Interactive predictive toxicology with Bioclipse and OpenTox - Open Source Software in Life Science Research - page 29

second Bioclipse paper describing the scriptability [19], a recently
published description of the integration of these tools [10], and the paper
describing the technologies used to glue together the components [20].
For the user of the platform it suffi ces to know that all functionality of
the Bioclipse-OpenTox interoperability is accessible both graphically
and by means of scripting. Table 2.1 shows an overview of all currently
available functionality.

Bioclipse-OpenTox functionality from the Graphical
User Interface is also available from the scripting
environment. Scriptable commands (left column) and
descriptions (right column) for various groups of
functionality are provided in this table

Table 2.1

Authentication
login(accountname, password) Authenticate the user with OpenSSO

and login on the OpenTox network.

logout() Logout from the OpenTox network.

getToken() Returns a security token when Bioclipse

is logged in on the OpenTox network.

Computation
calculateDescriptor(service,
descriptor, molecules)

Calculates a descriptor value for a set
of molecules.

calculateDescriptor(service,
descriptor, molecule)

Calculates a descriptor value for a
single molecule.

predictWithModel(service, model,
molecules)

Predicts modeled properties for the
given list of molecules.

￿ ￿ ￿ ￿ ￿

predictWithModel(service, model,
molecule)

Predicts modeled properties for the
given molecule.

Data exchange
createDataset(service) Creates a new data set on an OpenTox

server.

createDataset(service, molecules) Creates a new data set on an OpenTox

server and adds the given molecules.

createDataset(service, molecule) Creates a new data set on an OpenTox

server and adds a single molecule.

addMolecule(dataset, mol) Adds a molecule to an existing data

set.

( Continued )