Nav: Home

EDGE bioinformatics brings genomics to everyone

November 29, 2016

LOS ALAMOS, N.M., Nov. 29, 2016 -- A new bioinformatics platform called Empowering the Development of Genomics Expertise (EDGE) will help democratize the genomics revolution by allowing users with limited bioinformatics expertise to quickly analyze and interpret genomic sequence data. Researchers at Los Alamos National Laboratory and their collaborators at the Naval Medical Research Center developed EDGE, which is described in a paper recently published in Nucleic Acids Research.

"We realized that while next-generation sequencing instruments are becoming more widespread and more accessible to the average biologist or physician, the bioinformatics tools required to process and analyze the data were not as user-friendly or accessible," said Patrick Chain, of Los Alamos' Biosecurity and Public Health group and EDGE team lead. "Given the large number of applications where sequencing is now used, a robust bioinformatics platform that encapsulates a broad array of algorithms is required to help address questions a researcher may have. We sought to develop a web-based environment where non-bioinformatics experts could easily select what pipelines they need and rapidly obtain results and interact with their data."

Stopping the spread of disease--from naturally occurring or manmade threats -- requires an in-depth understanding of pathogens and how they work. To this end, the ability to characterize organisms through accurately and rapidly comparing genomic data is an important part of Los Alamos' national security mission.

Technology advancements have fueled the development of new sequencing applications and will flood current databases with raw data. A number of factors limit the use of these data, including the large number of associated software and hardware dependencies and the detailed expertise required to perform this analysis. To address these issues, Chain and his team have developed an intuitive web-based environment with a wide assortment of integrated and pioneering bioinformatics tools in pre-configured workflows, all of which can be readily applied to isolate genome sequencing projects or metagenomics projects.

EDGE is a user-friendly and open-source platform that integrates hundreds of cutting-edge tools and helps reduce data analysis times from days or weeks to minutes or hours. The workflows in EDGE, along with its ease of use, provide novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks. This bioinformatics platform is described as an initial attempt at empowering the development of genomics dxpertise, as its name suggests, for a wide range of applications in microbial research.
EDGE has already helped streamline data analysis for groups in Thailand, Georgia, Peru, South Korea, Gabon, Uganda, Egypt and Cambodia, as well as within several government laboratories in the United States.

The paper "Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform" was published in Nucleic Acids Research in partnership with the Defense Threat Reduction Agency, the Naval Medical Research Center-Frederick and the Henry M. Jackson Foundation.

About Chain

Patrick Chain earned his master's of science in microbial genomics from McMaster University and his doctoral degree in molecular microbiology and molecular genetics at Michigan State University. He is currently leading the Bioinformatics and Analytics Team and the Metagenomics Program within the Biosecurity and Public Health group at Los Alamos National Laboratory.

His background is in microbial ecology, evolution, genomics and bioinformatics, having spent the past 20 years using genomics to study various microbial systems, including the human microbiome, other environmental metagenomic communities, various isolate microbes or single cells, including bacterial and viral pathogens as well as fungal, algal, plant and animal systems.

He currently leads a team of researchers whose charge is to devise novel methods, algorithms and strategies for the biological interpretation of massively parallel sequencing data.

About Los Alamos National Laboratory

Los Alamos National Laboratory, a multidisciplinary research institution engaged in strategic science on behalf of national security, is operated by Los Alamos National Security, LLC, a team composed of Bechtel National, the University of California, BWXT Government Group, and URS, an AECOM company, for the Department of Energy's National Nuclear Security Administration. Los Alamos enhances national security by ensuring the safety and reliability of the U.S. nuclear stockpile, developing technologies to reduce threats from weapons of mass destruction, and solving problems related to energy, environment, infrastructure, health, and global security concerns.

DOE/Los Alamos National Laboratory

Related Bioinformatics Articles:

Embracing bioinformatics in gene banks
Scientists from the IPK have explored, within a perspective paper, the upcoming challenges and possibilities of the future of gene banks.
New bioinformatics tool identifies and classifies CRISPR-Cas systems
Designed to improve the utility and availability of increasingly diverse CRISPR-Cas genome editing systems, the new CRISPRdisco automated pipeline helps researchers identify CRISPR repeats and cas genes in genome assemblies.
AMP Iissues consensus guideline recommendations for NGS bioinformatics pipelines
The Association for Molecular Pathology, the premier global, non-profit molecular diagnostics professional society, today published 17 consensus recommendations to help clinical laboratory professionals achieve high-quality sequencing results and deliver better patient care.
A new tool to decipher evolutionary biology
A new bioinformatics tool to compare genome data has been developed by teams from the Max F.
Advances: Bioinformatics applied to development & evaluation of boron-containing compounds
The interest for developing boron-containing compounds as drugs is increasing after some successful cases.
When life sciences become data sciences
The University of Freiburg offers Europe-wide infrastructure and service in Bioinformatics.
Bioinformatics brings to light new combinations of drugs to fight breast cancer
A bioinformatics analysis of pairing 64 drugs used to treat breast cancer allows researchers at IRB Barcelona to identify 10 previously untested combinations with potential to tackle resistance to breast cancer treatment.
New bioinformatics tool tests methods for finding mutant genes that 'drive' cancer
Computational scientists and cancer experts have devised bioinformatics software to evaluate how well current strategies distinguish cancer-promoting mutations from benign mutations in cancer cells.
EDGE bioinformatics brings genomics to everyone
A new bioinformatics platform called Empowering the Development of Genomics Expertise (EDGE) will help democratize the genomics revolution by allowing users with limited bioinformatics expertise to quickly analyze and interpret genomic sequence data.
VirusDetect, a new bioinformatics pipeline for virus identification released
A new bioinformatics analysis tool developed by researchers at the Boyce Thompson Institute can help scientists to identify all known and novel viruses and viroids within small RNA datasets on a local to global scale.
More Bioinformatics News and Bioinformatics Current Events

Trending Science News

Current Coronavirus (COVID-19) News

Top Science Podcasts

We have hand picked the top science podcasts of 2020.
Now Playing: TED Radio Hour

Teaching For Better Humans 2.0
More than test scores or good grades–what do kids need for the future? This hour, TED speakers explore how to help children grow into better humans, both during and after this time of crisis. Guests include educators Richard Culatta and Liz Kleinrock, psychologist Thomas Curran, and writer Jacqueline Woodson.
Now Playing: Science for the People

#556 The Power of Friendship
It's 2020 and times are tough. Maybe some of us are learning about social distancing the hard way. Maybe we just are all a little anxious. No matter what, we could probably use a friend. But what is a friend, exactly? And why do we need them so much? This week host Bethany Brookshire speaks with Lydia Denworth, author of the new book "Friendship: The Evolution, Biology, and Extraordinary Power of Life's Fundamental Bond". This episode is hosted by Bethany Brookshire, science writer from Science News.
Now Playing: Radiolab

Dispatch 3: Shared Immunity
More than a million people have caught Covid-19, and tens of thousands have died. But thousands more have survived and recovered. A week or so ago (aka, what feels like ten years in corona time) producer Molly Webster learned that many of those survivors possess a kind of superpower: antibodies trained to fight the virus. Not only that, they might be able to pass this power on to the people who are sick with corona, and still in the fight. Today we have the story of an experimental treatment that's popping up all over the country: convalescent plasma transfusion, a century-old procedure that some say may become one of our best weapons against this devastating, new disease.   If you have recovered from Covid-19 and want to donate plasma, national and local donation registries are gearing up to collect blood.  To sign up with the American Red Cross, a national organization that works in local communities, head here.  To find out more about the The National COVID-19 Convalescent Plasma Project, which we spoke about in our episode, including information on clinical trials or plasma donation projects in your community, go here.  And if you are in the greater New York City area, and want to donate convalescent plasma, head over to the New York Blood Center to sign up. Or, register with specific NYC hospitals here.   If you are sick with Covid-19, and are interested in participating in a clinical trial, or are looking for a plasma donor match, check in with your local hospital, university, or blood center for more; you can also find more information on trials at The National COVID-19 Convalescent Plasma Project. And lastly, Tatiana Prowell's tweet that tipped us off is here. This episode was reported by Molly Webster and produced by Pat Walters. Special thanks to Drs. Evan Bloch and Tim Byun, as well as the Albert Einstein College of Medicine.  Support Radiolab today at