# BIOL398-05/S17:Class Journal Week 14/15

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## Contents

## Nika Vafadari Reflection Questions

- Combining biological and mathematical approaches to scientific questions is very valuable since both fields offer different skills and techniques that can aid in solving various problems. For example, while biology provides us with an understanding of the complex systems in nature, such as the way various microorganism including yeast function, mathematics allows for the modeling and production of concrete data that explains these systems. Without the combination of these two fields, the studies of many researchers would be stunted especially since mathematics has provided researchers with the ability to analyze their results and determine whether or not statistically significant data exists.
- Looking back at my reflections on the Janovy and Stewart readings I have realized that throughout the course of this semester I have been able to experience and see the workings of many of the points these authors discuss. For example, Janovy brings up the point that scientific beliefs are always open to modification, something that was definitely stressed in class especially with our reviews of various scientific papers that introduced new information about yeast, such as the function of their metabolism and nutrient consumption. However, in order evaluate new information researchers must share their publications for peer review since it allows other researchers to confirm their results and even offer modifications in order to improve the understanding and knowledge of the scientific community. This notion also points to another topic discussed in class, that research especially in these two fields often builds upon itself with the involvement of researchers with different scientific backgrounds and understandings of certain areas.
- Throughout the course of this class I gained a better understanding of the function of transcription factors within a cell and the development and function of gene regulatory networks that control the response to various environmental stresses, such as cold shock. This knowledge has strengthened my understanding of the Dahlquist Lab research project and even provided me with the opportunity to gain hands on experience analyzing the microarray data sets produced from efforts of the wet lab team, allowing me to gain a better understanding of mathematical approach utilized to solve the question of which transcription factors control the early response to cold shock in yeast. As for my heart, I have definitely come to better understand the importance of working together in teams. Working with other people, as biologists and mathematicians do when working towards solving various scientific questions, is a vital aspect of research since it allows for the generation of various approaches to a single issue, which can propel a project. For example, when working on the various modeling projects throughout the semester, I found that working with my fellow classmates even when our projects had different goals, allowed for the integration of ideas, which lead to modifications and improvements to my own model. As for my hands, I definitely gained the most knowledge in this area with the various technical skills I learned throughout the course of the semester. For example, I gained a better understanding of the various functions of excel and was even introduced to multiple programs I had never worked with, such as Matlab. However, this introduction to these new programs strengthened various vital skills, such as perseverance and determination, which are both important when it comes to working towards understanding a new concept and adapting to new situations.
- In addition to the values of dedication and hard work that I gained throughout the semester, I definitely learned the importance of meticulously paying attention to my work, especially when working with large quantities of data. Double checking your work and carefully following protocol can prevent errors that can stunt a research project. These skills are definitely skills that can be employed to the rest of my studies here at LMU, graduate school and even in my career.

### Acknowledgments

I certify that this individual journal entry was completed by me and not copied from another source.

**Nika Vafadari 17:41, 2 May 2017 (EDT)**:

## Lauren M. Kelly Reflection Questions

**What is the value of combining biological and mathematical approaches to scientific questions?**- There is a lot of value in combining biological and mathematical approaches to scientific questions. Statistics, such as ANOVA, can tell you if your data is statistically significant. Significant data is crucial when approaching scientific questions. Mathematics also allows you to see another more analytical side of biology that can shed light on certain conclusions and give you the opportunity to see things in a different way.

**Looking back on your reflections on the Janovy and Stewart readings from the Week 1 Class Journal, do you have any further insights to share? Have your answers changed to those original reflection questions? Why or why not?**- In week 1, I said that when I heard the term mathematics, I thought of numbers, symbols, and complicated formulas. Now, I think of the various ways in which mathematics can be integrated into biology and the applications it has in the real world. The "numbers, symbols, and complicated formulas" now have more meaning. I also did not consider myself a mathematician. After a semester in this class, I can see myself on my way to becoming a mathematician. I am starting to get more comfortable using mathematics regularly, but I know I still have a long way to go.

**What did you learn in this class?****With your head (biological and/or mathematical principles)**- I learned more about how transcription factors react to the environment. I also learned that a system of differential equations can essentially be made out of thin air in order to model the growth of a population, and that it is not an easy task.

**With your heart (personal qualities and teamwork qualities that make things work or not work)?**- I learned that, despite the content of the class being difficult, having the opportunity to work together with some of my best friends made it much more enjoyable. The long nights spent in Seaver 120 working on presentations and other group-work greatly enhanced my teamwork abilities and taught me how to work efficiently. I also learned that I am a hands-on learner. Running different simulations in matlab greatly increased my understanding of the topic.

**With your hands (technical skills)?**- I can now do a lot more on the computer than I could before, especially with Excel and Matlab. Matlab was a completely foreign program to me at the beginning of the semester, but now I feel that I have a pretty decent understanding of it and would like to learn more about how it works.

**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 using the ANOVA skills I learned in Excel. I will also use everything I learned about how to make a scientific presentation for the rest of my career. This summer, I hope to be able to utilize what I learned about making and giving presentations in the research symposium at U of O.

### Acknowledgements

I certify that this individual journal entry was completed by me and not copied from another source. Lauren M. Kelly 23:20, 3 May 2017 (EDT)

## Cameron M. Rehmani Seraji Reflection Questions

**What is the value of combining biological and mathematical approaches to scientific questions?**- The value of combining biological and mathematical approaches to scientific questions is you can analyze the question using biology and mathematics and determine the best way to answer the question using biology, mathematics, or biology and mathematics.

**Looking back on your reflections on the Janovy and Stewart readings from the Week 1 Class Journal, do you have any further insights to share? Have your answers changed to those original reflection questions? Why or why not?**- Looking back on my reflection on the Janovy and Steward readings from the Week 1 Class Journal, I did not mention anything about statistics in my answer and that has been important aspect when analyzing the models. Also, I think because I am currently taking Genetics that my definition of a gene has changed compared to when I was in Cell Function because the classes have different focuses and I think this made it difficult sometimes to think back to remember the Cell Function definition. My answers have not changed very much from what I originally put in Week 1 because my answers in Week 1 were very broad in respects to Biology and Mathematics.

**What did you learn in this class?**- I learned a lot about building models for metabolic pathways and gene regulatory networks and how you can combine biology and mathematics to answer scientific questions.
**With your head (biological and/or mathematical principles)**- One mathematical thing I learned about was the different statistical methods that can be used to interpret data. One biological thing I learned about was microarray data and how it can be used to tell if genes are being induced or repressed.

**With your heart (personal qualities and teamwork qualities that make things work or not work)?**- Some important personal qualities I was able to further practice in this course included teamwork, time management, and problem solving.

**With your hands (technical skills)?**- I learned wiki syntax, how to use OpenWetWare, how to use MATLAB, and many other programs that can be used to generate models

**What lesson will you take away from this class that you will still use a year from now?**- I will take away from this class an understanding of how biology and mathematics can be used together to develop models, increased computer skills including wiki syntax, MATLAB, and Mircosoft Excel, and lastly being able to work as team and think logically how to solve complicated problems.

### Acknowledgements

I certify that this individual journal entry was completed by me and not copied from another source.

[***Cameron M. Rehmani Seraji 00:51, 4 May 2017 (EDT)**:[Category:BIOL398-05/S17]]

# Margaret J. ONeil Reflection Questions

**What is the value of combining biological and mathematical approaches to scientific questions?**- The value of combining biological and mathematical approaches to scientific questions is that you can use math to run experiments that would be much too expensive and time intensive to do in a wet lab setting. Through combining biological and mathematical approaches in problem solving, you are able to create models that better explain what is going on in the biological systems. In a much broader sense, when math and biology are combined, you can determine the significance (if there is any) in the results of a biological experiment as well.

**Looking back on your reflections on the Janovy and Stewart readings from the Week 1 Class Journal, do you have any further insights to share? Have your answers changed to those original reflection questions? Why or why not?**- Looking back on my reflection on the Janovy and Steward readings from the Week 1 Class Journal, I said I didn't consider myself a mathematician, which I now feel is most definitely false. Between this class and in doing research this semester, I feel much more well versed in applied mathematics than I have before. I also neglected to mention graph statistics and statistics in general when asked what first came to mind when I thought of the term mathematics. Now both are most definitely at the forefront of my mind when I think of math.

**What did you learn in this class?**- I learned more about the nitty-gritty of the GRNmap prokect, which gave me more appreciation for the effort that went into generating the data I now take for granted. I also became a lot more comfortable in using MATLAB and OpenWetWare though the experience.
**With your head (biological and/or mathematical principles)**- A mathematical principle I learned, or rather came to better understand, was through the chemostat modeling assignment, and being tasked with creating a series of equations to model the chemostat. Through doing this, I came to better understand the principles behind the GRNmap model and how mathematical models of biological systems are generated.

**With your heart (personal qualities and teamwork qualities that make things work or not work)?**- One teamwork quality I was able to learn is how to effectively teach people about the inner workings of the GRNmap project. Because I was the most experienced with using the programs, and understanding what various outputs of the models meant, I spent a good portion of time helping others and teaching them about the project, which in turn helped me to better understand the wokr myself.

**With your hands (technical skills)?**- I learned how to more efficiently use Microsoft Access, MATLAB, OpenWetWare, and Excel.

**What lesson will you take away from this class that you will still use a year from now?**- I will take away from this class a better understanding and appreciation of the GRNmap project as a whole. I will also walk away from this semester with more technical skills with a variety of useful programs, and a stronger ability to solve complex problems.

### Acknowledgements

I certify that this individual journal entry was completed by me and not copied from another source. Margaret J. Oneil 02:04, 4 May 2017 (EDT)