This journal entry is due on Saturday, April 27 at midnight PST (Friday night/Saturday morning).
Individual Journal Assignment
- Store this journal entry as "username Week 12" (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 "BIOL388/S19" category to the end of your wiki page.
Please meet with your partner (either face-to-face or virtually) at least once when preparing this assignment. Even though you may work together to understand the assignment, your journal assignment must be completed individually. It is not acceptable to do a joint assignment and copy it over to each others' journal page.
- Angela and Ali
- Fatimah and Leanne
- Austin and Brianna
- Ava and Edward
- Desiree and Sahil
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:
- The purpose: what was the scientific purpose of your investigations?
- Note that this is different than the learning purpose.
- 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.
- 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.
- A scientific conclusion: what was your main finding for today's project? Did you fulfill the purpose? Why or why not?
- The Acknowledgments section.
- 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.
- 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.
- 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.
- If you need to reference content, include the formal citation in your References section (see below).
- You must also include this statement:
- "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
- Sign your Acknowledgments section with your wiki signature.
- The References section. 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:
- documents, including the scientific literature
- Do not include citations/references to sources that you did not use.
- You should include a reference to this week's assignment page.
- The references should be formatted according to the APA guidelines.
Developing a Yeast-in-the-Chemostat Model
Reconsider Table 1 of the Tai et al (2007) journal club paper and do some research on chemostats.
- Find some reference material (books, papers, preferably not random internet sites) on chemostat growth processes, so that you can answer these questions.
- The yield quantity Y Glu/X: this is a ratio of what quantities? Be specific and relate to the 2-nutrient chemostat model from class.
- The flux qGlu is a ratio of what quantities? Be specific and relate to the 2-nutrient chemostat model from class.
- Convert residual glucose and residual ammonia from mM to grams.
- Determine the length of time the chemostat is operated before data is collected.
- Determine as many model parameters as you can from these data: use the "warm" data and both glucose- and ammonium-limited data.
Develop a simulation model for a 2-nutrient chemostat.
- Modify the MATLAB files chemostat_script.m and chemostat_dynamics.m to simulate a 2-nutrient chemostat. You will find those codes in the zipfile here. This task will require the equations we developed in class.
- Use what parameters you have determined from the data to simulate the system.
- Do the graphs show the system going to steady state?
- Do the steady states match the Table 1?
- Be sure to save the graphs and upload them to your journal.
- Store your shared journal entry in the shared Class Journal Week 12 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 "BIOL388/S19" category to the end of the wiki page (if someone has not already done so).
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?
- Does this paper provide more detail on its experimental methods?
- What else do you wish these papers reported on their methods and/or results?