We provide the ability to launch a versions 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 two versions that we offer are:
- A Sampler of Pathway Logic models of cellular processes ranging from a bacterial metabolic synthesis pathway to signal transduction in a macrophage model.
- STM8 -- a collection of signal transduction networks modeling cellular response to different stimuli. Each network is curated from experimental evidence using the Pathway Logic (PL) representation system and the Pathway Logic Assistant (PLA). The collection also includes a network (Death) modeling the different paths leading to cell death.
- 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.
- VMac, an executable model of signaling processes in a macrophage derived from the Macrophage Map.. The model includes respsonse to signals such as interferons, interleukins, chemokines, pathogen molecules and more. It also includes subnetworks leading to phenotypes such as macrophage activity, apoptosis, and production of reactive species, cytokines and chemokines.
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). Choose the Always trust option or else it will quietly fail.
To use the webstart versions of the PLA Launchers mentioned above:
Downloadable PLA ClientTo sidestep the webstart infrastructure, simply download PLAclient.zip:
[iop@serrano ~/Desktop]$ unzip PLALauncher.zip Archive: PLALauncher.zip creating: PLALauncher/ inflating: PLALauncher/launcher-STM8 inflating: PLALauncher/launcher-sampler inflating: PLALauncher/lib/iop.jar inflating: PLALauncher/lib/online.jar [iop@serrano ~/Desktop]$or if it went into your Downloads folder on a Mac, just click on the icon and drag the PLALauncher folder onto the Desktop. Now cd into that directory and execute the desired launcher script. You can also just open the folder and double click on the desired launcher too.
[iop@serrano PLALauncher]$ ./launcher-samplerYou 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. To be guided through this process take a look here On windows you may have to rename the launcher file to launcher-sampler.sh (or launcher-STM8.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. For the sampler these are the appropriatye tour.
- 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
- Guided Tour for the VMac model