BioPAX at Virtual Cell: News/Updates
Lots of updates have happened since, which are unfortunately not tracked
August 14, 2008
Uploaded the newest Sybil JAR files and changed some names:
So sybil.jar used to be the file that needs the other JARs to run and is now the JAR that can run alone.
- - Renamed the JAR that needs all the other JARs, from sybil.jar to sybilCore.jar
- - Renamed the JAR that can run alone, from sybilAll.jar to sybil.jar
- - Renamed the folder in the resource folder that contains the JARs, from oldjars to sybiljars
August 14, 2008
- - Sometimes species references were mentioned multiple time in reactions, now fixed.
- - Compartment table now has explicit "none" option for external (useful to correct a wrongly entered choice)
- - Generation of SBML IDs has weaknesses: Names are unconveniently long, and cause occasionally problems with VCell if longer than 64 characters. Also, Sybil's id generation depends on Jena's way of splitting of URIs into namespace and local name, which is not based on any standard and might not always be well behaved. Also, if two different URIs end up with the same local name, this causes problems (though this should be extremely rare). There should be generation of short labels and a stronger scheme for generating IDs.
- - Sybil has not really been tested against files other than from Rectome.
August 1, 2008
RELEASED as a downloadable JAR file
July 14, 2008
Sybil now uses BioPAX properties SHORT-NAME, NAME and SYNONYMS, before falling back to taking the local part of the URI.
July 10, 2008
Sybil now allows input in process table. Select a table cell and a combo box will appear. Options include:
- - Select [new], and a dialog will appear to enter the URI of a new node (should be a valid URI - something like "w/s1", where "w/" is the namespace and "s1" is the local name, is fine). Sybil tries to give you an existing URI as a sample.
- - Select [?] to denote that node is unspecified
- - You can always go back to nodes entered previously (e.g. after you entered more than one node in the same cell).
July 3, 2008
New Sybil features:
- - There now is a locking mechanism allowing resources (e.g. data) to be locked by a task to prevent corruption by multiple tasks manipulating it at the same time, for example, if a user presses a button twice. Buttons which start tasks can now be disabled if the needed resources are locked. Example: The classes panel's "next"
- - All tasks now register with a central task list when they start and unregister when they finish. This allows also to set the mouse cursor to "busy" when any task is running and back when no task is running.
- - The layout of the port panel is reworked, making it cleaner and more robust under resizing.
June 26, 2008
The process table, a table containing information about processes and participants is done.
Now, one can see the effect of different assumptions:
- - Open a data file
- - Select tab "port"
- - On panel "port", select tab "input"
- - Press button "update". The name of the data file should now appear under "Data files"
- - Press button "next". This should bring you to the next tab - "classes". This takes time depending on size of input file.
- - Choose assumptions about which class is united, then press "next". This again may take time. Then, it should take you to next panel, "stuff", where you should see a table. The table has two columns "stuff" and "entity". Depending on which classes are chosen united, the cells of the stuff column should be empty (if not united) or be a copy of the entity (if united).