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Pathway editing with Node-RED

· pathways,programming,technology

Trying to find an appropriate tool for editing pathways has not been easy. Even the search terms have been hard to work out. You’ll be presented will specialised biology pathway editors when you search for ‘pathway’ editor and you can get some very pretty and complex graphs searching for ‘network’ editors, these do not let you add data to the nodes however.

I have found a couple of promising programs that we will have to look into more in the future (Dia and DotEditor). For now, however, we have settled on using Node-RED.

Node-RED was certainly not built for this use but we have been able to make a pathway editor out of it anyway. After ignoring that you can incorporate JavaScript functions and dumping all of the default nodes it feels like we’re maybe selling Node-RED a bit short. Nevertheless, the GUI was what we really needed.

And so, we set about making some new custom nodes for our purposes. We needed some nodes into which we could put the data that describes what is happening at each step of the pathway. The guides provided by Node-RED made it a simple task and I got on with designing the data forms. The further you delve into customising the nodes the trickier it gets to find help and I did hit my limit on trying to code multiple tables and nest them. I was probably being a bit ambitious there. In the end, it has been more efficient for us to extract a lot of this data out into spreadsheets anyway so I have been able to achieve everything we needed.

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I have been impressed by the amount of customisation that can be done in the creation of new nodes; everything can be changed dynamically if you want it to be. There are a couple of things we could have done with. The ability to add more than one line to the title displayed on the nodes and the ability to move where the inputs and outputs are on the node which would allow a clearer layout. I did end up creating this tangle of a wires due to the limitations.

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That said, for a tool that we are using outside its design, it has been very useful and easy to use. Our goal is to have an editor that allows anyone to jump on and start making pathways. Node-RED is very intuitive to use and helps us towards that aim.

By Harley Johnson