Services

I strongly believe in making computational resources widely available. For this reason all of my programs are written so as to be reusable. Either directly by using the .NET assembly, or via an SBW integration. I also provide W3C web services which can be readily used from other languages or operating systems. On this page you can find a collection of them.

SED-ML Services

 

A set of methods that allows to create SED-ML documents easily. Either directly from an SBML model, or by converting to and from SED-ML script.

test service | WSDL

Layout Services

 

To make it easy to visualize SBGN or SBML Models with the Layout / Render Packages, the following uris accept the posting of an SBML model.

GenerateImage

This action generates a PNG for a posted SBML / SBGN file. Should the file contain no SBML Layout, one will be generated. So how does this work. The URL to use is:

http://sysbioapps.dyndns.org/Layout/GenerateImage

You simply post to this URL the following HTTP Form elements:

file         - the SBML file
scale        - an optional floating point scale for the image (defaults to 2)
height       - scale image to fit the height
width        - scale image to fit width 

If height is given, width needs to be given as well.

GetLayoutSBML

This action simply loads the given SBML file, and writes it out using the SBML Layout library. Should no layout, exist, one will be generated. The URL is:

http://sysbioapps.dyndns.org/Layout/GetLayoutSBML

You simply post to this URL the following HTTP Form elements:

file         - the SBML file

Example

So for example, if you wanted to post a local file to the service with curl, you'd run:

curl -X POST -F file=@".\BorisEJB.xml" http://sysbioapps.dyndns.org/Layout/GenerateImage -o out.png

lets take the arguments apart:

  • -X POST post FORM data
  • -F file=@filename post filename to the URL
  • http://sysbioapps.dyndns.org/Layout/GenerateImage the URL
  • -o out.png write the resulting PNG to the current directory as out.png.

On the SBW home page we also provide the Web Service Creator that allows you to generate W3C web service wrappers to all installed SBW modules. Among those: roadRunner, the SBML translators and the SBML layout support.