SIDEKICK: Genomic data driven analysis and decision-making framework

Doderer, Mark; Yoon, Kihoon; Robbins, Kay A.

doi:10.1186/1471-2105-11-611

Cited by 4 publications

(3 citation statements)

References 32 publications

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“…We use the SideCache suite in a number of our own web services and as the basis for the Sidekick [ 10 ] client side application. Table 1 summarizes three services currently running under our own SideCache deployment at visual.cs.utsa.edu.…”

Section: Resultsmentioning

confidence: 99%

SIDECACHE: Information access, management and dissemination framework for web services

Doderer

Burkhardt²,

Robbins

2011

BMC Res Notes

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BackgroundMany bioinformatics algorithms and data sets are deployed using web services so that the results can be explored via the Internet and easily integrated into other tools and services. These services often include data from other sites that is accessed either dynamically or through file downloads. Developers of these services face several problems because of the dynamic nature of the information from the upstream services. Many publicly available repositories of bioinformatics data frequently update their information. When such an update occurs, the developers of the downstream service may also need to update. For file downloads, this process is typically performed manually followed by web service restart. Requests for information obtained by dynamic access of upstream sources is sometimes subject to rate restrictions.FindingsSideCache provides a framework for deploying web services that integrate information extracted from other databases and from web sources that are periodically updated. This situation occurs frequently in biotechnology where new information is being continuously generated and the latest information is important. SideCache provides several types of services including proxy access and rate control, local caching, and automatic web service updating.ConclusionsWe have used the SideCache framework to automate the deployment and updating of a number of bioinformatics web services and tools that extract information from remote primary sources such as NCBI, NCIBI, and Ensembl. The SideCache framework also has been used to share research results through the use of a SideCache derived web service.

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Section: Resultsmentioning

confidence: 99%

SIDECACHE: Information access, management and dissemination framework for web services

Doderer

Burkhardt²,

Robbins

2011

BMC Res Notes

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“…It builds on the Sidekick [23] framework. Pathway Distiller was built using Adobe Flex and Action Script 3 which produces a Adobe Flash movie that runs in a user's web browser.…”

Section: Methodsmentioning

confidence: 99%

“…We developed a web-based application, the Pathway Distiller ( http://cbbiweb.uthscsa.edu/PathwayDistiller ), which provides access to our integrated pathway database base, pathway enrichment and three methods of pathway consolidation. It builds on the Sidekick [ 23 ] framework. Pathway Distiller was built using Adobe Flex and Action Script 3 which produces a Adobe Flash movie that runs in a user's web browser.…”

Section: Methodsmentioning

confidence: 99%

Pathway Distiller - multisource biological pathway consolidation

et al. 2012

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BackgroundOne method to understand and evaluate an experiment that produces a large set of genes, such as a gene expression microarray analysis, is to identify overrepresentation or enrichment for biological pathways. Because pathways are able to functionally describe the set of genes, much effort has been made to collect curated biological pathways into publicly accessible databases. When combining disparate databases, highly related or redundant pathways exist, making their consolidation into pathway concepts essential. This will facilitate unbiased, comprehensive yet streamlined analysis of experiments that result in large gene sets.MethodsAfter gene set enrichment finds representative pathways for large gene sets, pathways are consolidated into representative pathway concepts. Three complementary, but different methods of pathway consolidation are explored. Enrichment Consolidation combines the set of the pathways enriched for the signature gene list through iterative combining of enriched pathways with other pathways with similar signature gene sets; Weighted Consolidation utilizes a Protein-Protein Interaction network based gene-weighting approach that finds clusters of both enriched and non-enriched pathways limited to the experiments' resultant gene list; and finally the de novo Consolidation method uses several measurements of pathway similarity, that finds static pathway clusters independent of any given experiment.ResultsWe demonstrate that the three consolidation methods provide unified yet different functional insights of a resultant gene set derived from a genome-wide profiling experiment. Results from the methods are presented, demonstrating their applications in biological studies and comparing with a pathway web-based framework that also combines several pathway databases. Additionally a web-based consolidation framework that encompasses all three methods discussed in this paper, Pathway Distiller (http://cbbiweb.uthscsa.edu/PathwayDistiller), is established to allow researchers access to the methods and example microarray data described in this manuscript, and the ability to analyze their own gene list by using our unique consolidation methods.ConclusionsBy combining several pathway systems, implementing different, but complementary pathway consolidation methods, and providing a user-friendly web-accessible tool, we have enabled users the ability to extract functional explanations of their genome wide experiments.

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