Bug fixes in SimpleModel, SimpleReaction, Subsystem. New features added to Subsystems. #9
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…mode does not work
…anges to others. Also not working for species not in list of shared resources. Also setting size using system size in volume mode amounts
…e, and connect all working. Need to fix the volume mode and make it consistent all over.
…PTG_transport graph generate for multiple inputs
… led to bugs which need to be fixed. simulatevariableinputs bioscrape method improved, along with many other changes
…rking yet in the new framework for combinations inside a System
…and it has been removed from the code. tutorial.py is working but combineSubsystem is not. minor fixes needed
Subsbml setup
… modes. Volume mode also works perfectly, virtual mode works too. combine does not depend on share now. All valid SBML models generated in SBML l3v2.
…rting to latest SBML level and version (l3v2). IPTG transport example working with this commit
…attribute was used which is obsolete in SBML L3v2
…t, SBML Model inside, and make all the basic settings using a standard set of preassigned values. An important bug fix in createSimpleReaction in SimpleModel class, to allow for reactions which create or degrade a particular species into nothing (when product/reactant missing).
…th numbers in species names/ids
…th numbers in species names/ids (#3)
…iableInputs method modified and multiple bugs fixed. Accepts lists for compartments, plotting options in a single plot or a matrix using subplots (not yet working).
…heir concentrations. fixed minor bug in simulate variable inputs for compartment species in else loop set to species id, replaced now with blank string, so optional keywords arguments should work. also added **kwargs to this function argument
…in SimpleModel class
* modified SimpleReaction.py to fix bug for creating simple reaction with numbers in species names/ids * bug in create unit definition in simple model fixed * added gitignore to remove temp files to go to github repo, bug fixes in SimpleModel class
* modified SimpleReaction.py to fix bug for creating simple reaction with numbers in species names/ids * modified iptg transport circuit. Improved membrane model. simulateVariableInputs method modified and multiple bugs fixed. Accepts lists for compartments, plotting options in a single plot or a matrix using subplots (not yet working). * added varying alhl and varying gfp dna plots to guide experiment on their concentrations. fixed minor bug in simulate variable inputs for compartment species in else loop set to species id, replaced now with blank string, so optional keywords arguments should work. also added **kwargs to this function argument * iptg transport working with modifications to variable input simulations
…te unit tests so that further code developments have backward compatibility. IPTG transport example renamed to main_IPTG_transport for better visibility.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Bug fixes to 0.1 version.