MarkUs - Revision history

Smith: /* Java Security */

2015-03-06T23:33:25Z

‎Java Security

Smith: /* Java Requirements for Viewing MarkUs Results */

2015-02-11T16:59:55Z

‎Java Requirements for Viewing MarkUs Results

Smith: /* Java Security */

2015-02-11T16:19:34Z

‎Java Security

Smith: /* Java JRE Version */

2015-02-11T16:17:42Z

‎Java JRE Version

Smith: /* Java JRE Version */

2015-02-11T16:16:58Z

‎Java JRE Version

Smith: /* Java Requirements for Viewing MarkUs Results */

2015-02-11T16:16:20Z

‎Java Requirements for Viewing MarkUs Results

Smith: /* Result Viewer */

2015-02-11T15:59:11Z

‎Result Viewer

Smith: /* Java Security */

2015-01-30T23:12:15Z

‎Java Security

Smith: /* Services (Grid) */

2015-01-30T23:03:21Z

‎Services (Grid)

Smith: /* Running MarkUs */

2015-01-30T23:03:04Z

‎Running MarkUs

← Older revision		Revision as of 23:33, 6 March 2015
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	*** https://honiglab.c2b2.columbia.edu.		*** https://honiglab.c2b2.columbia.edu.
	** Then click the "OK" button.		** Then click the "OK" button.
		+
		+
		+	[[Image:Java_Control_Panel.png]]
		+

@@ Line 18: / Line 18: @@
 The MarkUs results page includes the Astex molecular structure viewer, which is a Java applet.  Allowing this applet to run in a browser requires several steps. These are described below.
@@ Line 35: / Line 51: @@
 ** Then click the "OK" button.
 ====Browser Security====

@@ Line 21: / Line 21: @@
 ===Java Security===
-You will need to allow Java to run in the browser, and enable the MarkUs URLs.
+To use the Astex molecular structure viewer in the browser, you will need to allow Java to run in the browser, and enable the MarkUs URLs.
 On Windows, this can be done by going to Control Panel -> Java -> Security.

@@ Line 39: / Line 39: @@
 '''Windows'''---
-As of early 2015, On Windows, if you wish to use the Java JRE in Firefox or the default version of Chrome (both of which are 32-bit browsers), you must install a 32-bit version of the JRE.  This may also apply to other browsers.  You can have both 32 and 64 bit versions of Java installed on the same machine, if you have a 64-bit version of the operation system.
+As of early 2015, on Windows, if you wish to use the Java JRE in Firefox or the default version of Chrome (both of which are 32-bit browsers), you must install a 32-bit version of the JRE.  This may also apply to other browsers.  You can have both 32 and 64 bit versions of Java installed on the same machine, if you have a 64-bit version of the operation system.
 '''Mac OS X'''---

@@ Line 38: / Line 38: @@
 The molecular structure display works in any modern Java version, including Java 7 and Java 8 JREs.  You should install the latest version available.
-Windows---
+'''Windows'''---
 As of early 2015, On Windows, if you wish to use the Java JRE in Firefox or the default version of Chrome (both of which are 32-bit browsers), you must install a 32-bit version of the JRE.  This may also apply to other browsers.  You can have both 32 and 64 bit versions of Java installed on the same machine, if you have a 64-bit version of the operation system.
-Mac OS X---
+'''Mac OS X'''---
 On Mac OS X, the MarkUs applet should run in Firefox, Chrome or Safari.  See [https://www.java.com/en/download/help/sysreq.xml Java 7 System Requirements] for further information.

@@ Line 15: / Line 15: @@
 ==Java Requirements for Viewing MarkUs Results==
-Display of MarkUs results directly in geWorkbench requires a 32-bit JVM, such as included with certain installer versions of geWorkbench.  The built-in browser in geWorkbench will not run with a 64-bit JVM.  However, in those cases where the built-in browser cannot be used, geWorkbench will allow the user to open the MarkUs results in an external browser.  There are several steps described necessary for setting up Java security to allow the viewer applet to run in the browser.  These are described below.
+MarkUs results will be displayed either directly in geWorkbench, using a built-in browser, or in the case where a 64-bit Java Virtual Machine is in use (now the default on all platforms) the user can click a link to display the results page in an external web browser window.
 ===Java Security===
-On the Mac and Windows, you will need to allow Java to run in the browser, and enable the MarkUs URLs.
+You will need to allow Java to run in the browser, and enable the MarkUs URLs.
 On Windows, this can be done by going to Control Panel -> Java -> Security.
@@ Line 36: / Line 38: @@
 The molecular structure display works in any modern Java version, including Java 7 and Java 8 JREs.  You should install the latest version available.
-On Windows, if you wish to use the Java JRE in Firefox or Chrome, you must install a 32-bit version of the JRE.  This may also apply to other browsers.  You can have both 32 and 64 bit versions of Java installed on the same machine, if you have a 64-bit version of the operation system.
+Windows---
-On Mac OSX, the MarkUs applet should run in Firefox, Chrome or Safari.  See [https://www.java.com/en/download/help/sysreq.xml Java 7 System Requirements] for further information.
+Mac OS X---
 ====Browser Security====

@@ Line 105: / Line 105: @@
 ===Result Viewer===
-The result of the analysis is returned to a web-browser window displayed within geWorkbench.  The run may take a considerable amount of time to finish, and partial results will be displayed.  The window does not auto-refresh.  To see the most recent results, right-click on the result display window and select "refresh".  A banner will indicate how many steps have yet to be finished for the current run.
+The run may take a considerable amount of time to finish, and partial results will be displayed.  The window does not auto-refresh.  To see the most recent results, right-click on the result display window and select "refresh".  A banner will indicate how many steps have yet to be finished for the current run.
 Before the first results are available, the results page may display a field for entering a Private Key.  If a private key was requested, it has already been generated and is available in the [[Workspace]] data node name. This field will disappear once the the first results area available.  You do not need to enter anything into this field in the results viewer.

← Older revision		Revision as of 23:03, 30 January 2015
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	10. If the "Private Key" checkbox was checked, copy down the private key from the new result node in the [[Workspace]].		10. If the "Private Key" checkbox was checked, copy down the private key from the new result node in the [[Workspace]].
−
−	~~==Services (Grid)==~~
−	~~To select the grid service for MarkUs,~~
−
−	* Click on the Services tab.
−	* Push the "Grid Services" button. This will retrieve available MarkUs grid services from an index server.
−	* Select the radio button for the desired grid service.
−
−
−	~~[[Image:MarkUs_Services_grid_selected.png]]~~
−
−
−	~~See the [[Grid_Services \| Grid Services]] section for further details on setting up a grid job.~~

	==References==		==References==

@@ Line 130: / Line 130: @@
 . Inspect and adjust if desired the parameters to DelPhi.  DelPhi calculates the electrostatic field around the molecule.
-. MarkUs is available in geWorkbench as a local or grid service.  Both local and grid job submission are asynchronous and to the same server, so there is no advantage to using the grid service.
+. MarkUs is available in geWorkbench only as a local service. The grid service has been discontinued.
 The figure below shows the local service as selected.
@@ Line 145: / Line 145: @@
 . If the "Private Key" checkbox was checked, copy down the private key from the new result node in the [[Workspace]].
 ==Services (Grid)==