Convert Tabs to Selection Box where appropriate eg in Plots
GUI improvements:
General
fill empty spaces in widgets (tables should fill space vertically)
DONE unify button layout of CCopasiWidget derivatives ("Commit", "Revert",...), buttons should be divided into left and right aligned group
move units behind input fields
DONE remove separator line between the buttons and the rest from all widgets
add "wait" cursors whereever needed
DONE loading a model when in the annotation (or notes tab) will display the annotation (or notes) of the loaded model after load -> reset tabs status when loading a model
hide all method parameters behind a button
boolean values in parameter widgets should be displayed as a checkbox
show parameters for subtasks with parameters of complex tasks
have separate sets of options for subtasks in complex tasks
add "copy" button to "new" and "delete" buttons where applicable, e.g. functions, species, reactions, (compartment)
DONE when clicking on a species or reaction in the tree view, COPASI scrolls to the top sometimes
Model Widget
DONE Change "Rate Law Interpreation" & combo box to checkbox "Apply Stochastic Correction to Kinetic Laws".
Compartment Widget: see general
DONE Change "Compartment Name" to "Name" and "Contained Metabolites" to "Metabolites"
"DONE Use Initial Expression" checkbox -> "Initial Expression" checkbox
DONE Disable "expression" Box instead of hiding it
DONE "Trigger Expression" Box and "expression" Box are too large
DONE Replace radio button by combo box -> "Calculate at assignment time" & "Calculate at trigger time"
DONE align the delay checkbox with the "expression" box
parameter overview:
DONE move title and save button above the table
DONE add value for global parameters
DONE (save data) exports the model values with "space" separators instead of "tab"
DONE (save data) exported parameters are not ordered as the GUI display
ODE display:
DONE white background
DONE PNG export with transparent background
Content MathML export
matrices widget:
diagram widget:
DONE table is too small
enable the disabled buttons
Task branch in tree should have a widget that displays common settings like "update model" or "activated"
Steady State Widget:
remove calculate Jacobian -> is done automatically anyway (only do this if the calculation of the Jacobian has no significant influence on calculation time)
Steady State Results:
Combine the Complete and Reduced Jacobian and make the selection between the two in the table
DONE Move "Stability" tab before "Jacobian"
Elementary Flux Mode Widget:
DONE remove separator line after title
allow people to "make species fixed"???
allow people to change the "reversibility" of reactions???
Elementary Flux Mode Result:
DONE "Filter Expression" -> "Search"
Search in tables as well -> move search field above tabs
Mass Conservation:
Mass Conservation Result:
Time Course:
DONE find a way to make it apparent that the feedback widgets are not editable, e.g. use label background, label foreground
do stability analysis for time course -> add checkbox
Time Course Result:
add Tab for Fluxes, Stability & Jacobian
MCA:
MCA Result:
DONE change the "Bars" button to a changing pictogram
add bitmap view option
tweak table layout
Lyapunov Exponents
Lyapunov Exponents Result
DONE layout needs tweaking
Time Scale Separation Analysis
Time Scale Separation Analysis Results
DONE replace radio buttons by the actual time and frame number values
DONE save data to file needs to be behind title
DONE rename button to "save data"
Parameter Scan
DONE decrease padding around items
DONE remove exclamation mark from "...Create!" button
Optimization
hide only a subset of the parameters
shorten parameter names & show complete name on tooltip
display parameters similar to Gepasi -> better use of space
layout of expression widget needs tweaking
don't use +-infinity as defaults, 10e-6 - 10e6
check for duplicate parameters
Optimization Result
DONE add range and original value to table
graphical display of result and minimum and maximum within a range bar
Parameter Estimation
see optimization
move the "Duplicate for each Experiment" button and change the text, e.g. "multiply" (Q: Where is the best place to move the button?)
Parameter Estimation Result
see optimization
Parameter Estimation Experimental Data
enforce uniform data structure per file -> get rid of some of the widgets
check for errors only on OK button press
Sensitivities
DONE rename "Function" and "Variable" to "Effect" and "Cause"
DONE add tooltip to explain "Effect" and "Cause"
add functionality to select set of objects for the "Effect" and the "Cause"
Sensitivities Results
see MCA result
Output Specifications
Plots table:
DONE activate all/deactivate all
Plots
DONE tabs need to go -> list view
DONE put type and log checkboxes into one line
Reports
DONE rename to report templates
associate files with reports in report definition???
DONE change "ReportDefinition" to "Template" and "Target" to "Filename"
Functions
DONE add copy functionality
DONE remove separator line above buttons
DONE fix button layout
annotation of predefined functions
paste Gepasi function documentation into notes field of functions
DONE make "General" lower case
DONE add windows menu to menubar to display all COPASI windows
make plot/report task aware, e.g. associate them with one or more taks so that they only get done for these tasks
tree:
add "hover" feature that displays the elements children
tables:
add "hover" for table cells and headers that display the full cell content
usability: new elements can not be entered continuously, user has to click last entry to enter next element
annotations:
DONE create links that lead to the database
Output assistant
DONE add more items
DONE only display relevant output items
remove the "empty" item
DONE remove exclamation mark from "Create!" button
DONE shorten names (e.g. remove "Plots of" from titles
