Reserve Words in SyMBA Templates

In SyMBA templates, there are many reserved words to allow the web interface to interpret your intentions correctly. To ensure that they do not conflict with any real words you might wish to use, they are all prefixed with net.sourceforge.symba.keywords. . Below is a list of reserve words that may be used in the template, and a short definition of their meaning. In the following sections, which of these reserved words are allowed in the different sections are defined.

  • net.sourceforge.symba.keywords.noDatafile : used to let the web interface know that this application of a protocol has inputs and/or outputs that do not contain data files (only materials).

  • net.sourceforge.symba.keywords.dummy : used to show that the XML element in the template isn't itself the one to copy into the users's experiment, but is instead a dummy object that is meant to be copied into a real object before saving.

Create Your Input XML

Describe Your Material

Inputs to the assays that create your data files are generally FuGE Materials.

Name Your Material

You should name your material using a number of reserve words to modify the behaviour of the dummy Material in the web interface. Any Material you put in your SyMBA template will remain untouched by users: instead, a copy is made of the Material, and the appropriate user-defined parameters are added before it gets associated with a particular user's experiment.

Reserve Words for Material

Below is an example name attribute for a GenericMaterial in a SyMBA Template. A full explanation of how this name was built follows.

 Material Characteristics net.sourceforge.symba.keywords.dummy Noname Notreatment for Recording Protocol (Component of Carmen Electrophysiology Investigation)

  • "Material Characteristics" : Anything before the "Dummy" Keyword will be used to title the fieldset that the material metadata is grouped into in the web interface.

  • "net.sourceforge.symba.keywords.dummy" : This keyword MUST be used in the Material name, as it tells SyMBA that this is not a real Material. It is also a keyword that is used in the Search methods within SyMBA so that Dummy Materials won't be shown in search results.

  • "Noname" : This keyword ensures that the user isn't asked for a general name for their Material. This value would otherwise go into the "name" attribute of the user's GenericMaterial element. If you want to control the name of the Material (e.g. through an ontology term), you should use this keyword.

  • "Notreatment" : This keyword will disable SyMBA's default display of a text box that would allow users to enter free text about the treatments of their Material. You may wish to disable this if you have specific parameters describing your treatments.

  • "for Recording Protocol (Component of Carmen Electrophysiology Investigation)" : This section is REQUIRED, and must contain the full name, including the "(Component of...") section, of the Protocol that this Material will be associated with as an input material.

Describe the Parameters of the Protocol Application (PA)

Name Your PA

You should name your material using a number of reserve words to modify the behaviour of the dummy Material in the web interface. Any Material you put in your SyMBA template will remain untouched by users: instead, a copy is made of the Material, and the appropriate user-defined parameters are added before it gets associated with a particular user's experiment.

Reserve Words for PA

Below is an example name attribute for a GenericProtocolApplication in a SyMBA Template. A full explanation of how this name was built follows.

 Parameters Associated with Creating the Data File Dummy for Real-Time PCR Protocol (Component of MiMage Investigation)

  • "Parameters Associated with Creating the Data File" : Not used by the web interface, but useful for the template developer as a comment.

  • "Dummy" : This keyword MUST be used in the PA name, as it tells SyMBA that this is not a real Material. It is also a keyword that is used in the Search methods within SyMBA so that Dummy Materials won't be shown in search results.

  • "for Real-Time PCR Protocol (Component of MiMage Investigation)" : This section is REQUIRED, and must contain the word "for", the full name, including the "(Component of...") section, of the Protocol that this PA will be associated with.