CTii

CTii: Cell Tomography Intuitive Interface    A Java GUI application facilitating the tasks of scientists performing the Omnimatch 3D template matching experimentations.

Acknowledgment

This work was carried out in the context of the BiG Grid project, with financial support from the Netherlands Organization for Scientific Research (NWO). The work, described in this document, is developed in collaboration with 3DEM groups at the university of Utrecht (UU) and Leiden University Medical Center (LUMC).

1- Introduction

Cell Tomography Intuitive Interface (CTII) is a Java GUI application which aims at facilitating the tasks of scientists performing the omnimatch 3D template matching experimentations [lebbink 2007 ]. In addition to the main processing component, CTII also provide two other components for pre/post processing of the input/output electro microscopy files. Within the current version of the document, we only focus on the main processing component (3D template matching).

From the usage point of view, CTII is very sensitive, since it involves the set-up of a number of sensible parameters whose adjustments require appropriate expertise and skill in the application domain.

2- Installation

a- Requirements

CTII is an interface to assist the scientist in setting the proper environment for running and monitoring 3D template matching experiments. It also helps in organizing and classifying the output results. In order to properly, use the CTII interface, the following pre-requirements are needed:

• Omnimatch software must be properly installed and functional. From now on, we will refer to $omnimatch_home as the path to omnimatch software. (Omnimatch software can be downloaded from: ….).
• In order to use the workload management system (Torque), the user must provide a job submission script which, sets up the appropriate environment to run omnimatch and launches the jobs. CTII expects a script file named psb_script_header.sh located under $omnimatch_home. An example that script is given in Annex 1.

b- Installation

CTII installer is created using winzip/winrar and can be downloaded from: ….

To install CTII, you simply need to decompress the installation package 'CTII.rar'. After installation is complete, it will create a new CTII directory with the following structure and items:

• dist: a subdirectory containing the JAR files needed by CTII (CTII.jar)
• dist/lib: a subdirectory containing the different third party libraries used by CTII (jgraph, etc.)
• ctii.bat/ctii.sh: a script to launch CTII Interface for Windows and Unix respectively
• config.xml: descriptions file containing the graphical representation and the description of the omnimatch workflow experiment. This file is only editable through the CTII graphical user interface.
• settings.properties: a property file used to configure CTII. It specifies the remote location on which omnimatch will run and sets up the proper environment to use. This file is only editable through the CTII graphical user interface.

c- Running CTII

You can run CTII by issuing the following command:

• Java -jar CTTI.jar Or
• CTTI.bat on windows
• CTII.sh on UNIX

Figure 1 illustrates the CTII main User Interface, which is composed of: 1) a top-toolbar, 2) a three-tab panel with a central/body area, and 3) a bottom-toolbar.

3-Configuration

Most of the CTII configuration is done in the property file 'settings.properties'. This file is read by CTII at startup. It presents the setting information in a graphical interface to be updated and confirmed by the user. This interface is shown in Figure 2. Essentially; the user needs to feed CTII with connection information and working environment on the remote host, where omnimatch software is installed (cluster or grid interface).

• Host Name: specifies the host name of the machine where to launch omnimatch (e.g. lisa.sara.nl).
• User Name: specifies an existing user on the host machine.
• Password: specifies the user password on the host machine.
• Input directory: specifies where omnimatch input files are located.
• Output directory: specifies the base directory where to create output files along with a summary file for each run.
• Job script: specifies the job submission script which, sets up the appropriate environment to run omnimatch and launches the jobs.

4- Usage

As illustrated in figures 1&2, CTII GUI is composed of a top-toolbar, a three-tab panel with a central body, and a bottom-toolbar.