9 min read

Remote Learning with ROSALIND

By Arizona Milotich on Feb 11, 2021 12:47:57 PM

An Interview with Janice and Harrison of Jericho High School

As COVID-19 has forced many researchers to work from home, so too has it forced students to learn remotely.  Two researchers of Jericho High School’s class of 2022 found ROSALIND on a quick Google search and have since been using the platform to showcase Diabetes research for their Senior project. I spoke with Janice and Harrison about their experience using ROSALIND over a Zoom call.

 

It's fascinating how deep you have gone in your research for this school project! Where did you first learn about gene expression and RNA-seq?

Janice: My first exposure to gene expression and RNA sequencing was at the beginning of the summer, actually, because we realized that we had to have a bioinformatics project by the end of the summer. So I just watched YouTube videos. I tried taking some other online courses. I know our school gave us an online course to help us learn more about RNA sequencing. But those lessons were still really complicated, it was hard for me. 

Harrison: Our research teacher from school runs a summer program and she was kind enough to give us access to the data science courses that they were taking. And so that's originally how I learned about gene expression and RNA. But I've also tried to learn more on my own because, like Janice said, it was very fast paced, so I would go on Youtube to understand it.

 

How did you first hear about ROSALIND?

Janice:  I first heard about ROSALIND browsing through a Google search. I was looking around for a [bioinformatics] platform that didn't require any coding, because I have a bioinformatics project coming up. I have no real experience with coding and data science, but I really am passionate about biology. And I was just doing an Internet search about any platform that might exist that could help me with this. 

Some of the ones that came up were ones that also required you to upload the data. Basepair came up and the OMICS course. They all require you to have data that you have to upload to them. And even downloading the data off of public domains can be difficult, it requires all these things like separate softwares to download. But Rosalind was the only one where you could just simply take the project’s accession number and just copy and paste it. And it does like pretty much everything for you. 

Harrison: Originally going into this summer, I was thinking that I'd be able to do a wet lab project, but unfortunately, because of Covid, we weren't able to get that opportunity. I knew that I would need to do a data science-based project. And so originally, I tried to learn how to code. Because my goal was to be able to have a research project by the end of the summer I found that if I were to take the time to learn how to code, it either wouldn't come out to the quality that I would want it or I would run out of time. 

And so I started looking for platforms and originally I found a different platform that was very confusing. Then Janice recommended Rosalind. It's very intuitive, unlike the other platforms that I was trying to use. And like Janice said, it's very simple. All you have to do is copy and paste the accession number and it does a lot of the stuff for you as long as you know what you're doing.

 

What level of biology have you completed at school? and what studies have you completed on your own?

Janice: I took AP Chem this year and I took Intro to Research 9 and Research Science Research 10. And then on my own, I've done a research project since 8th grade relating to cancer. And last summer, I did research on obesity. 

By myself, I read science journals about different biology topics, I read a lot of science journals about cancer especially.

Harrison: I've also taken science, biology and chemistry, but on my own, I've also self studied AP Bio and AP Chem. 

I also have a little bit of a background in research. I took science research 10 this year and most of my research that I was working on was focused more on molecular biology. Specifically looking at the effects of mechanotransduction, which is how cells respond to physical signals like force or changes to cell elasticity. I've also taken a biochemistry course this summer.

 

How did you teach yourself how to use the platform?

Janice:  I taught myself how to use the platform by calling the people at Rosalind. I also used the videos on the main page website, it gives like a brief tutorial about how to use Rosalind. 

I clicked around and just tried to figure out what each button does as well. And then I also watch some of the video tutorials that come along with Rosalind to teach myself.

But whenever I had a question I was able to ask the Rosalind team and they'd get back to me within a few hours. It was really quick and easy to reach out if I ever had any question, it was answered very quickly. 

Harrison: A lot of the videos that came with the platform were very helpful. I think a lot of the learning that I did was just by clicking around and seeing what they did and what plots came up. And just being able to say, OK, this is the thing that Rosalind came up with. And then I wrote down what each button did so that I could reference it for the future. But so given how many buttons are there, it would take awhile. But it actually didn't write many down because a lot of the buttons are pretty self-explanatory. 

 

What area of research are you most interested in? 

Janice: I'm most interested in cancer based research and in research relating to the immune system. I think it's so fascinating how our body has this innate protection to all kinds of diseases. I’m interested in how we can boost that in order to cure some of these diseases, enhancing your own body’s system to make it better at fighting off these diseases. In cancer, I'm focusing on CAR t cell therapy, which is also related to the immune system and how to genetically edit T cells to better target cancer. 

Harrison and I also worked on a project together for a local competition, called Medical Marvels where we spoke about vaccines.

Harrison: I'm also interested in biology, but I tend to find biochemistry and molecular biology more interesting. And that tends to be where my research is.

Just being able to predict what happens at a macroscopic level based on a change in one molecule. To watch a small molecule have such an important influence on your body's function. I think that's really cool.

 

What is your favorite feature of ROSALIND? 

Janice: My favorite feature is easily the pathways. I like how it shows which genes are up, regulated and down regulated in the pathway and relates it back to a bigger context. 

Harrison: I was also just about to say the pathways. Not only does ROSALIND show the specific genes that were analyzed in the dataset, but also puts the result into context which is even more important for understanding the results. Having ROSALIND just essentially do that for you and you’re able to see the results and it's mapped out. Intuitively, I think it is very, very useful.

 

What would you like everyone to know about ROSALIND and using ROSALIND?

Janice: I would like everybody to know that it's very, very simple to use because it's like we said before, like this, you have to enter the project accession number. And it's the easiest way to upload data and run the analysis.

You can get the analysis really quickly and it gives you all the heat maps, and all the basic bioinformatics tests it can run for you. 

[ROSALIND] just gives you all of the information so quickly and so easily that it's really helpful, especially for people who don't have a lot of experience with data science, but are interested in biology. And it's like perfect for them. 

Harrison: Rosalind is a great platform. If you don't know a lot about bioinformatics but you're interested in doing bioinformatics research, I think my advice would be to just don't be afraid to play around with it. Upload a dataset and then just experiment and see all the capabilities that ROSALIND is able to do. And I think that's the best way to learn because you'll be able to see how intuitive the platform really is. 

 

What future discoveries motivate your interest in Biology the most?

Janice: CAR t cell therapy research is really innovative and there's a lot that can be done with it. And I hope to help implement it as a therapy in solid tumors because it has a really high remission rate in leukemia and lymphoma. 

A discovery that motivates me would be to answer: How can we help improve CAR t cell therapy implementation in solid tumors? If we figure that out, it would be a near universal cancer treatment. I think that that's going to be a major breakthrough. So that's what motivates me the most is if I can help contribute to that in any sense.

Harrison: I guess my answer to this question is probably much more broad than what Janice is talking about. I think just being able to come up with a cure or even just a treatment that makes people’s quality of life better. I think just being able to contribute to that is what motivates me. 

 

What has been the latest piece of research that gives you the most hope or that you’ve found the most interesting?

Janice: So given the times right now, I think the most hopeful research is actually about Covid. I think the AstraZeneca vaccine that they're coming up with at Oxford University is the most hopeful thing we have right now. That in such a short amount of time we've come up with, and we're coming up with, all these vaccines and there's so much promise from this particular vaccine. 

 

What is your dream job? 

Janice: I'm not 100 percent sure about my dream job because when I was younger, I was really set on being a doctor. And before that, a lawyer.

More recently I've been branching out a bit more. But I think that in the end, I'm still most interested in the STEM field. So I might want to take a route towards medicine. If I do become a doctor, I would either want to do radiology or interventional neurology. 

Harrison: I'm actually not sure at all. I just know that whatever I do in the future, I want to be able to help the world by using science or anything that I'm able to contribute. 

 

What message do you have for fellow students interested in genomics?

Janice: Genomics is a great thing to be a part of because it has an application that’s bigger than yourself. You’re basically helping to solve some of the world’s biggest diseases. You shouldn’t get discouraged when it gets hard, because especially from our experience during Covid, Harrison and I haven’t been able to do wet lab research and we’re very limited. But we’re both still interested in it and if you’re interested in it, just keep following through with it. 

Don't let any limitation get in your way because, for me at least, I always see it as if I stop now, I'm not going to be able to help others in the long run, even if it's hard for me now. 

You just have to push through it. And any limitation that comes, you just have to overcome it. If you're really, truly passionate about it and you can always ask others for help, there's so many people out there who are willing to help, like the people at ROSALIND and our teachers at school. Reach out if you feel discouraged. You always have this support system. And just keep in touch with what you’re passionate about. 

Harrison: I would say just go for it right now. The world isn't necessarily built for young scientists to be able to have an impact at such a young age. The most of the messages that we get are just to wait until you're more knowledgeable or more experienced. But piggybacking off what Jenna said, just go for it. The worst thing that could happen is that you reach out to someone that has experience and they say no or they don't respond.  In other words, there's more consequences to it if you don't go for it than there are if you did.

 

In conclusion, here are some of my takeaways from my discussion with Janice and Harrison: 

Takeaway #1- ROSALIND helped Janice and Harrison run bioinformatics on publicly-available Diabetes research data. Without ROSALIND they would not have access to the analyses, would not be able to interact with the results, and would be limited on making discoveries on the data. 

Takeaway #2- ROSALIND is an easy to use, intuitive interface. Researchers like Janice and Harrison, with no bioinformatics experience are still able to run their own pipelines and get to their results quickly.

Takeaway #3- Like Janice and Harrison advise, go for it. Even in the middle of the pandemic, there are ways to keep making discoveries on your research and our team at ROSALIND is happy to help. 

So knowing all this, and given this unique moment in time, how are you analyzing the results of your research?

You can access Janice's Type 1 Diabetes Showcase here: https://rosalind.onramp.bio/showcase/T1D

Arizona Milotich

Written by Arizona Milotich

Arizona is a Research Success Advisor at OnRamp and is responsible for researcher onboarding to the ROSALIND platform. Customers enjoy working with Arizona for her friendly and knowledgeable instruction of transciptomic and epigenomic studies.