[Scientific
FAQ]
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Usually it's one of the following reasons:
If you get the "[404] Not Found" error, first check if the URL really is correct (no typo). If that is the case and you still get the error message try changing your character encoding (i.e. the browser's settings in preferences/fonts/encoding or view/encoding). Depending on these settings, some browsers encode URLs with an underscore differently and send a wrong request to our server.
Genomatix
graphics are interactive so you can show and hide most elements in your
results following your needs. For maximum flexibility our graphics are Java
applets.
To view them, a reasonably recent installation of Sun Microsystem's Java
Runtime Environment is required. At the moment any version >=
1.5.0 will
work. Please note that the built in Java Virtual Machine provided by the
various Microsoft Windows operating systems is not sufficient, you have
to install a Java VM yourself. You can download the Java Runtime Environment
either by clicking the "Java Get Powered" button to the
right or by selecting your download manually on this
page.
For a more detailed overview of the applet's features, please see this page.
If you installed Java correctly (you didn't get any error messages from the Java installer) it can still be impossible for you to see our graphics. Check the following:
In some cases Java could be disabled in your browser settings. Please make sure this is not the case by following these click paths:
If you are using a 64-bit operating system such as Windows XP 64-bit or Linux 64-bit you will not see the Java graphics using Java 64-bit only since Sun is not providing the necessary plugins.
Workaround for Windows: users should install the standard 32-bit Java on their 64-bit Windows system and then start the 32-bit version of Internet Explorer (it is already installed on the system in parallel to the 64-bit version) or the 32-bit version of Firefox (it is only available as 32-bit version at the time of this writing).
Workaround for Linux: We recommend that users install a 64-bit package of Java, start Konqueror (a browser like Firefox), then enter Java's executable path (execute "whereis java" in a shell) in the Konqueror Java settings (go to Settings -> Configure Konqueror -> Java & Javascript). Konqueror will then be capable of showing Java graphics without the need of a plugin.
There is another solution which requires in depth experience in administrating Linux systems: if you really need to use Firefox on 64-bit Linux you have to install a complete 32-bit environment within your 64-bit system, then you can install both Firefox and Java as 32-bit versions within that environment. Please understand that we cannot help with setting up 32-bit emulation on 64-bit Linux systems.
The more elements are shown in the generated graphics, the more memory will be needed for displaying them. Without any changes you will probably get this error when more than 20 MB of memory are used, no matter if you have 4 GB of memory installed because the Java Virtual Machine is set to use a limited amount of memory per default. To be able to view more complex result graphics you have to add -Xmx200m to the list of runtime parameters of the Java plugin which will assign 200MB of memory to the virtual machine. (You may use higher values, e.g. -Xmx512m, but be sure not to specify more than half the memory that is physically installed in your computer!)
Changing the memory settings on Windows or Linux/Unix:
Then within the Java Control Panel select the "Java" tab. Click the "View..." button shown under "Java Applet Runtime Settings". Enter or add '-Xmx200m' into the "Java Runtime Parameters" field. Click "OK" in the "Java Runtime Settings" window and "OK" or "Apply" in the "Java Control Panel" window to save the changes.
Restart your browser after these changes!
Changing the memory settings on Mac OS X:
Mac OS X 10.3 and 10.4:
Open the Java Preferences. (Applications -> Utilities -> Java -> J2SE 5.0 -> Java Preferences) and select the "General" tab. Then enter or add '-Xmx200m' into the "Java Applet Runtime Parameters" text field. Click "Save" (at the bottom right) to save the changes.
Restart your browser after these changes!
Users running MacOS X 10.5 that have installed the "Java for Mac OS X 10.5 Update 2" on their system please see the Apple Knowledgebase Article HT3210 at http://support.apple.com/kb/HT3210 for more information on how to set parameters for the Java Applet.
Open "Java Preferences" in your "Utilities" folder (/Applications/Utilities/Java Preferences)
Click "Restore Defaults" in the upcoming window. Then select "Java SE 6 64-bit" in the "Java Applet Plugin" section and click the "Options" button.
Type '-Xmx200M' into the upcoming "Runtime Parameters" field. Confirm the setting by clicking the "OK" button.
Optionally repeat this step for the "Java SE 6 32-bit" selection.
Restart your browser after these changes!
Changing the memory settings for Konqueror on Linux:
Open the Konqueror settings, then select the "Java & JavaScript" section. Enter or add '-Xmx200m' into the "Additional Java arguments" textfield. Click "OK" to save the changes.
Restart your browser after these changes!
Java needs a continuous range of physical memory which it can use. Of course it cannot use memory which isn't even installed in your computer - or which is already used by other programs. So to be on the safe side never allow Java to use more than half of your physically installed memory when specifying the -Xmx parameter.
If you are accessing the internet through a web proxy which is not configured for reverse lookups in your institution's DNS system and which you specified by its IP address (e.g. 192.168.100.215), Java will try to find out the corresponding hostname (proxy.mycompany.com) and wait for this (non-existing) answer for about 5-10 seconds every time the graphics data are fetched from our servers. This will happen again whenever you simply reload the page, not only the first time when the applet (display program) is being loaded. In that case please specify your proxy by its hostname (proxy.mycompany.com) or - if it doesn't have a hostname - contact your friendly system administrator and ask for a reverse DNS entry for your proxy server. Further information can be found in Sun's Java bug database.
Unfortunately this happens sometime with all Mozilla-based browsers (Firefox, Camino) on MacOS X. This seems to be a MacOS X related problem, as we don't see it on other platforms. We recommend using Safari on the Mac. If you can't use Safari for any reason, Opera can be used alternatively.
Web browsers usually cannot print plugin content, they simply print a white area where the graphics should be. For that reason our interactive Genomatix Java graphics provide additional functionality: click on the blue disk icon which you will find in every graphics area in its icon tool bar. This will save the complete page including all graphics elements into a directory of your choice. Within that directory you will find an HTML file and one or more JPEG files. Open the HTML file with your web browser and you will see the page you were viewing before - but this time all graphics are simple non-interactive JPEG images. They have the big advantage to be printable without any problems by the normal print function of your browser.
Please make sure to export into a really existing directory (not into "Computer" or "Network"). You need write permission for this directory. If your graphics output is really complex, there might not be enough memory to display and print your graphics. Please try enlarging the memory your Java Virtual Machine may use or try to reduce the complexity of your graphics.
If you are using Windows Vista and Internet Explorer Java is only allowed to save into C:\Users\<username>\AppData\LocalLow\ and its subdirectories. This comes from the new security policy introduced by the operating system. If you save your graphics into another folder, it will look as if it worked - but it almost certainly has not!
If something is still going wrong after you fixed all possible problems described here, please open the Java console and send us all output that is written there when the error occurs. The Java console is a text window where Java applets can output error information. Usually you cannot see this console because it is not necessary during normal work.
Activating the Java console on Windows, MacOS X or Linux/Unix:
Then select the "Advanced" tab. Open the "Java console" menu item and tick the "Show console" checkbox. Click "OK" or "Apply" or "Save" to save the changes. To switch back to the default behavior, select "Do not start console" and click "OK" or "Apply" or "Save" .
Restart your browser after these changes!
Activating the Java console for Konqueror on Linux:
Open the Konqueror settings, then select the "Java & JavaScript" section. Select "Show Java console" and click "OK". To switch back to the default behavior, untick the "Show Java console" checkbox and click "OK".
Restart your browser after these changes!
When you are browsing web pages, downloading files, retrieving data from servers in the internet, you (the client) are usually connecting directly to that server. Your client application (web browser, ftp program, Genomatix ChipInspector) sends commands to the server (web server, ftp server, Genomatix web server for ChipInspector) directly and receives the server's answers (web pages, the file, ChipInspector data) directly.
Many companies though are restricting internet access through firewalls, i.e. there is no communication possible between computers in the company's intranet and the outside world, the internet. To allow some (controlled) internet access to their employees, these companies usually run proxy servers. Configured correctly your client application will then send all requests to the proxy server which then decides if that special request is to be allowed or not. On approval the proxy server sends your request to the internet server
Please have a look at the web browser you are currently using. If your company is using a proxy server, your browser knows it - otherwise you could not be reading this text. Here's where you can find proxy settings for some common browsers:
If 32-bit and 64-bit Java are installed in parallel, the computer is not able to assign the correct JVM version. You can tell ChipInspector which Java version to use by editing the file "chipinspector.conf", which is located in the Genomatix installation directory under
"<INSTALLATION DIRECTORY>/Genomatix/etc/" or "<INSTALLATION DIRECTORY>/etc/" (for Windows and Linux)
"<INSTALLATION DIRECTORY>/ChipInspector.app/Contents/Resources/chipinspector/etc/" (for Mac)
Substitute the line
#jdkhome="/path/to/jdk"
by
jdkhome="C:\Program Files\Java\jdk1.6.0_04"
or whereever the 64-bit Java is located.
ChipInspector stores downloaded files (e.g. transcript information, annotation data) and user settings in the default working directory. You can change the working directory by editing the file "chipinspector.conf", which is located in the Genomatix installation directory under
"<INSTALLATION DIRECTORY>/Genomatix/etc/" or "<INSTALLATION DIRECTORY>/etc/" (for Windows and Linux)
"<INSTALLATION DIRECTORY>/ChipInspector.app/Contents/Resources/chipinspector/etc/" (for Mac)
Substitute the path in the line
default_userdir="<defaultPath>" (for Windows and Linux)by your path:
default_userdir="<yourPath>" (for Windows and Linux)Make sure to enter a valid path.
Every Java program such as ChipInspector runs within a defined environment, the Java Virtual Machine (JVM). When a Java program is started, the computer allocates a portion of its main memory (its RAM) to the JVM. When ChipInspector is first installed, the amount of allocatable RAM is calculated. However, this calculation may be too high depending on other programs running on your computer.
It is possible to decrease the portion of RAM for the JVM, thus giving ChipInspector less memory to ensure that the JVM (and thus ChipInspector) can be started:
...\chipinspector.exe -J-Xmx1300m -J-Dplugin.manager.check.interval=EVERY_STARTUP
Every Java program such as ChipInspector runs within a defined environment, the Java Virtual Machine (JVM). When a Java program is started, the computer allocates a portion of its main memory (its RAM) to the JVM. When ChipInspector is first installed, the amount of allocatable RAM is calculated. However, this calculation may be off or new hardware RAM may have been added subsequently.
It is possible to increase the portion of RAM for the JVM, thus giving ChipInspector more memory:
...\chipinspector.exe -J-Xmx1400m -J-Dplugin.manager.check.interval=EVERY_STARTUP
An example project is available on our server. It contains finished analyses. They are intended for examination by users who don't have access to raw data files or who would like to see the results of an analysis type for which raw data is (not yet) available at their institution.
The experiments are performed with publicly available data, which is referenced in the analysis description.
Currently, the ExampleProject contains two analyses:
Download the file ChipInspectorExampleProject.zip (file size 260 MB) and extract it into the "GenomatixProjects" directory in you home directory. In case you are working with Windows this is the following directory:
C:\Documents and Settings\<YOUR_USERNAME>\GenomatixProjects
Open the project in ChipInspector.
This message is shown only once, when the Java platform receives the first updates from Genomatix. From then on, the source for ChipInspector program updates is known and your computer will accept program updates automatically. And you do trust Genomatix, don't you?
With Internet Explorer 6, when using the combo box for gene input in MatInspector, some other elements (notably select boxes) are rendered on top of the gene list, as in this picture:
When a MatInspector result page is loaded in your browser, some initializing JavaScript functions are called, which are necessary for the interactive features of the result tables. If there are many and/or large output tables on the same page, these scripts can take some time to run. In rare cases, a message window might pop up on your computer, notifying you about an "unresponsive script". Usually your simply can ignore this message and just allow the script to continue.
The interactive handling of the result tables is deactivated if there are more than 50 sequences, more than 1000 matches in one sequence, or more than 2000 matches in all sequences in the output. In this case, please filter for the matrix families you are interested in before submitting your search to MatInspector (use the option "continue with subset definition from selected groups").
Please check the size of your file. Files larger than 2 GB cannot be uploaded via the browser
for technical reasons as almost all browsers have a general upload limit of 2 GB, i.e. files bigger
than this size should be zipped before uploading from your local computer
(supported formats are .gz, .z, .7z or .zip).
In case the compressed file is still too large, copy it to a file system that is available
for "Upload from GGA" (e.g. your workbench home directory).
Results generated via the GUI on the Genomatix Mining Station (GMS) can be directly accessed on the GGA. In order to allow this, the GMS projects folder has to be mounted on the GGA. Mounting the GMS projects folder can be done with the "Administration" interface of the GGA ("Administration -> Server Administration -> First time configuration -> Remote file systems (NFS)"), please see the GGA System Administrator's Guide (chapter "Remote file systems (NFS) settings / connection to GMS"). The local mount point must always be named exactly like the GMS's fully qualified domain name or IP address. Enter "gms.yourcompany.com:/home/gx_sesame/projects" as remote file system. If you are already NFS importing the projects folder from a NAS server into the GMS, you have to enter "nasserver.yourcompany.com:/path/to/projects" as remote file system.
As soon as the GMS projects file system is mounted on the GGA, the BED file upload option "import from the GMS" will be available. The file browser shows the name of the GMS and you can select files from your own projects as well as from publicly available projects.
The GMS does not export file systems mounted via NFS. Therefore, you have to edit the GMS mount point on the GGA and change the remote file system to the projects folder on your NAS server. Please go to the "Administration" interface of the GGA ("Administration -> Server Administration -> First time configuration -> Remote file systems (NFS)") and edit the GMS mount point. Change the "Remote file system" to "nasserver.yourcompany.com:/path/to/projects" and reboot the GGA. The "Local mount point" must not be changed.
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