Wolfram Alpha Turns 2: 'People Just Need What We Are Doing' (Ryan Singel/Epicenter)

Wolfram Alpha Turns 2: 'People Just Need What We Are Doing' (Ryan Singel/Epicenter)
TECHMEME | 29 MAY 2011
http://www.techmeme.com/110529/p7#a110529p7

Ryan Singel / Epicenter: Wolfram Alpha Turns 2: 'People Just Need What We Are Doing'  —  Steven ... read more

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Life Technologies announced the commercial release of LifeScope™ Genomic Analysis Software

Today, Life Technologies announced the commercial release of LifeScope™ Genomic Analysis Software. As BioScope™ software has been useful for bioinformaticists, LifeScope™ software is designed to be user-friendly for life scientists. Here are some LifeScope™ software highlights:

 

1. Performance is up to 5x faster than BioScope.

2. A new small RNA analysis workflow is available.

3. Auto-generated graphs and reports enable easier evaluation of analysis results.

4. Automatic data output viewing in Broad's IGV software.

5. Improved file processing efficiency is accomplished by working directly with the new, smaller XSQ file format.

6. Simplication of the configuration and management of analysis pipelines in the command line interface.

7. A re-engineered architecture maximizes a compute cluster environment.

 

Check out this video:

 

http://www.youtube.com/watch?v=2sd4dNoJ0_0

Optimized and Integrated Solutions for Every Need and Budget
Accelerate your analysis by running LifeScope™ Software on one of our optimized, high-performance computing Workstations or Clusters.  Both configurations come with LifeScope™ Software pre-loaded, performance tested, and ready to be licensed.  Learn more about the LifeScope™ Cluster and the LifeScope™ Workstation. If you prefer not to maintain your own compute infrastructure, opt for LifeScope™ Cloud (which provides the full power and sensitivity of the software in a massively scalable, convenient, and maintenance-free mode.

Kevin: WHAT IS THE PRICE? would Bioscope and Bioscope support remain free? Would unsatisfied Bioscope users be confident with Lifescope? Questions questions questions!

Just when you thought short read sequencing can't get longer

As 454 Preps Launch of Sanger-Length Reads, Early Customers Highlight Utility for De Novo Assembly

To assert its position as a provider of long-read high-quality next-gen sequencing data, Roche's 454 Life Sciences plans to commercially offer Sanger-length reads for its Genome Sequencer FLX by the end of next month, based on improved sequencing chemistry and an instrument upgrade.

Applications for the long reads, which the company has talked about for more than two years and had originally planned to launch in 2010 (IS 9/29/2009), include de novo assemblies of large and complex genomes, transcriptome sequencing, sequence capture, and shotgun metagenomics.

full length article here

bio-itworld RNA Editing Much More Widespread than Imagined

http://www.bio-itworld.com/els/2011/05/20/rna-editing-much-more-widespread-than-imagined.html

May 20, 2011 | Results published in Science yesterday suggest that the DNA-RNA-protein workflow that forms the basis of biology may not be as straightforward as we thought. Scientists found more than 10,000 points of RNA "editing" where RNA sequences did not match the DNA. The results suggest that RNA editing could account for human genetic diversity on a much larger scale than previously thought. Nature

Sean Grimmond shares his plans for his 5500xl upgrades at the Institute for Molecular Bioscience at the University of Queensland

 Sean Grimmond talks to us about the 5500xl installation at IMB

Posted by Michelle Brandhuber on May 25, 2011 6:46:18 PM

The 5500xl recently found its home at the Institute for Molecular Bioscience at the University of Queensland and Sean Grimmond shared his thoughts about what this means for the lab:

 

"The 5500xl is first step towards upgrading the SOLiD fleet at the Queensland Centre for Medical Genomics. We are currently working thorugh establishing new operating procedures for genome sequencing (long mate pair and barcoded Exomes) and transcriptome (barcoded whole transcriptome and small rnas) on the new platform.

 

Our plan is to make the 5500XL the engine behind all our large scale sequencing efforts at the QCMG. Our flagship project is Australia's pancreatic and ovarian cancer genome and transcriptome sequencing efforts which are part of the international cancer genome consortium. This program is seeing us sequence matched normal and tumor genomes/transcriptomes/methylomes for 500 cancer patients. We are particularly keen to employ exact call chemistry in these cancer genome studies and push the accuracy and sensitivity of mutation calling.  We also keen to broaden our efforts into stem cell transcriptome profiling by rnaseq on the 5500s, thanks to the higher throughputs/run.  Finally, we are also looking to start our first de novo genome sequencing experiments using a combination of The exact call chemistry and Torrent sequencing."

 

Sean Grimmond's lab certainly has a lot planned.  We are happy to hear they plan to fully take advantage of 5500xl pay-per-lane sequencing!

 

Check out the celebration and more photos here.

Open Science ...

http://www.guardian.co.uk/education/2011/may/22/open-science-shared-research-internet
The ability to collaborate quickly and transparently online is just one facet of a growing movement in research known as open science

UW Team Demonstrates Primate Exome Assembly Against Human Reference Genome

Link to full article

Excerpted

By Monica Heger

In order to overcome the challenges of using next-gen sequencing for de novo assemblies, researchers from the University of Washington demonstrated that it is possible to assemble a primate exome by aligning it to the human reference genome.

"It's feasible to sequence primate genomes, but assembly with short reads is still difficult," Renee George, a postdoctoral student in Willie Swanson's laboratory at the University of Washington, said in a presentation at this month's annual Biology of Genomes meeting in Cold Spring Harbor, NY.

To learn whether they could sequence and assemble a primate exome by aligning it to the human reference, the researchers first tested the method on the macaque monkey, which does have a reference genome. Their aim was to see if it is possible to capture primate exomes with human probes and align and assemble the resulting reads against a human reference genome.

Using Nimblegen's SeqCap EZ Exome in-solution kit, they used an Illumina Genome Analyzer to capture and sequence the exome to an average of 60-fold coverage with 76 base-paired end reads. They found good correlation after comparing the read depth of the macaque against two human controls.

"The exons that are captured well in humans are captured well in macaque," George said. Additionally, although read depths declined in the regions of the macaque genome that are more divergent from the human genome, they still remained well-covered.

The team verified the method by showing that the sequenced macaque exome was comparable to the coding regions of the macaque reference genome.

It next applied the method to two Old World monkeys — the colobus and vervet — and one New World monkey, the tamarin. None of the animals has a reference genome. 

Sensitive and fast mapping of di-base encoded reads.

Sensitive and fast mapping of di-base encoded reads.
Hormozdiari F, Hach F, Sahinalp SC, Eichler EE, Alkan C.
Bioinformatics. 2011 May 17. [Epub ahead of print]
PMID: 21586516 [PubMed - as supplied by publisher]