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Here you can find info and links to some usefull utilities avilable for you.
Follow the above link to add the ARE/GRE tracks to the standard genome browser. Make sure the tracks are not hidden if you can't see them.
The tracks are designed to integrate with HG18 (the NCBI36 2006 release). They also only cover the main genome, so regions out of the standard Chr1, Chr2, ... Chr22, ChrX and ChrY will not have data. The sites are also restricted to gene 3'UTRs according to the ENSEMBL gene models, which may be slightly different than the UCSC or RefSeq gene models in some cases. Lastly, The sites on the track annotate either the degenerate WTATTTATW or the larger ATTTATTTA of two or more overlapping pentamers (and likewise for GREs). The matching is exact with no mismatches allowed, and all possible sites in any given 3'UTR are shown. These parameters are slighlty different from those used in the ARED/GRED database but I beleive they are more suitable for the browser.
Click the above link and use labuser for both the username and password.
The above link automatically installs a small utility on your computer to allow you to connect to the server and run the applications. It should work with most browsers and systems. If you are asked to allow the application (or ActiveX) to be downloaded or installed please say yes. You may need to have administrator rights on the machine for this to work. The first time you access the above link it will take about a minute to download and install the utility. On subsequent times you will not have to go through any of this headache. If installing the utility fails, please contact me to see what can be done about it.
Using the control window that opens after you log in start the Proxcell version that you need. You will also find an Explorer icon, use it to run a file manager to allow you to copy image files to the server. This is necessary to allow the program to run at full speed on the server. Simply run explorer, then find the experiment files on your local drive (they are the drives named Clinet something). Copy those files to the Aquired Images folder on the server (located on drive D; follow the shortcut). Run Proxcell as usual (be sure to select the batch located in the Acquired Images folder on the server). When done, you can copy the result file to your local drive and then delete the experiment files from the server. Please be sure to clean up after your run or we will run out of space quickly. Note that files older than one month will be automatically deleted from the Aquired Images folder without notice, including results files, so be carefull! This policy may change in the future, we will see how it goes.
The server can run 4 or 5 instances of Proxcell simultaneously so you can process multiple batches in one go. Simply run Proxcell again for each batch. Just be sure not to run the same batch more than once at the same time or you may corrupt the files. When all is done, be sure to close all programs and then choose Sign Out from the control window. This will allow other users to log on to the server.
Here is a walkthrough of the process:
1. Click the above link (or goto http://brp.kfshrc.edu.sa/apps) and allow installation of the utility.
2. Log on to the service using labuser both as username and password.
3. Use the control window to run the application you need.
4. Use Explorer to copy files between the server and your computer.
5. In Proxcell, make sure to access the files on the server, not your local drive.
6. When all is set and done, use the control window to Sign Out
7. Feel happy !