CloVR

"Background

Next-generation sequencing technologies have decentralized sequence acquisition, increasing the demand for new bioinformatics tools that are easy to use, portable across multiple platforms, and scalable for high-throughput applications. Cloud computing platforms provide on-demand access to computing infrastructure over the Internet and can be used in combination with custom built virtual machines to distribute pre-packaged with pre-configured software.

Results

We describe the Cloud Virtual Resource, CloVR, a new desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing. In a case study, we demonstrate the use of CloVR to automatically process next-generation sequencing data on multiple cloud computing platforms.

Conclusion

The CloVR VM and associated architecture lowers the barrier of entry for utilizing complex analysis protocols on both local single- and multi-core computers and cloud systems for high throughput data processing."

http://clovr.org/

NSF Gives Three Life-Science Projects $1.2M Grant to Test Microsoft’s Azure Cloud

Three life-science projects are among 13 teams that will have free access to Microsoft’s Azure cloud-computing platform for two years as part of an agreement between Microsoft and the National Science Foundation.

The life-science projects, led by researchers at Virginia Polytechnic Institute; the University of North Carolina, Charlotte; and the J. Craig Venter Institute, were awarded a total of $1.2 million in grants under the program, which kicked off in 2010 (BI02/10/2010). The awardees were announced last week.

In addition to providing access to the cloud, Microsoft will provide a support team, tools, applications, and data collections to help the scientists integrate cloud technology into their research.

An NSF review board considered the “appropriateness” of each proposal to the Azure platform’s capabilities, Reed Beaman, a program director at the agency, told BioInform.

For example, he said, the reviewers considered the fact that the platform is very strong in so-called “embarrassingly parallel” computations and in its ability to deploy web services.

He observed that in addition to providing Microsoft an opportunity to test the limits of its cloud computing platform, the partnership saves research dollars that would otherwise have been spent on hardware.

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DNAnexus Launches First Complete Cloud-Based Solution for Genomic Variation Identification

DNAnexus, Inc. announces the availability of a comprehensive set of new informatics tools that enable life science researchers to efficiently analyze and manage large-scale genomic variation datasets in a cloud-based workflow. DNAnexus will discuss results from a study using this solution at the 12th annual Advances in Genome Biology and Technology (AGBT) meeting in Marco Island, Florida. 
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Cresset Introduces Newest Cloud Computing Enabled Application with FieldAlign V3.0

Cresset today announced that it has released a major new version of its FieldAlign package. FieldAlign V3.0 is the latest in Cresset’s new generation of “cloud enabled” applications, which support parallel, distributed computing by default. It can be deployed both as a traditional desktop application and as a command-line application distributed onto large computing servers. FieldAlign V3.0 also introduces native support for the Mac for the first time. 
FieldAlign is a powerful molecular design and 3D Structure Activity Relationship (SAR) tool which generates biologically relevant molecular comparisons, which can be used to find the root causes of activity or inactivity. FieldAlign helps chemists to gain detailed understanding of the SAR of their lead molecules and to use this to design the best next synthesis. 

FieldAlign V3.0 introduces a range of user features that improve productivity and customisability. Its command line interface supports scripting and workflow systems, and is now available on Windows, Linux and Mac platforms. It incorporates a new molecule table enabling filtering and sorting of lead molecules, using imported data or standard physical properties, such as wcLogP, TPSA, Rule of Five violations. The new molecule editor enables rapid design iterations, while the multi-processor support facilitates faster run times on modern computers. With the option to expand computational power by distributing remote FieldEngines and its enhanced integration with other chemistry applications, more flexible licensing options provide advanced user flexibility. 

“FieldAlign V3.0 is now much simpler to deploy throughout a company and easier to use. This gives medicinal chemists access to an intuitive and powerful tool that enables them to accurately evaluate the effect of small design changes before synthesis”, said Tim Cheeseright, Products Director at Cresset.