18.05.2018

The next release of Bio7 adds a lot of new R features and improvements. One minor change is that the default perspective after the startup of Bio7 now is the R perspective to emphazise the importance of R within this software.

The R-Shell view has been simplified and the R templates have been moved in it’s own simple view for an improved usability (see screenshot from R perspective below).

In addition the context menu has been enhanced to allow the creation of submenus from scripts found in folders and subfolders (recursively added) which you can create for a menu structure.
Scripts can be added created in R, JavaScript, Groovy, Jython, BeanShell, ImageJ Macros.
Java (with dependant classes) can be dynamically compiled and executed like a script, too.

Several improvements have also been added to the R-Shell and the R editor for an easier generation of valid R code. The R-Shell and the R editor now display R workspace objects with it’s class and structure in the code completion dialog (marked with a new workspace icon – see below).

R-Shell:

R editor:

In the R editor a new quick fix function has been added to detect and install missing packages (from scanned default packages folder of an R installation – has to be enabled in the Bio7 R code analysis preferences).

Also the detection of missing package imports are fixable (when a function is called but the installed package declaration is missing in the code but the package is installed to deliver the function).

The code assistance in the R-Shell and in the R editor now offers completions for, e.g., dataframes (columns) in the %>% operator of piped function calls:

In addition code assistance is available for list, vectors, dataframes and arrays of named rows and columns, etc., when available in the current R environment.

Code completion for package functions can now easily added with the R-Shell or the R editor which loads the package function help for both interfaces. The editor will automatically be updated (see updated editor marking unknown functions in screencast below).

Numerous other features, improvements and bugfixes have been added, too.

Bio7 2.8 will hopefully be available soon at:

https://bio7.org

Overview videos on YouTube

 

 

08.01.2018

I recently discovered on a high dpi display (Retina-Display) enabled 13’’ notebook that the latest release of Bio7 for MacOSX is not displayed in high dpi but in a lower resolution which makes text and icons blurry (scaled) and unnecessary strains the eyes when editing R scripts with the R editor.

So I uploaded a new, fixed version for MacOSX.

However, to fix an already downloaded version of Bio7 you have to open open the ‘/Bio7.app/Contents/Info.plist’ file with a text editor (right-click on Bio7.app, execute ‘Show Package Contents’ and open ‘/Contents/Info.plist’) and add the following lines before the </dict> tag:

<key>NSHighResolutionCapable</key>
<true/>

In addition to update the Info.plist file for the Operating System you have to open the Terminal (in ‘Applications/Utilities’) and execute the following command (default install directory – shell command is one line!):

/System/Library/Frameworks/CoreServices.framework/Frameworks/LaunchServices.framework/Support/lsregister -v -f /Applications/Bio7.app

Here some screenshots from before and after the fix was applied on a Retina-Display (zoom in for details):

Before:

After:

An updated version with the fix already applied can be downloaded here

See also:

Release notes for Bio7 2.7

 

20.10.2017

Beside a massive of amount of R packages and ImageJ plugins Bio7 can be extended with Eclipse plugins useful for data science and programming.

Some of them could also be very useful for R related developments (e.g., to develop R packages or distribute Shiny apps).

Installation of Eclipse Plugins

One  way to install Eclipse plugins is by using the Update Manager in the help menu (Help->Install New Software).

Thus the first step to install a plugin is to open the Update Manager and selecting the category “Eclipse Repository – http://download.eclipse.org/releases/neon” (see screenshot below!)

Another handy way of searching and installing Eclipse plugins is by using the Marketplace Client plugin which must be installed firstly with the Update Manager.

Search for the Marketplace Client (e.g., “marketplace”) plugin to filter, select and install the Marketplace Client.

The following plugins can be installed using either the Marketplace Client or the Update Manager.

Database Remote Files and Shells

EGit

https://marketplace.eclipse.org/content/egit-git-team-provider
The powerful Eclipse Git plugin to connect Bio7 with Git repositories.

TM-Terminal

http://marketplace.eclipse.org/content/tcf-terminals
A true native terminal with SSH,Telnet and Serial line support. Bio7 comes already with a pseudo-terminal but lacks the support of a pty connection and ANSI escape sequences (but can be controlled from a Bio7 API interface). The terminal can also be installed with the Update-manager searching for “tm” (see screenshot below).

Remote System Explorer

https://marketplace.eclipse.org/content/remote-system-explorer-ssh-telnet-ftp-and-dstore-protocols
A plugin to connect Bio7 with SSH, Telnet, FTP and DStore protocols.This plugin work very well with a remote connection and makes it easy to transfer data from a local workspace to a remote server. Remote files can be opened, edited and stored with the available Bio7 editors (e.g., a *.html file with the JavaFX editor – see screenshot below).
Apropos, please use an OpenSSH key for, e.g. a SFTPconnection!). It works great together with the TM-Terminal plugin.

DBWeaver

https://marketplace.eclipse.org/content/dbeaver
“DBeaver is free universal SQL client/database tool for developers and database administrators. It can work with any database server which has JDBC driver.” (source: website DBWeaver)
DBWeaver is a great database tool and plugin for Eclipse and can also be installed into Bio7 to control and edit R database connections.

Scripting Editors with Bio7 interpret support

The following three editors can be used within the current Bio7 process to execute scripts using the Bio7 interface. It is important however to create a language project first to profit from the advanced editor features.

Bio7 will recognize the opened editor type and interpret the current opened script with the embedded script interpreter of Bio7 when using the dedicated toolbar action.

Please use the context menu action “Open with” to open the scripts with the installed editors instead of the default Bio7 editors (Groovy, Jython/Python editors are available by default in Bio7).

Here a video installing and using the JavaScript editor as an general example.

JSDT

https://eclipse.org/webtools/jsdt/
JavaScript editor and development tools. Install with the Update-manager (search for JavaScript – see video above).

PyDev Editor

https://marketplace.eclipse.org/content/pydev-python-ide-eclipse
A very powerful Python editor which can be used to execute Bio7 Jython and Python scripts instead of the Bio7 default editor.
In addition Bio7 can use the PyDev editor to execute scripts running on the Bio7 Java classpath. If you open Jython/Python scripts with the PyDev editor the default Bio7 action will be visible to execute the scripts on the Bio7 classpath.

Groovy Editor

https://github.com/groovy/groovy-eclipse/wiki
(Add site: http://dist.springsource.org/snapshot/GRECLIPSE/e4.7/ to the Update Manager)
A more powerful Groovy editor. Can also be used with the Bio7 classpath if scripts are opened with this editor instead.

General programming editors and extensions

Eclipse CDT

https://marketplace.eclipse.org/content/eclipse-cdt-cc-development-tooling
Powerful C/C++ editor and development tooling.

Arduino C++ IDE:

https://marketplace.eclipse.org/content/arduino-c-ide
A great Arduino extension of the C++ editor of Eclipse. See this video for an introduction. Bio7 embedds some Java libs to communicate with an Arduino (see Bio7 examples).

Photran (comes with PTP)

https://eclipse.org/ptp/
http://www.eclipse.org/photran/
An Integrated Development Environment and Refactoring Tool for Fortran

Julia Editor

https://github.com/JuliaComputing/JuliaDT
A Julia editor in an early stage. But very promising.

Bash Editor

https://marketplace.eclipse.org/content/bash-editor
A bash editor for bash scripts. Perfect for the use with the above linked TM-Terminal and Remote Systems Explorer.

Jeeeyul’s Eclipse Themes

https://marketplace.eclipse.org/content/jeeeyuls-eclipse-themes
To install more themes into Bio7.

pde-tools

https://github.com/jeeeyul/pde-tools#crazy-outline
A plugin which adds clipboard history support and a crazy outline view.

WindowBuilder

https://marketplace.eclipse.org/content/windowbuilder
A very powerful builder for Graphical User Interfaces for SWT, etc.
In Bio7 a wizard is available to create a template for the builder (File->New->Bio7 Java Projects->Bio7 Java Project (WindowBuilder template)).
You can then open this template with the WindowBuilder to create interfaces (e.g., to create R interfaces using the new Bio7 R API). The created interface can be compiled dynamically with Bio7 (compiling the main class) and executed instantly in the current Bio7 process (see screenshot below)

More plugins can be found with the Eclipse Marketplace Client. It depends however how useful the plugins are in the context of Bio7.

 

 

 

19.10.2017

I released a new version of Bio7 for MacOSX.

(Screenshots: Bio7 with Dark theme enabled. Scrollbars are set to “When scrolling” in the preferences.)

For an overview of the new features please consult the release notes of Windows and Linux here:

Installation:

Download and extract the installation file from http://bio7.org.

If you start Bio7 a warning or error can occur because of the changes how Apple treats signatures! To allow Bio7 to start see this instructions for Yosemite and Sierra:

OS X Yosemite: Open an app from an unidentified developer

macOS Sierra: Open an app from an unidentified developer

If you have still problems with Sierra see this solution!

In addition For MacOSX you have to install R and Rserve.

To install Rserve open the R shell and then execute the menu action “Options->Install Rserve (coop. mode)”. This will download an install Rserve in your default R library location, see video below (please make sure that your default MacOSX R library install location has writing permissions! – normally you don’t have to worry about this on MacOSX!).

The special version of Rserve can also be downloaded here:
https://bitbucket.org/maustenfeld/bio7-new/downloads

For a manual installation in the R prompt type the following command to install the compiled package (replace with your file path!):

> install.packages(“Users/yourName/Downloads/Rserve_1.8-4_Mac_cooperative.tgz”, repos=NULL)

Installation of Useful R Packages

R packages which are useful in combination with Bio7 can easily be installed with the main menu “Scripts” action:

Scripts->R-Scripts->InstallDefaultRPackages

Bio7 Documentation and Examples

For more information about Bio7 please consult the soon updated Bio7 User Guide.

A plethora of Bio7 videotutorials can be found on YouTube.

The latest Bio7 examples can be downloaded (download and import as *.zip) from Github here!

 

17.10.2017

A new version of Bio7 for Windows and Linux is available. The MacOSX version will be released soon, too.

The application Bio7 is an integrated development environment for ecological modelling, scientific image analysis and statistical analysis. Beside many different tools it contains a complete Graphical User Interface for R.

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.

For  a short overview see this older video.

New Features:

General

• Improved the dark theme for Bio7 2.6 (see Windows and Linux screenshot below)
• Improved the default Bio7 theme (see Linux screenshot below)

• Improved the theming of some Bio7 views (e.g., tables, text editors)
• Added a new shortcut for Windows and Linux to show or hide the Bio7 main menus  – CTRL(CMD)+2, CTRL(CMD)+3). By default the application frame, toolbar and the status bar can be hidden, too. (see screenshot below with hidden window and menu – set the key shortcuts in the preferences!)
• Bio7 2.6 is based on Eclipse 4.7.1a
• Added the ‘Project Explorer’ view to many perspectives and deleted the ‘Navigator’ view in some of the perspectives (the ‘Project Explorer’ view displays errors and warnings and supports pasting of clipboard Java code, etc.)
• Added a break and interrupt action for the windows shell to end ,e.g., a ssh connection (CTRL+BREAK) or interrupt an ongoing shell process (CTRL+C)
• Added an API to send commands to the Windows/Linux/MacOSX shell
• Added SSH for Windows
• Added the embedded SSH application path to the shell
• Added a new ‘ImageJ Edit’ perspective to execute ImageJ scripts, macros side by side with the ImageJ-Canvas (see ImageJ section below)
• Added a easy to use R API for Java/BeanShell/Jython/Groovy/JavaScript to execute R commands or scripts in an extra job (thread)
• Improved several import/export scripts (now with Groovy) with the new Bio7 R API.
• Improved the Linux shell (added the default xterm path)
• The R package install script now works with a native R shell connection.
• Shiny applications can now be tested from all folders (not only project folder – e.g.; from Git folders)

R Editor

• Added an action to surround selected code with a “try and catch” skeleton
• Added an Project view/Navigator view popup action to start a shiny app in a arbitrary folder
• Added an action to open and insert a hex color in the editor
• Added a hoover dialog to display and replace selected hex and R colors (see screenshot below)

• Added an action in the hoover dialog to select hex colors
• Added an action in the hoover dialog to select default R colors by name (see screenshot below)

• Added a new database view to the R perspectives to store or apply database profiles and connections

• Added SSH support for the database view (also for Windows!). Bio7 comes bundled with the latest SSH version of Windows

• Improved the code completion of the R-Shell
• Improved the default R package install script for Bio7
• Restructured the R editor context menu

ImageJ

• Added a full featured ImageJ macro editor with the following features:
  • Dynamic error detection (grammar derived from the ECMA grammar by Bart Kiers)
  • Toolbar action to execute ImageJ macros
  • Syntax highlightening
  • Editor debugging support (reusing and implementing interfaces and methods from – same keyboard shortcuts)
  • Code completion (with browser help)
  • Code templates (add you own templates)
  • Info popups (text hoover)
  • Outline view (var variables, variables, methods and macros)
  • Automatic closing of braces, parentheses and strings
  • Automatic indention of functions,loops, etc.
  • Code folding
  • Code formatting (based on the Eclipse-javascript-formatter by Sebastian Moran)
  • Resize fonts functions (with Ctrl++ or CMD++, CTRL+- or CMD +-)
  • Font preferences
  • Mark occurences (scope independant)
  • A copy function for the ImageJ forum

• The ImageJ view menu is now right aligned and foldable to the left
• Updated ImageJ to version 1.51r
• Several bugfixes for the ImageJ compatibility

Download and Installation:

Windows:

Just download the *.zip distribution file from http://bio7.org and unzip it in your preferred location. Bio7 comes bundled with a Java Runtime Environment, R and Rserve distribution and works out of the box.

Linux:

Download and extract the installation file from http://bio7.org.

For Linux you have to install R and Rserve.

To install Rserve open the R shell and then execute the menu action “Options->Install Rserve (coop. mode)”. This will download an install Rserve in your default R library location, see video below (please make sure that your default Linux R library install location has writing permissions!).

The special version of Rserve can also be downloaded here:

https://bitbucket.org/maustenfeld/bio7-new/downloads

For a manual installation in the R prompt type the following command to install the compiled package (replace with your file path!):

install.packages(“Users/yourName/Downloads/Rserve_1.8-4_Mac_cooperative.tgz”, repos=NULL)

Installation of Useful R Packages

R packages which are useful in combination with Bio7 can easily be installed with the main menu “Scripts” action:

Scripts->R-Scripts->InstallDefaultRPackages

Bio7 Documentation

For more information about Bio7 please consult the soon updated Bio7 User Guide.

A plethora of Bio7 videotutorials can be found on YouTube.