BIOL368/S20:Week 2

This journal entry is due on Thursday, January 30, at 12:01am Pacific time.

Overview

The learning objectives for this assignment are:

• To explore an interactive model with genetics, biochemistry, molecular biology, and evolution components to gain a conceptual framework that links these fields of biology.
• To practice documenting your scientific workflow in the service of reproducible research.

Individual Journal Assignment

Homework Partners

• You will be expected to consult with your partner, in order to complete the assignment.
• Each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed).
• You must give the details of the interaction with your partner in the Acknowledgments section of your journal assignment.
• Homework partners for this week are:
  • Drew, Annika, Lizzy (Biochemistry)
  • Jenny, Christina, Carolyn (Evolution)
  • Madeleine, Nathan, Karina (Molecular Biology)
  • Jack, Maya, Sahil, Nicolas (Genetics)

Format and Content Checklist

1. 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).
2. Write something in the summary field each time you save an edit. You are aiming for 100%.
3. Invoke the template that you made as part of the Week 1 assignment on your individual page. Your template should contain:
   • A link to your user page.
   • A link to the template page itself.
   • A list or table of all of the Assignment pages for the course.
   • A list or table of all of your individual journal pages for the course.
   • A list or table of all the shared class journal pages for the course.
   • The category "BIOL368/S20".
4. Purpose: a statement of the scientific purpose of the assignment. Note that this is different than the learning objective stated on the assignment page. What science will be discovered by completing this assignment?
5. Combined Methods/Results (Electronic Lab Notebook): documentation of your workflow for this exercise. It should include:
   • The protocol you followed in enough detail for someone else to be able to conduct the same investigation. 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.
   • Answers to any specific questions posed in the exercise.
   • Screenshots and images to document your answers.
   • Data and files: links to all data and files used and generated.
     • 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:
       • 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. 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.
6. Scientific Conclusion: a summary statement of the main result of exercise/research. It should mirror the purpose. Length should be 2-3 sentences, up to a paragraph.
7. Acknowledgments section (see Week 1 assignment for more details.)
   • You must acknowledge your homework partner 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.
   • Acknowledge anyone else you worked with who was not your assigned partner. This could be the instructor, 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 copied any part of the assignment or protocol and then modified it, acknowledge that here and also include a formal citation in the Reference section.
   • 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 (four tildes, ~~~~).
8. References section (see Week 1 assignment for more details.)
   • Use the APA format.
   • Cite this assignment page.
   • Cite any protocols that you copied and modified (this must also be noted in the Acknowledgments section).
   • Cite any other methods, software, websites, data, facts, images, documents (including the scientific literature) that was used to generate content on your page.
   • Do not include extraneous references that you do not cite or use on your page.

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.
• Part IV: Evolution
  • Complete "A", "B", and "C" questions on pages 5 to 9.

Shared Journal Assignment

• Compose your journal entry in the shared Class Journal Week 2 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
• Create a header with your name, and then answer the questions in your own section of the page.
• You do not need to invoke your template on the class journal page.
• Any 'Acknowledgments and References you need to make should go in the appropriate sections on your individual journal page.
• Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
• Add the category "BIOL368/S20" to the end of the wiki page (if someone has not already done so).

Read

• Brown, T.A. (2002) Genomes 2, Ch. 3.3.2: The link between the transcriptome and the proteome (freely available on NCBI Bookshelf)
• Nirenberg, M. (2004) Deciphering the Genetic Code—a Personal Account. Trends in Biochemical Sciences 29: 46-54. DOI: 10.1016/j.tibs.2003.11.009 (also on Brightspace)
• Kaji, A., Kaji, H. (2004) The history of deciphering the genetic code: setting the record straight. Trends in Biochemical Sciences 29: 293. DOI: 10.1016/j.tibs.2004.04.005 (also on Brightspace)
• Moody, G. (2004) Digital Code of Life, Chapter 1, Hoboken, New Jersey: John Wiley & Sons, pp. 1-9. (on Brightspace)
• Hayes, B. (2004) Ode to the Code, American Scientist 92: 494-498. (on Brightspace)

Reflect

1. What is the biggest discovery that I made from these readings?
2. What part of the readings did I understand the least?
3. What is the relationship between the genetic code and a computer code?