Online PLA

We provide a version of PLA that may be accessed remotely from this web page, if you do not want to install PLA or if you are using a non-supported platform. We currently provide access to three PL models:

• SmallKB, a small proof of concept model, a guide to which can be found here.
• STM6, STiMuli version 6, an even more comprehensive model of cellular response to external stimuli (including the ligands Cd40lg, Csf1, Egf, Igf1, IL1, Ins, Tgfb1, Tnf, and Lps), a detailed guide can be found here.
• Protease, a network model of gram+ bacterial proteases here.
• Mycolate, a complete model of the Mycobacterial Mycolic Acid Biosynthesis Pathway, a detailed guide can be found here.

The current version is version 3.0 (February 2010).

You can either download a PLA client application, which will run by talking to our server at SRI, or you can use Java's webstart to achieve the same effect (if webstart works for you). The webstart approach seems to work for Windows and Linux (Java 1.6 is your best bet here). There are problems with webstart on Mac OS X for Java versions prior to 1.6, though you will be asked to trust it. You need to click the Always trust option or else it will quietly fail.

Webstart Versions (SmallKB, STM6, Protease & Mycolate)

To use the webstart version of the PLA for:

• SmallKB click here!
• STM6 click here!
• Protease click here!
• Mycolic Acid Biosynthesis click here!.

Downloadable PLA Client

To sidestep the webstart infrastructure, simply download PLAclient.zip:

• PLAclient.zip (463K)

and if your browser doesn't unzip it, you'll need to do this too. Assuming you have put the zip on your Desktop:

[iop@serrano ~/Desktop]$ unzip PLAclient.zip 
Archive:  PLAclient.zip
  creating: PLAclient/
  inflating: PLAclient/PLAremote     
  inflating: PLAclient/PLAremote2     
  inflating: PLAclient/PLAremote3    
  inflating: PLAclient/PLAremote4
  inflating: PLAclient/online.jar    
  inflating: PLAclient/iop.jar       
[iop@serrano ~/Desktop]$ 

or if it went into your Downloads folder on a Mac, just click on the icon and drag the PLAclient folder onto the Desktop. Now cd into that directory and execute the PLAremote script. For the SmallKB model:

[iop@serrano PLAclient]$ ./PLAremote 

For the Mycolate model:

[iop@serrano PLAclient]$ ./PLAremote2 

For the STM6 model:

[iop@serrano PLAclient]$ ./PLAremote3

The STM6 model is bigger still, hence so additional patience is required. For the Protease model:

[iop@serrano PLAclient]$ ./PLAremote4

Using Online PLA

Now would be a good time to try out one of our two guided tours:

• Guided Tour for the SmallKb model
• Guided Tour for the STM6 model
• Guided Tour of the Protease Network
• Guided Tour for the Mycolate model

Bug Reporting

Please report problems to pla-support@csl.sri.com.