Galaxy Bioinformatics Platform performs COVID-19 Analysis, Scientists don’t know how SARS-CoV-2, which causes COVId-19, is going to evolve, but they say it won’t leave soon. Human coronaviruses have been identified for the first time during the mid-1960. The existing disease is a new disease for humans.
Around 100 organisations, mainly academic laboratories and genome sequence facilities have already contributed genomic data to the pandemic study. Genomic data are critical because it helps to identify the development of the virus and can provide key insights into how it can be stopped. Many of these teams have experience working to speed up genome sequencing with HIV, Ebola, Zika, flu, and hepatitis C, as has previously been done.
However, the SARS-CoV-2 is distinct.
Sergei Pond, a professor of biology at Temple University in Philadelphia, said: “This community did not expect this many data quickly. “It is in real-time that we see that epidemic develops. The current outbreak is unique. This is unique. Never before has it happened.
The Galaxy project, which was one of the world’s largest web bioinformatics platforms, is collaborated by Pond and his colleague Anton Nekrutenko of the State of Pen. On the platform more than thirty thousand biomedical scientists work for about 500 000 jobs a month.
Since 2013, a large percentage of Galaxy users have been powered by the Texas Advanced Computing Center (TACC), which has enabled scientists rapidly and seamlessly to resolve difficult problems where their personal computer or campuses are not sufficient.
“We have quite a database of users, and we have many instances around the globe — the biggest case in America is TACC,” said Nekrutenko, a Biochemistry and Molecular Biology professor. Galaxy started in 2005, in the state of Penn, with Nekrutenko and his close associate James Taylor.
On April 2, 2020, at the age of 40, he passed away unexpectedly, at the age of 40, at the age of Taylor, professor of biology and computing at Johns Hopkins University. Here is published the official Galaxy Project eulogy.
Since 2013, the Texas Advanced Computing Center (TACC) has been providing data analysis to a significant percentage of the galaxy user, enabling researchers to solve difficult problems quickly and seamlessly in cases where the personal computer or the campus cluster are not enough. “We do 100,000 analyzes a month and are currently spiking with regards to the use and viral testing.”
The researchers use parallel processing and Big Data Analytics to perform most of their analyzes on Stampede2’s and Jetstream’s supercomputers. Moreover, Galaxy uses Bridges platform for genome assembly applications at the Pittsburgh Supercomputing Center (PSC) that require large amounts of common memory. The Extreme Science and Technology Discovery Environment (XSEDE) allocate these systems to researchers who are funded by the National Science Foundation. These systems are provided with supercomputer resources.
“The open public resources of XSEDE are for us a way of demonstrating the value of a public cloud, which is specially designed for research,” said Nekrutenko. “We are able to analyze everybody in the world with proven tools and solid workflows. We believe TACC and PSC are ideal platforms for this use of the assigned XSEDE resources.
As a famous expert in the development of infectious diseases, Pond develops software tools and methods for researchers. He and Nekrutenko are currently working feverishly on a number of federally-funded research projects that integrate tools developed by the Pond laboratory to bring them into and into Galaxy. “We are in a good position to deal with the current issue with SARS-CoV-2 since for a number of years we have worked in this domain,” said Pond.
The Pond methods enable scientists to trace the sources and development of viruses. He has developed a wide range of tools named HyPhy for the analysis of infectious diseases in particular. Researchers can undertake robust, reproducible SARS-CoV-2 genomic sequences analysis by working together with Galaxy and HyPhy. The company is also leading an NIH grant, which puts tools in the Galaxy for HIV analysis.
“These are conceptually the same instruments for SARS-CoV-2 study. In the SARS-CoV-2 worldwide research community, we can mainly resolve all genomic data analysis needs, “says Nekrutenko.
100-150 virus genomes were available in February 2020. This is because diagnostic and research laboratories worldwide sequence and deposit these genomes into large, central databases. This number is increasing exponentially in March and is growing faster. “There might be 50,000 genomes for everything we know next week,” said Pond.
The objective is to decrypt these data to understand in real-time if the virus has anything unique before it affects the course of the pandemic.
In the past, many interesting analyzes have been carried out after the outbreak, such as SARS, MERS, Ebola, and Zika. Mainly because, unlike what is happening now, the outbreaks were contained before they became a pandemic. Furthermore, researchers did not have the technology they needed to sequence until about five years ago.
Galaxy Bioinformatics Platform performs COVID-19 Analysis
“Your tools now have to be installed and running very quickly and you have public data analysis infrastructure,” said Pond. “Everything develops live. The analysis is turned around as fast as the data centres.
The SARS-CoV-2 is mutating more slowly than influenza on the positive side because of an enzyme that reacts during synthesis with RNA and replication with RNA. “It means we have to be able to create a successful, rather uniform vaccine,” said Pond. “You may take the Japanese sequence and the Africa sequence and will be very similar to each other, so we can develop a fairly reliable vaccine with high confidence.” Anton Nekrutenko says, “We can essentially resolve the global research community’s genomics analysis demand for SARS-CoV-2.”
People are expected to become a seasonal infection with SARS-CoV-2, so scientists need to look for changes to develop and possibly develop a new vaccine every year. Our immune systems will eventually develop host immunity. However, it takes time and time — months to years — through the people.
“The first step is to produce the variation of the genome and to find the most important of all the thousands of positions we can look at. We help to concentrate on where there might be some interesting evolutionary dynamics, “says Pond.
Researchers know that there are 30,000 basic pairs in the virus — three times greater than influenza or HIV. “A virus is as large as a virus can be before molecular replication is confronted with fundamental constraints,” said Pond. “It mutates slowly compared to influenza or HIV, but mutates in mammals or bacteria much more quickly than genome simply because it undergoes rapid cycles of replication.”
Their aim is to enable researchers to perform this analyzes irrespective of the location in Nekrutenko, Pond and other Galaxy-workers. “For instance, if someone generates data sets in Africa or China or Brazil, they could use Galaxy to carry out analysis on an established, uniform basis. We have established equal opportunities for analyzes carried out by different laboratories to be comparable, “said Nekrutenko.
“We have a situation here in which we don’t know what will happen,” said Pond. “We look forward, then, to try to analyze these data predictively. For a scientist, it’s very exciting because it’s a unique opportunity that never happened before. I feel that all have to make their best contribution. And it is definitely something to do to provide data analytics.
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Galaxy Bioinformatics Platform performs COVID-19 Analysis
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