BIOL398-04/S15:Class Journal Week 14

Lucia I. Ramirez

Interpretations

• Look at the uploads of at least one other group in the class. State which group you compared yours to. Is there any overlap between your group and theirs with regard to which genes are in the networks (there should be at least for CIN5, GLN3, HMO1, and ZAP1)? If so, do the weights compare? Are there any weights that indicate activation in one network and repression in another? If so, what do you make of it?
  • It seems that no one was able to attain weighted networks.

Reflection

Reflect back on your learning for this project and for the entire semester and answer the following:

1. What is the value of combining biological and mathematical approaches to scientific questions?
   • This is very valuable because we are now able to see visually what genes are affecting and controlling other genes. Being able to see the mathematical representation of what we know or are still trying to understand biological concepts has been extremely interesting!
2. Looking back on your reflections on the Janovy and Steward 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?
   • My answers haven't really changed.

Lucia I. Ramirez 02:59, 28 April 2015 (EDT)

Lauren M. Magee

Interpretations

• Look at the uploads of at least one other group in the class. State which group you compared yours to. Is there any overlap between your group and theirs with regard to which genes are in the networks (there should be at least for CIN5, GLN3, HMO1, and ZAP1)? If so, do the weights compare? Are there any weights that indicate activation in one network and repression in another? If so, what do you make of it?

Reflection

Reflect back on your learning for this project and for the entire semester and answer the following:

1. What is the value of combining biological and mathematical approaches to scientific questions?
   • Biology and mathematics have different strengths and area of focus. Biology offers an understanding of life's complex systems, but mathematics is able to do what we would never have the years to complete. Mathematics can model real or hypothetical systems from which we can gain a more holistic view of life. When combining these two disciplines, we are highlighting each fields talents to assist the other, which creates a more complete picture and promotes the ideal that all disciplines are connected and can assist one another to create a more effective product.
2. Looking back on your reflections on the Janovy and Steward 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?
   • My answers have no change from that initial reflection, because as a Biomathematics major, I hold interdisciplinary approaches in very high regard. I would identify myself as both a biologist and a mathematician, but I believe that to be easier for me since I have had the opportunity to gain experience in both fields. I don't think there needs to be a specific skill set to label oneself either a biologist or a mathematician, I think it is more of a frame of mind and inquisitive nature to learn more about earths systems and the human experience. After completing the modelling, I can see clearly the intersectionality that is necessary between mathematics and biology in a very different way than I am accustomed to. I focus more on statistics as it relates to biology, so it is interesting to see more computer science and theoretical mathematics become so influential.

Lauren M. Magee 00:54, 28 April 2015 (EDT)

Alyssa Gomes

Interpretations

• Look at the uploads of at least one other group in the class. State which group you compared yours to. Is there any overlap between your group and theirs with regard to which genes are in the networks (there should be at least for CIN5, GLN3, HMO1, and ZAP1)? If so, do the weights compare? Are there any weights that indicate activation in one network and repression in another? If so, what do you make of it?

Reflection

Reflect back on your learning for this project and for the entire semester and answer the following:

1. What is the value of combining biological and mathematical approaches to scientific questions?
   • Biology helps explains the why and math explains how. I have always thought that but especially through procedures in this class have they become more interlinked by modeling and Matlab scripts. It is very different from the math I was expecting to do, but by combining both you can combine the how and why very easily in order to gain a deeper understanding of the what. Using this we will continue to learn and adapt more and more to scientific and mathematical advances.
2. Looking back on your reflections on the Janovy and Steward 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 one of my answers from the week 1 journal i noted that math is to see patterns. Through some of the research done in this class, my complex journal club 2 assignment and more, I've learned not all math will show patterns and a conclusive answer. Sometimes, rather, it helps reveal hidden discrepancies that would otherwise not be noted. I still believe in the way math and biology come together in different ways, but now I've seen much more of the complexities that come along with it, especially with trial and error methods. Sometimes it is easy to see something that may be off and just call it a weird conclusion, when in reality it is a math error or scientific method error. I've learned that because the combination of biology and math brings in a new level of foundation, we must understand each piece very carefully in order to really understand the whole assignment, experiment, or whatever it may be.

Alyssa N Gomes 23:28, 29 April 2015 (EDT)

Natalie Williams

1. What is the value of combining biological and mathematical approaches to scientific questions?
   • In combining mathematics and biology, we are finding ways to define and understand functions and processes that various systems undergo. In applying a mathematical equation to a process, we hopefully describe laws that are universal under many conditions. With universality of equations, we can apply these equations to other processes to better understand what occurs in nature.
2. Looking back on your reflections on the Janovy and Steward 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 gathering the data and determining significance, I am still amazed by all the work that must be done to get to just having the adjacency matrix for the input sheet. The one matrix for our selected GRN is not the only possibility from the data. Multiple versions can be run with varying outputs. These results elicit multiple interpretations and more than one can be correct. Even with the help of mathematics, which is concrete, interpretation of data varies and does not give conclusive results every time.

Kristen M. Horstmann

Interpretations

Look at the uploads of at least one other group in the class. State which group you compared yours to. Is there any overlap between your group and theirs with regard to which genes are in the networks (there should be at least for CIN5, GLN3, HMO1, and ZAP1)? If so, do the weights compare? Are there any weights that indicate activation in one network and repression in another? If so, what do you make of it?

• I looked at Tessa's and Alyssa's powerpoint of figures and we actually had many genes in common. Both of our networks included: ACE2, ASG1, CIN5, CYC8, FKH2, GLN3, HMO1, MIG2, MSN2, PDR1, RIF1, SFP1, SNF6, STB5, SWI5, YHP1, YLR278C, YOX1, and ZAP1. Actually, it seems the only gene that Kara's and my network had that Tessa's and Alyssa's did not was GAT3.
• CIN5->ASG1: in ours, positive weight (activation), in theirs, negative (repression)
• CIN5->MIG2: both extremeley high weights, but their estimated-b was highly positive and ours was very negative
• YHP1->GLN3: both positive, but in ours, the estimated was higher than theirs.
• MSN2->CYC8: ours was slightly positive, while both of theirs was extremely negative

%*There were some bar graphs of theirs that did not seem to have a pair with ours, but I felt their axis labels did not quite align with their chart so it was hard to tell which was which at times

• It makes sense, their network is different than ours, so there's no reason to expect that theirs should be similar or identical to ours. However, some of the weights were the same, which might make sense because since the majority of our genes were so similar, the chances of some of them not being affected by our respective deleted strains means that they behave the same regardless. This especially makes sense since ZAP1 was only connected to ACE2, Kara's and my network should be fairly similar to the genes that their deleted gene was unaffected by.

Reflection

Reflect back on your learning for this project and for the entire semester and answer the following:

1. What is the value of combining biological and mathematical approaches to scientific questions?
   • Biology and math are much more similar than many people would think. The value of combining these two is that it helps us further understand both topics- math helps strip the biology side to step-by-step equations and not a microscopic mystery, while biology helps find and explain how some of these more intense math equations fit with the natural world. I think the biggest value math brings to scientific questions is that by being forced to break it down into small steps help make the science less of a mystery and makes it easier to comprehend what's happening on a smaller level.
2. Looking back on your reflections on the Janovy and Steward 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?
   • I'm not sure if my answers have really changed. I guess I would consider myself a biologist/mathematician more so than before, but I would still never use those titles to describe myself as such. I still feel like those titles are far too prestigious to describe me, someone who knows very little relative to the massiveness of both fields. I think my response about "hiding math" with the Stewart reading is somewhat funny after this semester, as none of us could hide from all the math that we did this semester, yet the clearest outputs we produced were in GRNsight, a great program who does exactly that- hide math. It's just interesting because for us, doing all the math was what helped us understand, only to input it to create a picture to make it easier for everyone else to understand. I'm starting to think that's a big aspect of biomath and bioinformatics- making sure to streamline our work to the point that we can hide all the math we did in order to explain it to others.