ASU professor awarded Chan Zuckerberg Initiative grant to support software essential to biomedicine

September 29, 2021

MDAnalysis — an open-source software used by thousands of scientists for the analysis and manipulation of molecular simulations — was recently recognized by the Chan Zuckerberg Initiative with an Essential Open Source Software for Science (EOSS) grant for the significant contribution it has on the field of biomedicine. 

The $374,087 grant will provide funding to improve and maintain the MDAnalysis software over the next two years. The team behind MDAnalysis is led by Oliver Beckstein, associate professor in Arizona State University’s Department of Physics. Portrait of ASU Associate Professor Oliver Beckstein Oliver Beckstein, associate professor in ASU’s Department of Physics, was recently recognized by the Chan Zuckerberg Initiative with an Essential Open Source Software for Science (EOSS) grant to support MDAnalysis — an open-source software used by thousands of scientists for the analysis and manipulation of molecular simulations. Download Full Image

The grant is part of the fourth cycle of the EOSS program, with a total of $11.1 million in funding for 35 new grants to support maintenance, growth, development and community engagement for tools that are widely used in biomedical imaging, genomics, cell biology, bioinformatics and other fields. In addition, the Chan Zuckerberg Initiative also awarded $4.9 million to 14 proposals led by previously funded EOSS grantees for initiatives dedicated to advancing diversity and inclusion in their contributor communities.

With more than 10,000 downloads a month, MDAnalysis has grown exponentially since it was first developed 13 years ago.

“It started as a small project of a graduate student and over the years attracted developers from all over the world and has become one of the most used packages of its kind for the analysis of molecular simulations, especially in the biosciences, but also in materials sciences, and it's also used in the pharma industry,” Beckstein said. “However, over all this time, the developers were never really paid to work on this software — it's all been volunteer work.”

Over the years the software has been maintained by graduate students and postdoctoral researchers, with assistance from research software engineers and assistant professors. Now, MDAnalysis will have the resources to support a number of developers so that they can focus on the software and work on improving it in a number of ways.

"We are incredibly proud of Dr. Beckstein for receiving the Chan Zuckerberg Initiative grant,” said Patricia Rankin, chair of the Department of Physics in The College of Liberal Arts and Sciences. "The Beckstein Lab's work in biophysics of membrane protein and their work on open-source software for the analysis of biomolecular simulations continues to demonstrate innovation within the Department of Physics. These awards will allow Dr. Beckstein and his team to continue their work, and we cannot wait to see the innovative work they produce next."

Beckstein shared more about the software and how the grant will propel this work forward.

Question: How would you describe MDAnalysis?

Answer: Computer simulations at the molecular scale have become a very important tool in the molecular sciences, namely understanding the function of biological systems from individual proteins to the interactions between cells and viruses, and the development of new materials. These simulations run on the biggest supercomputers in the world and produce huge amounts of data. MDAnalysis is a software package that enables researchers to efficiently and easily work with these data and analyze them. Novices and experts can use MDAnalysis because it provides both ready-made tools for common tasks but also fully documented programmatic access to all the data structures and algorithms that one needs to develop completely new solutions.

Q: What goals do you hope to achieve with the support of the Chan Zuckerberg Initiative grant? 

A: We want to speed up some of the core of our code so that it works faster, even for very big simulation systems with tens of millions of atoms. Our users always desire higher performance. But there's generally no funding to be had for such important work because most granting agencies prize novelty over what is often seen as "incremental" work, even though it has an enormous impact when thousands of researchers can get their results in a fraction of the time. The grant allows us to do something that we could normally not do. Another common problem in the molecular computational sciences is that everybody writes code and all research relies on this code, but not enough researchers make their code available. This leads to widely recognized problems: Research is difficult or impossible to reproduce, and effort is wasted due to code duplication when other researchers need to solve similar problems. Although MDAnalysis comes with a growing number of essential analysis tools that everybody can use and modify, these tools cannot cover all the new and creative use cases that scientists come up with. Therefore, we will make it easier for other researchers to share and publicize their code in the form of "code packages" named “MDAnalysis-Kits.” The grant will allow us to build the tools and documentation so researchers can turn their research code into a high-quality professional software package based on MDAnalysis. We hope that researchers will welcome the opportunity to make their work available to the large MDAnalysis user community.

Q: When did this project come about, and what interests you most about this work?

A: MDAnalysis was started by Naveen Michaud-Agrawal in 2006, then a graduate student at Johns Hopkins University. Another graduate student, Elizabeth Denning and I (then a postdoc at Johns Hopkins) used it and contributed code. We decided to open-source MDAnalysis in January 2008. Naveen eventually left academia, but Elizabeth and I continued work on MDAnalysis. Over the years, both users and contributors grew. By now, MDAnalysis is cited more than 1,700 times in the scientific literature, we have had more than 130 individuals contributing code so far and we now have a core developer team of about nine people who collectively steer the project, run workshops or write proposals together. Obviously, we use MDAnalysis everywhere in our own research, so it’s great to have a good scientific multipurpose tool at hand that allows us to implement our own new ideas. Overall, I am most happy about the fact that MDAnalysis is not just a useful piece of software for so many but that MDAnalysis has become its own thriving community that is known to be very welcoming and inclusive. 

Q: Who will be a part of your team, and how long do you anticipate working on this project? 

A: The team leading the work on the grant are Irfan Alibay, a postdoc at the University of Oxford in the U.K.; Lily Wang, a PhD student from the Australian National University in Canberra; Fiona Naughton, a postdoctoral researcher at the University of California, San Francisco; and Richard Gowers, who works as a lead developer for a cheminformatics company in the U.K. We will also hire a postdoctoral student here at ASU. The grant runs for two years, but even after then I foresee that I will continue to be involved in MDAnalysis.

Emily Balli

Communications Specialist and Lead Writer, The College of Liberal Arts and Sciences

How low did it go? Study seeks to settle debate about oxygen in Earth's early atmosphere

September 29, 2021

Scientists have long debated how much molecular oxygen was in Earth’s early atmosphere. About 2.4 billion years ago, there was a rise in oxygen that transformed Earth’s atmosphere and biosphere, eventually making life like ours possible. This transition is called the “Great Oxidation Event.” But how much oxygen was in the atmosphere before this time? 

A team of scientists, led by former Arizona State University doctoral student Aleisha Johnson, has been working to unravel the mystery of how the stage was set for the Great Oxidation Event. Artist’s rendition of what the Earth could have looked like in the Archean Eon, from 4 billion to 2.5 billion years ago. Artist’s rendition of what the Earth could have looked like in the Archean Eon, from 4 billion to 2.5 billion years ago. Image by Peter Sawyer/Smithsonian Institution Download Full Image

Using computer modeling, Johnson and her team determined how much oxygen might have been present at Earth's surface before the Great Oxidation Event — and the implications for life on early Earth.

“We all breathe oxygen, and we all live on the only planet known where that is possible,” says Johnson. “With our study, we're one step closer to understanding how that happened — how Earth was able to transition to, and sustain, an oxygen-rich atmosphere.” 

The results of their study have been published in Science Advances.

The long-standing puzzle

Geoscientists studying the rock record of Earth have found seemingly conflicting evidence about Earth’s early atmosphere. On the one hand, the “fingerprints” of oxygen found after the Great Oxidation Event are mostly missing before that time, leading some scientists to argue that it was absent. 

But recent discoveries suggest at least some breakdown of common minerals that react vigorously in the presence of oxygen, and at least some supply to the oceans of chemical elements like molybdenum that accumulate in rivers and oceans when oxygen is present. The conflicting lines of evidence create a long-standing puzzle.

An emergent view of Archean terrestrial oxygen production. Before oxygen filled Earth's atmosphere, it may have been produced in shallow oceans and soils. Shallow soils in proximity to microbial communities (green in figure) may have had oxygen, unlike the overlying atmosphere. As a result, weathering signatures such as molybdenum enrichments in shales predate the Great Oxidation Event. Image by Johnson et al./ASU

“The evidence seemed contradictory, but we knew there must be an explanation,” said Johnson, who is currently a National Science Foundation postdoctoral fellow at the University of Chicago. 

To help resolve this puzzle, Johnson and her team wrote a computer model that uses what is known about the environmental chemistry of molybdenum, the reactions of minerals with small amounts of oxygen, and measurements others have made of molybdenum abundances in ancient sedimentary rocks, to figure out the range of oxygen levels that was possible in Earth’s atmosphere before 2.4 billion years ago. 

“This computer model helps us quantify how much oxygen is actually needed to produce the chemistry that is visible in the rock record,” said Johnson.

What the team found was that the amount of oxygen needed to explain the molybdenum evidence was so small that it wouldn’t have left many other fingerprints. 

“There’s an old saying that ‘absence of evidence is not evidence of absence,’” said study co-author Ariel Anbar, who is a professor at ASU’s  School of Earth and Space Exploration and School of Molecular Sciences. “Until now, our ideas about oxygen being absent before the Great Oxidation Event were mostly shaped by an absence of evidence. Now we have reason to think it was there — just at lower levels than could be detected before.”

The findings support other lines of evidence suggesting that oxygen was being produced, possibly by biology, long before the Great Oxidation Event. That, in turn, helps scientists in their quest to figure out what changes in the Earth’s systems caused one of the most important transformations in Earth’s history.  

“Our hope is that these constraints on ancient atmospheric oxygen help us understand the cause and nature of the Great Oxidation Event. But this isn’t just about Earth history. As we begin to explore Earth-like worlds orbiting other stars, we want to know if oxygen-rich atmospheres like ours are likely to be common or rare. So this research also helps inform the search for life on planets other than our own,” said Johnson.

The additional authors on this study are Chadlin Ostrander of Woods Hole Oceanographic Institution, Stephen Romaniello of the University of Tennessee, Christopher Reinhard of the Georgia Institute of Technology, Allison Greaney of Oak Ridge National Laboratory and Timothy Lyons of the University of California, Riverside.

Karin Valentine

Media Relations & Marketing manager, School of Earth and Space Exploration