BIPS

BIPS: A Semester in Review

May 17, 2021 By Becca Wolf in Research Tags: BIPS, computer science, plant science

Maria Lusardi showing how she connects the pH sensors to the Arduino. | photo by Becca Wolf, Bond LSC

By Becca Wolf | Bond LSC

As the semester comes to an end, Bioinformatics in Plant Sciences (BIPS) close the school year with a lot of accomplishments: one team earned Best Abstract honors at the Mizzou Undergraduate Research Forum, three teams have papers in the review process, one team got their research published in a journal, and two BIPS members were even selected to share their work at the Research Day in Jefferson City, MO.

These teams did not get to these places on their own.

BIPS is in its 3^rd year at Bond Life Sciences Center as an undergraduate program that pairs a plant sciences or biology student with a computer science or engineering student. Most students come in with little to no knowledge on the other’s major but are committed to work together on a project that requires both disciplines.

“I liked how I was able to work with Maria who has different experiences and knowledge than what I do and to be able to work together to create this cohesive project that we’ve been working on all semester. It’s been really rewarding,” Emily Walter said.

Walter, a plant sciences major, worked in the David Mendoza lab at Bond LSC this semester with Maria Lusardi, a computer sciences major.

They focused on using pH sensors with maize grown in a hydroponic system to track the acidification of the root environment when plants were grown with different nutrient availability. Lusardi first worked on tuning the remote pH sensors while Walter established the right hydroponic conditions for maize.

“I’ve been working with a lot of different things. I started out looking at Python [coding language] a lot and trying to get different Python scripts to work, but at the end I worked more with data analysis,” Lusardi said. “I tried to learn a new language so that I could make some applications that would make it easier for us to look at our data.”

They presented their research in Mizzou’s spring Undergraduate Research Forum. The forum was held online this year.

“The presentation talks mostly about the different brands of sensors we used and compared in the experiment and the different data sets,” Lusardi said. “It was more focused on the set up of the plants themselves.”

Walter and Lusardi received a Best Abstract award at the forum.

“It was really cool because I was watching the closing ceremonies and then they said our names. I was surprised, I wasn’t expecting to actually win and be a part of the top best abstracts,” Walter said.

Walter credits BIPS for helping her and Lusardi be comfortable presenting their research poster. The two presented in front of members of BIPS before the forum and received critiques.

“It was nice to know what to improve upon. It was also cool to see what other people were working on and learn about other projects,” Walter said. “I definitely expect to be doing similar stuff like this and hopefully will present live in the future.”

This success is the ultimate goal of BIPS.

“I think it’s very rewarding because you see them at the beginning when they have no idea what the project is,” Mendoza said. “At the beginning, they start by just following instructions, but, little by little, they start getting an understanding of what they are trying to do and start doing things by themselves.”

Mendoza was the principal investigator who initiated BIPS through a National Science Foundation grant.

“We now know the recipe for success, and we want to keep the program growing,” Mendoza said.

Both Walter and Lusardi have learned a lot about the other’s major.

“There are different knowledge and skill sets that you learn that you wouldn’t normally do on your own if you’re just a plant sciences or computer sciences major. It’s a good way to see how those interact to create something more,” Walter said.

Mendoza hopes that BIPS can keep this momentum going next year.

“In the end, the hope is that they learned that moving across fields is not impossible and that you can learn from a different field. You don’t have to be isolated in what you thought would be the rest of your career,” Mendoza said.

Beyond counting: computer science partnership helps speed up plant science experiments

May 12, 2021 By Lauren Hines in Research Tags: BIPS, computer science, high-throughput phenotying, plant science

Janlo Robil, graduate student in the Paula McSteen lab, came up with the GrasVIQ project after he finished a project that required him to count hundreds of plant leaf veins. | photo by Lauren Hines, Bond LSC

By Lauren Hines | Bond LSC

It’s not surprising that researchers feel discouraged when pursuing projects that involve plant leaf vein density analysis. Manually counting individual leaf veins and measuring their density to understand how nutrients are transported in plants can take weeks of tedious work.

That’s how Janlo Robil was feeling when he was working on a maize leaf project while rotating through the Paula McSteen lab in 2016 in Bond LSC.

Now, researchers can cut that time down to just minutes.

As part of the Bioinformatics in Plant Sciences (BIPS) program, undergraduate and graduate students in plant sciences and computer science have come together to create the first phenotype image analysis system for monocot plant leaf veins called, GrasVIQ.

The GrasVIQ software can process photos of grass leaves, automatically detect and count vertical grass leaf veins and calculate various quantitative measurements such as vein density, width and separation. These measurements help analyze leaf vein network patterns.

“The time that you use for collecting data, you can already use for analysis,” said Janlo Robil, head of the project and graduate student in the McSteen lab. “It will also help you in your decision about the direction of your research because the faster you get the data, then the better idea you have if you still need to pursue this or not.”

The project was spurred by Robil in 2017 when he went to a seminar by Filiz Bunyak, assistant research professor in the Electrical Engineering and Computer Science Department.

Bunyak was presenting her group’s interdisciplinary image processing and computer vision research, including their work on plant phenotype analysis. Robil got the idea to apply it to plant leaf veins.

“It started from a simple question,” said Ke Gao, co-author and graduate student in the Electrical Engineering and Computer Science Department. “Can we help them do their analysis faster with repeatable quantified results? We were hopeful we could use our previous experiences in plant image analysis to help Janlo and his lab conduct their analysis more efficiently.”

However, the project was on hold until 2019. Robil simply didn’t have the time or manpower for this project until he heard about the BIPS program.

“I think [the BIPS program is] a very good way of promoting interdisciplinarity in research,” Robil said. “Had I not asked the computer science people to collaborate with me, I would still be manually counting veins right now, and not using software to quantify veins more quickly. I think interdisciplinarity can move science forward and faster, literally.”

The software can identify the vertical veins with 95% accuracy and 92% accuracy for transverse veins when compared to the manual quantification.

“Without any doubt, we believe that the software can do a better job by just the rate of it,” Robil said.

The GrasVIQ phenotyping image analysis software can classify and quantify stained veins of grass and corn leaves. doi.org/10.1111/tpj.15299

While the software saves plant science researchers time and energy, it also provides computer science students something as well.

“Collaborating with plant scientists gives us the opportunity to leverage our expertise in engineering, algorithm development, and mathematical models to contribute to the solution of a real-world problem,” Gao said.

BIPS pairs undergraduate and graduate students from plant sciences and computer science together to work on a project. For undergraduate Claire Neighbors in the McSteen lab and computer science undergraduate Michael Boeding, this was their first published paper.

“It’s super exciting,” Neighbors said. “It feels good like all my hard work meant something.”

Neighbors was the one who had to create the images and do the manual counting to compare to the software’s counting. She said the process took her months.

“It was worth something so that we could make this software valid,” Neighbors said. “Someone had to put in the hours to be able to make those ground truths to show that this software works. So, it feels really good that I was able to contribute something.”

While the software has much to offer, the researchers believe it could be better. Robil thinks vein classification can be improved using machine learning even though the software achieves a detection accuracy of more than 90% for vertical veins.

The current software is designed to be used by scientists and does not have a very friendly user interface. Building a better user interface and further improving the analytics using machine learning approaches are future goals for Gao. GrasVIQ will enable generations of training data for these machine learning-based improvements.

Nonetheless, the software provides an escape from endlessly counting veins.

“We learned how to quantify the veins quickly, but like a year from now, that isn’t going to be what’s taking us months to do,” Neighbors said. “It’s going to be figuring out why this gene made the veins look weird or produced less or thinner, thicker, which is going to make things more efficient in the future.”

More information about the project can be found in, “GrasVIQ: An Image Analysis Framework for Automatically Quantifying Vein Number and Morphology in Grass Leaves.” The paper was published on April 29 in The Plant Journal. The study was done by Janlo Robil, Ke Gao, Claire Neighbors, Michael Boeding, Francine Carland, Filiz Bunyak and Paula McSteen. The Bioinformatics and Plant Sciences (BIPS) program is funded under the National Science Foundation, Cellular Dynamics and Function MCB-1818312 to David Mendoza-Cozatl (University of Missouri, Columbia).

BIPS: Bringing Plant Science and Engineering Together

February 3, 2021 By Becca Wolf in Research Tags: bioinformatics, BIPS, computer science, plant science

Nick Dietz and Marianne Slaten observing a plant in the lab. | photo by Becca Wolf, Bond LSC

By Becca Wolf | Bond LSC

Technology advancements have always driven scientific discoveries in order to perform in depth research, but that has never been more true today.

“A couple of decades ago it was perfectly fine to be an engineer and a biologist and live in your own world,” David Mendoza said. “But as science has advanced, we depend more on mathematics and computer sciences now.”

Mendoza, principal investigator at Bond Life Sciences Center and associate professor of plant sciences, created a program to help develop those skill in the next generation of scientists.

Bioinformatics in Plant Sciences (BIPS) was born in 2016. The undergraduate program pairs plant science or biology majors with computer science or engineering majors. Through research, field trips, and journal clubs, undergraduate students learn how to collaborate on projects and how the two fields help each other.

While Mendoza is the PI who initiated BIPS through a NSF grant, students from all labs are welcome in this program. More recently, a second NSF grant in collaboration with Gary Stacey has allowed the program to expand. BIPS identifies labs that have projects with both computer and biology components for students to work on. Students can also come to BIPS with a project already in mind.

Graduate Student Mentors

BIPS is run by students, for students, with a handful of graduate student mentors and undergraduate students in the program.

The graduate student mentors run weekly meetings, invite in guest speakers, and organize the journal clubs, which is where students review scientific publications and discuss them. Graduate mentors, Marianne Slaten and Nick Dietz, have enjoyed their time and responsibilities at BIPS.

“We make sure they’re on track and don’t get stuck. We want them to become well-rounded researchers,” Slaten said. “It’s a really novel opportunity to jumpstart the next generation of researchers.”

While BIPS cannot go on a field trip this year or have in-person speakers, Slaten and Dietz have come up with alternatives to keep undergrads engaged.

“We’ve been doing workshops showing different bioinformatics tools that can be used to address different research questions,” Dietz said. “We’re also having them do journal club, which gives them a better understanding of the literature surrounding what they are studying. We’re trying to normalize the experience as much as we can, even though everything’s virtual right now.”

A Bioinformatics in Plant Sciences (BIPS) meeting in progress. | photo courtesy of Nick Dietz, Bond LSC

Undergraduates

Undergrads are put into research teams and begin working.

Many projects start with a biology student cataloguing physical plant traits and a computer science or engineering student creates a way to take images of the plants and organize data and information.

“Some of the files you work with are so big you can’t even open them in Excel, so there’s always room for computational people that really know how to harness all that data,” Slaten said. “The files are just so big that your computer crashes. It takes additional skills to know how to deal with that data.”

While a majority of their projects focus on phenotyping, BIPS is looking to branch out into other areas.

“A big problem in biology right now is big data, which you can’t get through that if you don’t have computer science,” said Maddy Creach, a junior from Walter Gassmann’s lab at Bond LSC. “It’s interesting to see the way computer scientists look at problems and that has definitely made me a better researcher, especially since I know 1,000% more about computer science than I did when I started.”

Creach has found that her two years in BIPS helps her think about new ways to think about research.

“A big thing that I have gotten out of BIPS is how to manage my own project,” Creach said. “It’s on me to communicate with my partner and get stuff done and put work towards it, because no one else going to tell me to do it.”

In addition to working on their research and participating in journal club, the undergraduate students are expected to make a poster each year to present their research either at Life Sciences Week or at the Undergraduate Research Forum. Since the pandemic has limited or canceled these events, the students now submit a video of their work online for others to watch.

BIPS’ Impact

Building research and collaboration skills has helped everyone involved.

“I’m learning as much from them as I’m teaching them, so that’s been really awesome,” Slaten said.

Students also hone their communication skills.

“I didn’t realize being a good mentor is a skill set, it’s something you can cultivate over time,” Dietz said. “Oftentimes as students, we think of mentors as either good or bad, you either have it or you don’t. But it’s actually a skill that you can develop over time and I’ve picked that up since I’ve been helping run the program.”

But all remember it’s a learning process.

“Everyone’s really fun and easygoing, no one is judgmental because there is a range in expertise,” Creach said. “There are no dumb questions.”

BIPS has helped many students become well-rounded in their research abilities and is always looking for more students.

“The world is a big place that is moving at a fast pace, and if they don’t get on the train, they are going to miss it,” Mendoza said. “It’s that simple. There’s so much happening in real time, that if you don’t learn how to integrate technology into your research, you’re going lag behind.”

For more information on BIPS or to apply, contact David Mendoza or go to Bioinformatics in Plants (BIPS).