Online PLA

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.

The sampler launcher allows you to select one of seven 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.
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.

The STM8 launcher allows you to select one of more than forty PL response networks. The networks are describe in the STM8 guide along with a guided tour of the Death network. The guide can be found here. The current version is version 6.0 (2018-02-25).

The launchers start a PLA client, which will run by talking to our server at SRI. For Linux and Windows you can download a launcher folder with a script and required dependencies. These seem to work for Windows and Linux (assuming you have Jave installed , at least Java 1.6 or higher). For Mac users the launcher is provided as a downloadable app that is stand-alone and doesn't require you to have Java installed.

Downloadable PLAOnline App

On Mac OS X there is an app for each launcher: PLAOnline for STM8 and PLAOnlineSampler for the Sampler collection. You simply download a zip of the app,

<appname>.zip

unzip and open the app.

Downloadable PLA Client

Simply download PLAclient.zip, it includes launchers for both collections:

PLALauncher.zip (about 2.5M)

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 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-sampler

You 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 PLA

Now would be a good time to try out one of our many guided tours. For the sampler these are the appropriatye tour.

While for STM8 there is:

Guided Tour for the STM8 models

Bug Reporting

Please report problems to [email protected].