Knitr with Bio7

16.04.2015

In Bio7 it is possible to write a documentation in knitr. A simple visual and textual HTML editor (based on JavaFX) and an embedded Latex editor (based on TeXclipse) helps in the creation of a *.html or *.pdf documentation. For the *.pdf creation a TeX environment has to be available (Windows e.g. MiKTeX).

Overview video:

Note that there is still a bug in the visual JavaFX HTML editor (JavaFX SWT bug) to select text in the visual part of the editor. A workaround is to use the combination of Shift- or Ctrl-key and a mouse-click.

In upcoming releases more improvements for R reports will be available in Bio7.

 

Bio7 2.0 for Windows 32 bit Release

24.03.2015

Because of some requests of a Windows 32 bit version of Bio7 2.0 I uploaded a built to sourceforge.

Release notes:

  • Updated R to version 3.1.3
  • Updated ImageJ to version 1.49p
  • Added some ImageJ dialog options (to stay on top, e.g., the ROI Manager)
  • Updated Java to version 1.8.40
  • Updated the JavaFX embedded SceneBuilder to Java 1.8.40

If you don’t know Bio7 here is an overview of the features (not only R):

Bio7 can be downloaded here:

http://bio7.org

Documentation and Videos Tutorials:

Documentation

Video Tutorials YouTube

 

 

Solving CentOS 7, Fedora Problems at Startup Wrong Layouts

02.02.2015

Here I describe some notable Linux distribution errors which can be corrected with the following startup options (1) and CSS changes (2).

1. Startup Problems

There seems to be problems with CentOS 7  in general. If the application does not start correctly, e.g., the Bio7 window will not be shown then add the following arg (e.g., with a text editor) to the Bio7.ini file in the Bio7 base folder (installation folder).

–launcher.GTK_version
2

This arg had to be added like this in the*.ini file (see screenshot – don’t place it wrong else an error will occur!):

centosarg

After saving the file Bio7 should be started on CentOS 7 (see screenshot below)! Please note that you can also adjust the Java memory there.

centos7

Another rare error occuring in Fedora is described here!.
However I tested Bio7 on the latest Fedora release and Bio7 started without any problems.

2. Layout Problems

If the layout of your distribution seems to be distorted (e.g., maximize buttons are to small – could be occuring in the default layout of Fedora and CentOS!) this can be corrected in the Bio7 CSS. The file can be found under:

/yourBio7folder/plugins/com.eco.bio7.themes_2.0.0.201412011620/css/e4_default_win7.css
(win7.css was reused for Linux so please don’t wonder)

The following changed css attributes will correct the height of the toolbars (changed attributes in bold):

.MPartStack {
……………………………………
color: ‘#org-eclipse-ui-workbench-INACTIVE_TAB_TEXT_COLOR';
 swt-tab-height: 36.0px;

}

.MPartStack.active {
…………………………………..
swt-shadow-visible: false;
 swt-tab-height: 36.0px;
}

/*Important to set height for the view menus!*/
CTabFolder {
swt-corner-radius: 15.0;
swt-tab-height: 36.0px;
}

Of course you can change other attributes as well, e.g.,  if you want to change a color.

 

 

 

Bio7 2.0 for Linux Released!

01.02.2015

I released the Linux version of Bio7 2.0 (see screenshot below).

screenlinux

For an overview of the new Bio7 features follow the link: Bio7 2.0 new features

Added Linux features:

  • A new Java menu action (in the Scripts menu) is available to start a Py4J server which can communicate to Java and CPython (if enabled in the native preferences of Bio7 and Py4J is installed in the local Python distribution). With this feature it is, e.g., possible to transfer ImageJ values to CPython or call the Bio7 Java API.
  • Improved the embedded native pseudo terminal to send signals to a process tree (e.g., SIGINT = STRG+C).
  • Added an option in the native preferences to interpret a Python script with a a native CPython interpreter >=3.0.

Installation:

Download Bio7 and simply unzip the Bio7 archive file in your preferred location. Bio7 comes bundled with a JRE so you don’t need to install Java separately. The Bio7 application was tested on Ubuntu 14.04 (minimum requirement).

R features:

For the Linux version of Bio7 2.0 R and Rserve have to be installed. For the use in Bio7 Rserve has to be compiled with a special flag to enable the cooperative mode (see below).

In a shell simply execute:

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

The command will compile and install the Rserve package in your default Linux R application. This is necessary to share the R workspace when you switch from a local Rserve connection to the native Bio7 R console (see this video for an explanation of the new connection mode in Bio7).

Please note that the default R package location of Bio7 is: /usr/lib/R/site-library

The location (and the path to R) can be changed in the R preferences of Bio7 (e.g., menu: R->Preferences).