ICYMI, iGEM organization's overall goal and the projects that are carried out as part of the annual competitions are highly related to this topic: http://igem.org/Main_Page
In general, it is hard to find a biological system that will give you a reliable and generic compiler framework (a la LVM) unless you better scope your problem and/or goal; but there are small problems for which we have nice implementations/solutions (a la software design patterns). The challenging part is to mix and match parts that will help you solve specific problems.
So the answer really depends on what you want to do with such a system and what parts of the already available solutions that you don't like.
There are many suggestions here, but make sure to check Cancer Commons community out as they are trying to help patients and their close relatives for exactly this type of queries: https://www.cancercommons.org/home
I know, right? I was really happy when I learned that this branch of the CS is also referred to as evolutionary, because I was inspired by the evFold approach, which is related to evolution in multiple organisms. This is a bit confusing for people coming from the biological science domain, but also nice that we share some terminology between two fields ;)
cool! Thanks for sharing the link to your project. I am not really a Ruby expert, so wasn't able to figure out how you calculate the couplings. I will be more than happy to compare the results across these two tools.
The PDFs that come out of igraph layout are not that pretty. The screenshots I used on the blog post are generated with Cytoscape 3.1.1, which gives better layout and better styling options. For Angular.js, I went with "partialCorrelations_0.3.sif".
that is partially true: single file apps will never have couplings in this manner. One extension to this project would be to find couplings between particular regions of the file and then even single file apps will start falling down. I think it is not true that if you cannot find any coupling using this tool, your software is well-designed; it would just mean this tool is not smart enough to capture those bad designs.
Couplings between different regions of the files, however, are relatively harder to find and requires some more thinking in terms of implementation.
right now, it is not really tied to GitHub; but only expects you to give a git repository URL. Coupling it GitHub will allow more information on the system, for example knowledge on commits that resolve issues on the tracker. That is a long-term goal of this project.
Thanks for the pointer; didn't know about that plug-in. As a long term Intellij Idea user, implementing this as a plug-in to Intellij is one of the things I would like to do in the short term. Would be really great to make the tool let you know about possible coupling as you work on the project.
Let me know if you can get your hands on a list of related plug-ins, I am really curios to see them in action.
agreed; those kind of linkages are not necessarily due to bad design but are, on the contrary, intrinsic to the design of the language you code in. Ideally I should consider these kind of things and exclude such pairs (X.cpp <-> X.h) from the final results, but this is still pretty much work in progress.
In general, it is hard to find a biological system that will give you a reliable and generic compiler framework (a la LVM) unless you better scope your problem and/or goal; but there are small problems for which we have nice implementations/solutions (a la software design patterns). The challenging part is to mix and match parts that will help you solve specific problems.
So the answer really depends on what you want to do with such a system and what parts of the already available solutions that you don't like.