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Blankenberg D.,Pennsylvania State University | Kuster G.V.,Pennsylvania State University | Coraor N.,Pennsylvania State University | Ananda G.,Pennsylvania State University | And 6 more authors.
Current Protocols in Molecular Biology | Year: 2010

High-throughput data production has revolutionized molecular biology. However, massive increases in data generation capacity require analysis approaches that are more sophisticated, and often very computationally intensive. Thus, making sense of high-throughput data requires informatics support. Galaxy (http://galaxyproject.org) is a software system that provides this support through a framework that gives experimentalists simple interfaces to powerful tools, while automatically managing the computational details. Galaxy is distributed both as a publicly available Web service, which provides tools for the analysis of genomic, comparative genomic, and functional genomic data, or a downloadable package that can be deployed in individual laboratories. Either way, it allows experimentalists without informatics or programming expertise to perform complex large-scale analysis with just a Web browser. © 2010 by John Wiley & Sons, Inc.


Williams J.M.,OpenHelix LLC | Mangan M.E.,OpenHelix LLC | Perreault-Micale C.,OpenHelix LLC | Lathe S.,OpenHelix LLC | And 2 more authors.
Briefings in Bioinformatics | Year: 2010

The amount of biological data is increasing rapidly, and will continue to increase as new rapid technologies are developed. Professionals in every area of bioscience will have data management needs that require publicly available bioinformatics resources. Not all scientists desire a formal bioinformatics education but would benefit from more informal educational sources of learning. Effective bioinformatics education formats will address a broad range of scientific needs, will be aimed at a variety of user skill levels, and will be delivered in a number of different formats to address different learning styles. Informal sources of bioinformatics education that are effective are available, and will be explored in this review. © The Author 2010. Published by Oxford University Press.


Mangan M.E.,OpenHelix LLC | Williams J.M.,OpenHelix LLC | Kuhn R.M.,University of California at Santa Cruz | Lathe W.C.,OpenHelix LLC
Current Protocols in Molecular Biology | Year: 2014

Electronic data resources can enable molecular biologists to quickly get information from around theworld that a decade agowould have been buried in papers scattered throughout the library. The ability to access, query, and display these data makes benchwork much more efficient and drives newdiscoveries. Increasingly, mastery of software resources and corresponding data repositories is required to fully explore the volume of data generated in biomedical and agricultural research, because only small amounts of data are actually found in traditional publications. The UCSC Genome Browser provides a wealth of data and tools that advance understanding of genomic context for many species, enable detailed analysis of data, and provide the ability to interrogate regions of interest across disparate data sets from a wide variety of sources. Researchers can also supplement the standard display with their own data to query and share this with others. Effective use of these resources has become crucial to biological research today, and this unit describes some practical applications of the UCSC Genome Browser. © 2014 by John Wiley & Sons, Inc.


PubMed | OpenHelix LLC
Type: Journal Article | Journal: Briefings in bioinformatics | Year: 2010

The amount of biological data is increasing rapidly, and will continue to increase as new rapid technologies are developed. Professionals in every area of bioscience will have data management needs that require publicly available bioinformatics resources. Not all scientists desire a formal bioinformatics education but would benefit from more informal educational sources of learning. Effective bioinformatics education formats will address a broad range of scientific needs, will be aimed at a variety of user skill levels, and will be delivered in a number of different formats to address different learning styles. Informal sources of bioinformatics education that are effective are available, and will be explored in this review.


PubMed | OpenHelix LLC
Type: | Journal: Current protocols in molecular biology | Year: 2014

Electronic data resources can enable molecular biologists to quickly get information from around the world that a decade ago would have been buried in papers scattered throughout the library. The ability to access, query, and display these data makes benchwork much more efficient and drives new discoveries. Increasingly, mastery of software resources and corresponding data repositories is required to fully explore the volume of data generated in biomedical and agricultural research, because only small amounts of data are actually found in traditional publications. The UCSC Genome Browser provides a wealth of data and tools that advance understanding of genomic context for many species, enable detailed analysis of data, and provide the ability to interrogate regions of interest across disparate data sets from a wide variety of sources. Researchers can also supplement the standard display with their own data to query and share this with others. Effective use of these resources has become crucial to biological research today, and this unit describes some practical applications of the UCSC Genome Browser.

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