The application Bio7 is an integrated development environment for ecological modeling, statistical and scientific image analysis. The application itself is based on an RCP-Eclipse-Environment (Rich-Client-Platform) which offers a huge flexibility in configuration and extensibility because of its plug-in structure and the possibility of customization.
Features:
- Creation and analysis of simulation models.
- Statistical analysis.
- Advanced R Graphical User Interface with editor, spreadsheet, ImageJ plot device and debugging interface.
- Spatial statistics (possibility to send values from a specialized panel to R).
- Image Analysis (embedded ImageJ).
- Fast transfer of image data from ImageJ to R and vice versa.
- Fast communication between R and Java (with RServe) and the possibility to use R methods inside Java.
- Interpretation of Java and script creation (BeanShell, Groovy, Jython, JavaScript).
- Dynamic compilation of Java.
- Creation of methods for Java, BeanShell, Groovy, Jython and R (integrated editors for Java, R, BeanShell, Groovy, Jython).
- Sensitivity analysis with an embedded flowchart editor in which scripts, macros and compiled code can be dragged and executed.
- Creation of 3d OpenGL (Jogl) models.
- Visualizations and simulations on an embedded 3d globe (World Wind Java SDK).
- Creation of Graphical User Interfaces with the embedded JavaFX SceneBuilder.
Bio7 is now available as a Maven Tycho built and can be created locally. All plugins and features are now available in one Github repository.
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For the built Eclipse must be installed locally (please use this distribution: Eclipse IDE for RCP and RAP Developers).
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Download and install Java 21 JDK (Adoptium JDK can be downloaded here: https://adoptium.net).
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Download and install the latest Maven release (https://maven.apache.org/).
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Import all Plugins and Features from the bio7 Git repository (https://github.com/Bio7/bio7).
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Expand the com.eco.bio7.targetplatform plugin. Execute "Set as Active Target Platform" and then execute Reload Target Platform". See also: https://www.vogella.com/tutorials/EclipseTargetPlatform/article.html
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Open a shell and navigate to the main Maven *.pom in the Git repository (in the downloaded Git repository, e.g., on MacOSX: 'cd /Users/xxxx/git/bio7/').
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Execute the parent *.pom in the shell with: 'mvn -f com.eco.bio7.aggregator/pom.xml clean install' (or with 4 cores available: 'mvn -T 4 -f com.eco.bio7.aggregator/pom.xml clean install').
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The Bio7 built is now available in the com.eco.bio7.product plugin (in the targets/products folder - refresh the folder if not visible!).
To start Bio7 after a successful built a JDK is required. In the Bio7.ini file (can be opened with a text editor) a default path is given which points to an embedded local JDK. Just copy a JDK to the given location to start Bio7 (rename the top folder to 'jdk'). For more information about the -vm option which points to a JDK, see: https://wiki.eclipse.org/Eclipse.ini
To start Bio7 within Eclipse for testing and development navigate to the com.eco.bio7.product plugin and open the Bio7.product file. Then execute the "Launch an Eclipse application" action.
https://www.vogella.com/tutorials/EclipseTycho/article.html
https://tycho.eclipseprojects.io/doc/latest/
Huge thanks to Matthias Mailänder who made this new Bio7 Maven Tycho built possible.