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Online platform designed to improve reproducibility, scientific collaborations

Online platform designed to improve reproducibility, scientific collaborations

Genomic wet labs are incredibly complex operations. Now a team of researchers, assisted by RISE engineers at Penn State’s Institute for Computational and Data Sciences, has developed an online platform to help scientists keep track of these complex processes, making them more efficient, less expensive and their experiments more reproducible. be for other teams. Credit: National Cancer Institute/Unsplash

For centuries, scientists relied on a pen or pencil and a reliable lab notebook to ensure their experiments could be understood and replicated by colleagues. Now that experiments can span dozens of steps and hundreds of materials, produce gigabytes of data that supercomputers need to process and share with collaborators around the world, the lab notebook may no longer be enough.

In a recent study, the researchers report developing an online platform that could help genomic researchers track experiments from conception to publication, maintain accurate data for quality control purposes and facilitate potential reproducibility efforts.

Called the Platform for Epi-Genomic Research, or PEGR, the system is designed as a tool to help experimental life science labs (or wet labs) keep track of highly complex operations and turn raw data into scientific insights. For example, instead of relying on meticulous handwritten notes, PEGR incorporates two-dimensional barcodes — called rapid response or QR codes — to electronically collect and track detailed information about samples as they go through the experimental process.

PEGR’s efficiency may improve reproducibility, a key rationale for developing the tool, according to William Lai, an assistant research professor, Cornell University, and previously an assistant research professor of biochemistry and molecular biology, Penn State. Reproducibility, a critical step in the scientific process, requires scientists to review their work to ensure it is accurate, safe and functional in real-world applications.

“It is already widely recognized that reproducibility is not just an issue in life sciences, but in all STEM (science, technology, engineering and medical) fields,” Lai said. “There has been story after story of research teams claiming to have discovered something and a few years later we find that no one has reproduced those results outside of the lab that generated the findings. PEGR is an approach to follow to get to grips with experimental processes – what a user uses and when do they use it – so we can improve reproducibility.”

Being an online platform, PEGR can connect scientists around the world to facilitate reproducibility efforts. The platform also focuses on the rapid development of genomic research equipment — including robotic sampling and high-throughput sequencers that can run many experiments simultaneously — that create massive amounts of data, according to Danying Shao, research and development engineer for the Institute for Computational and Data Science’s (ICDS) Research Innovations with Scientists and Engineers, or RISE, team.

“There’s no question that there is a data explosion happening in bioinformatics,” said Shao, who helped design the platform. “Big data sets are being generated at an unprecedented rate. For example, a single sample can generate gigabytes of data. And if we sequence hundreds of samples, you can see that we can get to the level where we can get terabytes of data.”

According to the researchers, who published details about the system in Genome BiologyPEGR is integrated with the Galaxy platform, an open-source scientific workflow system. PEGR is designed to monitor the sample and sequencing experiment, manage the processing of the data, and then produce reports and visualizations of the experimental results.

In the first few runs with the platform, the researchers are already experiencing early benefits.

“As an example, recently a technician had a series of failed experiments, so we went to PEGR and by examining the experimental metadata, we realized they were using a bad batch of a particular chemical,” Lai said. “Now, historically, the process of finding the cause of the failed experiments could have taken months — if not, a year or two — rather than finding the source right away.”

RISE-powered research

According to RISE team leader Chuck Pavloski, the PEGR project is just one example of how members of RISE are helping Penn State researchers and the research community at large. Pavloski likens the team to a bond of researchers with computational tools and expertise that can increase the power of science to address key scientific and societal challenges.

“The RISE engineers are basically the glue between science and today’s computing needs,” says Pavloski. “In other words, they enable the scientists to be what they do best. We behave in the same way as a staff scientist in a national laboratory, paving the way for our scientists to explore their fields and develop their research ideas.” pursue.”

This RISE-powered collaboration can help scientists with traditional computational research questions, such as offering advice on best practices for using Penn State’s Roar supercomputer to provide ways to optimize and improve code, but the team can also apply in-depth knowledge of academic research to collaborating with scientists on cutting-edge, interdisciplinary projects.

“The RISE team is made up of masters and PhD level scientists who have a deep understanding of how science works, but work outside their field all the time,” says Pavloski. “For example, we have a trained meteorologist who also works on biochemistry or genomic projects, or we have engineers on our team who can help scientists in astronomy or biochemistry.”

This interdisciplinarity offers another advantage. RISE team members can use the best computational science practices in one area for investigations in other areas or disciplines.

“We also provide a strong link to new technologies, such as using artificial intelligence techniques or exploring the use of graphics processing units or GPU computation in a research project,” Pavloski said.

RISE engineers also collaborate with data visualization specialists to help scientists create compelling visualizations for their work, and to take advantage of new immersive technologies, such as virtual reality and augmented reality, to explore data in in-depth ways.

Future use

The researchers hope that PEGR, which is open source, could benefit the entire scientific enterprise, save time, money and headaches, and lead to everything from a better understanding of the genome to better medical treatments that reach patients faster.

In the future, the researchers could explore whether the online platform could be expanded beyond use in wet labs and for use in translational science, which would help scientists bring treatments and solutions to the real world.

“This platform was originally designed around basic research, but we are actively working to move it to the translational biomedical field in the future,” says Lai.


A new open access portal for human immunological data and tools


More information:
Danying Shao et al, PEGR: A flexible management platform for reproducible epigenomic and genomic research, Genome Biology (2022). DOI: 10.1186/s13059-022-02671-5

Provided by Pennsylvania State University


Quote: Online platform designed to improve reproducibility, scientific collaborations (2022, June 24) retrieved June 25, 2022 from https://phys.org/news/2022-06-online-platform-scientific-collaborations.html

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