COSC 348: Lab10

Overview: Microarray data analysis (lab 1/2)

The 1st part: Discusssion of the scientific paper on microarray data analysis:

Scott L. Pomeroy et al. (2002) Prediction of central nervous system embryonal tumour outcome based on gene expression. NATURE vol. 415, pp. 436--442.

The paper can be downloaded here

IMPORTANT: Submit 1 page report in which you describe what the paper was about (worth 1% of the final mark).

The 2nd part: We will re-analyse some of the data from the paper using the data analysis software NeuCom. Please follow these steps to make sure you can access and run NeuCom on you lab computer in the virtualised Student Desktop:

On a Computer Science undergrad lab computer (running OSX), log in with your assigned Computer Science credentials (*not* your University ID).
Once logged in, start a web browser (Safari, Chrome or Firefox) and browse to this URL: https://student.desktop.otago.ac.nz/vpn/index.html
On the web dialogue box you will need to authenticate with your University ID and password (*not* your Computer Science credentials this time)
If the Citrix Receiver application does not start up automatically, click the Student Shared Desktop link in the middle of the window. After a short period you should be presented with the Student Desktop. If desired, full-screen this window by using the XenDesktop Toolbar pull-down menu at top centre of the window.
Run Neucom application from the Start Menu >> Course Specific Resources >> Computer Science >> Neucom Student V0.919 (*not* the debug mode version)
Note: Neucom docs and datasets appear under Computer >> Teaching Volume (T: drive) >> CompSci >> NeuCom >> bin >> win32
When finished using the Student Desktop, either disconnect the session by way of the XenDesktop Toolbar pull-down menu at top centre of the window or log off via the Start Menu within Windows. Disconnecting from a session will allow you to continue with the same session at a later time, with all applications running as you left them at the time you disconnected.

Further info:

When using Windows Explorer you may be asked whether the virtual desktop is allowed to navigate and access local files on the local lab computer. Select "Read/Write access" to allow any of your documents stored on your Computer Science networked home directory to be accessible through the virtual desktop, and vice versa. The local file systems will appear as "Local Disks C,D,H etc" within the Student Desktop. Any files created within the Student Desktop would be, by default, stored in H:\RedirectedFolders\ - typically Documents, Downloads folders etc.
Please report any malfunctioning of the Student Desktop or NeuCom to cshelp@cs.otago.ac.nz

In order to test the functioning of NeuCom you can start working on lab11

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