# BIOL398-04/S15:Class Journal Week 15

### From OpenWetWare

## Contents |

## Lucia I. Ramirez

**What did you learn in this class?**

- I was definitely able to apply my knowledge learned from last semester's Cell Function course into our main projects. This class gave me more practice with Matlab and I learned how to use it to model biological data, first deriving a set differential equations. While working in group projects, I realized that my input was heavily based on my math skills and quickly understanding the mathematical concepts expressed in this class. In that, I took on the challenge of understanding cell functions and processes through a mathematical representation, which I found quite engaging. I also learned how to navigate through the openwetware website, gaining the habit of frequent notations/commentary.

**What lesson will you take away from this class that you will still use a year from now?**

- I have realized that each person has a different point of view when engaging in group projects, especially when the group is composed of people with different majors. Although I wasn't the best at explaining the biological aspects of our class projects, I was easily able to conduct the math portions expected in this class. Because of this experience, I have realized the importance of having a diverse group of people in any group setting (diverse meaning educational background/different areas of expertise). Over more, seeing the collaboration between Dr. Dahlquist and Dr. Fitzpatrick, each person should be able to explain their unique and different ideas so that everybody is in the same page, which might be a common challenge among interdisciplinary fields.

Lucia I. Ramirez 22:52, 6 May 2015 (EDT)

## Lauren M. Magee

- What did you learn in this class?
- With your head (biological and/or mathematical principles)
- Even though I have studied biology, I was unfamiliar with cold shock experiments and their importance. Additionally, I was familiar with mathematical principles, but had never outlined a biological system with a mathematical model or used the program of MatLab. Therefore, it is within these areas where I say the most growth within my understanding.

- With your heart (personal qualities and teamwork qualities that make things work or not work)?
- The majority of the partner assignments I completed in this class were with Lucia, and I honestly couldn't have asked for a better partner. Not only does she keep me on task, but her engineering background offers new perspectives to our assignments. Her strengths differ greatly from my own as she has more of an analytical mind and I'm more of a creative thinker. We worked well together both contributing to problem solving and the overall interpretation of our results. Overall, I personally feel I gained a keen eye for detail. This class challenges me to read everything through completely and to think critically about the subject matter. Every assignment is so clearly outlined that the only way to fail is to step of the path that has been cleared for us.

- With your hands (technical skills)?
- I have had previous experience with a lot of other programs (R, SAS, SPSS, and Excel), but I had never worked with MatLab. It's quite similar in set up to the other programs, but the overall programming language is very unique. There is always a bit of a learning curve when getting involved with a new analysis program, but I think my passed exposure aided me in my understanding. I have also never had the opportunity to see a model created using a coding program, so understanding and then running the MatLab model in this class was something new to me, but moving forward I would be able to create my own with the example of the one used in this class.

- With your head (biological and/or mathematical principles)
- What lesson will you take away from this class that you will still use a year from now?
- I may not remember how to program in MatLab, or how to prepare a data set for STEM, or GRNMap, but I will remember that biological system can be modeled using mathematical modeling and computer programming. I will remember the importance of interdisciplinary research and I will be excited to engage with it outside of the university setting.

Lauren M. Magee 13:37, 28 April 2015 (EDT)

## Kara M Dismuke

- What did you learn in this class?
- With your head (biological and/or mathematical principles)
- In terms of the principles, I think this class taught me a great deal about models as well as certain concepts within biologically. I learned how to derive equations of a particular model and how subsequent parameters act as constraints on these equations. While we did not write much of our MATLAB code, I did experience how these equations were translated into code in order to harness the power of a computer to generate results/outputs, as opposed to trying to do things by hand. Biologically speaking, my last exposure to biology was sophomore year of college when I took Bio 101 and Bio 111, and prior to that, it was the biology I was exposed to in my freshman biology class in high school. It is safe to say, my background in biology is not extensive; however, as opposed to the broad, survey-based approach by which I have been taught biology in the past, I appreciated the approach in this class, namely that we dove into more in depth to study certain biological phenomena (i.e. the effects of ammonia concentration on nitrogen metabolism and the regulation of gene expression). In this class. I learned more about these specific principles/processes within Biology- most of which I had little understanding of prior to this class.

- With your heart (personal qualities and teamwork qualities that make things work or not work)?
- This class reminded me the importance of teamwork and collaboration. Having my peers as resources proved to be extremely helpful when I had questions or when problems arose. In addition to interacting with other students in the class, I found that interacting with the professors also proved to be helpful as they could offer their guidance and expertise. In addition to not being afraid to ask questions, this class also certainly reminded me how important it is to follow directions. And, then, even when directions are followed, it taught me that often times problems still arise as research is a messy endeavor.

- With your hands (technical skills)?
- Technically speaking, I feel a bit more equipped to work within MATLAB, and while we never wrote our own code, I feel more more confident that I would have an easier time learning to do so because I have a basic understanding of how the program works. In addition, this class helped to reinforce my working knowledge of Excel, and reminded me of things to consider when formatting a PowerPoint presentation.

- With your head (biological and/or mathematical principles)
- What lesson will you take away from this class that you will still use a year from now?
- I think this class taught me how being intentional about dedicating time and effort to something and surrounding myself with people are also working towards the same goal, can have solid results. I say this because as I reflect upon my experience in the class, I see that my understanding and confidence levels increased dramatically from the course's beginning to the course's end. I distinctly remember how lost I felt when I read that first Journal Club paper, and yet, not only did I come to understand the content of the paper, I have more confidence in myself to be able to understand any scientific paper (should I put enough time into it and have certain resources).

--Kara M Dismuke 18:52, 3 May 2015 (EDT)

## Alyssa Gomes

- What did you learn in this class?
- With your head (biological and/or mathematical principles)
- In this class I learned a lot about the scientific method. Although I had taken Bio Lab before I didn't realize the necessity of such meticulous notes, but for me, once I went back and tried to fix errors in our final project, it was hard to find where I wouldn't missed out because reading from my instructions were sometimes overall not very clear. I learned a lot about the significance of modeling and its applications to science. Although I had worked with MatLab and Mathematica before, I hadn't yet made a script to apply to something other than a simple book problem.

- With your heart (personal qualities and teamwork qualities that make things work or not work)?
- In this class learned so much about teamwork. I wouldn't have been able to make through this class as far without the help of my amazing partner Tessa, and the entire class as a whole. Oftentimes we would find ourselves in the computer lab at the same time or the library and were able to work constructively, helping one another answer the others' questions, especially for those of us more geared on a math background or a biology background, needing assistance on the other. I also learned that for me personally, staying persistent is key. Sometimes in class I would feel discouraged because I was falling behind on our in-class procedures because I was reading my own screen, the projector screen, whoever was speaking while trying to conduce something. I realized that to stay with it, I cannot let myself get discouraged and keep working to catch up and understand in brevity what was happening. Some classes are hard to ask questions in, and this class I felt very comfortable about it, seeing as oftentimes when one student would ask a question, it would help answer another student's.

- With your hands (technical skills)?
- Although I had worked with Matlab before, like mentioned above, I had never had the chance to apply it to anything but book-style problems. Being able to apply it to a model made it exciting (yet difficult) in order to understand each of the parameters and how they contribute as a whole to the model. Also, at my job on campus, I currently work a lot with Excel, modeling growth rates and percent increases. However, there was a lot about Excel that I had not previously known, that would have made my work much simpler at times, such as dragging techniques and transpositions.

- With your head (biological and/or mathematical principles)
- What lesson will you take away from this class that you will still use a year from now?
- A year from now I will be preparing for graduation. I'm not quite sure what I'll be doing long term at all but more than anything this class taught me to keep striving for the end goal. As this project was part of Professor Dahlquist's research, it was not something to abandon halfway through due to difficulty. Through the help of the many resources around me, not just the internet, but my peers, co-workers, professors, mentors, I can use their help to allow me to finish that end goal. I definitely learned to much more meticulous with my work, double checking it and taking it slow, even if it means it will take longer. Sometimes when you're so eager to reach that end goal, you'll sacrifice the care and true worked needed for something. In the end, it ends up taking much longer to find your error and retrace your steps. Overall, it was a great class, and while I learned a lot about biology and mathematics, I think most of all, I learned about myself.

Alyssa N Gomes 00:41, 5 May 2015 (EDT)

## Kristen M. Horstmann

- What did you learn in this class?
- With your head (biological and/or mathematical principles)
- More than anything I think I learned about the cell function and the microbiological workings of transcriptional factors and the cell. Thanks to engineering and internships, I had some experience in Matlab and Excel before, but my biology background is rather weak. So I felt I had to put in extra effort to understand some of the vocabulary and basic cellular steps. I also enjoyed seeing how much math and differential equations can fit into the natural phenomena in biology, as so many people do not realize the overarching power that math has that it can explain almost anything.

- With your heart (personal qualities and teamwork qualities that make things work or not work)?
- Like mostly everyone else is saying, the importance of working together was very evident all semester. All of us had different skills- some better in bio, some in math- and it was sometimes necessary to reach out to someone else to get more information on science or math. After switching out of engineering and into biomath (although still in the process), I have been very aware of how I've been feeling about my classes this semester. So another big thing my heart learned through this class is how happy I am with the choice I made. Yes, this class was a lot of work and I had to make sure to keep up with the Bio aspect, but it's nice to know that something I used to dread in engineering (Matlab...) is now something I only kind of dislike. I feel like this is because I enjoy the applications we have been working on and seeing how math and bio fit together more so than seeing the technical math and physics side.

- With your hands (technical skills)?
- I definitely learned more with Matlab, but also feel like keeping up with the electronic notebook became a very important technical aspect for me. Kara and I experienced many difficulties with our graphs and data inputs throughout these final weeks, so we realized how vital it was to be able to go back into our work from weeks ago in order to troubleshoot and try to redo the assignment. Writing down details and steps proved to be very important and became a skill that I will make sure to use more in the future.

- With your head (biological and/or mathematical principles)
- What lesson will you take away from this class that you will still use a year from now?
- I think that making sure to intentionally split up some of the longer assignments will stick with me. I am typically the type of person who likes to finish something in one sitting if possible, but with some of these assignments, that was nearly impossible. With the longer assignments towards the end of the semester, it became necessary to carefully plan which aspect was going to be done which day. I also feel like I will still be using Matlab and Excel a lot. This summer, I will be helping a professor at the university back home with his research, and it wasn't until he had learned that I had taken two Matlab-focused classes that he wanted to include me because none of his biology students have a programming background. Even though it's not my favorite program in the world and it will still take a long time and a lot of practice before I feel like I am an expert, having these technological skills are very valuable and I do think I will try to keep them up a year from now.

Kristen M. Horstmann 19:47, 6 May 2015 (EDT)

## Tessa A. Morris

- What did you learn in this class?
- I learned a lot more about modeling and how to combine mathematics and biology. I have always been interesting in biology and mathematics, but I never truly understood how the two could be combined. I learned that you have to be patient with everyone and learn how to work with people who have different strengths. It is not always easy to work with other people, but collaboration is an important part of being a scientist. On a technical level I leaned how to use Matlab and many of the other programs. I have a stronger background in biology and math, rather than programing or any kind of computer science, but it has always interested me.

- What lesson will you take away from this class that you will still use a year from now?
- I will take away that hard work pays off and that it is important to work with people with different strengths. Combining different subject makes for more interesting and efficient research and new scientific progress.

Tessa A. Morris 01:10, 7 May 2015 (EDT)

## Jeffrey Crosson

- What did you learn in this class?
- With your head (biological and/or mathematical principles)?
- I learned how gene networks generally interact with each other, how this is measured, and mapped. I also learned how to create and analyze differential equations from dynamic interactions. Of course I've learned many other things too.

- With your heart (personal qualities and teamwork qualities that make things work or not work)?
- I've learned how to collaborate with people with completely different skill sets.

- With your hands (technical skills)?
- I learned how to how to conduct statistical analysis and make clever manipulations in Excel. I also learned of some more features of MATLAB.

- With your head (biological and/or mathematical principles)?
- What lesson will you take away from this class that you will still use a year from now?
- There is an immense amount of genetic interactions occurring at every moment in every organism on this planet, even the simple ones.

Jeffrey Crosson 1:57, 6 May 2015 (EDT)

## William A. C. Gendron

- What did you learn in this class?
- With your head (biological and/or mathematical principles)
- I learned a lot on both the biological and mathematic fronts. I never really learned much about yeast or experiments that invovled using yeast as model organisms so it was fascinating to learn about all of the ways that things need to be controlled to limit other variables. In terms of mathematics, I learned how to apply a lot of the different concepts that I had learned in my previous courses. I never really used them in context so this was a nice change.

- With your heart (personal qualities and teamwork qualities that make things work or not work)?
- I usually make sure to select people who I am familiar with to work with, but this forced me to adapt to the situation and the person. I will take these skills to future projects and be able to gauge how to engage that individual better.

- With your hands (technical skills)?
- I was able to relearn everything about Matlab that I had previously forgotten.

- With your head (biological and/or mathematical principles)
- What lesson will you take away from this class that you will still use a year from now?
- I will remember the general concepts and apply them to create models. I also believe that this experience has taught me how to go about using these programs and approaching new problems.

**William A. C. Gendron 02:27, 7 May 2015 (EDT)**: