Bio7 User Guide Version 3.3 (work in progress)

© 2005-2021 M. Austenfeld

Updated: 21.07.2021

1 Why Bio7?

1.1 Ecological Background

The application Bio7 was originally developed for the chair of experimental and systems biology (Bio7) to create and analyze spatially explizit simulation models on dry acidic grasslands on inland sand dunes. Only specialists like Corynephorus canescens, Polytrichum piliferum, etc. can settle on this nutrient poor water limited sandy soils. Additionally high temperatures on the surface of the soil and erosion make it very hard for other species to settle there. In comparison to other ecosystems this habitat is less complex in its species structure and nutrient dynamics which facilitates monitoring of vegetation dynamics to identify the driving forces or key factors of the system. With the exploration of this ecosystem several questions and hypothesis should be answered and verified. Because many specialized plants and animals occur in this habitat the main question is, how we can protect and preserve this valuable ecosystem at all. Also the key factors are from high interest and can maybe serve to identify similar processes in more complex systems like the tropical rainforest. From various experiments in these systems we have knowledge about seed dispersal, competition, and nutrients availability or dependencies from different species which are typical for this habitat. We use the capabilities of this application to express the features of this system in syntactical rules for simulation.

Figure 1.1 Dry Acidic Grasslands

2 Getting started

2.1 Installation

2.1.1 System requirements:

2.1.2 Installation:

2.1.2.1 Installation:

2.1.2.2 Windows

2.1.2.3 R, Rserve installation for MacOSX, Linux

2.1.2.4 Rserve local installation (compiled for cooperative mode on Linux and MacOSX, 64-bit platforms)

1install.packages("C:/xxx/Rserve_1.8-8.zip", repos=NULL)

1install.packages("/Users/xxx/Rserve_1.8-8.tgz", repos=NULL)

1install.packages("/home/xxx/Rserve_1.8-8.tar.gz", repos=NULL)

2.1.2.5 Build of Rserve in cooperative mode on Linux or MacOSX (if necessary!)

1sudo PKG_CPPFLAGS=-DCOOPERATIVE R CMD INSTALL --build Rserve_1.8-8.tar.gz

1sudo PKG_CPPFLAGS=-DCOOPERATIVE R CMD INSTALL --build Rserve

2.1.3 R Windows specific:

2.1.4 Useful R packages

2.1.4.1 R packages Linux specific:

2.1.5 R Markdown

1Sys.setenv(PATH="/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin")

1Sys.setenv(PATH="/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Library/TeX/texbin:$HOME/bin")

1Sys.setenv(PATH="/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:$HOME/bin")

1Sys.setenv(PATH=paste(Sys.getenv("PATH"),"C:/pandoc”, sep=""))

Figure 2.10 The main R preferences with a startup command to set the path for pandoc in R

2.1.6 LaTeX

2.1.6.1 Linux

1sudo apt-get install texlive-latex-extra
2sudo apt-get install lmodern

2.1.7 Windows only (if needed)!:

2.1.8 Portable (Windows):

2.1.9 Examples for Bio7:

2.1.10 Increased Java memory Windows/Linux

2.1.11 Increased Java memory MacOSX

Figure 2.12 Open the package (1) on MacOSX to change the Bio7.in file (2) for more Java memory, etc.

3 The Platform-Architecture

Figure 3.1 Window components of Bio7

3.1 The Toolbar

Figure 3.2 Toolbar of Bio7

3.1.11.1 Toolbar from left to Right:

1. Play/Pause: Starts or stops a simulation run. This action will start or pause a default calculation thread of the application. The calculation thread then repeatedly calls a special method (called run) in a compiled Java class if available (which extends a special class called “Model”). In the submenu the Control view can be opened to change the execution interval of the calculation thread.
2. Setup: Invokes a Java setup method if available in the compiled class.
3. Reset: Resets the discrete grid (if opened) in the application. This action will reset all states in the Quadgrid (Hexgrid) arrays to the value 0.
4. Counter-Reset: Resets the counter to null. This action will reset the time to the value 0 and will also update the default charts. The values of a special list which automatically stores the count of enabled states in a simulation run will also be deleted.
5. Random: Distributes selected states in the discrete field (if opened). There are two random functions available in the menu of this item to randomize the field. With a special action landscape patterns can be produced (see 4.10.3↓).
6. LibreOffice: This action will open a connection to LibreOffice. If you select this action Bio7 tries to connect to LibreOffice with the LibreOffice API (Application Programming Interface). The path to LibreOffice will be fetched from the Preferences and can be adjusted there (Windows: If LibreOffice is installed, it will be automatically fetched from the Windows Registry if possible. Sometimes the Windows path to LibreOffice has to be adjusted, too. With this connection some actions are available (see 9.3↓)
7. R: Will open a connection to R by means of a Server (Rserve). This action will connect Bio7 to the Rserve application which builds a connection to the statistical tool R (see 4.7↓). In the submenu of this action the started R process can be terminated or killed if necessary.
8. Print: Prints the content of an opened editor. If an editor in Bio7 has been opened this method will print the content.
9. Create new Projects and Files: With this toolbar menu Bio7 projects with default files can be created easily without to create the project and files individually (fast mode).

3.2 The Menu

• The File menu offers methods for the import and export of projects and files which can be extended with BeanShell, Groovy or Jython scripts.
• The Edit menu offers several methods for the work with the different editors in Bio7.
• The Preferences menu opens the preferences of the Bio7 application (see 6.1↓).
• The Scripts menu (with several submenus) is extendable for self-defined scripts (BeanShell, Groovy, Jython, R scripts and ImageJ macros) in different categories.
• The R menu offers methods for the interaction with R and to transfer data to the embedded R application (see 4.7.1↓).
• The LibreOffice menu offers actions for acquiring and setting values from and to LibreOffice. Three further methods can transfer data to R or BeanShell which facilitates data acquisition through the options of LibreOffice application (see 9.3↓).
• With the Window menu perspectives and views can be opened and the editor area can be activated in a Bio7 perspective. In addition custom perspectives can be stored with an action available in this menu.
• The menu Help offers help for the application and the possibility to make updates and installations of new components for Bio7 (see 7↓).

4 The Perspectives of Bio7

1. Click the Open Perspective button on the shortcut bar on the left side of the Workbench window. (This provides the same function as the Window  ▷  Open Perspective menu on the menu bar.)
2. To see a complete list of perspectives, select Other... from the drop-down menu.
3. Select the perspective that you want to open. When the perspective opens, the title bar of the window changes to display the name of the perspective. In addition, an icon is added to the shortcut bar, allowing you to quickly switch back to that perspective from other perspectives in the same window.

4.1 Resource Perspective

Figure 4.1 The Resource perspective with opened context menu of the Navigatior view

4.1.1 The Navigator

4.1.2 The Editor Area

4.1.3 The Console of Bio7

Figure 4.2 The Console view of Bio7 with opened menu

1. The script consoles (Beanshell, Groovy, Jython) can interactively communicate with the Bio7 application or simply interpret different instructions in the selected scripting language.
2. The Shell pipes commands to the underlying OS with a pseudo-terminal.
3. The Native R and Native Python consoles pipe commands to the different applications (Please adjust the paths to the language environments in the Preferences! See: 10.1↓).
4. The default enabled Console Output only displays errors and prints messages. In addition it pauses the REPL (read–eval–print loop).The Console is responsible for the:
   1. Output messages for the interpreters and connected applications.
   2. Output messages of the embedded Java compiler (compiler warnings, infos, etc.)
   3. Output of the R interpreter (Rserve warnings, etc.) and evaluated expressions in R.

4.1.3.1 Menu of the Console View

4.1.4 The Snippets View

Figure 4.3 The Customize... dialog of the Snippets view available in the context menu

4.2 SceneBuilder Perspective

Figure 4.4 JavaFX SceneBuilder Perspective

4.3 ImageJ Edit Perspective

Figure 4.5 The ImageJ Edit perspective optimized for typical image analysis tasks

4.3.1 ImageJ-Canvas

• The ImageJ canvas is embedded in Bio7 as a tabbed SWT interface.
• The Toolbar of ImageJ is integrated in an RCP view (when called from the menu Window ▷ ImageJ-Toolbar as a detached view).
• Two extra actions have been added to compile or interpret current opened sourcecode on the ImageJ classpath only (OSGI seperated plugins classpath: Plugins ▷ Compile Java and Plugins ▷ Interpret Script)
• Several actions for the image data transfer to R are available in a special detached view (see 4.9↓)
• The menu of the integrated application has been reprogrammed as a SWT view menu which is similar to the original ImageJ menu.
• All images are opened in tabs and can be edited if activated.
• External plugins are supported. Installed plugins extend the ImageJ menus of Bio7 ImageJ view dynamically.
• The menus can be updated dynamically (if a new plugin has been added) with the “Refresh Menus” action.
• Macros can extend the main menu of Bio7 and can be created like in the regular version.
• For more information about these plugins visit the different websites (for available manuals!).
• The ImageJ API is accessible by means of the embedded compiler or with BeanShell, Groovy, JavaScript, ImageJ Macro or Jython scripts.

• Opening the toolbar of ImageJ (ImageJ-Toolbar as a detached view - see below)
• Opening a control panel for the Points panel with methods for the exchange and adjustment of images between ImageJ and the Points panel.

4.3.1.1 ImageJ Toolbar

Figure 4.6 The ImageJ toolbar integrated as a detachable view

4.3.1.2 ImageJ Plugins And Macro Paths

• Bio7/plugins/com.eco.bio7.image_x.xx.xx/plugins
• Bio7/plugins/com.eco.bio7.image_x.xx.xx/macros

4.3.1.3 ImageJ preferences

Figure 4.7 The ImageJ Preferences

4.3.1.4 Compilation of ImageJ plugins

4.4 R ImageJ Analysis Perspective

Figure 4.8 R ImageJ Perspective

4.4.1 ImageJ Interactions with R

Figure 4.9 Image-Methods view

4.4.1.1 Image Transfer to R

• The action in (5) transfers selected image data in an easy way without the need of an opened ROI Manager in ImageJ. The image data of the current selection (one selection) from one or multiple images (opened tabs) can be transferred to R in the selected datatype of the combobox of action (9).
• The action in (7) transfers the selected pixels (Freehand, Rectangular etc.) with or without a signature as a matrix to R. The transfer type can be selected, too! The ROI Manager with ROI selections has to be active. Selected ROI Manager ROI selections (or all ROI’s if no ROI is selected) for all layers (opened tabs in the ImageJ view) are transferred automatically with an selected or incremental signature! If a stack is among the opened images only the first slice (layer) will be transferred.
• The action (8) transfers the selected pixels of the selected ImageJ selections (Freehand, Rectangular etc.) in a stack with or without a signature as a matrix to R. The transfer type can be selected, too! The ROI Manager with selections has to be active and the selected image must be a stack! All selections for all slices are transferred automatically with an selected or incremental signature! A stack can also represent multispectral or hyperspectral image data which selectively should be transferred to R! Note that image folders can be dragged on the toolbar or the ImageJ canvas to load the images as a regular or virtual stack (in a virtual stack only the displayed data is loaded into the RAM of the computer).

4.4.1.2 Supervised Classification with ImageJ and R

Figure 4.10 Pixel RM Stack action to transfer selected pixels (RM = ROI Manager)

4.4.1.3 Transfer of Selection Coordinates

4.4.1.4 Geometry Selections View

1. Selection coordinates as list: If this option is selected selections from an available ROI Manager of ImageJ are transferred as a simple 2D list to R.
2. Spatial Data (R package ’sp’ required): If this option is selected data can be transferred with the ’sp’ R package as the following objects in R:
   1. SpatialPolygons or SpatialPolygonsDataFrame (if an available R dataframe has been selected - Add selected data frame action!)
   2. SpatialLines or SpatialLinesDataFrame (if an available R dataframe has been selected- Add selected data frame action!)
   3. SpatialPoints or SpatialPointsDataFrame (if an available R dataframe has been selected- Add selected data frame action!)

Figure 4.11 The Geometry Selections view to transfer ImageJ selection data to R.

The option Transfer as centroid coordinates transfers the selections as centroids of a grid cell instead of the top-left coordinate of a grid cell. This can be useful or necessary for point data to transfer the point selections in the center of a grid cell (see 4.12↓)! The option Add projection from georeferenced file allows the georeferenced transfer of the selection data from an raster image (e.g., *.geotiff). Please note that the file has to be in a projected into a Projection Coordinate System! Typically the image selection data originates from a georeferenced image which then is selected with the Transfer to R! action to extract the spatial information for the creation of a georeferenced spatial object in the R workspace.

Figure 4.12 Transfer of point selections as centroids (left image: GIS display of transferred point vector data, right image: ImageJ display of selections)

Figure 4.13 Transfer of different selection ImageJ types (right image) and the result in a GIS display (left image))

4.4.1.5 Cluster And PCA Analysis

Figure 4.14 Cluster dialog to perform a cluster analysis from selected layers (tab images)

4.4.2 Thumbnails

Figure 4.15 Thumbnail browser

1. With the 5->,10->, 15-> buttons you can select how many thumbs should be created in a row
2. The Small, Medium, Large labelled buttons will create preview images with a size of 100*100, 150*150 or 200*200 pixel.
3. The Open button opens the directory which should be displayed.
4. The Mag. button enables or disables the overview navigation panel.
5. The Rec. button enables the recursive search for images in selected folders (up to 1000 images!)
6. The combobox will adjust the level of magnification. The thumbs will be resized by means of the lens (blue rectangle in the right panel for the overview!).

• *.gif, *.jpeg,*.png, *. bmp,*.tiff (with preview!)
• *.pnm, *.pcm (without preview!)
• *.txt (e.g. macros, results!)
• *.roi (single ROI!)
• *.zip (Stacks, ROI Manager files!)
• *. LUT (Pseudocolor Image Look-Up Tables - A pseudocolor image is an image (8, 16 or 32-bit) with a look up table color assigned to it.

4.4.2.1 Mouse Actions Thumbnails Browser

4.5 The 3d Perspective

Figure 4.16 3D Perspective with the opened Java editor

4.5.1 The Space View

1public void setup(GL2 gl,GLU glu,GLUT glut){
2// Please enter your Java OpenGL setup code here
3​
4}  public void run(GL2 gl,GLU glu,GLUT glut){
5// Please enter your Java OpenGL code here
6 
7} 

4.5.1.1 Time

Figure 4.17 Time panel

4.5.1.2 Space

Figure 4.18 Space panel

4.5.1.3 Model

Figure 4.19 Model panel

4.5.1.4 Texture

Figure 4.20 Texture panel

4.5.1.5 Height Map

Figure 4.21 Height Map panel

4.5.1.6 Camera

Figure 4.22 Camera panel

4.5.1.7 Light

Figure 4.23 Light panel

4.5.1.8 Image

Figure 4.24 Image panel

1. Please do not call an OpenGL method from a different thread.
2. Generally create the following objects and models in the setup method: TextRenderer objects, Texture objects and *.obj models This ensures that the created objects in Fullscreen mode will be recreated with the correct gl context.

4.6 The WorldWind Perspective

Figure 4.25 The WorldWind Perspective with the opened Java editor

4.6.1 Control

Figure 4.26 Control panel

4.6.2 Default Layers

Figure 4.27 Default Layers panel

4.6.3 Layers

Figure 4.28 Layer panel

4.6.4 Render

Figure 4.29 Render panel

4.6.5 Measure

Figure 4.30 Measure panel

4.6.6 Projection

Figure 4.31 Projection panel

4.7 The R Perspective and Menus

4.7.1 R Menus in the Bio7 Main Menu

1. Start Rserve starts R with a Rserve connection.
2. With the Load Workspace action R workspaces can be loaded.
3. The Save Workspace action saves the current workspace.
4. Evaluate Expression opens a dialog where R expression can be evaluated. The evaluated expression will be displayed in the Console of the Bio7 platform.
5. Evaluate Selection evaluates the selected line in the R editor and then jumps to the next line. In Rserve mode the line will be parsed and only evaluated if an expression is valid. Else it will be added to a string buffer until a valid R expression is given by the evaluated lines (use STRG+C or the R-Shell view action to interrupt!)
6. The Evaluate Clipboard action evaluates R scripts which were transferred before to the clipboard.
7. The Get Clipboard Data action will transfer data from the clipboard to the workspace of R and is stored in a dataframe “clip”.
8. The action Remove all objects removes all objects from the current workspace.
9. Start RGui with Workspace action starts the standard R shell or RGui with the current workspace if started on theWindows OS (The path to the temporary file can be adjusted in the Preferences of Rserve).
10. The Preferences action opens the main R and Rserve preferences of Bio7

4.7.2 The R Perspective

Figure 4.32 The R Perspective

4.7.2.1 The Table View

• In the File menu the following imports and exports are supported:
  • Import: Excel (1997-2007, 2010), CSV, Bio7 XML (to load formatted spreadsheets with images)
  • Export Excel (1997-2007, 2010), Text, Bio7 XML (to save formatted spreadsheets with images)
• The Edit menu consists of several actions for copy and paste data, and edit sheet cells properties (color and size).
• The Sheet menu embeds several actions to create a new sheet, rename the sheet (or simply double-click on the tab!) or change the amount of rows and columns in the sheet.
• With the R menu data in the spreadsheet can be transferred to the R workspace as dataframes (with or without head) or as vectors of different types from selected data. Key combinations in a sheet work to select single values or portions of data (Strg + Mouse Click - select single cells, Shift + Mouse Click - select blocks). All cells of a row or column can be selected in the header (border) of the sheets.
• The Scripts menu can be extended with custom Groovy, BeanShell, Jython, R scripts (see 10.4↓).
• In addition a context menu is available which support typical actions like cut, copy, paste and delete (the typical keys for those actions work, too - Strg+x, Strg+c, Strg+v).

4.7.2.2 File Import for CSV Data

Figure 4.33 The CSV Reader dialog to import *.csv data

4.7.2.3 The R-Shell View

Figure 4.34 The R-Shell view in the R perspective

• With the Eval action valid R expressions (single and multiple seperated with a semicolon) can be evaluated.
• The Load and Save actions can save or restore evaluated commands stored in the available history (up to 100 commands!) of an R session.
• The RDocu action opens the documentation of R in an external Webbrowser.
• The ? action opens the documentation for a given keyword (package, method, etc.) in an internal webbrowser of Bio7.

• The List action updates the data view of an active R workspace.
• The Del action removes selected data view variables (2) from the R workspace (single and multiple selections are possible! - Strg+left-click or Shift+left-click).
• The GC action triggers the garbage collection of R to free up space from the RAM.
• The Clear action clears the display (3) of the right console.
• The Font action opens a font dialog for the adjustment of the fonts in the data view and display.
• The ? action opens information about the use of the different actions available.

• Show - Displays the values of the selected variable.
• Summary - Summarizes the values of the selected variable.
• Filter - Filter actions for the R workspace to display only selected data structures.
• Converts - Actions to convert a variable to a selected datatype.
• Transfer to Table - Actions to transfer data of the R workspace to the Table view of Bio7.
  • Dataframe with Head: This action transfers a selected R workspace dataframe in the data view to the Table view in a new sheet. The first row will be transferred as the header.
  • Dataframe: The same action as above but without a header.
  • Matrix: This action transfers a selected R workspace matrix in the data view as a new sheet in the table view.
  • Vector to Rows: This action transfers selected R workspace vector data to a row of a selected Table sheet starting at the selected table cell position of the sheet.
  • Vector to Columns: This action transfers selected R workspace vector data to a column of a selected Table sheet starting at the selected table cell position of the sheet.
• Script Menus (below Transfer to Table menu item!) - Custom scripts can be saved in a special folder or subfolders (see: 10.4↓) to extend the context menu. Some default menus and scripts are available as examples.

• The key A transfers selected data values to the textfield (1) and concatenates the variables with a comma character.
• The key C transfers selected data values to the textfield (1) and concatenates the variables with a plus character.

Figure 4.35 The R Snippets view

4.7.2.4 The Packages view

Figure 4.36 The Install Packages tab

Figure 4.37 The Load Packages tab

Figure 4.38 The Attached Packages tab

4.7.2.5 The Plot Data View

Figure 4.39 The Plot Data view with context menu

4.7.2.6 The R Editor

Figure 4.40 The R editor with the opened context menu

The R editor of Bio7 supports the syntax of the R language. If an R file is created with the default wizard the extension of the created R script file is *r. If you have an *.r file outside the workbench, this file can simply be dropped to a project of Bio7. If a R file has been opened, the toolbar of the Bio7 application displays a new action item for the interpretation of R scripts (if a connection to the Rserver and R has been established).

Figure 4.41 The R editor with errors and warnings. Error and warning quick fixes are indicated with a light bulb icon. Quick fixes can be opened (and applied) when hovering over the underlined error or warning.

4.7.2.7 The Database View

1. Install the ODBC drivers and R packages (odbc, DBI)
2. Select one available default profile
3. Update the login data on the Database and (if enabled) SSH Tunnel tab. In additon customize the Custom Disconnect Code for a live connection. Please note if no database password should be stored for the database connection leave the password field blank. For each live database connection a password dialog will be opened to ask for the username and password (handy if you don’t want to store the database password or the password should be hidden in a public area)
4. Store the current profile with the Add Connection Profile action
5. Use the Connect action to establish a database connection
6. Use the Disconnect action to execute the R code given in the Custom Disconnect Code textfield

• The Add Connection Profile action stores the current settings of the Database and SSH (if enabled) entries in a new profile and adds the selected name to the list of available Stored Profiles (saved as a XML file in Bio7).
• The Delete Stored Profile action deletes the current selected profile and removes the profile from the Stored Profiles list.
• The Use SSH Tunnel option adds the settings of the SSH Tunnel tab to the database tab settings which will be previewed in the Preview textfield.
• The Preview textfield shows the current settings of the database and SSH connection which can be stored as a database profile.
• The Insert in Editor action transfers the database connection code to the current opened editor.
• The Connect action establish a connection with the credentials given from the Database and SSH Tunnel tab. The connection is stored in the variable con
• The Disconnect action executes R code given in the textfield Custom Disconnect Code (available to control the SSH connection!)

Figure 4.42 The Connection tab

1. The List ODBC Drivers action searches for available ODBC drivers on the OS and add them to the ODBC Driver list
2. The ODBC Driver list let you select a ODBC driver for a database connection by name found by the action List ODBC Drivers
3. The Server textfield to enter the server address of the database
4. The Database textfield to enter the database name of the connection
5. The Port to enter the port of the database
6. The User textfield to enter the username.If empty a login dialog will automatically be opened for the username and password
7. The Password textfield to enter the password of the database connection. If empty a login dialog will automatically be opened to enter the username and password

Figure 4.43 The Database tab

1. The SSH Host textfield and Port spinner for the server address and port of the SSH connection
2. The Username of the SSH connection (password should be stored in the SSH key!)
3. The Sleep spinner to execute the sleep command on the remote server (default to 10s)
4. The Private Key file textfield and file dialog action to set the location of the private SSH key
5. The Local Port to set the port for port forwarding (This setting lets you specify a local port that will be forwarded to your remote host and remote port)
6. The Custom arguments textfield to change or add custom SSH client options

Figure 4.44 The SSH Tunnel tab

4.7.2.8 Plotting

Figure 4.45 A R Plot opened in ImageJ as the default device

4.7.2.9 R Debugging Interface

1. The Debug Trace Action to start the debugging process.
2. The Stop action to stop the debugging process.
3. The Next action to go to the next statement.
4. The Continue action which continues with the execution without single stepping.
5. The Step Into action to step into function calls.
6. The Finish action to finish the current loop or function.
7. A Help action to display R debugging console commands.

Figure 4.46 R debugging perspective with debugging toolbar actions enabled.

1. Set a breakpoint.
2. Set a conditional breakpoint - Syntax e.g. : if (x==5) browser() which is a wrapper for: trace(fun, quote(if (x == 5) browser())).
3. Edit a conditional breakpoint.
4. Delete a selected breakpoint.
5. Delete all breakpoints.

4.7.2.10 R Plot Preferences

Figure 4.47 Rserve preferences to select and adjust the R plot device

In the preferences several options are available to adjust the R plots. The default plot size can be changed in the textfield Device Definition (or the whole plot definition). Beside the option to plot images in ImageJ it is possible to open plots in different applications. Some templates in the preferences can be selected to switch e.g. to a *.pdf (multiple plots can be displayed) or *.svg plot (displaying a single plot) which will be opened with the default registered software if available – for *.svg i recommend http://www.inkscape.org to improve the plot appearance). Antialiased image plots can be enabled with the Image Cairo option. To change the default Device Definition in the textfield press the action Apply. With the Special image plot options plots can be opened in individual image tabs or macros can be excuted after image creation (handy if you automatically want to scale images after plot creation). Please note that the preferences will be saved if you press the OK or Apply button.

4.7.2.11 Help

Figure 4.48 The Help Browser

4.7.2.12 Rserve preferences

Figure 4.49 Main Rserve preferences

• The path to the R install location.
• The default package install location.
• The Path to temporary R folder options sets the path to the Bio7 R temp folder. In the temp. folder some plot images and R files are temporarily stored.
• The Install path at startup option installs a registry path to R in the Windows registry (deprecated).
• The option Check at startup for running R process(es) warns for running R processes which can interfer a newly started R/Rserve native process.
• The Rserve startup arguments can be adjusted to start Rserve with custom arguments.
• The R startup arguments can be adjusted to start R with arguments when started together with Rserve.
• The Rserve TCP client port option configures the running Rserve client port of the rserve application.

4.7.2.13 R Editor

4.7.2.14 Native R Excution

4.7.2.15 Create R Packages

• Build PDF From .Rd to create PDF documentation of *.Rd files.
• Check R Package - To check if the package is properly configured.
• Build R Package - to start the build process of the package
• Install R Package - to install the R package.

Figure 4.50 Dialog to create R package skeleton

4.7.2.16 Create R Packages with the devtools package.

• Setup - Setup R package in (project) folder (devtools)
• Load All - Simulates installing and reloading (devtools)
• Document - Updates the documentation, etc. (devtools)
• Test - Tests the packages (devtools)
• Install - Installs the packages
• Build - Builds the packages
• Check - Checks the packages
• Build Windows - Builds the package on Windows
• Run Examples - Runs all examples of the package
• Check Manuals - Checks all manuals
• Release - Releases the package

4.8 Document Perspective

4.9  The HTML Perspective

Figure 4.51 The HTML Perspective

The HTML perspective is a special perspective to create websites with the HTML editor of Bio7. The HTML editor will be opened if a *.html file is selected or created. It contains two tabs to switch between the source editor and a text interface based on JavaFX. Projects are stored and displayed in the Navigator view (left) which is also displayed by default in this perspective. You can use the Bio7 file wizard to create a new *.html site. With the Open In Browser action the created content can be displayed in the default browser of the OS (embedded as a Browser view below the editor).

4.10 The 2d Perspective (hidden by default)

Figure 4.52 The 2d Perspective

4.10.1 The Quadgrid

1/*A simple example to show how to produce and set random cells!*/
2​
3int rand; // A random number variable!
4​
5public void run() {
6	for (int y = 0; y < Field.getHeight(); y++) {
7​
8		for (int x = 0; x < Field.getWidth(); x++) {
9			rand = (int) (Math.random() * Bio7State.getStateSize());
10			Field.setState(x,y,rand);
11			Field.setTempState(x,y,rand);
12​
13		}
14	}
15​
16}

4.10.1.1 Transfer Quadgrid Data and Patterns to R

• Transfer of population counts: The first action transfers population counts of all current states to R. The counts can be deleted in the toolbar with the Counter Reset action (see 4.10.5↓).
• Transfer of pattern: The second action transfers the current state pattern as a matrix to R.

4.10.2 The Hexgrid

Figure 4.54 The Hexgrid view

4.10.3 Randomize the Quadgrid (Hexgrid)

• Maxlevel (maxlevel) adjusts the maximal number of recursions. The default action creates a 2 ^Maxlevel* 2 ^Maxlevel grid pattern from activated states (integers) in the quadgrid.
• Standard deviation (sigma) adds the intial standard deviation.
• Fractal dimension (H) this parameter determines the fractal dimension (D = 3 - H)
• Random additions (addition) turns random additions on/off.
• Seed (seed) adjusts the seed value for the random number generator (the action Shuffle creates a random number)
• With the Create Weights action state changes (if changed in the quadgrid) are considered and the amount of weights are set with equal proportions in the textfield. It is possible to change the value (proportion in the Quadgrid) for each state in the textfield individually.
• The Create Image option can be selected to create a random pattern with float numbers in ImageJ (e.g. for a height map or continous clumbed nutrient matrix). The default values can be multiplied with a scale factor in the Scale box.

Figure 4.55 Midpoint 2D dialog to create random patterns

4.10.4 The Linechart and the Piechart

4.10.5 Recording the Amount of States over Time

4.10.6 The Time and Space Control

• The first slider (Speed) is responsible for the calculation speed of the calculation thread. It can be set to values from 10-1000 units.
• The visible sliders below (Fieldsize) can be moved to values from 1 to 2000. They are responsible to adjust the field size of the different grids in Bio7 (Quadgrid, Hexgrid) The maximum field size which can be adjusted in Bio7 is a field size of 2000*2000. When moving the sliders for the field size several views will be updated instantly. TheQuadgrid panel will be updated when a resize event takes place (the Hexgrid panel and the visualization of 3d panel only if opened). After resizing the new indexes (2d grid array) are instantly accessible (e.g. programmatically).
• When the checkbox Resize after adjust is activated the resizing takes place after the button Resize has been pushed. This is recommended when the field size is >400 because the resizing then is done in one call. Info: The speed of a resize event is also dependant on the amount of grid panels which are currently visible in the Bio7 window (e.g. Quadgrid, Hexgrid or 3d panel!).

4.10.7 Spreadsheet

4.10.7.1 Spreadsheet Toolbar

• With the toolbar textfield new states can be defined (press the + button or press Return).
• Selected states in the “Delete” column can be deleted with the “Delete” action.
• If a state in the spreadsheet is selected the state can be set in the quadgrid (via the mouse device - click or drag).

4.10.8 File Storage of Patterns

4.10.8.1 The State View

4.11 Custom Perspective, Views and Menus

4.11.1 Custom Views

Figure 4.56 Custom JavaFX view

4.11.2 Custom Menus

4.11.3 Custom Startup

• BeanShell, Groovy, Jython, R, JavaScript, ImageJ customizations or imports at startup.
• Open or close a custom perspective or a view.
• Execute a startup setup in the different panels.
• Invoke an action from the Bio7 platform.
• Import libraries.
• Start a server application at startup.

5 The Editors of Bio7

5.1 General Features

• Before creating a file, a Project has to be created where the files can be placed (File ▷ New ▷ General ▷ Project).
• A file can be created by using a wizard, which can be activated in the File menu. (File ▷ New ▷ Other ▷ xxx) or in the context menu of the Navigator. (e.g.: New ▷ Other ▷ xxx).
• The file itself will be opened in the editor area, which can be hidden or shown in a perspective by selecting the action Window ▷ Show/Hide Editor.

Figure 5.1 Dialog to create projects and files with a wizard for the different editors

5.1.1 Editor Code Templates

Figure 5.2 Editor code templates

Figure 5.3 Template preferences

5.1.2 Preferences of the Editors

5.1.3 The R Editor

5.1.4 R Markdown Editor

5.1.5 LaTeX Editor

5.1.6 HTML Editor

5.1.7 Java

Figure 5.4 The Java editor of Bio7 with opened context menu

Since Bio7 2.0 the JDT Java editor is used to edit Java source files. A description of the JDT editor can be found on the Eclipse documentation website http://help.eclipse.org/luna or in the Bio7 help.

5.1.7.1 Since Bio7 1.7.1 Full Class and Multiple Class Compilation is Supported!

Figure 5.5 Java compiler preferences to switch e.g. between dynamic classbody (deprecated) and (multiple) class compilation (1). The editors colours and fonts (2) can be adjusted, too.

5.1.8 BeanShell and Groovy

1. Need for speed in complex applications: The embedded Java compiler compiles the Java code to bytecode while the interpreted languages interpret the code which is much slower and sometimes is not sufficient for resource intensive calculations (though compiled code will be executed also very efficiently by BeanShell, Groovy or Jython!). However new versions of the different interpreters close this speed gap more and more.
2. Scripting capabilities: With BeanShell, Groovy (and Jython) it is possible to create highly dynamic applications with customized scripts. Script templates like the snippets can easily be recycled for custom modifications. Scripts can be used to extend the Bio7 Script menus.
3. Direct interaction: With the BeanShell, Groovy (or Jython) console you can interact directly with the methods and integrated API’s of Bio7.

5.1.8.1 Special Actions in the Context Menu of the Java and BeanShell/Groovy Editor

1. Add Block Comment: Surrounds the selected code with a block comment.
2. Remove Block Comment: Removes a selected block comment. (A precise selection is necessary!).
3. Format Java: Formats regular Java code (To work with BeanShell or Groovy please create Java code inside the BeanShell/Groovy editor!).
4. Format selected Java: Formats only the selected code. This is sometimes necessary if the formatter can not format the entire code.
5. R Source Conversion: Converts Rscript code. This converter helps to convert R expressions for the use e.g. in an BeanShell or Groovy script using the Rserve API.

5.1.9 The Python/Jython Editor

1# A Jython example which overrides the run method
2# of the inherited Model class of Bio7!
3# The method run can be called from the Start/Pause action
4# of the Bio7 toolbar!
5​
6class jythonClass(Model):
7​
8def run(self):
9#print index
10Field.chance();
11Field.doPaint();
12​
13#We instantiate the class!
14model = jythonClass()
15#We set the class as the compiled class!
16Compiled.setModel(model);

5.1.9.1 Native Python Execution

1# A Python Py4J example which transfers values
2# from the ImageJ Results table and plots them with
3# the Matplot lib.
4# For this example Py4J has to be installed in Python
5# and the Py4J Server has to be started!
6​
7import numpy as np 
8import matplotlib.pyplot as plt 
9from py4j.java_gateway import JavaGateway 
10from py4j.java_collections import JavaArray
11​
12gateway = JavaGateway() 
13results=gateway.jvm.ij.measure.ResultsTable 
14analyzer=gateway.jvm.ij.plugin.filter.Analyzer
15​
16#get the results from the Java ImageJ API!
17rt=analyzer.getResultsTable() 
18res=rt.getColumn(0) 
19lastCol=rt.getLastColumn();
20​
21values=[[0 for x in range(len(res))] for x in range(lastCol+1)]
22for x in range (0,lastCol+1): 
23	vals=rt.getColumnAsDoubles(x) 
24	if (isinstance(vals,JavaArray)): 	
25		print (’’)   		   		
26		for y in range (0,len(res)): 			
27			values[x][y]=vals[y]
28​
29#Plot the values!
30plt.boxplot(values) 
31plt.show()

5.1.10 The ImageJ Macro Editor

Figure 5.6 The opened ImageJ Macro editor

In the ImageJ Edit perspective several views are arranged to support the creation and execution of ImageJ Macro files. A special debugging interface is available in the Debug view.

5.1.5 The Flow Editor

• It can be used to create complex sensitivity analysis for created models
• It can serve as a guide for complex analysis of all tools offered by Bio7.
• Or it simply can be used to visualize complex workflows.

Figure 5.7 The Flow editor

If the editor is opened default actions will be added to the Bio7 toolbar (1) and a new menu will appear in the menubar of the application. Additionally, a specialized context menu will be available for calling different methods inside the Flow editor. In the flowchart of Bio7 files can simply be dragged from the Navigator view (2) of Bio7 and dropped into the Flow editor (3) of the application. According to their file extension these files are executed in the sequence of the flow which has been created. A created Flow editor file has the extension *.ecoflow. Some other files will be handled by default from the Flow editor when they are dragged from outside the workspace. Executable files (*.exe) will be executed, too and it is also possible to execute these files with an argument (by creating a file with the extension *.argument). Files from external that have different extensions will be executed according to their registration in the system environment. Furthermore an Outline view (4) on the left will show an overview of the flow - if the flow cannot easily be displayed in the main window because of its size a blue rectangle will be displayed in the Outline for a flow selection. The selection is the area of the flow which can be displayed in the main Flow editor window. A new Palette bar (5) will also be displayed for inserting flowchart elements in a newly created file.

5.1.10.1 Execute and Verify a Flow

5.1.10.2 The Palette of the Flow Editor

1. Start : The start of the flow - necessary for execution !
2. Stop : The end of the flow - necessary for execution !
3. Loop : A loop will repeat a sequence in the flowchart. The number of iterations can be adjusted with an integer value directly in the shape (click and hold ca. one second to edit).
4. Decision : A decision in the flow will execute an if statement. According to a self defined condition a static variable (Bio7Flow.setDecision(“true”)) can be set to true or false. The direction of the flow then depends on the linked connection which can be set to true or false in the properties dialog (select the connections to set the values).
5. Info : A single line label for an info which can be edited in the shape.
6. Connection: To determine the sequence of the flow Connections are available to connect components. If selected in the Palette directed connections can be drawn from component to component.
7. Selections can be made with the Marquee tool and the Select tool (multiple selections are possible).

• With the Zoom In, Out actions it is possible to zoom in or to zoom out in the flow (by using the combo box or the lens items). If an opened flow was changed, the toolbar items for undo and redo could be used to undo or redo changes in the flow.
• Furthermore components can be deleted with the Delete item and so removed from the flow (or by pressing the delete key).
• If more than one component is selected the alignment actions (Align Width, etc.) and the Match Width/Height actions will be available to align shapes to the first selected shape or adjust the width or the height of selected shapes to the properties of the first selected component.
• Additionally the added menu Flowaction in the menubar of Bio7 offers three further options for the alignment and layout of the components.
• When the option Rulers is selected and marked rulers in the flow will be made visible for the exact layout of the flow components. By dragging horizontal and vertical lines from the ruler (like it is known from image software) components can easily be aligned to the visible ruler lines. The alignment will be supported by artificial lines (red lines) which occur when the alignment criteria are met.
• The option Grid will enable a grid in the flow. When enabled, the components can be arranged in discrete coordinate steps according to the default grid size in the flow. Furthermore artificial lines will occur (green lines) with the enabled option Snap to Geometry when a translated component matches the alignment of another component in the flow. The grid size can be adjusted in the context menu of the Flow editor.

1. The options Manhatten Router and Shortest Path action are responsible for the layout of the connections.
   1. The Shortest Path action applies the shortest path algorithm to find paths around obstacles in the flow.
   2. The Manhatten Router algorithm will use rectangular lines for connections in the flow.
2. The Save action will save the current flow to the before defined file (Save as in the Bio7 main menu available!).
3. The Save Image action will save an image in the formats *.gif*, *.jpeg, *.ico to a file. The current size of the flow will determine the pic size (the rulers display the size of the flow in pixel. So be cautious not to store large images with a resized flow !).
4. The Debug Mode option enables a visualization of the current flow by colouring the active shape white to mark files that are currently interpreted or compiled, etc. A mouse-click on the flow deletes marked components.
5. Size Layout Grid opens a dialog to resize the grid (layout) if enabled.

1. The File/Loop/Info/Condition property displays the following attributes in dependence of the selected component:
   1. The filepath of a dropped component (relative path in the workspace. This path will be used for execution!)
   2. The amount of loops which should be made when the loop component has been selected.
   3. An info text if the info component has been selected.
   4. When a decision component has been selected this property will be interpreted as a scripting expression in BeanShell.
2. The filetype property shows the extension of the selected file, which has been dropped into the flow (has no effect on the other components).
3. The properties Height,Width, X,Y display the size of the component and the location inside the flow which can also be adjusted in the properties view.
4. There are two properties if a connection is selected.
   1. The property LineStyle can be set to dashed or solid (by default the style is solid).
   2. The Boolean property is important when a decision is created in the flow. The property can be set to true or false.

1. A start and a stop component have to be placed in the flow and they have to be connected with the components for a regular Bio7 flow.
2. A flow follows the outgoing direction (directed graph) marked with an outgoing arrowhead.
3. Files:
   1. A dropped file in the flow editor (rectangular shape) can only be connected with another file or by means of a loop which connects on or two files.
   2. A file component has to have one outgoing connection.
   3. Files in the flow editor will be executed sequently by means of the information in the file property and the filetype property (the appropriate interpreter or program will be selected automatically).
4. Loops:
   1. A loop can have one incoming and one outgoing connection.
   2. A loop cannot be the first component (after the start) in a Bio7 flow.
   3. It is possible to execute a loop with one file component.
   4. Loops can be created nested. The loops are executed “iteratively” (not “recursive” !).
   5. A loop can be connected (point) to a decision .
5. Decisions:
   1. A decision gets an input from a component and has to have two outgoing connections. One connection has to be set to false and the other has to be set to true.
   2. A decision can be connected to another decision (else if).
   3. A decision cannot be connected (point) directly to a loop.
   4. It is allowed in Bio7 to place a decision right after the start.
   5. The condition of a decision component can be set directly in the properties view or in the component itself. The static variable decision has to be set to "true" or "false" (type: String) to follow a connection with the appropriate value - (API method: BatchModel.setDecision(“true”);).
6. Info: An info component can be placed outside the connected flow for an information display. It is also allowed to draw connections to a file component as a pointer (optionally you can mark this connection with a changed line style).

6 Preferences

6.1 The Bio7 Preferences

6.1.1 Application Paths

Figure 6.1 Bio7 path preferences

6.1.2 Script Paths

6.1.3 Bio7 Editor Preferences

• Preferences Bio7 ▷ Preferences xxx-Editor for changing the default colours.
• Preferences Bio7 ▷ Preferences xxx-Editor ▷ Template Editor xxx to change the default templates.

6.1.4 Preferences Rserve

6.1.5 Default Platform Preferences

7 Help

8 Update Manager

Figure 8.1 The Update Manager

With the update manager Eclipse plugins can be easily installed or deleted. Update sites can be added as a installation source for existing external plugins. Installed third party plugins locations can be managed in the Available Software Sites preferences. Plugins can be deinstalled following the already installed link - it is even possible to return to a certain state of installation because the Eclipse Framework registers all configurations dates and changes. For more information about the update manager please consult the Eclipse documentation http://help.eclipse.org.

9 Additional Views and Interfaces

9.1 Additional Eclipse views in Bio7

• The Bookmarks view is a view which shows marked bookmarks in all language editors of Bio7 to easily find points in code which have to be edited.
• The Tasks view in the R-Editor serves as a marker for plots in the source code. For all other editors it can be used to leave some information about tasks that have to be done or as information in the Bio7 language editors (They can be marked with different priorities!).
• The Problems view to indicate compiler error and problems.
• The Cheat Sheets view can be used to load created Cheat Sheets from Eclipse.
• The Progress view shows information about running jobs in the application. Each time a job has started this progress view can be opened in the progress dialog of the status bar.

9.2 Java and Script Interaction with R

1. Custom GUI’s can be created in Java or in the script interpreters and the values can be evaluated in R. After evaluation the results can be sent back to the interpreters workspace or to a method in Java.
2. Build frontends for R methods with a scripted language (e.g. in JavaFX or SWT).
3. Interaction between R and the API of ImageJ to automize image analysis tasks.
4. Extend the script menus of Bio7 with R methods called by the script interpreters.

9.3 LibreOffice features of Bio7

1. To receive or transfer values from or to the spreadsheet of LibreOffice it is necessary to open a spreadsheet. This can easily be done with the action LibreOffice ▷ Open Spreadsheet. After a spreadsheet has been opened (also possible by means of a small API) the spreadsheet can be filled with values by hand or with values from a file (in the opened spreadsheet menu of LibreOffice call the menu action: Insert ▷ Sheet from file).
2. With the action Data to R LibreOffice spreadsheet values can be transferred to the active R workspace by means of the Rserve connection (the columns will be stored as lists and the selected values as a dataframe).
3. With the action Data with head to R numeric values (type double) with a head can be transferred directly to R.
4. With the action Send Bio7 counts counted values of the activated states in a simulation for all time steps are transferred to an opened spreadsheet which then can be stored to all kinds of data files.
5. There is also a small API available for the transfer of data (get and set), inserting new sheets, getting values from sheets and the marking of the data in a spreadsheet (see Bio7 Snippets and Bio7 API docs).

10 What else ?

10.1 Native Preferences

Figure 10.1 Native preferences of Bio7

• None will simply startup Blender without a Python script execution (arguments can be specified in the Blender Arguments).
• The option Interactive Shell if selected starts the Python connection as an interactiv shell (argument: --python-console). A special script customization is possible by defining code elements which will be executed before and after the editor code (the default code in the two textfields redraws the 3d GUI of Blender!)
• The option Python Script starts Blender and executes the editor script in Blender Python without an interactive shell.
• With the Blender Arguments additional arguments can be specified for the startup of Blender (e.g. with the option None some rendering tasks can be executed instead of executing a python script).

10.2 Drag, Drop, Compile and Start

10.3 Drag and Drop Files

10.4 Install Eclipse, R, ImageJ Plugins or Packages in Bio7

1. To install (suitable) Eclipse plugins the Update-Manager can be used to install plugins from a remote website.
2. R packages can be added in two different ways. One way is to use the package installer GUI of Bio7. Additionally the command line in R can be used to install packages.
3. ImageJ plugins (*.class or *.jar files) have to be installed in the plugins folder of ImageJ which is is located in Bio7: Bio7/plugins/com.eco.bio7.image_x.xx.x/plugins. Note: In the ImageJ Eclipse plugin the typical ImageJ folder structure can be found!
4. Groovy, BeanShell, Jython, JavaScript and R scripts, as well as ImageJ macros can be dropped to special folders to extend the default Bio7 menu (startup) functionality. The folders which are scanned by default are shown in the table below.

10.5 Bio7 Themes

Figure 10.2 Dark theme of Bio7 MacOSX

10.6 Install Git

Figure 10.3 Installation of the EclipseGit plugin

10.7 Bio7 Browser

Figure 10.4 The Bio7 Browser view

10.8 Uninstall Eclipse Plugins

10.9 Programming Examples for Bio7

11 Literature and Links

11.1 Scientific Libraries Available in Bio7

• JScience http://jscience.org/
• Colt http://dsd.lbl.gov/~hoschek/colt/
• Math http://jakarta.apache.org/commons/math/
• Weka http://www.cs.waikato.ac.nz/ml/weka/
• JTS http://www.vividsolutions.com/jts/JTSHome.htm
• Joone http://sourceforge.net/projects/joone/ JDMP http://www.jdmp.org/

11.2 Documentation and Programming Links:

• BeanShell http://www.beanshell.org/
• R http://www.r-project.org/
• Rserve http://www.rforge.net/Rserve/
• ImageJ http://rsb.info.nih.gov/ij/
• JavaCompiler http://www.janino.net/
• Groovy http://groovdehaus.org/
• Forums http://www.nabble.com (search for the different applications BeanShell, R, ImageJ, Janino)

12 Addendum

• To use programmatically: Work.openView("Id");
• Example: Work.openView("com.eco.bio7.quadgrid");

• To use programmatically: Work.openPerspective("Id");
• Example: Work.openPerspective("com.eco.bio7.perspective_2d");
• A saved custom perspective is available by it’s name !
• Example: Work.openPerspective("Custom"); //if saved as “Custom”
• Bio7 API : A small API is integrated in Bio7. The API is available within the help of Bio7.

13 Definition of Expressions

• Area of Analysis: A name for the area in the Points panel which is marked by a green rectangle for spatial point patterns.
• Programmatically: Using programming to accomplish a task.
• Namespace (BeanShell) : A namespace in which methods, variables, and imports (class names) live.
• Workspace (R): A saveable environment in which methods, variables and objects exists.
• Workspace (Bio7): The location where the projects and files are stored.
• Calculation thread: A time dependent execution of a compiled method (ecomain) in Bio7 started, e.g. with the Play/Pause button.
• Discretize: In Bio7 the process of transferring continuous data to discrete data.
• IDE (Integrated Development Environment): a type of software that assists in developing software.
• Snippets: In Bio7 a small piece of programming source code to demonstrate some of the Bio7 features.