Bio7 1.5 released!

Release notes:

General:

Built upon Eclipse 3.6.1.

Now works with the latest Java version! (Windows version bundled with the latest JRE release).

Removed the Soil perspective (now soils can be modeled with ImageJ (float precision). Active images can be displayed in the 3D discrete view (new example available).

Removed the database perspective and the plant layer. You can now built any discrete models without any plant layer.

Removed several controls in the Control view. Added the “Custom Controls” view. In addition ported the Swing component of the Time panel to Swt.

Deleted the avi to swf converter in the ImageJ menu.

Now patterns can be saved with opened Java editor source. If this file is reopened and dragged on Bio7 the pattern is loaded, the source is compiled and the setup method (if available) is executed. In this way model files can be used for presentations ->drag, setup and run. The save actions are located in the Speadsheet view toolbar.

More options available to disable panel painting and recording of values (if not needed for speed!).

New Setup button in the toolbar of Bio7 to trigger a compiled setup method if available.

Removed the load and save pattern buttons from the toolbar of Bio7. Discrete patterns can now be stored with the available action in the spreadsheet view menu.

New P2 Update Manager available in Bio7.

Updated the Janino Compiler.

New HTML perspective added with a view which embeds the TinyMC editor.

New options to disable painting operations for the discrete panels.

New option to explicitly enable scripts at startup (for a faster startup).

Quadgrid (Hexgrid)

Only states are now available which can be created in the “Spreadsheet” view menu easily. Patterns can be stored and restored as usual but are now stored in an *.exml file.

New method to transfer the quadgrid pattern as a matrix to R.

New method to transfer the population data of all quadgrid states to R.

ImageJ:

Update to the latest version (with additional fixes).

Fixed a bug to rename the image.

Thumbnail browser can now open images recursevely(limited to 1000 pics), the magnifiyng glass can be disabled, too.

Plugins can be installed dynamically with a drag and drop operation on the ImageJ view or toolbar (as known from ImageJ).

Installed plugins now extend the plugin menu as submenus or subsubmenus (not finished yet!).

Plugins can now be created with the Java editor. New Bio7 Wizard available to create a plugin template.

Compiled Java files can be added to a *.jar file with a new available action in the Navigator view (if you rightclick on the files in the Navigator). In this way ImageJ plugins can be packaged in a *.jar.

Floweditor:

Fixed a repaint bug in the debug mode of a flow (now draws correctly the active shape in the flow).

Resize with Strg+Scrollwheel works again.

Comments with more than one line works again.

New Test action to verify connections in a flow.

Debug mode now shows all executed Shapes.

Integrated more default tests (for the verification of a regular flow).

A mouse-click now deletes colored shapes in a flow (e.g. in debug mode).

Points panel:

Integrated (dynamic) Voronoi, Delauney visualization (with area and clip to rectangle action).

Points coordinates can now be set in double precision.

Transfer of point coordinates to R now in double precision.

Bio7 Table:

New import and export of Excel 2007 OOXML.

Row headers can now be resized with the mouse device.

R:

Updated R (2.12.1) and Rserve (0.6.3) to the latest version.

New help action in the R-Shell view.

New action to display help for R specific commands in the embedded Bio7 browser (which opens automatically).

New Key actions to copy the selected variable names to the expression dialog (c=cocatenate (+), a=add (,)).

New action to transfer character or numeric vectors horizontally or vertically in an opened spread (Table view) at selection coordinates.

Empty spaces in the filepath are now allowed under Windows if Rserve is started with a system shell or the RGUI (for the tempfile select a location in the Preferences dialog which is writeable) is started.This works also for the RGUI action.

Improved the search for the “Install packages” action (option “Case Sensitive” added).

API:

New API methods available!

And:

Many fixes since the last version!

Installation

Important information:

A certain firewall software can corrupt the Bio7 *.zip file (as well as other files).
Please ensure that you have downloaded a functioning Bio7 1.5 version. In addition it is also reported that a certain antivirus software detects the bundled R software (on Windows) as malware. Often the R specific “open.exe” is detected as malware. Please use a different scanner to make sure that the software is not infected if you have any doubts. For more details see:

http://r.789695.n4.nabble.com/trojan-at-current-development-version-td3244348.html

System requirements:

It is recommended that your computer should have at least
1024 mb ram and a 1ghz processor.
A 3d Graphics Card which is OpenGL enabled (only necessary for the Spatial view and
the embedded WorldWind view.
To use the OpenOffice-feature of Bio7 an installation of OpenOffice >= 2.0 is
required. The path to OpenOffice will be automatically fetched by Bio7 from
the registry or is adjusted (Linux) to the default path (See section 8: The Bio7 Preferences).

Installation Windows 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) file.

After the first start:

Please select 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!).

R Windows specific:

Because Windows Vista is very sensitve 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 this release is now:
Bio7\plugins\Bundled_R_2.12.1\R\site-library
At this location inside of Bio7 the packages will be installed by default (if not changed!).
If needed: to write the package location path (Bio7 and Rgui) 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 1.5 please install the R package “rgdal” which is needed for some 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.

R Linux specific:

To use R from Bio7 please install R with a package manager.
Also the installation of the Rserve 0.6.3 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->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 packages tripack and rgdal which are needed for the import/export rgdal scripts and for the voronoi plotting feature (you can also install them
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
This worked on Ubuntu 8.04 – 9.10

Customisation Linux:

If after the startup of Bio7 the Swing fonts are to small you can adjust them with a correction factor
in the properties file (Bio7/plugins/com.eco.bio7_1.5.0/bin/imports/swinglinux.properties) e.g. 3 for +3.

In this release you have also the possibility to use the Swing “Nimbus” look and feel.
In combination with the gtk Nimbus theme which is available here:

http://vale.homelinux.net/wordpress/2007/09/29/nimbus-beauty-for-your-ubuntu-desktop/

you get a nice option for a native look and feel of Bio7 1.5.

Screenshots:
Screen1.xcf
Screen2.xcf

You can enable this again in the properties file (Bio7/plugins/com.eco.bio7_1.5.0/bin/imports/swinglinux.properties).

To plot *pdf files with the plotting features of Bio7 another properties file is available
to select your favourite Pdf application (Bio7/plugins/com.eco.bio7_1.5.0/bin/imports/pdflinux.properties)
By default evince is used!

If the R shell is opened from the R menu a path with a load command for the workspace is copied
to the clipboard. If you want to work with you favourite GUI you can then simply paste
the command from the clipboard to work with the stored workspace.

With Bio7 1.5 the default shell (to open R) can be changed (Bio7/plugins/com.eco.bio7_1.5.0/bin/imports/linuxshell.properties) to open the R console in a gnome terminal instead of a Xterm terminal.
With the gnome terminal the clipboard feature can be used reasonably.

Examples:

On the Bio7 SourceForge website you can download examples for the Bio7 application.
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).



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