BIOL368/F16:Week 2

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This journal entry is due on Tuesday, September 13 at midnight PDT (Monday night/Tuesday morning). NOTE that the server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00.

Overview

The purpose of this assignment is:

1. To understand the nature of models and modeling and connect this with the process of science.
2. To review key concepts in the central dogma of molecular biology and evolution.
3. To learn the skills needed to create and maintain a high quality electronic laboratory notebook.

Individual Journal Assignment

• Store this journal entry as "username Week 2" (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 "BIOL368/F16" category to the end of your wiki page.

Homework Partners

You will work in groups of three for this week's assignment. Please sit next to your partner in class. You will be expected to consult with your partner, in order to complete the assignment. However, unless otherwise stated, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed). Homework partners for this week are:

• Matthew Allegretti, Jordan Detamore, Zachary Goldstein (Genetics)
• Shivum Desai, William Fuchs, Mia Huddleston (Biochemistry)
• Isai Lopez, Mathhew Oki, Avery Vernon-Moore (Molecular Biology)
• Courtney Merriam, Anindita Varshneya, Colin Wikholm (Evolution)

Background

• Schnell, S. (2015). Ten Simple Rules for a Computational Biologist’s Laboratory Notebook. PLoS Comput Biol, 11(9), e1004385. DOI: 10.1371/journal.pcbi.1004385
• Aipotu (formerly Molecular Genetics Explorer) home page.
  • Follow the Download link on the left side of the page to download the Windows or Mac versions of this software.

Protocols

Assignments to sections are listed under the Homework Partners section above.

• Part I: Genetics
  • Complete the "Specific Tasks to do with this tool" beginning on page 8.
  • Complete the tables and questions on pages 9-12.
  • When the protocol says "Data Blog", this means your wiki journal for this week (electronic lab notebook).
• Part II: Biochemistry
  • Complete the "Specific Tasks for this section" beginning on page 11.
  • Complete the tables and questions on pages 11 to 14.
  • When the protocol says "Blog", this means your wiki journal for this week (electronic lab notebook).
• Part III: Molecular Biology
  • Complete the "Specific Tasks for this section" beginning on page 7.
  • Complete the tables and questions on pages 7 and 8.
  • Assigned to: Nicole Anguiano
• Part IV: Evolution
  • Complete "A", "B", and "C" questions on pages 5 to 9.

Electronic Lab Notebook

• Schnell, S. (2015). Ten Simple Rules for a Computational Biologist’s Laboratory Notebook. PLoS Comput Biol, 11(9), e1004385. DOI: 10.1371/journal.pcbi.1004385

Complete your electronic notebook for your assigned part of the Molecular Genetics Explorer project on your individual journal page. Your notebook entry should contain:

• The purpose: what was the purpose of your investigations?
• Your 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 on your page and modify them as to what you actually did, as long as you provide appropriate attribution.
  • Take advantage of the electronic nature of the notebook by providing screenshots, links to web pages, links to data, etc.
• Your results: the answers to the questions in the protocol, plus any other results you gathered.
  • Usually it makes sense to embed your answers to the questions/results in the "methods" in the order in which you obtained them.
• A scientific conclusion: what was your main finding for today's project? Did you fulfill the purpose? Why or why not?

Data and Files

• Files left 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:
  • [Upload the files to this wiki.]
  • Upload the files to [Box].
  • Back them up on your personal flash drive.
• 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.

Acknowledgments

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

1. You must acknowledge your homework partner or team members with whom you worked, giving details of the nature of the collaboration. 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.
     • Sign this statement with your wiki signature.
2. Acknowledge anyone else you worked with who was not your assigned partner. This could be Dr. Dahlquist (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. If you need to reference content, use your References section (see below).
4. You must also include this statement unless otherwise noted: "While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source."

References

• 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:
  • data
  • facts
  • images
  • documents, including the scientific literature
• The references in this section should be accompanied by in text citations on your page that refer to these references.
• The references should be formatted according to the APA guidelines.
• For more detailed guidelines, please see the document Guidelines for Literature Citations in a Scientific Paper that you were given on the first day of class.

Shared Journal Assignment

• Store your journal entry in the shared BIOL368/F16:Class Journal Week 2 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
• Link to the shared journal entry from your user page.
• Link the shared journal page to this assignment page.
• Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
• Add the "BIOL368/F16" category to the end of the wiki page (if someone has not already done so).

Before Reflection

We will begin our process of shared reflection in class on September 6 by answering the following questions. On your honor, please give your answers without referring to any external sources. For the moment, answer them on paper or in a Word document without committing them to the BIOL368/F16:Class Journal Week 2 page, so that everyone comes up with their own answer independently.

1. What is the definition of a model?
2. What is the definition of modeling?
3. How does modeling relate to the scientific method?

After the class discussion, please add your answers to the BIOL368/F16:Class Journal Week 2 page so everyone can see each others answers.

Reading and After Reflection

Read the following:

• Eaton, C.D., Callendar, H.L., Dahlquist, K.D., LaMar, M.D., Ledder, G., Schugart, R.C. (2016) A “Rule of Five” Framework for Models and Modeling to Unify Mathematicians and Biologists and Improve Student Learning, submitted on 20 June 2016 to the journal PRIMUS: Problems, Resources, and Issues in Mathematics Undergraduate Studies for an upcoming special issue on interdisciplinary conversations.

On your honor, after you have read the paper, answer these questions on the BIOL368/F16:Class Journal Week 2 page:

1. What is the main take-home message of this paper?
2. What is the definition of a model?
3. What is the definition of modeling?
4. Were you engaged in modeling for this week's assignment? If so, how? If not, why not?