Technical FAQ

We have collected here the most common questions regarding Delta2D, and its function and technical background. If you can't find your question here, don't hesitate to send us an email at info@decodon.com or contact us in another way.

1. How do I register the full version of Delta2D?
2. Why can't I change the Memory Settings in Delta2D under Windows Vista?
3. How can I transfer spot boundaries from one gel to another?
4. How does Delta2D compute the statistical measures (mean, rsd etc.) shown in the statistics table?
5. Why are spots shifted when exported from one and imported to another gel?
6. "JDK 5.0 or newer cannot be found on your machine"
7. How can I uninstall Delta2D manually?
8. How Can I tell Delta2D 3.6 and older to use a proxy for license- or update requests?
9. How can I set a proxy for Delta2D 4.0 and newer?
10. Why is Delta2D so slow when working with large projects?
11. What can I do when I have problems opening the 3D rollup?
12. How can I find or change the place where Delta2D saves the settings?

How do I register the full version of Delta2D?

Background information: The single-machine version of Delta2D is copy-protected by a license file that is specific to you and your computer. Initially, you get a generic license file. Registering a license gives us the information we need to make a specific license file for your computer.

• After installation, please start Delta2D. You will be prompted for a license file. Please click on the "Import" button and select the license file you either found on your cd, received by e-mail or downloaded from your private download area.
• The dialog now shows a button "Register". Please click on the button and follow the instructions to send us your registration request by email. The registration request contains an identification code for your computer. Meanwhile you can start using Delta2D in Demo mode.
• We will process your request and send you the valid registration key, or a new license file corresponding to your computer.
• (Re-)Start Delta2D to obtain the registration dialog again and complete the registration with the registration key or the registered license file we sent by email.
  • Option 1: you received a license key. A license key looks like this: FXWEH-WJVXQ-XPQ5H-HWFEB-JSFBW-XYFLN-NBMWX-5XY4U-9WMJ7
    In the licensing dialog, click on the button "Enter license key". Copy the license key from your e-mail into the dialog and press OK.
  • Option 2: you received a license file. The license file ("registered license file") contains a key that is specific to your computer. Please save the file from your e-mail to some place on your computer. In the Delta2 registration dialog, click on "Import license file" and select the license file.
• Now your copy of Delta2D is fully licensed and operates in full mode.

Why can't I change the Memory Settings in Delta2D under Windows Vista?

Although I am logged in as administrator, Delta2D says

Can not write memory preferences to C:\Program Files\DECODON\Delta2D\etc\delta2d.conf. Start Delta2D as an administrator.

How can that be?

From Windows Vista on Microsoft introduced a new security mechanism, called User Account Control (UAC). This mechanism is meant to prevent users from damaging their system accidentally or unknowingly, and, as one consequence of it, even users with administrative rights do have to start programs explicitely as administrator if they want to run a program with elevated rights.

To run a program one time as an administrator

1. Right-click the program that you would like to run as an administrator and select Run as administrator.
2. At the User Account Control dialog box, select Continue.

After the user authorizes the elevation, the program will launch and run with the user's full administrative access token.

For more details about UAC please have a look at Microsofts Tech Net site, or for a brief overview see the Wikipedia article.

How can I transfer spot boundaries from one gel to another?

To transfer spots, right click on the thumbnail of the gel in the Project Manager which contains the spots you want to transfer, and choose Transfer Spots to Gel from the context menu. You will be able to choose your target gels in the context menu.

Please note: Since warping informations between gel images are necessary for transferring spots from one gel image to one or more others, it only works within a project and between gel images with valid warping informations.

How does Delta2D compute the statistical measures (mean, rsd etc.) shown in the statistics table?

Let's start with the mean. It is computed for every replicate group, using the relative volumes of the spots in a group. The formula for the mean is

The relative standard deviation is shown in the column rsd, in percent. The absolute standard deviation is a measure of the spread of sample values, it is defined as

The relative standard deviation (rsd) is computed by normalizing the standard deviation with the mean, and then multiplying by 100 to get a percentage value:

The median is defined such that at most half the spots in the group have values less than the median and at most half have values greater than the median. It is computed by sorting the intensities and then taking the middle one (if the number of spots is odd), or the average of the two middle ones (if there is an even number of spots). So, if

are the sorted spot quantities then the median is defined as

Ratios are computed according to the setting at the top of the quantitation table. By default, it is the quotient of the group means of relative spot volumes. The denominator of the ratio is always taken from the first group displayed in the project manager. Hold the mouse pointer over the ratio column heading, the tooltip will show details about the ratio computation. You can have the ratio is displayed in terms of fold change, where negative values mean decreases. For example, a fold change of -3 means a threefold decrease. To switch between normal and fold change display, go to the Preferences dialog and use the "Show Ratio of Spots as Fold Change" checkbox.

Delta2D computes t-Test values for certain pairs of replicate groups. The test is a unpaired two-sided Student's t-Test, with the assumptions of equal unknown variance and unpaired samples. The null hypothesis is that both groups have equal means. Delta2D computes the p-value, which is the probability that a test statistic at least as significant as the one observed would be obtained assuming that the null hypothesis were true (i.e. the differences in quantities are the result of mere chance). The value q shown in the statistics table is derived from the p-value as follows:

So higher values mean a higher probability that the null hypothesis is false. The value q is the t-Test value shown for the test applied to every group vs. the first one displayed in the project manager.

Why are spots shifted when exported from one and imported to another gel?

The function of exporting and importing spot boundaries is meant only for two main purposes:

1. Having the possibility to make detailed snapshots of spot detection with different or certain parameters
and
2. Having the possibility to exchange single gels and / or their data with other users without the necessity of copying the complete pool.

This presumes that spot boundaries belong to the image they were detected on. Thus it is not necessary and for the aspect of reproducibility even not wanted to consider warping to any other gel image when importing spots. If you want to transfer spots from one image to another, you can use the feature "Transfer Spots", available from the context menu of the image thumbnails in the Project Manager.

"JDK 5.0 or newer cannot be found on your machine"

When trying to start Delta2D I get this error message and nothing happens.

Usually there is no necessity for an extra java installation for using Delta2D. The phenomenon you experience is very likely a mixup of 32-bit and 64-bit Versions of Delta2D, as if there was an installation of 32-bit Delta2D which was upgraded with a 64-bit update, or vice versa.

To resolve this we recommend a complete new installation of Delta2D:

• Locate all previous installations of Delta2D which could be mixed up with your working installation. Please look at:
  C:\Program Files\DECODON\Delta2D   (for 64-bit installation on Vista64 or 32-bit installation on Vista32) and
  C:\Program Files (X86)\DECODON\Delta2D   (for 32-bit installation on Vista 64-bit)
• Make a backup of the folders for having the license file and in case there are customized settings you might want to reproduce easily
• Remove or rename the original folders Delta2D (This is, by the way, the crucial part of the manual method of uninstalling Delta2D manually, when the automatic uninstall fails. Additionally you might want to remove the entries from the start menu and the desktop)
• Download a copy of Delta2D from your Private Download Area and make sure you take the one you need (32/64-bit), whereas we always recommend the 64-bit version for 64-bit systems.
• Install Delta2D, and, on being requested for the license, take the file license.lfk from your previous installation.

How can I uninstall Delta2D manually?

Sometimes, when you try to uninstall Delta2D, the automatic uninstall fails. In this case you have to uninstall Delta2D manually.

Uninstalling Delta2D manually is basically done in three steps:

1. Remove the program files
1. (Optionally) Remove the user files and settings
2. Remove the Start Menu shortcuts
3. Remove the uninstall entry in the software part of the control panel

1: Remove the program files:

• Open the Windows explorer ("My Computer")
• Find the installation folder of Delta2D. Default location is C:\Program Files\DECODON\Delta2D
• You can delete recursively the complete folder "DECODON".

1a: Optionally you can delete your private settings and files for Delta2D:

Please make sure that you did not save any important data you do not want to loose in this location before deleting it!

• locate your user home. Depending on your Windows system, this is something like:
  C:\Documents and Settings\<your-login-name>\   (Windows XP)
  C:\Users\<your-login-name>   (Windows Vista)
• Delete the folder ".Delta2D" (please note the leading dot in the name)

2: Remove the Start Menu shortcuts:

• Click on Start -> All Programs and locate the entry "DECODON Delta2D" or similar (this name can be modified during the installation process)
• RIGHT click on the entry and choose "Delete" from the context menu
• Confirm with OK if you are warned that this will affect all users etc.

3: Remove the uninstall entries from the Installed Software Control Panel:

• Click on Start -> Execute
• Type in   regedit   and hit Enter (if regedit doesn't work, try regedt32)
• locate the registry key

  HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Uninstall

• Delete the unwanted key, here: "DECODON Delta2D XX" where XX stands for the version


• Optionally you can delete the other keys created by the Delta2D installation:

  HKEY_LOCAL_MACHINE\SOFTWARE\DECODON

  HKEY_LOCAL_MACHINE\SOFTWARE\ej-technologies

  (Please check if this key contains other subkeys being not related to Delta2D or DECODON in any way. If this is the case, please do not delete the complete key, but only the subkeys connected to Delta2D.)

  
  

  HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager\Environment\DELTA2D_HOME

  HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager\Environment\DELTA2D_JAVA_HOME

Please note, that doing other modifications to the registry of your windows installation can seriously damage your windows installation, which can lead up to a inoperable windows installation. This would require a complete new installation of Windows and all software programs on your computer!

How Can I tell Delta2D 3.6 and older to use a proxy for license- or update requests?

Delta2D needs to contact our web server for three possible reasons:

1. to validate special, so called 'web checked' licenses
2. to use Scouts for aquisition of data from web-based databases
3. to check for updates

If your network situation demands to set your internet browser to use a proxy, then Delta2D very likely will need the same settings, otherwise you will see error messages saying that the license server or the update server could not be connected.

There are two alternatives to specify a proxy for Delta2D 3.6 and older:

Delta2D.vmoptions

you will need adminstrator privileges for this procedure

• locate your Delta2D installation folder, on Windows something like "C:\Program Files\DECODON\Delta2D\3.6"
• Open the file "Delta2D.vmoptions" you can find there with any text editor
• add the following line(s) at the bottom:

  -Dhttp.proxyHost=proxyhost
  -Dhttp.proxyPort=portNumber
  

  where you specify proxyhost (resp. portNumber). The second line is optional and only necessary if the proxy port is other than 80.
• Save the file and start Delta2D

properties.ini

This file does not exist by default, but will be evaluated if it exists. It can be placed either in the Delta2D installation folder, where it will affect all users of Delta2D, or in the personal settings folder, where it will only affect the respective user, but, on the other hand, requires no adminstrator privileges.

• Open any text editor with a new, blank window
• add the following line(s):

  http.proxyHost=proxyhost
  http.proxyPort=portNumber
  

  where you specify proxyhost (resp. portNumber). The second line is optional and only necessary if the proxy port is other than 80.
• Save the file as properties.ini EITHER in the Delta2D installation folder (something like "C:\Program Files\DECODON\Delta2D\3.6", you will need administrator privileges) OR in your personal settings folder (<userhome>\.Delta2D)
• Start Delta2D

How can I set a proxy for Delta2D 4.0 and newer?

Delta2D needs to contact our web server for three possible reasons:

1. to validate special, so called 'web checked' licenses
2. to use Scouts for aquisition of data from web-based databases
3. to check for updates

If your network situation demands to set your internet browser to use a proxy, then Delta2D very likely will need the same settings, otherwise you will see error messages saying that the license server or the update server could not be connected.

Delta2D 4.0 and newer enables you to specify a proxy very easily:

Open the Options window (Delta2D menu: Tools -> Options) and switch to the "General" settings.

Choose the "Web" Tab.

The default setting is to use the system proxy settings. If you have specified proxy settings for your computer in the control panel these will be used by Delta2D as well. Please note, that the proxy settings are not apopted by Delta2D if your computer determines them by an automatic configuration script.

To specify individual proxy settings for Delta2D, simply tick the radio button Manual Proxy Settings and type in the host name or ip address and the proxy port into the respective fields.

If you are using a floating license it might be necessary to do additional adjustments. Please ask your network or computer administrator whether or not the Delta2D license server is reachable via the proxy. If yes, you are done with the proxy settings. If not, you will need to exclude the license server from proxying: please click on the button More you see below the proxy field. There you can specify the host name or ip address of your license server in the No Proxy Hosts: field. Multiple entries can be separated with a comma.

Please note, that if your proxy settings done here are not correct and hence Delta2D cannot contact the license server, it might happen, that Delta2D does not start any more. In this case you will have to edit the corresponding settings file manually to reenable Delta2D to start. You can find it in your Delta2D settings folder:

<your user home>\.Delta2D\config\Preferences\org\netbeans\core.properties

proxyType=2                                     # 0 = no proxy, 1 = system settings, 2 = as specified here
proxyHttpHost=yourproxhost                      # proxy host name or ip address
proxyHttpPort=4711                              # proxy Port, default is 80 or 8080
useProxyAuthentication=true                     # only necessary if authentication is required
proxyAuthenticationUsername=yourloginname       # only necessary if authentication is required
proxyAuthenticationPassword=yourpassword        # only necessary if authentication is required
proxyNonProxyHosts=localhost|127.0.0.1|foo|bar  # list of host names or ip addresses

You will not see all parameters in your file, only those you specified a value for.

Why is Delta2D so slow when working with large projects?

Probably you need to adapt Delta2D's memory settings: open the preferences dialog (in the project manager, go to Project / Preferences), change to the Memory tab and click on 'Recommend' or 'Recommend (Nice)'.

What can I do when I have problems opening the 3D rollup?

Please refer to this article explaining the details.

How can I find or change the place where Delta2D saves the settings?

Please refer to this short Howto for details on where Delta2D saves settings, where the demo data can be found and removed, how you can modify these places and other settings not being modifiable from Delta2D's options dialog.