<> = The ScrumPy Modelling Environment = == Running ScrumPy == Once [[ScrumPy/Installation|installed]], ScrumPy is simply run from your favourite shell: {{{#!highlight bash mark@Mark:~/model/work/Tomato$ ScrumPy }}} This will result in the appearance of this window. {{attachment:ScreenShot1.png}} The first text, in blue, is a greeting message from ScrumPy, followed by version information, the text in black serves a similar purpose giving information about the version of python you are using. Details will, of course vary between installations. The cursor ({{{>>>}}}) indicates that {{{ScrumPy}}} is waiting for you type something.The menu items will be described later. You will also see a certain ammount of diagnostic text appear in your terminal, something like this: {{{#!highlight bash StartScrumPy !!! /usr/lib/python2.6/site-packages /usr/lib/python2.6/site-packages/ScrumPy/tkGUI/StartScrumPy.py importing parser MySQLdb module could not be loaded No module named MySQLdb importing parser }}} These are not error messages, but internal diagnostic information. In particular, the {{{MySQLdb}}} message refers to an unused feature in a third party package, ignore it, as long as the window above appeared all is well. If libsbml cannot be found the following diagnostic will be seen {{{#!highlight bash !! !! couldn't import libsbml !! sbml not available !! }}} Under these circumstances, {{{ScrumPy}}} remains entirely functional, except yuo will not be able to read or write sbml files. In use {{{ScrumPy}}} will generate quite a lot of output on the terminal, and it is generally safe to ignore it. This output can be surpressed by redirecting stdout and stderr, e.g. {{{#!highlight bash mark@Mark:~/model/work/Tomato$ ScrumPy 2&>/dev/null }}} If you wish to keep the output, simply redirect to a file: {{{#!highlight bash mark@Mark:~/model/work/Tomato$ ScrumPy 2&>MyLogFile.txt }}} There occaissions when output on the terminal is useful in diagnosing specific problems in models, and these will be mentioned in the relevant parts of the documentation. == Loading a Model == A model is brought into existence by loading it into the modelling environment: {{{#!highlight python >>> m = ScrumPy.Model("FileName") }}} Note that {{{"FileName"}}} must be quoted. If {{{FileName}}} exists, {{{ScrumPy}}} will read it and present you with its' contents in an editor window. If {{{FileName}}} does not exist, {{{ScrumPy}}} will create a new, empty file, and open an editor window for you. Finally, if you do not specify {{{FileName}}} at all you will be presented with a file selection dialogue. If you have [[ScrumPy/Instalation#SBML|libsbml]] installed the file is in sbml format, it will be converted {{{ScrumPy}}} format, saved with a".spy" extension and it is then loaded as a normal {{{ScrumPy}}} file.