Group Project

(due Monday, April 5, 11:59pm)

Paper Format Requirements • 2000 words limit (not including figure captions or references) • 1.5 spaced • Normal margins • Times New Roman • 12 point font • 1.5 spacing • Justified paragraphs

Figures • All figures need a title, legend, axis labels and captions within the paper. • The caption should be detailed enough for the figure and caption to stand alone. • Tables should be included with all of your k-values and ODEs. • Required Figures:

o Original pathway including all fluxes and enzymes o Stoichiometric Matrix and J Equation o Altered pathway, shunted pathway, etc. o Table of all enzymes, reactions, k-values and ODEs o MATLAB plots of original pathway and altered/shunted pathway

References • MLA or APA format • No max for # references; minimum of 2 for cellular process and disease • Must reference papers discussing disease process

Submission • Submit a zipped file of both written report and MATLAB code with the title

“LastName_FirstName_Group_Project.zip” to Prof. Shevkoplyas

Some Comments: • Pathways should have at least 10 substrates • You are allowed to take a large existing pathway and break it down

o For example, how we took glycolysis, but only looked at upper glycolysis • Can assume pathways are irreversible, but the addition of a reversible pathway would be a

bonus

Helpful Link:

1. https://www.brenda-enzymes.org/ • Extensive database of enzymes

https://www.brenda-enzymes.org/
Ximena Medina Romero
Ximena Medina Romero
Ximena Medina Romero
Disease: Gluconeogenesis
Ximena Medina Romero
3/23/2021

Written Report Contents

1. Outline System & Disease: “Introduction and Background” – 10 points

• Introduction into the cellular process and the disease you picked. o Explain the importance of system and how the disease could inhibit/alter/etc. .it.

2. Explain how model was built: “Methods for Model Construction” – 30 points

• how equations were derived • what reactions were included/excluded • model assumptions • k-values • acceptable reasons to exclude an interaction

o interaction not confirmed in cells o interaction not relevant to disease/system

• unacceptable reasons to exclude an interaction o kinetic data not available

? make up a reasonable value and write down your assumption o my code won’t work

? keep trying and you’ll eventually get something ? o someone didn’t do this part of the report

3. Analyze the plots from you model: “Results derived from the Model” – 30 points

• Insert the plots from your model • Give statements about the concentrations you attained

4. Explain how model was modified for disease process and compare model output to what you would’ve expected and how this modified pathway would affect the biological system: “Model Modification for [disease/disorder]” – 30 points

• Is your model accurate? o Explain how you expected the models would look o Explain why the model may be inaccurate

? Explain how you could possibly fix it • Does your model reflect what actually occurs in nature? • What are the implications of the k-values you chose?

5. Bonus: include a reversible reaction somewhere in your pathway – 10 points

6. Project Reflection: include the grade you believe you deserve and the grade you believe each teammate (list by name) deserves and why.