Corporate Banner
Satellite Banner
Informatics
Scientific Community
 
Become a Member | Sign in
Home>News>This Article
  News
Return

Angry Birds Meets Bioinformatics

Published: Monday, July 23, 2012
Last Updated: Monday, July 23, 2012
Bookmark and Share
For years researchers have been looking for ways to improve patient care by making better use of health information.

So far, Big Data and Web 3.0, techie terms for massive stores of patient data and a unified global system to analyze it -- have not realized their full potential in medical research.

Meanwhile, you can cruise your favorite app store for hundreds of Web applications that analyze data, in many cases to create a smartphone game. No need to buy pricey hard drives or software packages. Ironically, the market asked Web browsers, the part of your computer that talks to the internet, to do so many things in recent years that this cheap, universal computing environment became an analytical powerhouse, especially when you network browsers together in "clouds."

Bioinformatics experts have looked on with envy, wishing they too had access to simple, powerful and free Web apps like those that drive Angry Birds. Now a team at the University of Alabama at Birmingham has made a start at delivering that.

As detailed in the July 20 edition of the Journal of Pathology Informatics, ImageJS is a free app system in some ways like Angry Birds, or perhaps more like Instagram, except that it analyzes tissue images instead of offering a digital shooting gallery or dressing up family photos. Specifically, the first ImageJS module enables pathologists to drag a digitized pathology slide into a Web app and analyze it for malignancy based on color changes that occur when cancer cells are exposed to standard dyes. But the developers' vision is more ambitious than that.

The pathology modules are the first in a series coming from Jonas Almeida, Ph.D., director of the Division of Informatics in the UAB School of Medicine Department of Pathology and corresponding author of the JPI study.

Future modules will seek to perform genomics analysis, make the system capable of cloud computing and enable doctors to compare their patient's data to similar cases stored in national databases. Such comparisons promise to increase diagnostic accuracy and rule out treatments that clash with a person's genetic signature.

"We created a new kind of computational tool that promises to make patient data more useful where it's collected," says Almeida. A demonstration is online on YouTube, and it's available from the Google Chrome App store, Google Code and Github.

"But ImageJS is an informatics experiment at this point; it will only become something special if pathologists embrace it," he says.

Public resources such as The Cancer Atlas, Gene Expression Omnibus and 1,000 Genomes Project have been generating massive data sets for years, but researchers are just beginning to harness it with Web apps to improve health-care delivery. To tap this potential, experts need apps that are neither overly complex nor require unsafe downloads of desktop applications.

The promise of ImageJS, Almeida says, lies in the willingness of pathologists to partner with biostatisticians at other institutions to write modules for this open-coded system that add value or resolve their specific problems. If that happens, ImageJS could come to resemble the social coding communities that surround smart phones, in this case to deliver better healthcare.

"Pathologists are extremely eager for this, but the barriers so far have made it frustrating," says James Robinson Hackney, M.D., a UAB pathologist who consulted on the ImageJS project. "It's great to watch a colleague's face when this system enables them almost instantly to accomplish a goal they had given up on using past applications."

The "ImageJS" name pays homage to the "ImageJ," an image-analysis program pioneered by the National Institutes of Health. ImageJ was written in the JAVA language and required hours of programming and security-breaching software to make the small changes needed to work with a hospital's system. Because hospital systems often prevent just such software downloads, its use has been limited there.

JAVA also posed challenges for the mobile Web and tablet platforms, which seldom support code written in languages other than the browser's native JavaScript, says Almeida. In contrast, the new ImageJS, a collection of Web-based algorithms written in JavaScript, enables researchers to change apps to fit their specific needs with a few lines of code and repeat each other's informatics experiments.

Most important, ImageJS code migrates from the code repository to the browser and eliminates the risks of travel-related data damage and exposure that violates patient privacy.

The central barrier to Web 3.0, an approaching era when all computers act as one to achieve new levels of collaboration and computing power, is that data compiled to date worldwide has been locked in silos that can't be searched, shared or analyzed.

While researchers hope to translate existing databases into the simple, universal Web 3.0 data formats that will allow this kind of sharing, they are also starting fresh. Almeida's team, for instance, will be attempting over the next year to build a database that offers future ImageJS users the option to store images and related analysis in a resource description framework or RDF.

Once data is stored in this format, it can be found by queries written in SPARQL, a simple computer language that can be learned by most people in a couple of hours. That is extremely important, says Almeida, because the next generation of bioinformatics must not remain the province of programmers. Instead, the researchers running the clinical trials and translational studies must write their own programs, which would add "stunning, new analytic value" to their research and feed into the new global databases.

The UAB team's work proceeds alongside other academic efforts, such as Tetherless World Constellation at Rensselaer Polytechnic Institute and ventures such as LinkedLifeData, Sindice and Hadoop.

Like a game, everyone's hoping to get to the next level. But for the field of bioinformatics -- and for patients -- the stakes are real, and they're much higher.


Further Information
Access to this exclusive content is for Technology Networks Premium members only.

Join Technology Networks Premium for free access to:

  • Exclusive articles
  • Presentations from international conferences
  • Over 2,400+ scientific posters on ePosters
  • More than 3,700+ scientific videos on LabTube
  • 35 community eNewsletters


Sign In



Forgotten your details? Click Here
If you are not a member you can join here

*Please note: By logging into TechnologyNetworks.com you agree to accept the use of cookies. To find out more about the cookies we use and how to delete them, see our privacy policy.


Scientific News
Computer Model Could Explain how Simple Molecules Took First Step Toward Life
Two Brookhaven researchers developed theoretical model to explain the origins of self-replicating molecules.
The Mystery of the Instant Noodle Chromosomes
Researchers from the Lomonosov Moscow State University evaluated the benefits of placing the DNA on the principle of spaghetti.
Web App Helps Researchers Explore Cancer Genetics
Brown University computer scientists have developed a new interactive tool to help researchers and clinicians explore the genetic underpinnings of cancer.
An Innovative Algorithm to Decipher How Drugs Work Inside the Body
Researchers at Columbia University Medical Center (CUMC) have developed a computer algorithm that is helping scientists see how drugs produce pharmacological effects inside the body.
How do Networks Shape the Spread of Disease and Gossip?
A team of mathematicians from Oxford University, University of North Carolina at Chapel Hill, and Rutgers University used a set of mathematical rules to encode how a contagion spreads, and then studied the outcomes of these rules.
AncestryDNA and Calico to Research the Genetics of Human Lifespan
Collaboration will analyze family history and genetics to facilitate development of cutting-edge therapeutics.
Informatics Tool Helps Scientists Prioritize Protein Modification Research
Researchers have developed a new informatics technology that analyzes existing data repositories of protein modifications and 3D protein structures to help scientists identify and target research on "hotspots" most likely to be important for biological function.
Software Differences can Skew Medical Scan Results
Differences in software can significantly skew results of medical scans commonly used in clinical care and research.
AMRI, PerkinElmer to Collaborate on Drug Discovery
Albany Molecular Research (AMRI) and PerkinElmer are collaborating to provide drug discovery infrastructure and services in AMRI's newly launched drug discovery center.
Exploring Living cells
JPK reports the exploration of living cells using nanoscale and single molecule techniques through the application of scanning probe microscopy.
Scroll Up
Scroll Down
Skyscraper Banner

Skyscraper Banner
Go to LabTube
Go to eposters
 
Access to the latest scientific news
Exclusive articles
Upload and share your posters on ePosters
Latest presentations and webinars
View a library of 1,800+ scientific and medical posters
2,400+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
3,700+ scientific videos
Close
Premium CrownJOIN TECHNOLOGY NETWORKS PREMIUM FREE!