COMBINE 2016 Day 2: pathwayDesigner

COMBINE 2016

Herbert Sauro

When pathwayDesigner was first written, there was no libSML, and his original parser remained inside his code for a long time – until this past summer, to be specific! There is also a direct link to libRoadRunner as he would like to make this into a realtime simulator at some point. There are now some new node styles, and has been doing some work on plugins. There are about 8 or 9 plugins to date, including parameter scanning, MCA (sensitivity) plugin appropriated from copasi, sliders, arrow designer. There is also an AutoLayout library in C++ which uses these the same algorithm as the original layout method in SBW. It also has Python bindings. Included with it is a test plugin which generates random networks so you can play with the layout options.

There is also a feature where you can generate Splines. There is also an antimony plugin which allows you to load in a network as text and it will be displayed in pathwayDesigner. There is even a Mac version in alpha available now. Within the next year, he’d like to finish the Mac version, the python plugin, the layout functionality, support for alias nodes and perhaps render extension. Longer term, he’d like to focus on that realtime simulator.

Please note that this post is merely my notes on the presentation. I may have made mistakes: these notes are not guaranteed to be correct. Unless explicitly stated, they represent neither my opinions nor the opinions of my employers. Any errors you can assume to be mine and not the speaker’s. I’m happy to correct any errors you may spot – just let me know!

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