1. Instructions - Download Bio7 (from the Bio7 website at http://bio7.org/). (Alternatively, it is directly from SourceForge at http://SourceForge.net/projects/bio7/. A copy of version 1.5 for Windows is also at http://www.jstatsoft.org/v49/i04/.) - Install Bio7 (see installation instruction below!). - After the first startup the "Resource" perspective for the e.g. file management and the editor area is displayed (the "Navigator" view on the left displays Bio7 projects and their files). - Start Rserve (press the button with the R logo in the Bio7 toolbar). - Create a new project in Bio7 ("File->New->General->Project")and copy the example file to the project. - Open the copied example file with the Bio7 Java editor (double-click on the example file!). - Compile the example file with the editor compile action ("compile source to method" - right button!) which is available in the toolbar after the editor has been opened. This action constructs a regular Java class from the source, compiles it and loads the class dynamically to the Java Virtual Maschine (no *.class file will be created! Everything is stored in the memory and each compilation replaces the previous loaded class in the Java Virtual Maschine). - Open the "3d" perspective (e.g. with menu "Window->Open Perspective->Other"). - Expand the "Time" item. - Press the Start/Pause action to execute the compiled Java method in the example file. More documentations can be found on the Bio7 website. Video instructions (Flash Tutorials) and a Bio7 forum for help are also available on the website. 2. Installation of Bio7 2.1 System requirements: It is recommended that your computer should have at least 1024 mb ram and a 1 ghz processor. A 3d Graphics Card which is OpenGL enabled (only necessary for the "Spatial" view and the embedded "WorldWind" view. To use the OpenOffice (LibreOffice) feature of Bio7 an installation of OpenOffice (LibreOffice) >= 2.0 is required. The path to OpenOffice will be automatically fetched by Bio7 from the registry (Windows) or can be adjusted in the Bio7 preferences (Windows, Linux, MacOSX) to the default path. For the MacOSX version a JRE >=1.6.0 has to be installed if not available on the OS by default (For Windows and Linux a JRE is bundled in the Bio7 installation package). 2.2 Installation Windows, MacOSX and Linux: The installation of Bio7 is similar to the installation of the Eclipse environment. Simply decompress the downloaded *.zip file in a preferred location on your file system. After decompressing with a standard zip-tool (like WinZip, Win Rar) the typical file-structure of an Eclipse based application will be created. To start the application simply double click on the Bio7.exe (Windows) or Bio7 (Linux, MacOSX) file. 2.3 After the first start: Please enable in the Preferences of Bio7 the option "Preferences->General->Always run in background" to disable the progress monitor dialog of Bio7. This avoids a blocking dialog in many operations of Bio7 (important for the integrated Flow editor!). 2.4 R Windows specific: Because Windows Vista, Windows 7, etc. is very sensitive to user rights etc. the package installation was reorganized in Bio7 1.4 for installable add-on packages inside of Bio7. The default add-on package location in a Bio7 release is now: "Bio7\plugins\Bundled_R_x.xx.xx\R\site-library" At this location inside of Bio7 the packages will be installed by default (if not changed!). Windows only (if needed)!: To write the R package location path to the Windows registry please start Bio7 with the enabled option "Install path at startup" to set the registry path to the bundled R location. By default this option is disabled not to harm any default user installation of R. In Bio7 x.x please install the R package rgdal which is needed for some spatial import and export scripts. Please note that the import scripts for spatial data can have problems with special text encoded filenames. If an rgdal import script produces an error the Rserver will probably die and you have to restart Rserve. 2.5 R Linux specific: To use R from Bio7 please install R with a package manager. Also the installation of the Rserve library is required. This can be easily done inside R by typing: > install.packages("Rserve", dependencies=TRUE) in the R console. After the installation of R the path to the R (if not using the default path) application has to be adjusted inside of Bio7 ("Preferences->Preferences Bio7"). In addition the path to the (add-on) packages install location has to be adjusted, too ("Preferences->Preferences Bio7->RServe Preferences"). Since Bio7 1.4 default paths are set which are usually correct for a Linux distribution. If Rserve is running you can then easily install the package rgdal with the Bio7 interface which is needed for the import/export scripts (you can also install it beforehand with R!). Linux: Scanner with Sane: If the Sane interface is not running by default please set a symbolic link (the shared library has to be found!): ln -s /usr/lib/libsane.so.1 /usr/lib/libsane.so 2.6 R MacOSX specific To use R from Bio7 please install the latest R. After the installation of R start R and install the Rserve package: > install.packages("Rserve", dependencies=TRUE) The default installation paths of Bio7 are pointing to a standard installation of R but can be adjusted in the preferences of Bio7 ("Preferences->Preferences Bio7"). In addition the path to the (add-on) packages install location can be adjusted, too if necessary ("Preferences->Preferences Bio7->RServe Preferences"). If Rserve is running you can then easily install the package rgdal with the Bio7 interface which is needed for the import/export rgdal scripts (you can also install them beforehand with R!). 2.7 Examples On the Bio7 SourceForge website you can download examples for the Bio7 application (recommended!). In addition the examples can be accessed on github. To install the Bio7 examples please import the examples from the Examples.zip file. "File->Import->Existing Projects into Workspace". Select the archive file "Examples.zip" and the two projects "Bio7 Examples" and "Ecological Modelling". Press "Finish" to import them into Bio7 (they will be imported to the workspace location). 2.8 Increased Java memory Windows and Linux For an increased Java heap space open the Bio7.ini file in the install directory of Bio7. In the file you can change the default memory settings e.g. the initial heap size -Xms and the maximum heap space -Xmx. MacOSX For an increased Java heap space open the Bio7 package (context menu if you click on the icon) then go to Contents->MacOS and open the Bio7.ini file with a texteditor. In the file you can change the default memory settings e.g. the initial heap size -Xms and the maximum heap space -Xmx.