We provide the ability to launch a version of PLA remotely from this web page, if you do not want to install PLA or if you are using a non-supported platform. The launcher allows you to select one of five PL models:
- SmallKB, a small proof of concept model, a guide to which can be found here.
- SKEML133, a model explaining SKMEL133 cell response to treatment by various drugs.
- STM7, Signal Transduction Model version 7, a comprehensive model of cellular response to external stimuli (including Adriamycin, Anisomycin, Bleomycin, anti-Cd40, Csf1, Egf, Etoposide, Hgf, Hydroxyurea, Ifna or Ifnb family members, Ifng, Igf1, IL1, IL2, IL4, IL6, IL12, Insulin, ionizing radiation, Lipopolysaccharide (Lps), Neocarzinostatin (NCS), Ngf, Pdgf, Phorbal 12-myristate,13-acetate (PMA), PolyIC, Serum, Sorbitol, Tgfb1, Various TLR9 ligands, Tnf, UV radiation, and Vegf), 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.
- GlycoSTM, a model of glycosylation extending the KEGG pathways. a detailed guide can be found here.
You can access the PLA Launcher, which will run by talking to our server at SRI, in one of two ways. You can download the client or you can use Java's webstart to achieve the same effect (if webstart works for you). Webstart comes with a myriad of security hurdles that may be too daunting, which is why we provide the alternative route. The webstart approach seems to work for Windows and Linux (at least Java 1.6 or higher is your best bet here). There are problems with webstart on Mac OS X, and the safest route may be to download the PLA Client (see below). Always trust option or else it will quietly fail.
To use the webstart version of the PLA Launcher:
- Launcher click here!
Downloadable PLA ClientTo sidestep the webstart infrastructure, simply download PLAclient.zip:
[iop@serrano ~/Desktop]$ unzip PLAclient.zip Archive: PLALauncher.zip creating: PLALauncher/ inflating: PLALauncher/launcher inflating: PLALauncher/lib/online.jar inflating: PLALauncher/lib/iop.jar [iop@serrano ~/Desktop]$or if it went into your Downloads folder on a Mac, just click on the icon and drag the PLALauncher folder onto the Desktop. Now cd into that directory and execute the launcher script. You can also just open the folder and double click on the launcher too.
[iop@serrano PLALauncher]$ ./launcherYou may need to temporarily modify your security settings on the Mac to be able to use the launcher, but thats just a sign of the times, unfortunately. On windows you may have to rename the launcher file to launcher.sh, then you should be able to launch it by clicking (assuming Oracle's java is in your PATH).
Using Online PLANow would be a good time to try out one of our many guided tours:
- Guided Tour for the SmallKb model
- Guided Tour for the SKMEL133 model
- Guided Tour for the STM7 model
- Guided Tour of the Protease Network
- Guided Tour for the Mycolate model
- Guided Tour for the Glycosylation model