Researchers at the Earlham Institute have introduced a groundbreaking software tool, MARTi, designed for the rapid identification and visualization of microbial threats. MARTi was initially created to detect pathogens in preterm babies. Today, it has become a nimble and flexible platform that’s applied in biosurveillance, agriculture, and even in use on research vessels in the Antarctic. With this groundbreaking tool, real-time analysis and visualization becomes a reality for metagenomics. It produces and drastically accelerates previously unattainable microbial threat assessment efficiency.
MARTi consists of two primary components: the MARTi Engine and the MARTi GUI. The MARTi Engine, developed on top of a Java backend, is the primary workhorse for analyzing many sequencing data simultaneously in an efficient manner. The MARTi GUI provides a browser-based visualization interface for users to explore and compare results in near real-time. This unique pairing of tools allows scientists and researchers to produce beautiful graphs and figures that are tailored for scientific publication and presentation.
Versatile Applications of MARTi
MARTi’s versatile working people as a valuable tool in a variety to inclusive environments. From agriculture to biosurveillance and security, it has shown its value — delivering near real-time results invaluable in emergency response scenarios. Director of the team at the Earlham Institute, Dr. Richard Leggett highlighted the flexibility of the software.
“MARTi has its origins in software we developed for really rapid identification of pathogens in preterm infants, but we’ve since adapted it to use in a wide range of settings including on board research vessels in the Antarctic, in agriculture, and in biosurveillance and security.” – Dr. Richard Leggett
The tool’s impact is clear even with the still new, real-time analysis of nanopore metagenomics. It enables researchers to examine all microbes inhabiting certain environments at once in record time. First author Dr. Ned Peel, a postdoctoral research scientist at Earlham Institute, emphasized its practical benefits.
“It’s operationally very lightweight; you can use it in-field for taxonomic classification on a standard laptop or undertake larger, complex analysis using high-performance computing.” – Dr. Ned Peel
MARTi provides amazing freedom of installation. You can install it on local machines such as desktops and laptops, or if you happen to have access to them, high-performance compute systems. This flexibility, in turn, allows the platform to serve user needs across an extremely diverse range of use cases and technical skill levels.
Immediate Impact on Research
One of MARTi’s most notable attributes is its unique capability to provide instant analysis results. This ability is what makes it an irreplaceable tool, especially when minutes are critical and time is of the essence. The software has since become the first-line analysis tool for any metagenomic project that comes through Dr. Leggett’s team.
“MARTi is now our first line analysis tool for any metagenomic project and we’re using MARTi in several current collaborations. Through testing both simulated and real data, we have demonstrated the robustness of results.” – Dr. Richard Leggett
This immediacy becomes all the more urgent in areas like biosurveillance, where the early diagnosis of a threat can trigger swift counter-response initiatives. With the capability to analyze and visualize data in real-time, we are better equipped than ever to intervene effectively and win the fight against microbial threats.
User-Friendly Design
The development team was particularly focused on user experience when developing MARTi. Their goal was to develop a tool equally powerful and robust as it is intuitive and easy-to-install.
“We’ve created a user-friendly tool that should be flexible, customizable, and easy to install.” – Dr. Ned Peel
The new browser-based GUI makes it incredibly easy to navigate. Users spend more time on their research and less time fighting with complex software workflows. This methodology fosters wider uptake and use by researchers in all disciplines.