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Rescooped by Alejandro Acosta from Tools for Learners
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Online video Tutorials ,Free University courses and training || OpenVideoTutorial.com

Online video Tutorials ,Free University courses and training || OpenVideoTutorial.com | science | Scoop.it

An open collection of Tutorials,Lectures and training Courses from top universities and colleges.10000+ free training courses.


Via Nik Peachey
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Sue Valdeck's comment, October 30, 2013 8:27 AM
On 30.10.13 looks like the site has closed down
Dawn Jensen's comment, October 30, 2013 1:54 PM
I see that Sue. Thanks for the catch. I don't know if it's temporary or not.
Dawn Jensen's comment, October 30, 2013 1:54 PM
I see that Sue. Thanks for the catch. I don't know if it's temporary or not.
Rescooped by Alejandro Acosta from The Steep Slope of Bioinformatics!
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I want to learn bioinformatics! A guide for complete beginners.


Via Neelima Sinha
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Scooped by Alejandro Acosta
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Llinás encontró la droga contra el Alzhéimer, solo falta la patente

Llinás encontró la droga contra el Alzhéimer, solo falta la patente | science | Scoop.it
El colombiano fue reconocido en España por sus descubrimientos sobre el cerebro. Su verdadero triunfo será ganarle la pelea al Alzhéimer. Entrevista de Margarita Vidal.
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Rescooped by Alejandro Acosta from Bioinformatics, Comparative Genomics and Molecular Evolution
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GPGPUs for bioinformatics | Oxford Protein Informatics Group


Via Arjen ten Have
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Arjen ten Have's curator insight, June 13, 2013 10:19 AM

GPUs come of age...........

Rescooped by Alejandro Acosta from Tools for Learners
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Draft. Write Better.

Draft. Write Better. | science | Scoop.it
Write better with Draft. Easy version control and collaboration to improve your writing.

Via Nik Peachey
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pohua-chen's curator insight, August 18, 2013 11:09 PM

Good for writing draft

Bart van Maanen's curator insight, August 28, 2013 6:16 AM

Dit is een mooie manier om je met schrijven te helpen, want je kan iemand uitnodigen je tekst te bekijken. Je kunt hem ook annoteren en versie vergelijken.

Nevermore Sithole's curator insight, March 12, 3:30 AM

Draft. Write Better.

Rescooped by Alejandro Acosta from Databases & Softwares
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Rainbow: a tool for large-scale whole-genome sequencing data analysis using cloud computing

Technical improvements have decreased sequencing costs and, as a result, the size and number of genomic datasets have increased rapidly.

Via Biswapriya Biswavas Misra
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Biswapriya Biswavas Misra's curator insight, June 29, 2013 11:40 PM
Abstract (provisional)Background

Technical improvements have decreased sequencing costs and, as a result, the size and number of genomic datasets have increased rapidly. Because of the lower cost, large amounts of sequence data are now being produced by small to midsize research groups. Crossbow is a software tool that can detect single nucleotide polymorphisms (SNPs) in whole-genome sequencing (WGS) data from a single subject; however, Crossbow has a number of limitations when applied to multiple subjects from large-scale WGS projects. The data storage and CPU resources that are required for large-scale whole genome sequencing data analyses are too large for many core facilities and individual laboratories to provide. To help meet these challenges, we have developed Rainbow, a cloud-based software package that can assist in the automation of large-scale WGS data analyses.

Results

Here, we evaluated the performance of Rainbow by analyzing 44 different whole-genome-sequenced subjects. Rainbow has the capacity to process genomic data from more than 500 subjects in two weeks using cloud computing provided by the Amazon Web Service. The time includes the import and export of the data using Amazon Import/Export service. The average cost of processing a single sample in the cloud was less than 120 US dollars. Compared with Crossbow, the main improvements incorporated into Rainbow include the ability: (1) to handle BAM as well as FASTQ input files; (2) to split large sequence files for better load balance downstream; (3) to log the running metrics in data processing and monitoring multiple Amazon Elastic Compute Cloud (EC2) instances; and (4) to merge SOAPsnp outputs for multiple individuals into a single file to facilitate downstream genome-wide association studies.

Conclusions

Rainbow is a scalable, cost-effective, and open-source tool for large-scale WGS data analysis. For human WGS data sequenced by either the Illumina HiSeq 2000 or HiSeq 2500 platforms, Rainbow can be used straight out of the box. Rainbow is available for third-party implementation and use, and can be downloaded from http://s3.amazonaws.com/jnj_rainbow/index.html.

 
Rescooped by Alejandro Acosta from Databases & Softwares
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A daily-updated tree of (sequenced) life as a reference for genome research

A daily-updated tree of (sequenced) life as a reference for genome research | science | Scoop.it
We report a daily-updated sequenced/species Tree Of Life (sTOL) as a reference for the increasing number of cellular organisms with their genomes sequenced.

Via Biswapriya Biswavas Misra
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Biswapriya Biswavas Misra's curator insight, June 19, 2013 12:56 PM

We report a daily-updated sequenced/species Tree Of Life (sTOL) as a reference for the increasing number of cellular organisms with their genomes sequenced. The sTOL builds on a likelihood-based weight calibration algorithm to consolidate NCBI taxonomy information in concert with unbiased sampling of molecular characters from whole genomes of all sequenced organisms. Via quantifying the extent of agreement between taxonomic and molecular data, we observe there are many potential improvements that can be made to the status quo classification, particularly in the Fungi kingdom; we also see that the current state of many animal genomes is rather poor. To augment the use of sTOL in providing evolutionary contexts, we integrate an ontology infrastructure and demonstrate its utility for evolutionary understanding on: nuclear receptors, stem cells and eukaryotic genomes. The sTOL (http://supfam.org/SUPERFAMILY/sTOL) provides a binary tree of (sequenced) life, and contributes to an analytical platform linking genome evolution, function and phenotype.