BIOL368/S20:Week 1

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BIOL368-01: Bioinformatics Laboratory

Loyola Marymount University

Spring 2020

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This journal entry is due on Thursday, January 23, at 12:01am Pacific time.


Overview

The learning objectives for this assignment are:

  1. To set up your individual user page on this wiki as an online resume or curriculum vitae (CV). This will allow the instructor, TA, 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 homework and projects in partners, small groups of three or four, 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).
  • 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 Cartmel & Jenny Chua
    • Annika Dinulos & Carolyn Egekeze
    • Christina Dominguez & Sahil Patel
    • Madeleine King & Jack Menzagopian
    • Nathan on & Maya Paniagua
    • Lizzy Urbina Hernandez, Karina Vescio, Nicholas Yeo

User Page Content Requirements

For this week only your individual journal page will be completed on your user page, according to the instructions below. Starting with Week 2, you will create a separate individual journal page to contain that week's work. For each subsequent week, you will create new individual wiki pages, one page per week.

For this week, 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 (CV). You must include the following content and demonstrate the wiki skills ( listed further below):

  1. Name
  2. Contact Information
    • Email address
      • We recommend that you obscure your email address so that web crawlers cannot pick it up and subject your account to spam. For example the instructor's address could be stated as "kdahlquist at lmu dot edu".
      • Also provide a link to email you through OpenWetWare, using the following syntax [[Special:Emailuser/username | Email username through OpenWetWare]].
        • For example, Dr. Dahlquist would use the code [[Special:Emailuser/Kam D. Dahlquist | Email Kam D. Dahlquist through OpenWetWare]] to set up a link to e-mail her.
    • LMU snail mail address (either your mailbox or departmental address)
  3. Education
    • Major
    • Expected graduation year
    • 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
  5. Research Experience (if applicable): 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
  6. Work experience
    • Position/title
    • Employer
    • Dates
    • Responsibilities
  7. Personal interests/hobbies
  8. What is your favorite aspect of biology and why?
  9. What is your favorite aspect of computer science and why?
  10. 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.

Talk Page

For quid pro quo, do this as well:

  • Write one question that you would like to know about me (Dr. Dahlquist) on my user talk page (linked previously), and I will answer them there. Make sure to sign your question with the standard MediaWiki "signature shortcut" (four tildes, ~~~~).

Individual Concerns (by email)

To keep your answers to the following questions private, please send an e-mail to Dr. Dahlquist answering to the following questions. Note, if your answer to a question is no, you still need to email me with your no answer:

  1. Do you have any worries or concerns about this class at this point?
  2. Is there anything else you would like me to know?

Practice your Wiki Skills

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, a discussion page, or a file upload), 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). For example, Dr. Dahlquist would create a page called [[Kam D. Dahlquist Week 2]].
  3. Link to a page within our Wiki: [[page title|optional visible label]]
    • Go to the People page and link your name to your own user page.
    • Also link to a page within the OWW wiki on your user page.
  4. Link to an external Web page: http://address or [http://address visible label]
    • The second form of the link is preferred because it looks neater on the page.
  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.
  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:BIOL368/S20]] for all of the wiki pages you create.
    • Instead of adding the category directly to your User Page, add it to your template instead (see number 13 below).
  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 (talk) 15:56, 6 January 2020 (PST)
    • You can fulfill this by posting your comment on Dr. Dahlquist's user talk page.
  13. Create a template for yourself and use 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]]. Dr. Dahlquist's template would be called Template:Kam D. Dahlquist]].
    2. Click on the Template redlink you just created and put content on this page that you will use over and over again. You must include the following set of navigation links on your template page:
    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 name}} 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. For example, Dr. Dahlquist's template would be {{Kam D. Dahlquist}}. For the rest of the semester, you will invoke your template on your individual journal pages and any other wiki pages you create.

Academic Honesty

As part of the Information Literacy learning objectives, you will be practicing how to appropriately acknowledge and cite sources for each of your weekly assignments. To accomplish this, each weekly individual journal assignment needs to conclude with an Acknowledgments and References section.

Acknowledgments

Your user page, and all other individual wiki pages that you create this semester must have an Acknowledgments section with the content listed 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 (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. For example, an appropriate statement could be (but is not limited to) the following:
    • I copied and modified the syntax for creating a wiki table from <user>.
  4. If you need to reference content (a journal article), that belongs in the References section where you will give a include a formal APA-formatted citation (see below).
  5. 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. An appropriate statement could be (but is not limited to):
    • I copied and modified the protocol shown on the Week 1 page.
  6. 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."
  7. Sign your Acknowledgments section with your wiki signature (four tildes, ~~~~).

References

Your user page, and all other individual wiki pages that you create this semester must have a References section with the content listed below.

  • 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, including software and/or websites
    • data
    • facts
    • images
    • documents, including the scientific literature
  • Do not include extraneous references that you do not cite or use on your page.
  • 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 Citation Guidelines page.
  • Cite the appropriate weekly Assignment page. For example, the citation for the Week 1 Assignment page is:
  • Even if you have nothing else to cite (which would be extremely rare), the References section must be present and include the citation to the appropriate weekly assignment page.

Shared Journal Assignment

  • Compose 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 :) )
  • 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, which for Week 1, is your user 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 and Reflect

Reflection Questions

Before reading the Denning articles (on your honor), answer the following questions;

  1. When you hear the term computer science, what comes to mind?
  2. When older relatives or friends hear the term computer science, what do you think comes to their minds?
  3. When younger relatives or friends hear the term computer science, what do you think comes to their minds?

Before reading the Janovy chapter (on your honor), answer the following questions;

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

After reading the Denning articles and the Janovy chapter, answer the following questions:

  1. What was the purpose of these readings?
  2. Which of the voices in the Voices of Computing article seem to appeal to you the most?
  3. Apply one of the seven principles from the Computing is a Natural Science article to something as "non-computer-science"-y as possible, either from other subjects or your daily life.
  4. What did you find most interesting or provocative about the Janovy reading?
  5. What does it mean to be a biologist? Do you consider yourself a biologist? Why or why not?
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