• Saturday July 5th 2008
• Do you want fries with that project?

Skip to Content

gemstone

resources:	Home Mailing List Installation Usage Developer Overview (Beta) Developer Case Study (Beta) Source Code Members Bugs Screenshots

Usage

• Overview
  
• Main Menu
• Service Registry
• Filesystem Viewer
• Security
• Service Content Area
• Settings
• Updates
  
• Garnet
  
• Apbs Example

Overview

The Gemstone framework is comprised of four main parts: the main menu and toolbar (on top), a service registry panel (left),
a filesystem view (right), and the main content area (center)

Main Menu And Login Toolbar

Service registry

The service registry consumes an RDF defined list of available application services for Gemstone to use.
By default, a locally stored registry is shown.  Add a new registry by typing in the address followed by clicking "Enter" or the "Go" button. To change registries, click the down arrow next to the "Go" button to bring up a menu of choices. To remove, change to the registry you wish to delete then click the down arrow and select "Remove Current Registry".

• The address of the currently selected registry is displayed above the  "Name" column
• To close the panel click the "X"-like button in the top right corner
• Clicking on the column picker   and selected "URL" will show the location of each service
• To resize the panel, hover your mouse over border until arrows appear, then click and drag to size
• Double click on a service name or choose "Open" on the context menu to open an application service into the content panel

Filesystem viewer

Support for basic filesystem browsing is provided with this utility.  

• The location of the currently selected root directory is displayed above the  "local" column
• To close the panel click the close button in the top right corner
• To change the root directory, double click anywhere around where it says "Filesystem"
• To resize the panel, hover your mouse over border until arrows appear, then click and drag to size
• Double clicking on a file is the same as selecting "Open" in the context menu 

   

Filesystem context menu items

Option:	Action:
Open	Performs the equivalent of opening the file in a typical web browser
Edit	Opens the file in a simple text editor
View Source	Opens the file in a read-only mode enhanced with find, highlight, and print capability
Open With...	Opens the selected file with either a simple flash molecule viewer (small pdb only) ,  QMView (Mac/Linux only) or Garnet. QMView must already be installed.
Refresh Filesystem	Manually refresh the filesystem panel to account for recent changes
Rename	Rename a single file
Copy	Copies the file's path to the clipboard (full copy support pending)
Delete	Removes a single file from the system. A directory can be removed only if it is empty. Deletions bypass your Recycle/Trash bin and are removed immediately

Security

    Before using web services that require https access with mutual authentication, you must first login using your GAMA account information. Gemstone retrieves your certificate which, if it is allowable by the service host, can be used to run jobs securely.

• To choose a GAMA server to use, select Options-->Settings or Gemstone-->Preferences on a mac. Entry, selection and removal is the same as with the service registry
• After clicking the "Login" button  you will be prompted to enter or create a "Master Password"  for the "Software Security Device", this separate password is needed to maintain the integrity of your certificate's private key and only needs to be entered once per login session
• After a final prompt for your certificate's password, you should see a popup with a message saying that your certificate is loaded.
• If there is any error during the process double check that your username and password are correct and valid for the chosen GAMA server

Service content area

    This area displays the interface for a service. Multiple services can be open at the same time including multiple instances of the
same service.  To close a service, click the "X" like button when the service you want to close is highlighted.

Settings

To run Gemstone some features of Gemstone successfully some additional user input is necessary.

• Temporary Directory - a location to deposit temporary files.  Defaults to /tmp/ on Linux and Mac,  <root>\Documents and Settings\<user>\Local Settings\Temp on Windows
• QMView Executable - (Linux/Mac only) location of QMView.new executable
• Babel Executable - (Linux/Mac/Windows) location of babel (or obabel.exe for windows)

Updates

    Gemstone will check to see if there are updates approximately once a day or you can check manually File-->Check for Updates.  Updates download silently in the background and you will be alerted to restart when finished. Running jobs and changed settings will not be disturbed. 

Garnet

Garnet is a lightweight Java-based molecular viewer bundled with Gemstone. To view a molecule (for instance a Gemstone XML molecule or pdb), right click it in the filesystem and choose Open With-->Garnet To use Garnet on a Linux system the Java plugin (from JRE 1.4.2 or above) must first be installed.

• In a Terminal, cd to Gemstone/xulrunner/plugins
• For Java 1.5.0 issue the command "ln -s /your_path_here/java/j2re1.5.0/plugin/i386/ns7/libjavaplugin_oji.so"
• For Java 1.4.2 issue the command "ln -s /your_path_here/java/j2re1.4.2/plugin/i386/ns610-gcc32/libjavaplugin_oji.so"

Running the APBS Web Service

To begin, open Apbs from the service registry.  The interface presented does not require that APBS be installed on your system to run.  Instead,  the parameters
and molecule input you specify are used to invoke the NBCR APBS  web service on a remote cluster. While most of APBS's command line functionality is captured by the web service and its interface used in Gemstone, there may be some features absent. For more information please visit

http://nbcr.net/services/apbs-ws.html for NBCR APBS web service documentation

http://agave.wustl.edu/apbs/doc/html/user-guide/index.html for the APBS manual

http://agave.wustl.edu/apbs/ for the APBS homepage

The APBS interface has five tab-panels each corresponding to an input or output category.
The service accepts standard PQR files as well as Gemstone XML files containing molecular information as well as APBS input parameters.

• To see the APBS input abbreviation of an item (eg bcfl for "Boundary Conditions" ) hover your mouse over the label

Calculation:

• Selecting "Binding Energy" for "Calculation Type" requires three molecules for input

• To choose molecules for an APBS run click "Select Molecule" to choose with a standard file-browser dialog or drag the PQR file from the filesystem viewer over to the molecule area

Grid:

• Molecules selected in the Calculation tab automatically appear in both "Center Grid On Molecule" menus.  In order to use this option check the box and choose a molecule in the menu

Physics:

• Ions are added by clicking the "Add Ion" button

File I/O

Choose they types of output you want to receive from APBS

Output

This panel is empty until a run has started 

Running a Job

There is one final option to set before starting your job: whether to run the job in non-blocking mode or not. For all jobs other than the 
shortest (5 minutes or less) you should leave "Non-Blocking" checked.  This is because non-blocking mode returns a unique job id for
each run that allows Gemstone to query the running job for status updates and gives the option to monitor ongoing progress in the form 
of console output produced by APBS.  In blocking mode Gemstone idles until the web service responds with output or an error. 

The following sequence represents what will happen during a normal non-blocking run and some things to watch out for

What you do	What Gemstone does	Pitfalls	Errors	Solution
Click "Run APBS"	Converts your input options and molecules into XML format	If your molecules are large this may take a moment. If a message saying "...Do you want to cancel this script?" click "Cancel" NOT Ok.	"Error: ......" You may have forgotten to enter some parameters	Fill in all parameters
	Invokes the web service.  "Run" is disabled and "Abort" is enabled	Do not abort the job at this stage.	The web service may throw a SOAPFault if your input cannot be passed to APBS (eg you tried pdb rather than pqr,  gave a pdime of 9000 processors)*	Change the specified parameters
	Panel focus switches from "Calculation" to "Output" and a new "Base URL" button appears.  The main  Apbs tab changes to include a job id. Your job has now started to run remotely.
Click on "Base URL"	Opens a browser window displaying an index page containing all input and output of the running APBS job
Click  "Abort Run"	Sends a message to the web service telling it to kill the running job
	"Message" displays "FAILED" and a popop alerts "Job Aborted"
Continuing as usual....	The web service is queried once a minute and updates the "Message" display accordingly.	If this state continues indefinitely check apbs.out and stderr to make sure nothing has gone wrong*.
	When the job completes, panel focus again shifts to "Output".  Input and Output are presented in rows with "Open" and "Save" buttons for each file		If there are no rows in the "Molecule Output" section check the output on the "Base URL" page*

*There may be a situation in which APBS, SGE or Axis fails in such a way as to prevent the web service from returning with a proper error condition

Output

All input and output of your job is available to view and download. "Open..." opens a browser window to view the data, "Save..." opens a file-browser
to save the item. You can also drag the "Save" button over to the filesystem viewer

NOTES TO OWNERS:

1. Look here for instructions on how to make your project releases publicly available, and our policy for posting releases to be picked up by the download mirrors.
2. To find out how to get your extension listed on update.mozilla.org read the instructions posted here:
   https://addons.update.mozilla.org/about/