Once more a spanking new shiny software –
Bio7 is a integrated development environment for ecological modelling based on the Rich-Client-Platformconcept of the Java IDE Eclipse. The Bio7 platform contains several perspectives which arrange several views for a special purpose useful for the development and analysis of ecological models. One special perspective bundles a feature rich GUI (Graphical User Interface) for the statistical software R.
For the bidirectional communication between Java and R the Rserve application is used (as a backend to evaluate R code and transfer data from and to Java).
The Bio7 R perspective (see figure below) is divided into a R-Shell view on the left side (conceptual the R side) and a Table view on the right side (conceptual the Java side).
Data can be imported to a spreadsheet, edited and then transferred to the R workspace. Vice versa data from R can be transferred to a sheet of the Table view and then exported e.g. to an Excel or OpenOffice file.
and
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
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