CSB-at-ZIB BioPARKIN issues

CSB-at-ZIB / BioPARKIN

Biology-related parameter estimation in large kinetic networks

http://www.zib.de/en/numerik/csb/software/bioparkin.html

GNU Lesser General Public License v3.0

4 stars 5 forks source link

issues

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Enable loading of SBML files/paths with umlauts, etc.

#77 moritzwade opened 12 years ago
1
Backend: Give constraints when computing sensitivities

#76 moritzwade closed 12 years ago
0
New feature: Handle constraints

#75 moritzwade closed 12 years ago
5
Display reaction graphically (in the entity detail view)

#74 moritzwade opened 12 years ago
0
Add UI (and logic) to manage simulation runs

#73 moritzwade opened 12 years ago
0
Repair the unit info on plot axes

#72 moritzwade opened 12 years ago
0
Add setting dialog with setting for global number display accuracy

#71 moritzwade opened 12 years ago
0
Try to build unit tests (general)

#70 moritzwade opened 12 years ago
0
Result data tables: Switch TableWidget to model-based approach

#69 moritzwade opened 12 years ago
0
Create dialog for importing SBML Shorthand

#68 moritzwade opened 12 years ago
0
Add Filter functionality to entity tree (need FilterModel + UI Widget)

#67 moritzwade opened 12 years ago
0
Remove dummy Species (and all references in Reactions!) when saving SBML file

#66 moritzwade opened 12 years ago
0
Think about implications of concentration vs. amount (of Species, etc.)

#65 moritzwade opened 12 years ago
0
Create "New York by Night" plot of sensitivities

#64 moritzwade closed 12 years ago
1
Visually highlight selected rows (Fit + sync to Param Sets/Parameters)

#63 moritzwade opened 12 years ago
0
Add console output during sensitivity calculation (if possible?)

#62 moritzwade opened 12 years ago
0
Add all needed features to create model from scratch

#61 moritzwade opened 12 years ago
0
Think about how to handle multiple experiment cases in the UI

#60 moritzwade opened 12 years ago
0
Add info to AssignmentRule (when to use, etc.)

#59 moritzwade opened 12 years ago
0
Add context info to Rate Rule (when to use)

#58 moritzwade opened 12 years ago
0
Think about and add "context info system"

#57 moritzwade opened 12 years ago
0
Add "first use" window with info + papers + licenses

#56 moritzwade opened 12 years ago
0
"Call to action" after starting the program

#55 moritzwade opened 12 years ago
0
Make compartments work with POEMcpp backend

#54 moritzwade opened 12 years ago
0
Create automated SBML tests (w.r.t. official Test Cases)

#53 moritzwade opened 12 years ago
0
Put updating results/plotting into Thread

#52 moritzwade opened 12 years ago
0
Add UI to see (and alter?) events

#51 moritzwade opened 12 years ago
0
Handle Algebraic Rules

#50 moritzwade opened 12 years ago
0
Handle SBML Functions in Backend

#49 moritzwade opened 12 years ago
0
Handle SBML Functions in GUI

#48 moritzwade opened 12 years ago
0
Add tooltip when new warnings arrive in WarningDialog

#47 moritzwade opened 12 years ago
0
Speed up plotting / updating of plot and table

#46 moritzwade opened 12 years ago
1
Clean up code

#45 moritzwade closed 12 years ago
0
Add more non-debugging log info

#44 moritzwade closed 12 years ago
0
Try to fix problems with BovCycle model

#43 moritzwade closed 12 years ago
1
Include Assigment Rules in ODE Viewer

#42 moritzwade closed 12 years ago
0
Plot subconditions over the course of (the user-defined) timepoints

#41 moritzwade opened 12 years ago
0
Investigate long loading time for gyncycle model

#40 moritzwade closed 12 years ago
0
Reuse backend objects (backend, Biosystem, Bioprocessor, etc.)

#39 moritzwade opened 12 years ago
0
Check __del__ error (swig?)

#38 moritzwade closed 12 years ago
0
Check for threshs when clicking sens. buttons

#37 moritzwade opened 12 years ago
0
Data Browser: Plot only selected columns

#36 moritzwade closed 12 years ago
0
Check: Sens. overview values (1e16?)

#35 moritzwade closed 12 years ago
1
Fix: Consecutive sens. overview plots/tables replace each other in results window

#34 moritzwade opened 12 years ago
0
Repair sync of source table checkboxes when clicking on de/select all buttons

#33 moritzwade closed 12 years ago
0
Simworbench: Mark parameters with assignm. rules in tabs: Sets/Sens/Fit

#32 moritzwade closed 12 years ago
0
Exclude parameters with assignm. rules from BioSystem

#31 moritzwade closed 12 years ago
0
Create automated SBML tests (wrt official Test Cases)

#30 moritzwade opened 12 years ago
0
Repair "Compute Sensitivities" menu entry

#29 moritzwade closed 12 years ago
0
Parameter Sets: Enable multi-selection

#28 moritzwade opened 12 years ago
0