BIOL388/S19:Class Journal Week 12

Ava's Journal Reflection

Review the Tai et al (2005) paper referred to in the Tai et al (2007) journal club paper.

1. Does this paper help with the individual assignment work?
   • Yes, it provides some of the necessary numbers and equations but not everything needed.
2. Does this paper provide more detail on its experimental methods?
   • Yes, this paper does give more background information but is still not easy to follow and r was never given so K and L cannot be determined.
3. What else do you wish these papers reported on their methods and/or results?]
   • I definitely wish that the authors of Tai et al had included a value for r, and also would have preferred if all of their parameter values and equations were in one place rather than searching around in an attempt to replicate the experiment. It almost feels like they have something to hide if they wanted to make the reader go to such lengths to find the specific numbers used in the equations.

Avalekander (talk) 19:10, 26 April 2019 (PDT)

Desiree's Reflection

1. Review the Tai et al (2005) paper referred to in the Tai et al (2007) journal club paper.
   • Does this paper help with the individual assignment work?
     • This paper does help a bit with the individual assignment work. It gives us values that we were then able to use to find a majority of the parameters that needed to be added to the MATLAB simulation of a 2 nutrient model.
   • Does this paper provide more detail on its experimental methods?
     • This paper does provide more intricate details on the experimental methods of the chemostat experiment. It provides more information than the 2007 paper on the strain conditions, the media makeup, and the ways that the data collected was analyzed for the experiment.
   • What else do you wish these papers reported on their methods and/or results?
     • I wish that these papers had reported the parameters that they used in their computer simulations, since the process to find them using the various amounts of data has been very confusing. It would also have been nice if the papers provided some of the experimental equations or even the code that they used to run the simulations.

Desireegonzalez (talk) 17:29, 26 April 2019 (PDT)

Brianna's Reflection

Review the Tai et al (2005) paper referred to in the Tai et al (2007) journal club paper.

1. Yes, the paper did somewhat help with the assignment because it provided specific parameters that were necessary to run the model.
2. I personally felt that the paper still wasn't giving enough information on their methods. I found myself still confused and unable to find some of the things needed.
3. I wish the paper was more specific on what parameters corresponded to each data collected so that it would make more sense trying to run the model on MATLAB. I still don't understand this stuff and I even tried to find things online to help but was still left confused.\

Briannansamuels (talk) 10:50, 26 April 2019 (PDT)

Austin Dias Reflection

Review the Tai et al (2005) paper referred to in the Tai et al (2007) journal club paper.

1. Does this paper help with the individual assignment work?

The Tai at al (2005) paper that was referred to in the Tai et al (2007) journal club paper provided assistance with completing the individual assignment. Particularly, this paper provided the inflow concentrations of glucose and ammonium. In the two nutrient MATLAB model these values are indicated as the parameters 'u' and 'v' respectively.

2. Does this paper provide more detail on its experimental methods?

This paper still does not contain extensive detail on the experimental methods that were used. Besides the inflow concentrations the paper does not provide other useful information that could be used to attempt to model the two nutrient chemostat experiment that was conducted in Tai et al (2007).

3. What else do you wish these papers reported on their methods and/or results?

I wish these papers provided more information that could be used to replicate their data. The fact that they made it so difficult to follow their methods and uncover parameters from their chemostat model is somewhat concerning. Specifically, I believe they should of explicitly stated the growth rate (r). The inclusion of this value would have made it a lot easier to solve for parameters 'K' and 'L' in our two nutrient chemostat model.

Alison's Reflection

1. Does this paper help with the individual assignment work?
   • This paper helps slightly because it provides us with some of the parameters required to run our model. Of course, the paper is necessary to base our model off of because it gives details about experimental method that is not provided in Tai et al. (2007). However, it does not make it easy to find many of the parameters still.
2. Does this paper provide more detail on its experimental methods?
   • Yes, this paper was referred to specifically in the 2007 paper so that they did not have to copy over all the methods. It did give us this missing information, but I would've preferred if they had just copied the methods over to the more recent paper.
3. What else do you wish these papers reported on their methods and/or results?
   • I wish that these papers were more specific about starting amounts of each nutrient and biomass. It would allow us to run a better model. Also, maybe more explicitly stating some of the parameters would be useful.

Alison S King (talk) 20:00, 25 April 2019 (PDT)

Angela's Reflection

1. This paper helps because it provided the basis for some of the parameters that were used in the model. It helped explain background methods needed to figure out how to calculate certain values/parameters.
2. Yes, this paper provided extra background details for the 2007 paper.
3. I wish these papers had a section or table where all the parameters and some of the equations were explicitly stated, so that the derivation of some of them could be more easily understood. Also the starting values would have been helpful to have when developing the 2-nutrient model.

Angela C Abarquez (talk) 00:13, 26 April 2019 (PDT)

Leanne's Journal Reflection

1. The Tai et al (2005) paper did help in the determination of parameters u and v (feed concentrations of glucose and ammonium). This then allowed us to be able to determine the amount of glucose consumed and the biomass at a steady-state
2. Yes, they provided the concentrations of what was in the media of each culture which allowed for the determination of u and v.
3. I wish the analysts provided what the maximum specific growth rate (r) was as this would of allowed us to determine K and L and run a complete model.

Leanne Kuwahara (talk) 12:05, 26 April 2019 (PDT)

==Fatimah Alghanem

1. Yes the paper help with the individual assignment work.
2. Yes this paper provides more parameters and discusses methods in more details.
3. I wish they provided r, K, and L and was more specific when discussing parameters used.

Falghane (talk) 15:15, 26 April 2019 (PDT)

Edward's Reflection

Review the Tai et al (2005) paper referred to in the Tai et al (2007) journal club paper.

1. Does this paper help with the individual assignment work?
   • Yes, because the assignment was based off of this paper. It provided several parameters. If they were not given directly, they were able to be calculated by converting units or by finding ratios.
2. Does this paper provide more detail on its experimental methods?
   • No, this paper did not give enough information to recreate the methods. At least, I found it very difficult due to my lack of knowledge of creating differential equations, finding values for certain variables, and creating MatLab scripts.
3. What else do you wish these papers reported on their methods and/or results?
   • I wish they would provide their methods on how they found their data. They did not go into detail on what database or programs they used to analyze their data to get their results. They provided an equation on Tai et al 2007, but it was not very helpful in what we did in our assignment. I never really gave much thought on breaking down the data of research papers, but I realize now that I would have no idea how to replicate these experiments.

Sahil's Reflection

1. Does this paper help with the individual assignment work?

• Yes, the paper helped with the individual assignment by providing direction and background for deriving the parameters used in MATLAB.

2. Does this paper provide more detail on its experimental methods?

• No, this paper referenced older publications, instead of writing out all of the experimental methods and parameters used.

3. What else do you wish these papers reported on their methods and/or results?

• It would have been nice if these papers included the experimental methods and numbers used more clearly in a table rather than surrounded by text. This made it harder to navigate through the paper to find the necessary information needed for this assignment.