# BIOL388/S19:Week 1

BIOL 388-01: Biomathematical Modeling

MATH 388-01: Survey of Biomathematics

Loyola Marymount University

This journal entry is due on Thursday, January 24, at midnight PST. (Wednesday night/Thursday morning).

## Overview

The purpose of this assignment is three-fold:

1. To set up your individual user page on this wiki as an online resume or curriculum vitae (CV). This will allow the instructors and other students in the course to get to know you. This page is also available to the public and can be used as a professional resume/CV.
2. To learn the skills needed to edit this wiki and set up your template, which you will use for all subsequent assignments in this course.
3. To begin the process of self-reflection on the shared journal page.

## Individual Journal Assignment

### Homework Partners

In this course you will be completing the research projects in groups of two, three, or as an entire class. To initiate this process, you will be assigned a homework partner for this week's assignment. 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:

• Angela and Fatimah and Savannah
• Austin and Desiree
• Alison and Leanne
• Ava and Sahil
• Brianna and Edward

### User Page

Set up your individual user page on this wiki (accessible via your username at the top of the page). Your user page should take the form of a résumé or, in academic circles, a curriculum vitae. Dr. Dahlquist and Dr. Fitzpatrick have such pages, both within this wiki (user page) and online in general. You may use those as starting points. As students, your information may be different from ours. At a minimum, you should include:

1. Name
2. Contact Information
• Email address (We recommend that you use do not use a "mailto" link for this, but follow the formatting to e-mail you through OpenWetWare.)
3. Education
• Major
• Upper division courses in biology, chemistry, math, and computer science that you have taken (including those in which you are enrolled this semester)
4. Career interests and goals (if you know)
• Description of any independent research projects in which you have been involved, including:
• Title of project
• Mentor's name
• List of presentations and/or publications resulting from the project
5. Work experience
• Position/title
• Employer
• Dates
• Responsibilities
6. Personal interests/hobbies
7. What is your favorite aspect of biology and why?
8. What is your favorite aspect of mathematics and why?
9. Feel free to customize your page in any way you wish, bearing in mind that this site is public and that you should present a professional face to the world.

### Individual Concerns (by email)

2. Is there anything else you would like us to know?

The previous sections listed the content that you need to provide on the wiki. In formatting your user page, demonstrate all of the following skills. Find a way to integrate them naturally into the content (e.g., do not say “Here is an image.” and put just any image on the page).

1. Every time you edit a page (whether it is a content page or discussion page), enter a meaningful description of your change in the Summary field at the bottom of the editor. This allows other users to easily see (say via the Special:RecentChanges or history pages) what has happened to the page since they last visited it.
2. Create a new Wiki page: [[new page title]] — When you include a non-existent link in a page (say, your user page), the software can tell that this page doesn't exist and colors it red instead of blue/purple. When you click on the red link, you are then given the option to edit (and thus create) the page.
• We suggest you practice this by creating your Week 2 journal entry page. The name for the page should be in the format "username Week 2" (i.e., that is the text you put between the square brackets when you link to this page).
3. Link to a page within our Wiki: [[page title|optional visible label]]
• Note that the bar symbol ( | ) is a separator that divides the wiki page name from the text that will be the visible link label on the page. It is optional, but makes your link look more professional.
• Go to the Students section of the course People page and link your name to your own user page.
• The second form of the link is preferred because it looks neater on the page.
• Note that for an external hyperlink, a space character separates the URL from the label, not a bar character ( | ), like in the internal wiki link syntax.
5. Use headings: === title === (number of equals signs indicates heading level)
• By convention, start your largest heading with two equals signs. The single equals sign is for the title of the page and is automatically created when you create the page.
• Show at least three levels of headers on your page, starting with two equals signs.
• Do not skip levels. For example "==" should be followed by "===", not "====".
6. Create a bulleted list: *
• Note that you can create sub-bullets underneath by using multiple asterisks, e.g., **, ***, etc.
7. Create a numbered list: #
1. Note that you can create numbered sub-lists by using multiple number signs, e.g., ##, ###, etc.
2. You can also mix bullets and numbers, e.g., *#, #*, or even #*#, etc.
3. Do not skip lines between items in your bulleted or numbered lists, or the wiki will not interpret your syntax correctly.
8. "Comment out" your Wiki code: <!-- commented-out Wiki text --> When you "comment out" your wiki code, the code will be visible on the Edit page, but will not be visible on the wiki page itself. "Commenting" is a common practice in coding that is used to explain the meaning of the code for someone else reading it. In this situation, commenting can be used to keep a rough draft of a wiki page invisible until you are ready for it to be seen.
• Note that the automatic comments placed on your User page by OpenWetWare will not count towards fulfilling this requirement.
9. Upload and display an image on your page. This is a two-step process:
1. Upload your image file: Click Upload file then follow the instructions to select and upload your file. Note the name of the file and make sure to type something in the Summary field.
2. Use the image on your page using the following syntax: [[Image:exact-name-of-image-file]]. Don't forget that the filename will include a file extension.
• REMEMBER: DO NOT SUBMIT COPYRIGHTED WORK WITHOUT PERMISSION! We suggest you include an image of yourself that would be suitable for a professional resume.
• The wiki is used by many different users. Make sure that your filename is unique to you. "image.jpg" is a very generic filename that could be potentially used by many people. "Myname.jpg" will be unique to you. Using a unique filename that identifies you as the author is important because files that are uploaded with the same name will overwrite each other. This is a great feature when you are updating your own file, but it is a terrible feature if your file gets overwritten by someone else's file!
• For further information on how to format your image on the page, see the MediaWiki image help page.
10. Upload another type of file (such as .pdf) and link to it on your page. This is also a two-step process.
1. Click Upload file then follow the instructions to select and upload your file. Note the name of the file and make sure to type something in the Summary field.
2. Link to the file you uploaded on your Wiki page: [[Media:exact-name-of-uploaded-file|visible label]] Don't forget that the filename will include a file extension.
• The wiki is used by many different users. Make sure that your filename is unique to you. "Resume.pdf" is a very generic filename that could be potentially used by many people. "Myname_resume.pdf" will be unique to you. Using a unique filename that identifies you as the author is important because files that are uploaded with the same name will overwrite each other. This is a great feature when you are updating your own file, but it is a terrible feature if your file gets overwritten by someone else's file!
• REMEMBER: DO NOT SUBMIT COPYRIGHTED WORK WITHOUT PERMISSION! We suggest that you include something professional, such as the Word or PDF version of your paper resume, a scientific paper you have written, etc.
11. Assign a category to your page: [[Category:category name]] This creates an automatic "table of contents" for the wiki. When you click on a category link at the bottom of a page, a new page opens giving you a list of all wiki pages that have been assigned that category.
• Throughout the course, you will use the category [[Category:BIOL388/S19]] for all of the pages you create.
12. Use the discussion/talk page to make a comment. Wiki etiquette requires that you sign your comments with your "signature": ~~~~ (4 tildes in a row). These tildes get converted automatically, for example, into: Kam D. Dahlquist 01:09, 10 January 2017 (EST)
13. Create a template for yourself and invoke it on your user page. A template is a block of wiki text that you want to use over and over again on various pages. Instead of having to either re-type that content or even copy-and-paste it multiple times, you can simply put the content on a special Template page. You then use code to invoke the template on any other page in which you want that text to appear. The advantage to using a Template is that when you make changes to the Template page, they will automatically appear on any other page on which the Template has been invoked. There are three steps to creating a Template.
1. Create your template page like you would create any other new wiki page, but using the prefix Template: as part of the page name. For example, your template should be called [[Template:username]].
2. Click on the Template redlink you just created and put content on this page that you will want to use over and over again.
3. Once you have added and saved the content to your Template page, you need to use your template on your user page. This is called "invoking" the template. To do so, invoke the template by using the following syntax: {{Template:username}} in the place you wish the content of the template page to appear. This will "expand" the template to its full contents on the actual page.

As discussed in class, each weekly individual journal assignment needs to conclude with an Acknowledgments and References section.

#### 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.

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), that belongs in the References section where you will give a include a formal APA-formatted citation (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."

#### References

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. 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.

## Shared Journal Assignment

• Store your journal entry in the shared Class Journal Week 1 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
• 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).

• Answer the "before" set of reflection questions at the end of this assignment.
• Read Chapters 1 and 5 of Letters to a Young Mathematician by Ian Stewart.
• Read Chapter 1 of On Becoming a Biologist by John Janovy, Jr.
• Answer the "after" set of reflection questions at the end of this assignment.

#### Reflection Questions

1. When you hear the term mathematics, what comes to mind?
2. Do you consider yourself a mathematician? why or why not?