Category Archives: Uncategorized

Cellular Automata on a 3D Globe

15.04.2014

One of the features of the next release of Bio7 is the possibility to run an ImageJ simulation (dynamic image data) georeferenced on the 3D globe with – and this is new – a default transparent color (see image with running “Game of Life” below).

screen

To run a simulation on a 3D globe with the current Bio7 version without a transparent color follow this tutorial:

Visualize dynamic images on the WorldWind globe

Scene Builder Integration in Bio7

11.12.2013

The JavaFX team recently announced the availability of a OpenSource Scene Builder API (“JavaFX Scene Builder Kit”)  to integrate the Scene Builder in a custom application (e.g. in an RCP application).

Reading this blog entry about a Netbeans integration i was tempted to integrate the SceneBuilder in my application, too.
So i started to create a perspective with different views for the Scene Builder components which are exposed by the API. Below you can see the first result using a MultiPageEditor to display the JavaFX canvas and the FXML source.

scenebuilder

I have to resolve some bugs in the implementation and the API is quite new so maybe some thing will be changed. However an integrated GUI builder shipped with Bio7 would be a great win to create custom views inside of one application.

 

 

Bio7 1.7.1 MacOSX Released

15.10.2013

Finally i released  Bio7 1.7.1 for MacOSX. This release is bundled with a Java Runtime Environment and the latest R version (3.0.2) for MacOSX. For the plot functionality eventually XQuartz has to be installed (if not already installed!).

Please note the installation requirements at the bottom of the page. Here are some screenshots for a first impression:

rmac2 rmac1 javamac imagejmac flowmac 3dmac
Installation Requirements:

  • MacOSX >=10.7.3 64-bit
  • Eventually XQuartz
  • Avoid blanks in the Bio7 installation path for the bundled JRE (Java Runtime Environment)

Eventually XQuartz has to be installed to use the default custom R plotting device of Bio7 on MacOSX. If you plot the first time with R and XQuartz is not available a dialog will inform you about the missing installation.

Installation:

Simply unpack the Bio7_1.7.1_Mac64.zip in your preferred location. A double-click on the Bio7 file in the created Bio7 folder will start the application from the local bundled JRE.

If you would like to use Bio7 with your installed R application:

Please install the Rserve package. After the Bio7 start adjust the path to R in the Bio7 Preferences.
Preferences->Preferences Bio7
You can get the path from the R application with the command:
> R.home()
E.g. path to R: /Library/Frameworks/R.framework/Resources. Also adjust the path to the install location of the R packages:
Preferences->Preferences Bio7->Preferences Rserve
You can get the path from your R installation by evaluating the expression
>.libPaths()
in the R console. If an error is indicated in the Bio7 preferences please adjust wrong paths to the correct location or adjust them to a temporary available location else you can’t save the preferences.

New Features:

For an overview of the new Bio7 features in this release please read the following posts:

New in Bio7 1.7
http://bio7.org/?p=2049

New in Bio7 1.7.1
http://bio7.org/?p=2112

Download:
Bio7 1.7.1 can be downloaded here.

Bio7 1.7.1 RC3 for MacOSX Released!

11.10.2013

I released a new bugfix version for Bio7 1.7.1 MacOSX. This release fixes some detected bugs which are listed below. This should be the last release candidate before the final release.

Bug Fixes:

  • Fixed a deadlock when a plot is opened from R in ImageJ (e.g. from the R-Shell)
  • PDF and SVG R plots are now created and opened with the default registered application on MacOSX
  • Rescaled some dialogs
  • Fixed a deadlock in ImageJ when converting images to a stack

To use the R features install the R Mac distribution available here. Furthermore Rserve has to be installed.

After the start adjust the path to R in the Bio7 Preferences (if the default path is not correct!).
Preferences->Preferences Bio7
You can get the path from the R application with the command:
> R.home()
E.g. path to R: /Library/Frameworks/R.framework/Resources

Also adjust the path to the install location of the R packages:
Preferences->Preferences Bio7->Preferences Rserve
You can get the path from your R installation by evaluating the expression
>.libPaths()
in the R console. E.g. Package install location: /Library/Frameworks/R.framework/Versions/3.0/Resources/library

If an error is indicated in the Bio7 preferences please adjust missing correct paths to the correct location or adjust them to a temporary available location else you can’t save the adjusted paths.

Eventually XQuartz has to be installed to use the default custom R plotting device of Bio7 on Mountain Lion. If you plot the first time with R and XQuartz is not available a dialog will inform about the missing package.

Installation Requirements:

  • MacOSX >=10.7.3 64-bit
  • R installation
  • Rserve package installation
  • Eventually XQuartz

If you detect any bugs please let me know.

 

Bio7 1.7.1 RC2 for MacOSX Released!

06.10.2013

I uploaded a new Release Candidate for MacOSX. This upload bundles a JRE so you don’t have to install the lates Java yourself. In adition i fixed some bugs related to the Update Manager (Now you can install e.g. the EGit plugin) and adjusted some default paths for the Mac (default LibreOffice location, default R location). Here some screenshots:

3dmac flowmac imagejmac javamac rmac1 rmac2

To use the R features install the R Mac distribution available here. Furthermore Rserve has to be installed.

After the start adjust the path to R in the Bio7 Preferences (if the default path is not correct!).
Preferences->Preferences Bio7
You can get the path from the R application with the command:
> R.home()
E.g. path to R: /Library/Frameworks/R.framework/Resources

Also adjust the path to the install location of the R packages:
Preferences->Preferences Bio7->Preferences Rserve
You can get the path from your R installation by evaluating the expression
>.libPaths()
in the R console. E.g. Package install location: /Library/Frameworks/R.framework/Versions/3.0/Resources/library

If an error is indicated in the Bio7 preferences please adjust missing correct paths to the correct location or adjust them to a temporary available location else you can’t save the adjusted paths.

Eventually XQuartz has to be installed to use the default custom R plotting device of Bio7 on Mountain Lion. If you plot the first time with R and XQuartz is not available a dialog will inform about the missing package.

Installation Requirements:

  • MacOSX >=10.7.3 64-bit
  • R installation
  • Rserve package installation
  • Eventually XQuartz

If you detect any bugs please let me know.