings in a systems biology approach demands that information on myriad signaling and biosynthetic pathways be accessible and interactive.

GeneGo is a Michigan-based developer of software packages for data analysis in drug discovery and systems biology. GeneGo has created a suite of software and database products that aim to facilitate analysis of the biology behind different types of high-throughput experimentation and understand the effects of small molecule drug compounds in human tissues.

GeneGo’s product suite is designed around MetaBase, a curated database containing information about biological pathways in human cells derived from the published literature. This content serves as an informational hub around which users can create gene and protein networks, so as to facilitate drug target selection and validation, the identification of biomarkers for specific diseases, or patient profiling in clinical trials. The MetaCore module can handle data from various input sources, such as microarray analyses of gene expression, analysis of single nucleotide polymorphisms, or metabolic profiling or high content screening (HCS). MetaCore contains user tools that enable the identification and prioritization of the most relevant pathways, networks and cellular processes affected by the condition. MetaDrug is GeneGo’s systems pharmacology platform used to predict human metabolites, toxicity and mode of action of novel small molecule compounds.

Last month, GeneGo announced the launch of two new products, MapEditor and MetaLink. The products are add-on modules in the MetaCore environment designed for integration, editing and mapping custom protein interaction data. With MapEditor, the user is able to create custom pathway maps starting from scratch, convert a network into a pathway map or edit one of the existing 500 proprietary maps from MetaCore. This allows users to develop new pathway maps based on proprietary data that is only accessible to their particular research team or company. GeneGo’s maps are currently available via the iPath Online BioAtlas from Invitrogen at www.invitrogen.com/ipath.

MetaLink allows users to upload their own protein association data produced by yeast-two-hybrid screens, gene co-expression, pull-down assays, text mining and other methods in MetaCore and build networks overlaying their interactions in the context of archival interactions. The accompanying gene expression and other “omics” data can be mapped and prioritized on the resulting customized networks.

Notes in a Lab
In September, Waters Corporation announced the launch of Waters eLab Notebook 3.0 Software, the company’s experimentation management software that is designed to automate the electronic capture of experimental results. eLab Notebook Software comprises a part of the company’s integrated Laboratory Informatics Suite, a portfolio of software applications for scientific data management, network integration, compliance management and laboratory productivity.

The new version of eLab Notebook Software enables laboratories engaged in chemical synthesis to operate more efficiently and collaboratively. It includes new features to manage reaction handling, automated stoichiometry calculations, searching of compounds and reactions, Markush structures (R-group), editing of synthetic and metabolic pathways, and registration of compounds and reactions.

The new version contains a collaborative authoring environment called The Scientific Workspace Editor. This functionality is designed to allow different groups to generate scientific content collaboratively and to share the work selectively before inclusion in an experiment. This feature works independently of the eLab Notebook’s compliance features. eLab Notebook is integrated with other software products in the Waters Laboratory Informatics Suite.

NuGenesis forms the core of Waters Laboratory Informatics’ suite of software tools. The platform is an automated electronic repository that stores and manages all types of scientific data to a centralized database. Empower is Waters’ chromatography data software product for gas and liquid chromatography data management.

E-mail Robert M. Frederickson at rfreder@yahoo.com.

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