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Overview of Help-Pages

Frequently asked technical questions


[Scientific FAQ]

1. Registered access to Genomatix programs

  1. I receive the error "Authorization failed" when trying to login with the account/password I received by email!
    What's wrong with my account or password?
  2. I changed my password, but I forgot it!
    How can I access MatInspector or GenomatixSuite anyway?
  3. When accessing the URL of the program (e.g. "mat_fam.pl") I get the error page "[404] Not Found"!
    What's wrong with the URL?

2. Proxy server problems

  1. What is a proxy server?
  2. Where can I find the proxy server settings my company uses?

3. Exporting results

  1. How to export a single result page?
  2. How to export a complete project?

4. ChipInspector 2.x

  1. I have installed Java 64-bit on my computer, but ChipInspector is not using it.
  2. How can I change my default working directory?
  3. I've installed ChipInspector without any problems, but ChipInspector does not start.
  4. How can I increase the memory for ChipInspector?
  5. I'd like to see an example analysis.
  6. When updating ChipInspector I see a warning sign: "Installing untrusted plugins is potentially insecure. Use unsigned or untrusted plugins at your own risk."

5. MatInspector 8.0

  1. In my Internet Explorer 6 browser, the drop-down list for selecting genes is partially covered by other form elements.
  2. I receive "unresponsive script" alerts when a MatInspector result page is created.
  3. Why am I not able to use the interactive features for sorting my MatInspector results?

6. Genomatix Genome Analyzer (GGA)

  1. The BED/BAM File Upload fails. The upload function lets me choose a file but I cannot go further from it. Clicking the "Submit" button does not work.
  2. How can I transfer my GMS results to the GGA for further analysis?
  3. Since I have moved the GMS projects folder to our NAS server, I am no longer able to access the GMS results on the GGA. The name of the projects folder on the GMS has not been changed, it is still /home/gx_sesame/projects/.

Answers

1. Registered access to Genomatix programs

  1. I receive the error "Authorization failed" when trying to login with the account/password I received by email! What's wrong with my account or password?

    Usually it's one of the following reasons:

  2. I changed my password, but I forgot it! How can I access GenomatixSuite anyway?

    Request a new password for your account. You only have to enter your email address and you will receive an email containing your username and your new password.
    If this does not work send an email to support@genomatix.de and ask them to reset your password to a new word (they can't look up the old password though).

  3. When accessing the URL of the program (e.g. "mat_fam.pl") I get the error page "[404] Not Found"!
    What's wrong with the URL?

    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.


2. Proxy server problems

  1. What is a proxy server?

    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

  2. Where can I find the proxy server settings my company uses?

    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:


3. Exporting results

  1. How to export a single result page?

    To export a single result in PDF format you can use your browser's print option, as all modern browsers allow printing to a PDF file. Some Examples:

  2. How to export a complete project?

    The result management's archive option allows downloading a project as a compressed tar file (.tar.gz) which includes PDF files for all results in the project.

4. ChipInspector 2.x

  1. I have installed Java 64-bit on my computer, but ChipInspector is not using it.

    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.

  2. How can I change my default working directory?

    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)
    default_mac_userdir="<defaultPath>" (for Mac)

    by your path:

    default_userdir="<yourPath>" (for Windows and Linux)
    default_mac_userdir="<yourPath>" (for Mac)

    Make sure to enter a valid path.

  3. I've installed ChipInspector without any problems, but ChipInspector does not start.

    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:

  4. How can I increase the memory for ChipInspector?

    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:

  5. I'd like to see an example analysis.

    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.

  6. When updating ChipInspector I see a warning sign: "Installing untrusted plugins is potentially insecure. Use unsigned or untrusted plugins at your own risk."

    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?


5. MatInspector 8.0

  1. In my Internet Explorer 6 browser, the drop-down list for selecting genes is partially covered by other form elements.

    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:

    Z-index bug

    This is a known issue of Internet Explorer 6 (and earlier versions) which is due to the implementation of the "Z-index" attribute of select-controls, as described in this Microsoft knowledge base article. Unfortunately, there is no work-around for this issue (the "iframe shimming trick" explained in several forum discussions, cannot be applied in our case), so the only possibility to circumvent this behavior is to upgrade your browser. (Microsoft changed the implementation of the Z-index in Internet Explorer 7)

  2. I receive "unresponsive script" alerts when a MatInspector result page is created.

    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.

  3. Why am I not able to use the interactive features for sorting my MatInspector results?

    The interactive handling of the result tables is deactivated if there are more than 50 sequences, more than 2500 matches in one sequence, or more than 4000 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").


6. Genomatix Genome Analyzer (GGA)

  1. The BED/BAM File Upload fails.
    The upload function lets me choose a file but I cannot go further from it. Clicking the "Submit" button does not work.

    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).

  2. How can I transfer my GMS results to the GGA for further analysis?

    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 Configuration -> Remote file systems"), 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/BAM 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.

  3. Since I have moved the GMS projects folder to our NAS server, I am no longer able to access the GMS results on the GGA. The name of the projects folder on the GMS has not been changed, it is still /home/gx_sesame/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 Configuration -> Remote file systems") 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.