R Improvements for Bio7 2.5


The next release of Bio7 comes with many new R features and improvements which were integrated since the last release.

In this post I like to present a subset of some new R documentation features of the upcoming Bio7 2.5 release.

1. R Markdown Editor:

I improved the R markdown editor of Bio7 and integrated some code templates, font colors and dynamic font resizing,  a default PDF viewer for all Operating Systems (pdf.js), an outline view, spell checking and some new preferences useful for a constant writing and preview of documents. For an improved writing and preview layout I added a new document perspective for Bio7 for the supported document types of Bio7 (LaTeX, rmarkdown, knitr, Sweave, etc.).



I also added a special rmarkdown compilation mode for a dynamic writing/compilation/preview of markdown documents according to a selectable time interval in the preferences.



On Windows you will also be able to open a word document in an embedded mode – on Linux and MacOSX the document is opened with the registered word viewer.



2. LaTeX:

Bio7 comes shipped by default with a full featured LaTeX editor (TeXclipse).
However for an easier default compilation and document preview I integrated several new dynamic actions without the necessity to built LaTeX documents.
Thus it is now possible to preview LaTeX documents inside the new custom display of Bio7 and I added several preferences to improve the compilation process and font rendering of Bio7 (BibTeX, XeLaTeX compilation, etc.).
In addition it will be possible to create presentations with the Beamer package and fullscreen the pdf presentation on different selected monitors (you can remove the toolbar and center the created pdf with a special key shortcut).



Beside this new R document features the new Bio7 release will also come with a lot of new features regarding the R editor, R-Shell,  built of R packages, Plot display (the default PDF display), etc.

For more information and updates visit: http://bio7.org




Dark Skin for Bio7 2.5


For the next upcoming release of Bio7 a new dark skin will be available. Here are some screenshots for Linux and Windows. Some UI elements of Windows are controlled from the OS and can’t be skinned at the moment.





New Icons for Bio7 2.5


Beside many changes for the next release I was able to find the time to update the icons of Bio7 for the next release. The icons are a subset of the FontAwesome icons and some custom icons and were created with Inkscape. They will be made available for free, too.  At the moment the icons are available in two resolutions (100%, 200%) and the larger icons will be used when working with a high DPI monitor (> x dpi). For the rules see:


Here are two screenshots:




Improved ImageJ plugin


Finally I had the time to improve the ImageJ plugin structure of the ‘Plugins’ view menu. Now the SWT menu structure of the plugin completely matches the AWT menu structure of  ImageJ (see screenshots below with some installed plugins).
Installed plugins, scripts and macros will be added to their defined menu path. Before this (current version) it was only possible to extend the SWT ‘Plugins’ menu and installed scripts and macros were only available if installed in the Bio7 main menu or by means of the ImageJ ‘Control Panel’.





In addition I improved the image ‘Type’ menu to show checked menu items according to the opened image (see screenshot below).


Finally the ImageJ shortcuts will be mapped to the SWT menu if not used by the platform with a higher priority (see screenshot below).


Some minor improvements will follow, too for the next update of the plugin which can be updated for Bio7 2.4 or any Eclipse environment soon.