# James P. McDonald Week 6

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#*We chose project 2: The chemostat model we’ve worked out does not predict the oxygen use and carbon dioxide production of Figure 1 B. Develop and analyze a model of the chemostat that includes oxygen and carbon dioxide. | #*We chose project 2: The chemostat model we’ve worked out does not predict the oxygen use and carbon dioxide production of Figure 1 B. Develop and analyze a model of the chemostat that includes oxygen and carbon dioxide. | ||

#Find at least one reference beyond the two terSchure et al papers that will be helpful to your modeling effort. Discuss in your journal the relevance of the reference. | #Find at least one reference beyond the two terSchure et al papers that will be helpful to your modeling effort. Discuss in your journal the relevance of the reference. | ||

- | #*Postma, Erik, et al. "Enzymic Analysis of the Crabtree Effect in Glucose-Limited Chemostat Cultures of ''Saccharomyces Cerevisiae''." Applied and Environmental Biology 55.2 (1989): 468-77. [[http://aem.asm.org/content/55/2/468.full.pdf+html | + | #*Postma, Erik, et al. "Enzymic Analysis of the Crabtree Effect in Glucose-Limited Chemostat Cultures of ''Saccharomyces Cerevisiae''." Applied and Environmental Biology 55.2 (1989): 468-77. [[http://aem.asm.org/content/55/2/468.full.pdf+html Paper 1 Link]] |

#*This paper will be useful because the experiment done in the paper deals with a chemostat containing a yeast population. There is a detailed section of the paper dedicated to the oxygen consumption and carbon dioxide production in the yeast. The information and data presented will be helpful in formulating a model for oxygen consumption and carbon dioxide in our project. | #*This paper will be useful because the experiment done in the paper deals with a chemostat containing a yeast population. There is a detailed section of the paper dedicated to the oxygen consumption and carbon dioxide production in the yeast. The information and data presented will be helpful in formulating a model for oxygen consumption and carbon dioxide in our project. | ||

#Find a mathematical reference, be it a textbook, a paper, or a website, that is relevant to your project topic. Discuss in your journal the relevance of the reference. | #Find a mathematical reference, be it a textbook, a paper, or a website, that is relevant to your project topic. Discuss in your journal the relevance of the reference. | ||

- | #*Bailey, J.E. "Mathematical Modeling and Analysis in Biochemical Engineering: Past Accomplishments and Future Opportunities." Biotechnology Progress 14.1 (1998): 8-20. [[http://onlinelibrary.wiley.com/doi/10.1021/bp9701269/full | + | #*Bailey, J.E. "Mathematical Modeling and Analysis in Biochemical Engineering: Past Accomplishments and Future Opportunities." Biotechnology Progress 14.1 (1998): 8-20. [[http://onlinelibrary.wiley.com/doi/10.1021/bp9701269/full Paper 2 Link]] |

#*This paper will be useful because it talks about mathematical modeling in steady state conditions such as in chemostats. The paper specifically touches on chemostats involving yeast populations. I have trouble with the modeling so this paper should prove to be a good resource when I am modeling our project. | #*This paper will be useful because it talks about mathematical modeling in steady state conditions such as in chemostats. The paper specifically touches on chemostats involving yeast populations. I have trouble with the modeling so this paper should prove to be a good resource when I am modeling our project. | ||

## Current revision

## Week 6 Assignment

- Select one of these project topics as what you will present next week.
- We chose project 2: The chemostat model we’ve worked out does not predict the oxygen use and carbon dioxide production of Figure 1 B. Develop and analyze a model of the chemostat that includes oxygen and carbon dioxide.

- Find at least one reference beyond the two terSchure et al papers that will be helpful to your modeling effort. Discuss in your journal the relevance of the reference.
- Postma, Erik, et al. "Enzymic Analysis of the Crabtree Effect in Glucose-Limited Chemostat Cultures of
*Saccharomyces Cerevisiae*." Applied and Environmental Biology 55.2 (1989): 468-77. [Paper 1 Link] - This paper will be useful because the experiment done in the paper deals with a chemostat containing a yeast population. There is a detailed section of the paper dedicated to the oxygen consumption and carbon dioxide production in the yeast. The information and data presented will be helpful in formulating a model for oxygen consumption and carbon dioxide in our project.

- Postma, Erik, et al. "Enzymic Analysis of the Crabtree Effect in Glucose-Limited Chemostat Cultures of
- Find a mathematical reference, be it a textbook, a paper, or a website, that is relevant to your project topic. Discuss in your journal the relevance of the reference.
- Bailey, J.E. "Mathematical Modeling and Analysis in Biochemical Engineering: Past Accomplishments and Future Opportunities." Biotechnology Progress 14.1 (1998): 8-20. [Paper 2 Link]
- This paper will be useful because it talks about mathematical modeling in steady state conditions such as in chemostats. The paper specifically touches on chemostats involving yeast populations. I have trouble with the modeling so this paper should prove to be a good resource when I am modeling our project.

## Class Links

- James P. McDonald
- BIOL 398 Home Page
- Week 1 Assignment
- Week 2 Assignment
- Week 3 Assignment
- Week 4 Assignment
- Week 5 Assignment
- Week 6 Assignment
- Week 8 Assignment
- Week 9 Assignment
- Week 11 Assignment
- Week 12 Assignment
- Week 13 Assignment
- Week 14 Assignment

## Journal Entries and Assignments

- Class Journal Week 1
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- Class Journal Week 13
- Class Journal Week 14
- James P. McDonald Week 2
- James P. McDonald Week 3
- James P. McDonald Week 4
- James P. McDonald Week 5
**James P. McDonald Week 6**- James P. McDonald Week 8
- James P. McDonald Week 9
- James P. McDonald Week 11
- James P. McDonald Week 12
- James P. McDonald Week 13
- James P. McDonald Week 14