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Old 07-24-2010, 04:45 PM   #1
Geneious
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Location: New Zealand

Join Date: Jul 2010
Posts: 22
Default Geneious Server Private Beta Trial Underway

Geneious Server Private Beta Trial begins
Four world-class research teams have recently begun putting Geneious Server™ through its paces. Our private beta partners are research teams lead by Dr. Charles Chiu at the University of California San Francisco, Associate Professor, Dr. David Edwards at the University of Queensland, Director of Scientific Computing, Dr. Ji He at the Samuel Roberts Noble Foundation and Associate Director, Dr. Mark Wall at Verenium Corporation. Research teams at each of these facilities have deployed Geneious Server and have begun testing the NGS and Phylogenetics modules. Their valuable feedback will ensure Geneious Server is a reliable, useful and robust platform when it becomes available later this year.

Geneious Server features three modules
Three modules of distinct functionality will be available at the launch of Geneious Server. Each of these will be priced individually, so you can choose to only have the modules that you require for your research or get all of them, and earn a discount.
NGS Assembly Module
Geneious Server makes next generation assembly easy. The power of Geneious Server to receive and run offloaded jobs, turns next-generation sequence data into now-generation sequence analysis. With the Geneious Server NGS Assembly Module you have unparalleled algorithm choice for your assembly and at the click of a button you can choose either the Geneious Assembler or select any of Velvet, Bowtie, BWA and Maq (SOAP2, MIRA, SaSSY, Cufflinks, TopHat coming soon) to assemble your data with confidence.

Phylogenetics Module
Many phylogenetics analyses can take significant computation resources, slowing down your own machine. The Geneious Server Phylogenetics Module allows you to offload ClustalW, MUSCLE, MAFFT, PHyML and MrBayes (with RAxML, PAUP*, SATé coming soon) to the Geneious Server freeing up your own computing resources.

Sequence Analysis Module
Geneious Server speeds up large-scale sequence analysis tools like BLAST, Smith-Waterman, HMMER and Fasta or take advantage of our integration with the accelerated algorithms on TimeLogic's DeCypher card to discover genes, patterns and motifs to annotate genomes more quickly than ever before.
Geneious Server to help sequence the wheat genome
One of the key Geneious Server private beta testers is Associate Professor David Edwards and his team at the Australian Centre for Plant Functional Genomics at the University of Queensland.

Following recent success characterizing the Brassica genomes in partnership with Bayer CropScience, BGI and KeyGene, David is moving on to an even bigger challenge: developing processes to characterize very large crop genomes. In particular, the polyploid bread wheat genome – a genome six times larger than the human genome. “These key crops are of great importance to farmers in Australia and around the world. Knowing the sequence for large genome cereal crops would revolutionize crop improvement, allowing breeders to select optimal parents for crop improvement,” says David.

To handle the challenge, the University of Queensland has built high performance computers designed specifically for the assembly of Illumina GAII genome sequencing data and developed their own assembler known as ‘SaSSY’ Geneious Server will manage the project’s huge volumes of data. A key part of the project is optimising SaSSY for the highly repetitive regions found in the wheat genome. David's team plan to eventually release SaSSY and many other tools as plugins for Geneious. “We want to get our tools out there in the most useful and user-friendly way possible. Geneious provides an easy to use interface, visualizations and great support, so we can focus on the algorithms and research,” David says.
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