BIOL368/F20:Help

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BIOL368-01: Bioinformatics Laboratory

Loyola Marymount University

Fall 2020

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Contacting LMU ITS Service Desk

Accessing Class Materials

  • All PowerPoint slides used by the instructor will be posted to this wiki or Brightspace before class so that you can download them and follow along.
  • All assignments and coursework will be carried out on this wiki.
  • Materials that cannot be shared publicly (copyrighted material, Zoom links, personal contact information, and grades) will be posted on Brightspace.
  • In-class Zoom sessions will be recorded on video and posted to Brightspace after the class period is over.

Using Zoom

MyLMU screenshot.png
  1. To login to Zoom, first login to MyLMU.
  2. Click on the "Accounts & Tech" tab. If you do not see the tab, click the hamburger icon (three-line icon).
  3. On the right, the last choice under "Software & Tools" will be "Zoom (web conferencing)". Click on the link to Zoom and it should take you to your LMU user profile page on Zoom.
    • If you don't have an account, an LMU Zoom account will be automatically created for you.
    • If you already have an account, you will see your Zoom home page.
  4. Click on the link sent to you via e-mail to join the meeting.
  5. If this is your first time using Zoom, the Zoom software will automatically be downloaded to your computer.
  6. Follow this link to test zoom on your device.
  7. To learn more about Zoom:
  8. If you are having issues using Zoom in the middle of class, you can always use your phone to call in to the meeting. The phone number will be on the meeting invitation e-mailed to you. If you do this, you will only be able to hear audio and talk through your phone, but you will be able to download and view the slides onto your computer. After the class is over, the video recording of the class will be posted on Brightspace.
  9. If you want to host your own Zoom meeting, please see these instructions written by Dr. Fujishige.

Accessing Zoom Support

There are three options to reach Zoom Support.

The Zoom support hours are 24 x 7, including public holidays, where agents or technical engineers are available for email or live chat.

Live chat or a phone call is the best option if you are in a meeting or trying to get something done.

  1. Live chat
    • Make sure you are logged in to your LMU Zoom account first (through MyLMU).
    • Select the "Help" blue bubble on the lower right-hand corner.
  2. Phone Call
    • US: 1-888-799-9666 ext 2
    • You might be asked to enter your ID number. Within Zoom, click the left navigation pane, select Profile and locate the Personal Meeting ID (xxx-xxx-xxxx).
  3. Online Submission (Ticket)
    • A ticket is mainly for non-emergency/non-immediate requests when you can wait a few hours or even a day or so for a response.
    • Online submission - click the "Submit a request" link. Make sure you are logged into LMU Zoom.

Web Conferencing Best Practices & Netiquette

Guidelines adapted from UW-Madison Webconferencing Best Practices and Dr. Martin's Netiquette Guidelines.

Preparing for Synchronous Zoom Session

  • Zoom in from a computer or tablet other than a mobile phone (assuming you have ready access to one), as you will want a large enough screen and a keyboard.
  • System Check: Complete a system and web browser check at least 24-48 hours prior to the first class session. This allows time to make any necessary changes (with the help of ITS Service Desk or Zoom Support, if necessary).
  • Internet Connection: Participate from a location with a strong and stable internet connection.
  • Close Other Applications on Your Computer: Particularly when presenting, any dropped connections from the web conferencing system can be very disruptive to a meeting. Close all other applications on the computer that are not necessary. This will help the software operate more efficiently, and will help to conserve the individual network bandwidth.
  • Quiet Location: Participate from a quiet location. To avoid disruption, post a note on your door, notify roommate and/or family that you're in a web conference.
  • Be On-Time: Call in 5-10 minutes before class starts to allow you sufficient time to test your audio/video, troubleshoot if there are any problems, chat informally with your classmates once I let you in from the waiting room (if used), and allow us all to start on time.
  • Audio Quality: If you have one available, use a headset with a microphone. It provides better sound quality and helps reduce background noise.
  • Come fully dressed: Recommended: Wear what you would normally wear (at least on top) if we were meeting in person for class.
  • Identity Yourself: Make sure your photo in Zoom is a recent headshot of you and the name that appears is the one you wish to be called by others. Your headshot (vs. a blank black square) will help me (and others) associate your name with your face and therein build community together as a class. Optional: you can also add in your personal gender pronouns (PGP). Example: "Kam Dahlquist (she/her)"
  • Check your background: When turning on your video, be aware of your camera’s line of sight. Put away things you don’t want others to see and make sure your background is not distracting to others. Use of virtual backgrounds is allowed, but don't worry about revealing a messy room if you don't have that capability. Do make sure potentially offensive or distracting objects are out of view of your classmates, including any housemates who might be engaged in activities which might draw undue attention to themselves.

During the Synchronous Zoom Session

  • Turn on your video: If you do not have sufficient bandwidth for video or have privacy or other concerns, please discuss these with me in office hours during the first week of class.
    • If you must turn off your video, consider turning it on at the very least at these times:
      1. at the beginning of class (to greet your classmates and me)
      2. at the end of class (to bid your classmates and me adieu)
      3. whenever you are speaking in class
      4. whenever you meet with a smaller group of classmates in Zoom breakout room sessions.
  • Mute: Mute your phone/microphone when not speaking. Every noise that is made, including paper shuffling, pencil tapping, typing, coughing, and chatting with others, will be heard by everyone else in the conference.
  • Avoid multitasking: Class is not the time for you to simultaneously workout, grocery shop, do household chores, drive/bike/travel from one location to the next, or attend to any other matters, particularly since active participation (orally and through the chat) will be expected.
    • Exception: I recognize that some of you may have to attend to loved ones at the same time you are in class, which is totally understandable in light of our pandemic realities.
    • If your children or pets make a cameo on screen, no worries and no need to apologize; attend to them as needed and rejoin when you are ready. You can even introduce them to us as your co-workers if they appear at an opportune (non-disruptive) time.
  • Stay Engaged: Either raise your hand (physically), use the "raise hand" feature, or just start typing in the chat whenever you wish to ask a question or make a comment.
    • Note that I might not notice that you are trying to get my attention right away--feel free to unmute yourself to get my attention.
    • If you notice that one of your classmates is trying to get my attention, help them out by pointing it out to me if I don't notice.
  • Use the chat: If for some reason you foresee having difficulties typing in the chat, have paper and pen ready so you can write your responses and show them on the screen.
  • Take care of yourself: If you need to take a break outside of the scheduled breaks we will take as a class, mute yourself, block your video, and then do your business, lest we get motion sickness from watching you move about and/or hear you going to the bathroom.
    • It is OK to eat or drink while in class, as long as it doesn't become distracting to yourself or others.

After the Synchronous Zoom Session

  • I will record our sessions and make them (including the group chat) available for students who weren't able to attend. Remember that trust will require us to keep what we've shared in class solely within the confines of the class, unless you've received explicit consent from your classmates to share. Please also refrain from posting screenshots or video clips from our class to others outside of it to maintain your classmates' and my privacy and to comply with LMU's policies.

Open WetWare Help

Some pages designed to help students become familiar with OpenWetWare.

Tips & Tricks

Please feel free to add any tips and tricks you have learned so the whole class can benefit from your knowledge.

Screenshots

  • Making a screenshot smaller: This may not be the most technical way, but it gets the job done. After the image you insert into the Edit page, add "thumb|upright=3.0". This command makes the image at thumbnail, then adjusts the thumbnail to a different size. For images you want to be wider, use a number greater than 1, for more vertical images, use a number less than 1. You can also center the image by using the "|center" command (Example: [[Image:This is an example.jpg|thumb|center|upright=2.5]]

Windows

  • To take a screen shot, press Ctrl and Print Scrn together. The contents of the active window will be saved on your clipboard. You may then paste into a graphics program (like Adobe Photoshop or Microsoft PowerPoint) and save the file.
  • An alternate method is to use the Snipping Tool.
    • Go to the Search field in Task bar and search for "Snipping Tool". Launch the tool.
    • Click on the "New" icon and then click and drag to select the area that you want to screenshot.
    • Go to the menu File > Save As and save your file.

Macs

Turning on File Extensions in Windows 10

  • The Windows 10 operating systems defaults to hiding file extensions. To turn them back on, do the following:
    Folder Options window
    1. Go to the Search menu (circle icon) "File Explorer Options" in the search field. Select the result.
    2. When the File Explorer Options window appears, click on the View tab.
    3. Uncheck the box for "Hide extensions for known file types".
    4. Click the OK button.
  • The computers in Seaver 120 are are set to erase all custom user settings and restore the defaults once they have been restarted, so if you have done this previously, you might have to do it again.

Setting the Download Options for FireFox and Chrome

  • For Mozilla FireFox (40.0.2 or higher)
    • Options set to default downloads to Desktop and to ask each time a file is downloaded
      • Go to the Options menu, General options
      • First, under the "Downloads" section, next to "Save files to" click the "Browse" button, select the Desktop, and click the OK button.
      • Second, click the radio button next to "Always ask me where to save files"
FireFox Download Settings.jpg
  • For Google Chrome (Version 44.0.2403.157 m or higher)
    • Options set to default downloads to Desktop and to ask each time a file is downloaded
      • Go to Settings page, click on link to "Show advanced settings"
      • First, under the "Downloads" section, click the "Change..." button, select the Desktop, and click the OK button.
      • Second, check the box next to "Ask where to save each file before downloading"
Chrome Download Settings.jpg

Compressing Files with 7-Zip

  • The 7-Zip file compression software has been installed on the computers in Seaver 120. (If you want to install this software on your own computer, go to the 7-zip Download page.) To compress a single file or a group of files, do the following:
    1. Select all of the files you want to zip together by clicking and dragging or control-clicking on the filenames.
    2. Right-click on your selection. In the context menu that appears, select the menu option: 7-Zip > Add to archive
    3. Make sure there is a meaningful filename in the field under the word "Archive:". If not, change it to something that is. Typically you will want to include your name or initials, a short descriptor of what the file contains, and the date in year-month-day format (yyyy-mm-dd).
    4. Select "zip" as the Archive format.
    5. You do not need to change any of the other defaults. Click OK. The zip file will appear in the same folder as the files you compressed.

What to do if there is a OpenWetWare outage

  • We recommend that when doing your journal assignments, "save early, save often". That is, work in short increments, saving your work in small pieces. This will help you avoid losing your work if there is an issue with the internet.
  • We also recommend that you begin your assignments well ahead of the deadline so that you have enough time to complete them on the wiki.
  • While we do not anticipate any problems, in the event of an OpenWetWare outage near a deadline, please do the following:
    • send an e-mail to the instructor notifying her of the outage, attaching a screenshot documenting the problem;
    • complete the unfinished portion of the assignment as a Word document and e-mail it to the instructor. Even though you are saving it as a Word document, write it in wiki syntax so that it can be saved back to the wiki when it becomes available again.

Other Useful Links

Online Biological Dictionaries