BIOL398-05/S17:Week 7

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BIOL398-05: Biomathematical Modeling

MATH 388-01: Survey of Biomathematics

Loyola Marymount University

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This journal entry is due on Thursday, March 2, at midnight PST. (Wednesday night/Thursday morning). Note that the OpenWetWare server registers time in the Eastern time zone, so it will say 03:00 AM at midnight PST.

Individual Journal Assignment

  • Store this journal entry as "username Week 7" (i.e., this is the text to place between the square brackets when you link to this page).
  • Create the following set of links. (HINT: These links should all be in your personal template that you created for the Week 1 Assignment; you should then simply invoke your template on each new journal entry.)
    • Link to your journal entry from your user page.
    • Link back from your journal entry to your user page.
    • Link to this assignment from your journal entry.
    • Don't forget to add the "BIOL398-05/S17" category to the end of your wiki page.

Electronic Lab Notebook

Complete your electronic notebook that gives the details of what you did for the assignment this week. Your notebook entry should contain:

  1. The purpose: what was the scientific purpose of your investigations?
    • Note that this is different than the learning purpose.
  2. Your workflow or methods: what did you actually do? Give a step by step account.
    • There should be enough detail provided so that you or another person could re-do it based solely on your notebook.
    • You may copy protocol instructions to your page and modify them as to what you actually did, as long as you provide appropriate attribution in the acknowledgments and references section.
    • Take advantage of the electronic nature of the notebook by providing screenshots, links to web pages, etc.
  3. Your results: the answers to the questions in the protocol, plus any other results you gathered. Your results will include some or all of the following: images, plots, data, and files.
    • Note that files left on the Desktop or My Documents or Downloads folders on the Seaver 120 computers will be deleted upon restart of the computers. Files stored on the T: drive will be saved. However, it is not a good idea to trust that they will be there when you next use the computer.
    • Thus, it is a critical skill for data and computer literacy to back-up your data and files in at least two ways:
    • References to data and files should be made within the methods and results section of your notebook, listed above.
    • In addition to these inline links, create a Data and Files section of your notebook to make a list of the files generated in this exercise.
  4. A scientific conclusion: what was your main finding for today's project? Did you fulfill the purpose? Why or why not?
  5. The Acknowledgments section, see below.
  6. The References section, see below.


In this section, you need to acknowledge anyone who assisted you with your assignment, either in person, electronically, or even anonymously without their knowledge.

  1. You must acknowledge your homework partner or team members with whom you worked, giving details of the nature of the collaboration. You should include when and how you met and what content you worked on together. An appropriate statement could be (but is not limited to) the following:
    • I worked with my homework partner (give name and link name to their user page) in class. We met face-to-face one time outside of class. We texted/e-mailed/chatted online three times. We worked on the <details> portion of the assignment together.
  2. Acknowledge anyone else you worked with who was not your assigned partner. This could be Dr. Dahlquist or Dr. Fitzpatrick (for example, via office hours), the TA, other students in the class, or even other students or faculty outside of the class.
  3. If you copied wiki syntax or a particular style from another wiki page, acknowledge that here. Provide the user name of the original page, if possible, and provide a link to the page from which you copied the syntax or style.
  4. If you need to reference content (such as the methods of a protocol) also acknowledge it here and include a formal citation in your References section (see below).
  5. You must also include this statement unless otherwise noted:
    • "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
  6. Sign your Acknowledgments section with your wiki signature.


  1. In this section, you need to provide properly formatted citations to any content that was not entirely of your own devising. This includes, but is not limited to:
    • methods
    • data
    • facts
    • images
    • documents, including the scientific literature
  2. The references in this section should be accompanied by in text citations on your page that refer to these references.
  3. Do not include citations/references to sources that you did not use.
  4. Generally, you should include a reference to that week's assignment page.
  5. The references should be formatted according to the APA guidelines.
  6. For more detailed instructions on how to cite journal articles, books, or web pages, please see the document Guidelines for Literature Citations in a Scientific Paper that you were given on the first day of class.

This Week's Exercise

For this week, you will be completing work on the model you began developing for the Week 6 assignment. Record your work on the model in your electronic lab notebook. In addition, you will then prepare a presentation to be delivered in class on Thursday, March 2 (see below).

Presentation Guidelines

  • You will prepare a 15 minute PowerPoint presentation that will present your mathematical model of nitrogen metabolism in yeast. Please follow these guidelines when creating your presentation. You will need approximately 15 slides (1 slide per minute) for your presentation. You will be graded according to this rubric.
    • Upload your slides to the OpenWetWare wiki by the Week 7 journal assignment deadline. You may make changes to your slides after the deadline and in advance of your presentation, but you will be graded on what you upload by the journal deadline.
  • Your presentation should follow the process of modeling shown on the left-hand side of this figure and cover the following content:
    • Title slide: title is statement of the main result of your model, includes your name, date, and BIOL398-05/MATH388-01
    • Outline slide: summary of the messages of your talk
    • Background, purpose, and significance of the model (think about this in relation to the TRACE documentation)
      • What is the question and hypothesis?
    • What are your simplifying assumptions?
    • How did you mathematize the model?
      • A list and explanation of the state variables needed to model the process of interest.
      • Your system of differential equations that model the dynamics.
      • An explanation of the terms in your equations.
      • A list and explanation of all the parameters your model requires for numerical simulation.
    • Exploration of the model.
      • Analysis of the steady-state.
      • Simulation of the dynamics with graphical output
    • A discussion of your results (the biological interpretation) and how they relate to the ter Schure et al. (1995)Journal of Bacteriology paper and other papers specific to your project.
    • Summary or Conclusion slide that mirrors your outline.
    • Every slide needs a title that is a statement of the main message or result of the slide, not a topic.

Shared Journal Assignment

  • Store your journal entry in the shared Class Journal Week 7 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
  • Link to your journal entry from your user page.
  • Link back from the journal entry to your user page.
  • Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
  • Add the "BIOL398-05/S17" category to the end of the wiki page (if someone has not already done so).


  1. In addition to the scientific conclusion for your project, reflect on what you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
  2. What is still not clear to you after having concluded this project?
  3. If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?