ACEDB HOW-TO

Creating a new object

  1. Edit --> Add/Alias/Rename
  2. Click on the name of the class for the new object
  3. Type in a name for the object in the yellow Name: box

    4.               OR
    Double-click on an empty object name (normal text, rather than boldface)
  4. The new object will appear in a separate window.
Note: objects can be implicitly created within other objects. See "Adding or changing information in an object".

Adding or changing information in an object

  1. Open the object you wish to change
  2. Hold down the right mouse button and choose 'Update'
  3. To create a new data item
    1. Click once on the object (not the tag) you wish to enter
      1. To create a new object
        1. type in the name of the object and press enter
        2. Note: this generates an empty object. You still need to create this object (see above) if you want to add information to that object. Empty objects show up as normal text, rather than boldface.
      2. To make a link to an existing object either
        1. double-click on the name of an object in another window
        2. Press TAB key and double click on an object in the Keyset window
  4. To delete an item
    1. Click once on the item you wish to delete
    2. Hold down the right mouse button and choose 'delete'
  5. To get out of a yellow box without changing the item, hold down the right mouse button and choose "Cancel"
  6. When finished, hold down the right mouse button and choose "Save"

Re-naming an object

  1. Edit --> Add/Alias/Rename
  2. Click on "Pick object"
  3. Double click on the name of the object, either in the upper-left hand corner of the object itself, or on a boldface link to the object in any other object. The name will appear in the yellow Name: box in the Add/Delete/Rename window
  4. Click on "Rename/fuse"
  5. Type in the new name in the yellow "Give new name:" box
  6. Click OK
  7. Note: The change will not appear in existing objects until you close them and re-open them.

Deleting an object

  1. Edit --> Add/Alias/Rename
  2. Click on "Pick object"
  3. Double click on the name of the object, either in the upper-left hand corner of the object itself, or on a boldface link to the object in any other object. The name will appear in the yellow Name: box in the Add/Delete/Rename window
  4. Click on "Delete"

    5. Note: The change will not appear in existing objects until you close them and re-open them.

Re-ordering items in an object

One shortcomming of ACeDB is that there is no simple way to change the order of items added to an object. Plan carefully before you enter items. If you have to change the order, rename the existing pathway object to some temporary name, can create a new pathway object with the original pathway name. Then copy the enzymes into the new object in the correct order.
 

Changing a model

Models can't be changed from within ACeDB. They must be changed by editing the file wspec/models.wrm. Do the following:
  1. Make a backup copy of wspec/models.wrm
  2. Change a model in wspec/models.wrm. It is usually best to change only one model at a time if at all possible, to avoid confusion.
  3. In ACeDB, gain write access (Edit --> Gain write access).
  4. Read in the new models.wrm file (Edit --> Read models). If the read is successful, no messages will be printed. If there are errors, a message window will pop up, telling the line(s) in the file that are incompatible with the existing models, or have incorrect syntax.
  5. Once you have successfully read in your new models, check the model in ACeDB to make sure it looks the way you want it to look In the main ACeDB window, click on the Models class, and a new keyset window will pop up. Double-click on the model you wish to see.

Dumping a database to a .ace flatfile

  1. Choose Admin --> Dump All
  2. In the file chooser, move to the directory where you wish the file to be written (Remember, clicking on ".." moves you up one directory).
  3. Click 'OK'. The Dump window will pop up.
  4. Click 'Yes' at the 'Should I proceed?" prompt.
  5. Hold down the right button and choose "Quit" to quit the Dump window.
  6. Your file will now be written with a name such as "dump_2000-03-28_A.1.ace".
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