The client of Monod Desktop has been certified on Mac OS X, Linux and Windows 2000.  You can refer to the technical notes for more details.

• Just launch BioSPICE Dashboard.
• Follow the BioSPICE Dashboard instructions to add Monod Desktop to the workflow editor.
• At the time of this write-up, the output of a tool running within BioSPICE Dashboard needs to be consumed (i.e., need to be specified as an input to another tool).  Just wire an appropriate tool (e.g., View Data Tool) to Monod Desktop to accept the output of Monod Desktop.
• Start the workflow

• A String object for the web browser path (e.g., /usr/bin/mozilla).  Note that Monod Desktop will use this web browser path only if it is run within the Dashboard.
• A SBML2 object
• A  Biodata object
  

• A Biodata object
  

• Just launch BioSPICE Dashboard.
• Follow the BioSPICE Dashboard instructions to add Monod Desktop to the workflow editor.
• At the time of this write-up, the output of a tool running within BioSPICE Dashboard needs to be consumed (i.e., need to be specified as an input to another tool).  Just wire an appropriate tool (e.g., View Data Tool) to Monod Desktop to accept the output of Monod Desktop.
• Add an analyzer or a source document to the workflow editor and wire it to Monod Desktop.
• Start the workflow

• Besides importing the SBML model as a Monod model, you can save the raw SBML as a Monod note.
• FYI: Currently, the Monod database schema does not fully support all the properties found in SBML level2 (e.g., listOfRules, listOfEvents, functionDefinitions, kineticLaw), the unsupported SBML properties will not be mapped to the Monod model during the import process.  You may find it useful to "import SBML file/object as a Monod model with note annotation".

• If your Monod server is not in the server list of the Monod login dialog, you can input it manually.

• Part of the standard Monod records (standardrecords.postrgres.sql bundled in the Monod tar file)  include records to create users in the database.  You can use the guest login for a quick tour of Monod.  Note that the permission access of a guest user is generally limited to the more common information.
  
• Login to web Monod to change the password of the administrator.
• Login to web Monod as the administrator and add new users.

• Use the main menu and select the appropriate menu item to create a new species or process.  For the time being, web Monod will be launched for such data creation.  In a future release later release, you'll be able to create species, process and category within Monod Desktop.

• Use the main menu and select the appropriate menu item to administer your permission preferences.  For the time being, web Monod will be launched for such task.   In a future release later release, you'll be able to administer the user preferences within Monod Desktop.

• If I am interested in looking up information about species "Ste5", launch Monod Desktop, go to the Species page of Data Miner, enter ste5 and press the submit button.
  
• Select ste5 and go to the Note Annotation page to view what the available notes I'm allowed to view.

• Double click (or right click to display the contextual popup-menu) on the note summary to view the note details.

• Double click on the Note Text tab to view the note text in expanded view (double click on the Note Text tab to revert to the original size).

•  Now that I learn from the note annotation that Ste5 is homologous to Far1.  I want to link this note to Far1 as well.  This can be done by using the Far1's contextual popup-menu to request "annotate with note".

•  Locate the note that I want to use and drag-and-drop to the bottom half of the "Annotating with Note" page.
• FYI (not shown): I can drag-and-drop more Monod data entities to the "Annotating with Note" page if I want to link the same note to all these data entities.

• Press the submit button on the "Annotating with Note" page to add the link.  Monod Desktop will notify me whether my annotation request is processed successfully.

Use Case-2: What if I want to use the interesting information I find in Monod to look up additional information in public web site?

• I want to find out which other yeast proteins are homologs of Ste5.  I use Ste5's contextual popup-menu to add Ste5 to the Workspace Navigator.

• I select Ste5 in the Workspace Navigator and select "External Link" to go to "Entrez Protein" to get the FASTA protein sequence for a BLASTP run.

• I can create a note annotation to attach to Ste5 and attach my BLAST result file to the note.  By choosing "Attach file from local file system", a dialog will be displayed for me to choose which file I want to attach to the note.
  
• FYI (not shown): To view the file details will launch web Monod.  The first time web Monod is launched from Monod Desktop, I'll need to login to web Monod.

• I can view the details of the attach file by going to the note details page, click on the "File Attachment" tab and double-clicking on the file of interest or right-clicking on the file of interest to bring up the contextual popup-menu.

• I can add an article to Monod by selecting "Create -> New Literature" from the main menu. 
  
• If I know the pubmed Id, I can use the Pubmed page to create a literature entry in Monod.

• If I know the citation information, I can use the Journal page to create a literature entry in Monod.

• I can use the Literature Data Miner to search on literature and use the contextual pop-up menu for navigation.

• FYI (not shown): I can also use literature as an annotation to other Monod data entities.