Of course, you are allowed to publish any and all figures from our software. That’s the whole point. The software is meant to create figures and give you results that can be directly published so you can save time and be more productive.
We would kindly ask that you either maintain the "(c) Advaita Corporation 2022” in the figure, or mention in the caption something like "Figure obtained with iPathwayGuide (AdvaitaBio)”. Just mentioning the software in the Methods would not be sufficient since it would not be clear what figures where produced with it.
I would like to take this opportunity to remind you a couple of things:
we are here to help if you need any help with the Methods section or even if you have any questions from the reviewers about anything to do with our analysis.
many figures can be customized in terms of content, order, etc. Some figures can be customized for colors, as well. Please let us know if you want us to show you how to do this.
once the paper is published, if you let us know, we may be able to highlight your research in a short piece that we can send to our mailing list. That will greatly increase the visibility of your research.