Comments (3)
The addGeneData function comes from the method of Lee et al, (2012), and we decided to stick to the original implementation as closely as possible. Our goal was to reproduce their results.
The method doesn't account for operator precedence, so you're right, in case of ambiguity it could return an incorrect result.
However, the models we used all have explicit parenthesis around the operators, so that was not a problem for us.
I would not recommend applying this code to a model that does not have explicit operator precedence encoded with parenthesis.
Anyway, the best approach would be to deprecate the string-parsing approach and migrate to the latest sbml-fbc specification, which uses an xml-tree based representation for GPR associations.
from transcript2flux.
Hi Daniel,
Thanks for your answer. I guess you’re right and you should not change the sequence if so many people have used it this way already. I just stumbled upon it because I wanted to speed up the process with my own code. I’m also in contact with Brandon Barker, the one responsible at opencobra and sent him my updated code which runs faster but indeed with operate precedence. Let’s see what happens.. Anyway thanks.
Kind regards,
Frans
From: Daniel Machado [mailto:[email protected]]
Sent: Monday, February 8, 2016 7:04 PM
To: cdanielmachado/transcript2flux [email protected]
Cc: Kloet, Frans van der [email protected]
Subject: Re: [transcript2flux] This code generates ambiguous results (due to addGeneData) (#4)
The addGeneData function comes from the method of Lee et al, (2012), and we decided to stick to the original implementation as closely as possible. Our goal was to reproduce their results.
The method doesn't account for operator precedence, so you're right, in case of ambiguity it could return an incorrect result.
However, the models we used all have explicit parenthesis around the operators, so that was not a problem for us.
I would not recommend applying this code to a model that does not have explicit operator precedence encoded with parenthesis.
Anyway, the best approach would be to deprecate the string-parsing approach and migrate to the latest sbml-fbc specification, which uses an xml-tree based representation for GPR associations.
—
Reply to this email directly or view it on GitHubhttps://github.com//issues/4#issuecomment-181440670.
from transcript2flux.
No problem. You're welcome to contribute with a patch if you want to. I prefer not to change it myself because (1) I want to reproduce the original publication results and (2) I think it's better to encourage people to migrate to the new sbml-fbc standard to represent GPR associations.
Best regards,
Daniel
from transcript2flux.
Related Issues (3)
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from transcript2flux.