BIOL398-05/S17:Class Journal Week 5

TRACE Documentation

Element 1

• Element one of TRACE documentation is applicable to the assignment. The model outputs are the equilibrium values for ammonium, glucose, and yeast. The context the model should be used in is a chemostat environment where yeast are grown. Conor Keith 23:28, 15 February 2017 (EST)
• This TRACE element applies to this weeks assignment. The model was used to find the equilibrium values of the concentrations of glucose, ammonia, and the biomass of yeast. The equilibrium values is the question that the model seeks to answer. Lauren M. Kelly 23:43, 15 February 2017 (EST)

Element 2: Model Description

• This TRACE element is applicable to the assignment. The model different equations explain what the model is. The first equation represents the residual ammonia, the second equation represents the residual glucose, and the third equation represents the equilibrium values of yeast. The model also explains how yeast growth depends on ammonia concentration and glucose concentration. Cameron M. Rehmani Seraji 00:22, 16 February 2017 (EST):
• Element 2 is applicable to this modeling assignment because there are many parameters and differential equations that go into the model used for this week's assignment. For Model 2, which was the primary model used (the non-trivial equilibrium values), the first equation represented the yeast population growth, the second represented the residual ammonium concentration, and the final equation represented the residual glucose concentration, all in terms of set parameters and state-variables. The state variables were c1 and c2 which represented the two nutrients, and y which represented yeast. The parameters u1 and u2 were used for ammonmia and glucose conc. repsectively, and V1 and V2 were the volumes in terms of c1 and c2. K1 and K2 rperesented the carrying capacities, q was the dilution rate, and R denoted relative efficiency. Margaret J. Oneil 04:06, 16 February 2017 (EST)

Element 3

• The source of the numerical data is the journal club paper. I am unsure of the quality of the numerical data obtained, but it does appear to be inconsistent with the models used in the assignment. The parameters are obtained from the experiment performed in the journal club paper. Conor Keith 23:28, 15 February 2017 (EST)
• This TRACE element is applicable to the assignment. The source of the numerical data is from the week 5 assignment page and from the journal club paper. The quality of the numerical data appears consistent with the model used in this assignment. Cameron M. Rehmani Seraji 00:22, 16 February 2017 (EST):

Element 4: Conceptual Model Evaluation

• This TRACE element is applicable to the assignment. The simplifying assumption of the model's design is that yeast growth is dependent on ammonia concentration and glucose concentration. Cameron M. Rehmani Seraji 00:22, 16 February 2017 (EST):
• Element 4 is applicable to the modleing assignment for this week. The simplifying assumption being made in designing the model is that yeast population growth is only dependent on the concentration of two nutrients, glucose and ammonia. The model was also designed intentionally to be a multiplicative nutrient use model rather than an additive model, so that it would better model dependency on the presence of both nutrients rather than modeling an ability of being able to grow the population using either glucose or ammonia. Margaret J. Oneil 04:06, 16 February 2017 (EST)

Element 5

• Element five does not appear to be applicable to this assignment. No software is designed and code is not needed to analyze the nutrient models in this fashion. Conor Keith 23:28, 15 February 2017 (EST)
• This TRACE element does not apply to this weeks assignment. As MATLAB was not utilized to complete the assignment, there is no computer code implementing the model. The model was worked out with pen and paper. Lauren M. Kelly 23:43, 15 February 2017 (EST)

Element 6: Model Output Verification

• Similar to element 7, this element involves determining whether or not the output of the data is accurate by analyzing whether it matches experimental observations and is a good fit. In addition it involves looking at the effects of environmental factors in shaping the output of the model to see how the output is swayed and finalized. During this assignment we attempted to verify the observations recorded in the journal article by reproducing a model of the data with the same parameters listed in the paper to observe if the output matches the observations. Nika Vafadari 02:49, 16 February 2017 (EST):
• Element 6 (1) applies to this week's modeling assignment because one of the goals of the homework assignment was to recreate a figure based on observations. In running the model and looking at specific parameters, we observed how well the model compared to each of our individual plots. The overall findings seem to indicate that the model output reasonably matches the observations. (2) is not as relevant to our model because we did not do any tweaking, save for the input of the different ammonia concentrations in order to create the graph. Margaret J. Oneil 04:06, 16 February 2017 (EST)

Element 7

• This TRACE element applies to this weeks assignment. Changing the parameters, such as u1, causes significant changes in the model output. As u1 got larger, the outputs of y*, c1*, and c2* changed. Lauren M. Kelly 23:43, 15 February 2017 (EST)
• This element involves looking at how the output from the model emerged in order to evaluate whether or not the model output can be trusted. During this assignment we analyzed the math behind several models, calculating the solutions that characterize equilibrium and thus affect data output, in order to grasp an understanding of how the data is produced. Nika Vafadari 02:49, 16 February 2017 (EST):

Element 8

• Model output corroboration is defined as comparing prediction made through modeling with independent data. However, during this assignment, while we solved for the equilibrium values on our own the parameters were not tweaked, but instead taken directly from the paper to recreate the data produced by the experiment. Thus the the data patterns were observed prior to the assignment and were used while developing the model thus model output corroboration does not apply entirely. Yet, it applies to the experiment in the article since the researchers in the journal article utilized model output corroboration by changing environmental settings and parameters in order to get the yeast to model their predictions. Nika Vafadari 02:49, 16 February 2017 (EST):

Acknowledgements

• Margaret J. ONeil compiled and reformatted structure of the shared journal entry to better reflect the single response for each TRACE element. Since all users' contributions were made on their own rather than made collaboratively, all individual bullet points were kept, and the signature of each user was copied at the end of their contribution
• Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

  'Nika Vafadari 02:49, 16 February 2017 (EST)

  Lauren M. Kelly 23:43, 15 February 2017 (EST)

  Conor Keith 23:28, 15 February 2017 (EST)

• Cameron M. Rehmani Seraji 00:22, 16 February 2017 (EST):

  Margaret J. Oneil 04:06, 16 February 2017 (EST)

Reference

• Grimm, V., Augusiak, J., Focks, A., Frank, B. M., Gabsi, F., Johnston, A. S., ... & Thorbek, P. (2014). Towards better modelling and decision support: documenting model development, testing, and analysis using TRACE. Ecological modelling, 280, 129-139. DOI: 10.1016/j.ecolmodel.2014.01.018

References

• Grimm, V., Augusiak, J., Focks, A., Frank, B. M., Gabsi, F., Johnston, A. S., ... & Thorbek, P. (2014). Towards better modelling and decision support: documenting model development, testing, and analysis using TRACE. Ecological modelling, 280, 129-139. DOI: 10.1016/j.ecolmodel.2014.01.018