Contributors

Contributors

The DIY Diagnostics Stream is made possible thanks to a generous donation from Bob and Cathy O’rear.

DIY is supported by the Freshman Research Initiative and the University of Texas at Austin.

Riley Welch

Riley Welch

My interest in the DIY Diagnostics stream was actually sparked long before my knowledge of the Freshman Research Initiative, and long before my enrollment in UT, and, if we’re being very specific, long before my acceptance to the university at all. As a senior in high school, my AP biology teacher offered us extra credit to attend Hot Science: Cool Talks at UT. The “Cool Talk” I ventured to was hosted by Dr. Andrew Ellington and it was all about self-diagnosis. Or rather, diagnosing yourself at home, made to be as simple as the at home pregnancy test. You do it at home and if you realize you have an illness that needs medical attention you can get to a doctors office. If you just have the common cold, you stay at home and save you and your doctor time. This was really interesting to me and it made lots of sense; finding something that saves time and money – I’m in! I’m also constantly looking for things that interest me, because it seems I have this chronic state of boredom I am trying to shake.

So, I did my one page write up of this extremely “hot” science, turned it in, got my five points of extra credit and moved on. Over the next however many months I ended up out of high school and at UT in the Freshman Research Initiative and was a few months away from having to apply to streams. As soon as I saw DIY Diagnostics I was reminded of that talk that had so caught my interest. I realized I couldn’t make any of the open houses and scheduled a meeting with the RE, Dr. Tim Riedel. And after that I was pretty sure there wasn’t another stream I wanted be in.

Being in the DIY Diagnostics lab is like being a real researcher, because you are a real researcher, which feels very hard at first for someone who has never been in a “real” lab before. You do everything on your own, and if you are me, you do it with a serious lack of confidence the first go around. By the end of the year I had mastered skills I didn’t even know existed before this class and was performing tasks that had taken me half an hour in the beginning of the year in half that time. The first time I felt like an actual scientist was during our weekly meetings when we were having a discussion that sounded like science and I understood all of it, and had responses and we were all formulating things together that would have sounded like garble to me three months prior.

One of my favorite diagnostics we did was using dog saliva. Now before I get into it, we did not get any valid results from experiment, not one person out of the 35-40 students. But I am starting to learn this is less about being distraught about failure and more about learning what to do differently the next time around. Those of us with dogs had to swab the dog’s mouth, fill out a survey on the dog’s behavior, then extract the DNA in the dogs mouth and see if we could link any of the DNA to behavioral characteristics. Pretty cool, I know, but it didn’t work. This semester I would like to figure out why it didn’t work, or at least how to get it to work. I love this stream because I am able to make my own decisions like that. And I’m sure if I suddenly develop a hatred for dogs and their saliva I have no doubt Tim would help me figure out something else to benefit the stream but also keep me from being totally miserable. DIY is a well-run, very interesting lab. I highly recommend it to anyone who wants to feel like a scientist and really have a integral part of their research experience. I will now refrain from making any puns involving Labrador retrievers and research labs, but I will include a picture of my photogenic dog whose saliva I have and will be testing.

 

 

Course Details

Course Details

COURSE CREDIT

Spring Semester:
(BIO 206L with BIO 102C) or
(CH 204 with CH 108)

Syllabus from Spring 2014

 

Fall Semester:
BIO 377, CH 369K, CS 378

Who is this stream for?

  • This is a young stream and you can help define what we do!
  • Science majors looking for computer experience
  • Computer Science majors looking for wet lab experience
  • Creative students comfortable with undefined open-ended projects

DIY Diagnostics student collecting water samples from Waller Creek.

DIY Diagnostics student collecting water samples from Waller Creek.

What will you do?

Students can expect to learn about the design process (how do I brainstorm innovative ideas that solve a problem in a new way?), biochemical detection (how do I develop a test that indicates the health of the patient?), interfacing with the virtual world (how do I make a website or app to interface the diagnostic output to a computer?), and machine learning algorithms and artificial intelligence computer programming (how do I tap into the vast array of diagnostic and social data available on the web to improve my diagnostic outcome?).

Specific skills include but aren’t limited to:

  • Design theory
  • Culturing bacteria
  • PCR
  • qPCR
  • isothermal LAMP PCR
  • DNA extraction
  • DNA sequencing
  • App programming
  • Website development
  • Image processing
  • Electronics
  • Data storage and manipulation
  • Machine learning and artificial intelligence (coming soon)
  • Social network analyses (coming soon)
Explore DIY Apps

Explore DIY Apps

Our researchers are working on a variety of diagnostic applications to help users with anything from determining the difference between a cold and allergies to tracking diseases on a global level.
Check out our tailored DIY App website for updates on current apps, and our App Gallery for a showcase of our survey applications.
Meet Our Student Researchers!

Meet Our Student Researchers!

Going to open houses can have an affect similar to that of an approaching avalanche. But don’t panic! Despite the wealth of streams available and all of the information to be absorbed, it’s completely possible to fall in love with a few research topics.

To help first semester freshmen here at UT with their FRI stream decisions, we’ve asked our Fall 2014 student researchers to write about their time with the DIY Diagnostics stream. Most of our researchers are sophomores, but we have several upperclassmen too, as well as mentors who have already finished their FRI coursework.

Our researchers have worked to extract bacterial RNA from saliva samples, find sulfur-producing microbes in fracking water, and search out chemical signatures in olive oil using TLC plates. By working to place diagnostic power in the hands of the consumer, we hope to help create more personal and safe health care and industrial diagnostic systems.

If you like what you read, make sure to stop by the DIY open houses.

Andrew Acosta

Andrew Acosta

I chose to be in the DIY Diagnostic stream because we have a diverse selection of opportunities available for research and lab experience. There are a variety of group projects available to become a part of, like the FRIome, frack water, and Waller creek projects, but we are also given the opportunity to develop our own research projects. I think it is also really cool that we learn how to code, because without this stream, I’m about 85% positive I would have never learned to code, and I’ve always wondered how it works.

I think I am most excited about the FRIome project simply because I’m a biology major and this field interests me. I have heard many times over here at UT, that there are more bacteria cells in/on your body than there are your own cells, so I definitely believe that these bacterium have to be effecting humans in some way, and FRIome could possibly help to determine how.

Being part of the research community at UT has helped me succeed because you get to meet a tone of ridiculously smart and friendly people and you also learn a lot of techniques that can help you in your future research or labs. I actually went into my Chemistry Lab course with a great understanding of techniques, lab protocols, and tools simply because I had a great learning experience in the DIY Diagnostic stream.

I think the funniest part of the stream was that many of us students would be so completely lost at times and think that everyone else knows what they are doing, but when you talk to students you realize we’re all on the same page. After the first couple of weeks, when all the students were settled in and friends were made, that is when the serious work went down because there was a great sense of community and everyone collaborated to achieve success and spread the skills we had just learned. I think that was a major experience of the stream.

Compared to other undergrads who have done research outside of this stream, or FRI in general, the DIY Diagnostics stream definitely puts a lot of emphasis on student participation. We are the ones collecting samples, analyzing data, and the results. I think it is very important to be a part of every step in the research and we are given every opportunity to do so. I see diagnostics as moving in the direction of primarily “at-home” diagnostics because they will generally be faster and cheaper, and guess what, this stream is called DIY (do it yourself) Diagnostics, and I see this DIY diagnostic stream as a way to force upon the world a more stringent focus on accessibility to technologies we have to capability to produce and help accelerate the production of “at-home” diagnostics.

Lindsey Alter

Lindsey Alter

What appealed most to me about the DIY Diagnostics stream was the way it combined biology and chemistry with computer science. I really liked the idea of learning to code and create an app that could actually be useful. When I went to the presentation during open house, Dr. Riedel was the most genuinely enthusiastic of all the research educators I heard speak. After hearing the pregnancy test example as a DIY diagnostic, it got me thinking of the many new diagnostics that would be useful to the public, such as a reliable at home strep test. Plus, I was excited to work in a stream that was just starting.

The diagnostic ideas I am most excited about is the ones that can come from the FRIome project, in which we are testing saliva samples to find correlative data between various health factors and bacterial abundance. I hope to help enlarge the database of samples so we can a large amount of samples sequenced. Then we can look at abundance of specific bacteria, and develop experiments that can lead to new diagnostics. In my Microbiology class, my professor briefly discussed how there are ongoing studies that are looking at the relationship between subjects’ microbiomes and obesity, autism, and immune response. The more I hear about the significance of the microbiome, the more excited I get for the FRIome project.

Being part of the research community has helped me with my time management skills in that I had to always get enough hours of lab time in each week. Also doing research has taught me that not getting expected results does not necessarily mean failure, and that I should always keep working to find solutions to problems I encounter.

I came into this stream with very limited knowledge in coding. The bit of coding we learned during the spring semester has been quite helpful. This summer I started working on an app that helps to speed up the process of which foods specifically are causing widespread food poisoning to hasten the recall process. Most of this app is not completed though.

My biggest “aha” moment so far was when I used the Qubit correctly. It took me several tries to get the technique right, so I was very excited when I got the machine to properly find the concentration of dsDNA in my samples.

 

I’m glad I have been able to start research so early in my undergraduate career.  I hope this opportunity will open doors for me to receive internships in other labs in the next couple of years. Hopefully in 20 years, we will be able to have our entire microbiomes sequenced, which would mean we would quickly be able to diagnose ourselves with things discovered to be  related to or caused by the bacteria that live in us. I hope to be part of this process of discovering how the microbiome affects the health of humans.

Salvador Arellano

Salvador Arellano

I can support anyone who claims that your first year at a university as a freshman is   new, confusing, and can be very daunting. When I entered my first semester here at UT, I immediately looked for something that I can be a part of so I could fit in somewhere. I knew I wanted to join something that would give me the opportunity to benefit others, to be able to discover new things through research, and use research to develop something that I can call my own. Through the UGS research methods class, I was taking at the time, I was able to learn about the Freshman Research Initiative.

After finding out about this great opportunity to get into the lab and begin research, I immediately filled out the paperwork needed to join. I then began to look into the many streams I could become a part of, and that is when I came across this brand new stream known as the DIY Diagnostics research stream. As I looked into what the stream was going to offer, such as being able to research new methods for diagnostics that you can develop for society, I just felt that it was the stream for me and I was luckily accepted into it after making it my first choice on my application.

 

I don’t regret my choice of stream at all till this day because of all it still has to offer. I’ve learned so much from this stream in just a semester, and much of it will stay with me as I continue on through my life. Perhaps the most important things to me that I’ve learned from this stream are the tools needed to research in a lab and how to code apps. I feel I joined the ranks of other researchers and scientists on campus, even if I don’t have the same amount of experience as some of them. The pride I can take in myself when I explain to others about this stream and the research I do is just incredible. The one part of the stream that I enjoy the most has to be the coding for the applications. In the beginning I didn’t quite like coding, but as soon as I got the hang of it I really started to appreciate it. The feeling of cracking the code and getting the app to work is just a great feeling for me. Continuing on my app work and advancing in my coding skills are the areas of the stream that I look forward to the most. I can completely recommend this stream to anyone who is interested in being in a fun environment while they learn the necessary skills to become a researcher, innovator, scientist, and app designer.

Alyssa Benavides

Alyssa Benavides

As I visited streams my first semester of college I was pretty intimidated for the most part. Although, DIY Diagnostics caught my attention because it was a new stream and Dr. Riedel seemed very eager to get things going in the lab. It was different from the other streams because we get to work on our own projects and whatever innovative idea we have we could test it out in the lab (of course with Dr. Riedel’s permission that is). If you fail somewhere within your experiment you would not be considered a failure in our laboratory. Dr. Riedel always tells us is go back to your protocol and check what step(s) you may have messed up on or what can you change to get the product you wanted in the first place. I’m extremely excited to keep developing my app with my lab partner Lisa, and hopefully get it to work within this semester. Also aside from that I will continue to either work on Waller Creek or testing for P. Gingivalis. I’m leaning towards the experiment that has less people on our lab working on it, because research needs to keep being done on these super awesome research experiments.

I talk to my parents all the time about the FRI and how much of a great experience it has all been. Aside from being in one of the best labs of the FRI, I’ve made great friends and study partners for other classes. FRI opens many doors if your research is done correctly. When I explain to people what exactly we do in our lab they say wow you’re so young and here you are doing research. For instance, my cousin who is a dentist, he thought our research on P. Gingivalis was a really interesting idea and he told me to keep researching on it and that he was proud that I was learning about this at such a young age.

Being in the research lab has been a great experience and I’m actually thinking about being a doctor and maybe doing research on the side because in research there is always something new to be found (random or not). Research needs to continue being done for all sorts of causes. As I stated before meeting great friends in the lab has really pushed me to study with them and do great in school so the research lab has had an impact on my success here at UT. Also, Dr. Riedel is someone who has also helped me be successful here at UT, whatever a student needs in lab he will get to it right away. If you’re dealing with a personal problem in your life Dr. Riedel is there to always talk to us and guide us in anything we need. For instance, after my first year at UT I was thinking of going back home to the university in my hometown because of the cost of attendance at UT. Dr. Riedel right away told me he was going to ask around for scholarship applications and see what he can find out for me. It is educators like this that you look up to and say I want to be just like them and think to yourself that your willing to help people always.

My experience within the FRI lab has been very memorable especially when trying to make an app. It was a challenge at first, but when I finally completed my first app and coding it was probably the happiest moment of my life. It took me many tries to finally get my app to work, but it was all worth it.

 

Diagnostics in 20 years will definitely be a lot bigger than it is right now because research has been evolving so that’s what I think but I could always be wrong. In 20 years I see myself more as a doctor than a researcher but I can always say I once did research in a diagnostics lab. FRI DIY Diagnostics is an experience I will never forget and I really want to stay in the lab as a mentor because the lab feels like my second welcoming home.