Pseudocode examples for Cytoscape Apps

[Hikmet Emre Kaya]

Hello everyone,

I am writing up my thesis (fingers crossed) and struggling to write pseudocode for my Cytoscape App (I might be overthinking about this). But it would make me a lot more comfortable if I see examples of pseudocodes in thesis or papers. I am looking up on Google Scholar but it would be great if you or someone you know has a published work.

Otherwise, I am also open to recommendations. I see LateX being used a lot.

Thanks in advance,

Warm regards,

Emre

[Christopher Churas]

Hi,

Unfortunately I can't think of a cytoscape paper with pseudocode in it, but you could look at some of the popular apps in the AppStore and look

at their publications. https://apps.cytoscape.org 

Another approach is just to search the literature for an algorithm similar to yours (or any algorithm) and oftentimes those

papers have pseudocode. 

For example, the node2vec paper has pseudocode: https://pmc.ncbi.nlm.nih.gov/articles/PMC5108654/

chris

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[Alex Pico]

Here’s a useful collection of Cytoscape App articles and also a recommended place to publish them: https://f1000research.com/gateways/cytoscapeapps

- Alex

[Gary Bader]

Hi Emre - here’s one:

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-4-2

Gary