BIOC-4010 Dry-Lab Resources

This repository includes codes, data, and files for the dry lab sessions of BIOC-4010 at the University of Windsor. It has been in use since the 2022W semester. The repository is being constantly updated for the most current semester. Not all materials are uploaded in this repository, some documents mentioned will be shared in the class, or through the Learning Management System (Brightspace).

This course is offered to Students from Biology or Biochemistry background with minimal experience in computer science.

If you are interested, you can take a look at my journey of choosing the Bioinformatics dry lab platform.

The material is released under Creative Commons license. You are welcome to adopt it to your course. I need to clean up the folders and codes, when I find some time to do it. Please send any comments to ytong_AT_uwindor_DOT_ca.

Currently it contains five dry-lab sessions. The plan is to

1. provide more details on the instructions;
2. expand on the sessions.

Tutorial #	Content
tut1	Linux basics and Regular Expression
tut2	Scoring matrices and dotplot
tut3	Sequence alignment and BLAST
tut4	Molecular Graphics with PyMOL
tut5	Molecular phylogeny

On March 24, 2023, GitHub updated its RSA SSH host key, in case you see a warning that REMOTE HOST IDENTIFCATION HAS CHANGED. Update local known_hosts file accordingly. A new instance of the Linux VM should not have an issue.

Before you start the Linux VM

To use the Linux VM:

• First login the Windows desktop using your UWindsor email address and your account password.

• Additional setup for the VM — you only need to do this once:

  • Setup shared folder, clipboard and file dragging
    • Start the Oracle VM Virtual Manager;
    • Select the 4010Lab, click Settings on the right panel;
    • In the pop-up dialog, click on Shared Folders, and select the "add new share folder" icon, and select the pull down menu next to "Folder Path";
    • It is recommended to select and choose the Downloads folder of the host
    • machine for sharing contents, check the 'Auto-mount' box, and click 'OK' to close the 'Add Share' dialog;
    • In the Settings of 4010Lab, choose General → Advanced tab and change Shared Clipboard and Drag'n'Drop from Disabled to Bidirectional.
    • Click 'OK' to close the '4010Lab - Settings'.

• Select the 4010Lab icon on the desktop, double click the icon to launch the Linux VM, or you can launch the VM from Oracle VM Virtual Manager. The actual number of icons in the desktop interface may be slightly different since new software may be added for other courses. But you should see a blue 4010LAB icon. You should be automatically logged into the Linux VM under the science account. The instructor or the GA/TA will provide you the password if needed.

• One final update to install the Guest Additions in the Linux VM — you only need to do this once:

  • Download the Guest Additions iso from http://download.virtualbox.org/virtualbox/6.1.32/ and save to Downloads folder of the host computer.
  • Launch the Linux VM
  • Inside the Linux VM, choose VBox_GAs_6.1.14, click mouse right button and select eject, the CD icon should disappear from the desktop
  • Outside the Linux VM in the Oracle VM VirtualBox menu, choose Devices → Optical Drives → choose the downloaded VBoxGuestAdditions_6.1.32.iso file.
  • A new CD icon will show up in the Linux VM and a pop-up dialog asking whether you want to run the software on the CD, choose Run, and enter the password to Authenticate.
  • After finish installation, restart the Linux VM.
  • You should be able to share content between the Linux VM and the host machine.

Sanity check

• Check the Linux VM desktop and make you see an icon labelled sf_Downloads which is the shared folder Downloads of the host machine.

• Open Notepad in the host machine type some text and copy by selecting and press Ctrl+C. In the Linux VM, start a Terminal, click mouse right button and choose Paste and see whether the text is pasted. Press Ctrl+C to break the input in the Terminal.

• Create a test.txt file on the host Windows desktop and see whether you can drag and drop into the Linux VM.

• Remember that the sf_Downloads folder in the Linux VM is the folder you can used to transfer files between the Linux VM and the host Windows computer. You can also use the Firefox browser inside the Linux VM to upload files to OneDrive or Brightspace.

• To make a screenshot, press the "PrtSc" button and the Linux will ask you where to save the screenshot. I suggest you save it in the sf_Downloads folder.

Navigate in the Linux VM

• 

Using the Linux VM for BIOC4010

The github bioc4010 repository has been cloned into the VM already, so after you login the Linux VM, start a terminal and type

cd bioc4010
git pull

to enter the bioc4010 directory to see the files and pull changes made to the repository. This will include all the changes made to the sub-directories.

If you have made changes to downloaded files, and have trouble pulling updates from github. Run the following command to put away these changes before you pull for the updates.

git stash
git pull

After you login the Linux VM and made the above updates, enter the directories corresponding to individual tutorial and follow the README.md file in each directory.