Resources

Biology Workbench

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The Biology WorkBench is a web-based tool for biologists. The WorkBench allows biologists to search many popular protein and nucleic acid sequence databases. Database searching is integrated with access to a wide variety of analysis and modeling tools, all within a point and click interface that eliminates file format compatibility problems.


BioPathways Workbench

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The Pathway Editor is a program for managing, visualizing, and editing signaling and metabolic pathways. Pathways may be created from scratch, accessed by opening a .path file, or downloaded from the LIPID MAPS website via the Pathway Editor application. Measured data may be downloaded by the program and displayed graphically in the context of the pathway


Lipid Maps

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LIPID Metabolites And Pathways Strategy (LIPID MAPS) is a multi-institutional effort created in 2003 to identify and quantitate, using a systems biology approach and sophisticated mass spectrometers, all of the major — and many minor — lipid species in mammalian cells, as well as to quantitate the changes in these species in response to perturbation.

Resources available include:


Signaling Gateway

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The UCSD-Nature Signaling Gateway Molecule Pages provides essential information on more than 3800 mammalian proteins involved in cellular signaling. The Molecule Pages contain expert-authored and peer-reviewed information based on the published literature, complemented by regularly updated information derived from public data source references and sequence analysis. The expert-authored data includes both a full-text review about the molecule, with citations, and highly structured data for bioinformatics interrogation, including information on protein interactions and states, transitions between states and protein function. The expert-authored pages are anonymously peer reviewed by the Nature Publishing Group. The Molecule Pages data is present in an object-relational database format and is freely accessible to the authors, the reviewers and the public from a web browser that serves as a presentation layer. The Molecule Pages are supported by several applications that along with the database and the interfaces form a multi-tier architecture. The Molecule Pages and the Signaling Gateway are routinely accessed by a very large research community.


VAMPIRE

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A collection of methods integrated into a web-based platform where users can detect differential gene expression and functional patterns in their microarray data. Utilizing the VAriance-Modeled Posterior Inference with Regional Exponentials (VAMPIRE) statistical framework, this analysis suite detects reliable differences in gene expression with increased sensitivity. With these results, users can then seamlessly detect overrepresentation of Gene Ontology terms, pathways, and motifs. Experts and non-experts alike can robustly analyze and gain physiological insight into their gene expression array experiments in one simple user-friendly platform, accessible from any web browser. The microarray analysis suite can be accessed at http://genome.ucsd.edu/microarray.