Featured Research

from universities, journals, and other organizations

Cloud computing method greatly increases gene analysis

Date:
September 9, 2010
Source:
Johns Hopkins University Bloomberg School of Public Health
Summary:
Researchers have developed new software that greatly improves the speed at which scientists can analyze RNA sequencing data. The software, known as Myrna, uses "cloud computing," an Internet-based method of sharing computer resources. Faster, cost-effective analysis of gene expression could be a valuable tool in understanding the genetic causes of disease.

Researchers at the Johns Hopkins Bloomberg School of Public Health have developed new software that greatly improves the speed at which scientists can analyze RNA sequencing data. RNA sequencing is used to compare differences in gene expression to identify those genes that switched on or off when, for instance, a particular disease is present. However, sequencing instruments can produce billions of sequences per day, which can be time-consuming and costly to analyze.

Related Articles


The software, known as Myrna, uses "cloud computing," an Internet-based method of sharing computer resources. Faster, cost-effective analysis of gene expression could be a valuable tool in understanding the genetic causes of disease. The findings are published in the current edition of the journal Genome Biology

Cloud computing bundles together the processing power of the individual computers using the Internet. A number of firms with large computing centers including, Amazon and Microsoft, rent unused computers over the Internet for a fee.

"Cloud computing makes economic sense because cloud vendors are very efficient at running and maintaining huge collections of computers. Researchers struggling to keep pace with their sequencing instruments can use the cloud to scale up their analyses while avoiding the headaches associated with building and running their own computer center," said lead author, Ben Langmead, a research associate in the Bloomberg School's Department of Biostatistics. "With Myrna, we tried to make it easy for researchers doing RNA sequencing to reap these benefits."

To test Myrna, Langmead and colleagues Kasper Hansen, PhD, a postdoctoral fellow, and Jeffrey T. Leek, PhD, senior author of the study and assistant professor in the Department of Biostatistics, used the software to process a large collection of publicly available RNA sequencing data. Processing time and storage space were rented from Amazon Web Services. According to the study, Myrna calculated differential expression from 1.1 billion RNA sequencing reads in less than 2 hours at cost of about $66.

"Biological data in many experiments -- from brain images to genomic sequences -- can now be generated so quickly that it often takes many computers working simultaneously to perform statistical analyses," said Leeks. "The cloud computing approach we developed for Myrna is one way that statisticians can quickly build different models to find the relevant patterns in sequencing data and connect them to different diseases. Although Myrna is designed to analyze next-generation sequencing reads, the idea of combining cloud computing with statistical modeling may also be useful for other experiments that generate massive amounts of data."

The researchers were supported by grants from Amazon Web Services, the National Institutes of Health and the Johns Hopkins Bloomberg School of Public Health.

The Myrna software is available for free download at http://bowtie-bio.sf.net/myrna.


Story Source:

The above story is based on materials provided by Johns Hopkins University Bloomberg School of Public Health. Note: Materials may be edited for content and length.


Journal Reference:

  1. Langmead et al. Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biology, 2010; 11 (8): R83 DOI: 10.1186/gb-2010-11-8-r83

Cite This Page:

Johns Hopkins University Bloomberg School of Public Health. "Cloud computing method greatly increases gene analysis." ScienceDaily. ScienceDaily, 9 September 2010. <www.sciencedaily.com/releases/2010/09/100908101933.htm>.
Johns Hopkins University Bloomberg School of Public Health. (2010, September 9). Cloud computing method greatly increases gene analysis. ScienceDaily. Retrieved October 25, 2014 from www.sciencedaily.com/releases/2010/09/100908101933.htm
Johns Hopkins University Bloomberg School of Public Health. "Cloud computing method greatly increases gene analysis." ScienceDaily. www.sciencedaily.com/releases/2010/09/100908101933.htm (accessed October 25, 2014).

Share This



More Computers & Math News

Saturday, October 25, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Real-Life Transformer Robot Walks, Then Folds Into a Car

Real-Life Transformer Robot Walks, Then Folds Into a Car

Buzz60 (Oct. 24, 2014) — Brave Robotics and Asratec teamed with original Transformers toy company Tomy to create a functional 5-foot-tall humanoid robot that can march and fold itself into a 3-foot-long sports car. Jen Markham has the story. Video provided by Buzz60
Powered by NewsLook.com
Microsoft Riding High On Strong Surface, Cloud Performance

Microsoft Riding High On Strong Surface, Cloud Performance

Newsy (Oct. 24, 2014) — Microsoft's Q3 earnings showed its tablets and cloud services are really hitting their stride. Video provided by Newsy
Powered by NewsLook.com
The Best Apps to Organize Your Life

The Best Apps to Organize Your Life

Buzz60 (Oct. 23, 2014) — Need help organizing your bills, schedules and other things? Ko Im (@konakafe) has the best apps to help you stay on top of it all! Video provided by Buzz60
Powered by NewsLook.com
Nike And Apple Team Up To Create Wearable ... Something

Nike And Apple Team Up To Create Wearable ... Something

Newsy (Oct. 23, 2014) — For those looking for wearable tech that's significantly less nerdy than Google Glass, Nike CEO Mark Parker says don't worry, It's on the way. Video provided by Newsy
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
 
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:  

Breaking News:

Strange & Offbeat Stories

 

Space & Time

Matter & Energy

Computers & Math

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:  

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile iPhone Android Web
Follow Facebook Twitter Google+
Subscribe RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins