Workflows for Microarray Data Processing in the Kepler Environment
News May 23, 2012
Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis demands, including integration with new data sources. Bioinformatics pipelines are usually custom built for different applications, making them typically difficult to modify, extend and repurpose. Scientific workflow systems are intended to address these issues by providing general-purpose frameworks in which to develop and execute such pipelines. The Kepler workflow environment is a well-established system under continual development that is employed in several areas of scientific research. Kepler provides a flexible graphical interface, featuring clear display of parameter values, for design and modification of workflows. It has capabilities for developing novel computational components in the R, Python, and Java programming languages, all of which are widely used for bioinformatics algorithm development, along with capabilities for invoking external applications and using web services.
This article is published online in BMC Bioinformatics and is free to access.
Giant Viruses Invent Their Own GenesNews
Three new members have been isolated and added to the Pandoravirus family. This strange family of viruses, with their giant genomes and many genes with no known equivalents, surprised scientists when they were discovered a few years ago. This new study notes that pandoraviruses appear to be factories for new genes – and therefore new functions.
Therapeutic CRISPR Could Be Cancer RiskNews
Therapeutic use of gene editing with the so-called CRISPR-Cas9 technique may inadvertently increase the risk of cancer, according to a new study. Researchers say that more studies are required in order to guarantee the safety of these ‘molecular scissors’ for gene-editing therapies.
Who Owns the Ocean? One Company Has Registered Half of All Marine Gene PatentsNews
A single corporation has registered nearly half of all existing patents associated with genes from marine organisms, according to a new study. Researchers from the University of British Columbia and the Stockholm Resilience Centre examined the patents associated with marine species and found that BASF, the world’s largest chemical manufacturer, has registered 47 per cent of the 12,998 genetic sequences from 862 marine species.