SBML4j python package

This is the python package to talk to a running SBML4j service instance.

Install

This package is available through pip To install use:

pip install pysbml4j

Usage

In your python project use

import pysbml4j

client = pysbml4j.Sbml4j()

This generates a client connection to a server running on

http://localhost:8080

To connect to a server running at different host use the 'Configuration' class

config = pysbml4j.Configuration("http://my-server-url:port")
client = pysbml4j.Sbml4j(config)

Then you can communicate with the running service using the client object.

client.listNetworks()

The main working object then is the 'Network' class.

myNet = client.getNetworkByName("NetworkNameFromNetworkList")

The following chapter describes the current options you have for working with the network element

Working with a network

Basic information

You can get a basic information dictionary for a network with

myNetInfo = myNet.getInfoDict()

GraphML

To get a graphML Representation use:

graphMLString = myNet.graphML()

You can provide the 'directed' attribute (true, false) to determine whether the resulting graph should be directed or not. The default is 'false'

There are more options, which I will provide documentation for shortly. Stay tuned.

To find out more about SBML4j visit the kohlbacherlab github repository