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Bio7 / News: Recent posts

Bio7 1.7.1 for Linux Released!

A new Linux version of Bio7 is available for download.
This release adds new features and improvements for the Linux platform.
For an overview please consult the Bio7 website:
http://bio7.org

Posted by Bio7 2013-09-24

Bio7 1.7.1 for Windows Released!

A new version of Bio7 for Windows is available. For an overview of the new features please visit the Bio7 website: http://bio7.org.

Posted by Bio7 2013-09-06

Bio7 1.7 for Windows Released!

A new version of Bio7 for Windows is available. For an overview of the new features please visit the Bio7 website: http://bio7.org.

Posted by Bio7 2013-08-08

Bio7 1.5 Mac (Beta) released!

A beta release of Bio7 1.5 for MacOSX (64-bit) is available!

Posted by Bio7 2011-07-22

New Flash Tutorials available!

New Flash Tutorials available for the latest Bio7 release. Please visit the website of Bio7 for the tutorials.

Posted by Bio7 2011-02-22

Bio7 1.5 released!

Bio7 1.5 released! For more details about this release please consult the Bio7 website which will be updated in the next days and weeks.

Posted by Bio7 2011-02-17

Bio7 1.4 for Linux released!

Today Bio7 1.4 for Linux was released.
For a first overview consult the new flash tutorials for 1.4
on the Bio7 website.
The release notes will be available on the Bio7 forum.

Posted by Bio7 2009-12-03

Bio7 1.4 for Windows released!

Today Bio7 1.4 for Windows was released.
For a first overview consult the new flash tutorials for 1.4
on the Bio7 website. During the week more information about
this release will be available on the Bio7 forum.
For a first installation follow the installation description for 1.3 available
on the Bio7 forum.

Posted by Bio7 2009-11-30

First try with MacOSX

Posted by Bio7 2009-09-30

Plans for the next release

In the next Bio7 release some new features are
planned or are already implemented.
Already implemented for example is a spreadsheet component which will ease the import and export of data.
Furthermore a Mac OS X version is planned for this year.

Posted by Bio7 2009-06-08

Bio7 1.3 for Linux released!

Posted by Bio7 2008-11-06

Bio7 1.3 for Windows released!

Posted by Bio7 2008-11-03

Information for the next release

In the next release of Bio7
several improvements will be
available:

An improved OpenOffice API (will accept empty spreadsheet cells as NA's and Strings, too).

An improved and very fast image transfer API for R and ImageJ
(Greyscale images up to 16000*16000 pixels can be transfered in one shot!).

Improved scripts for the Gis features.

Use of the new Rserve client API.

Furthermore some new useful features will be available, too.... read more

Posted by Bio7 2008-09-10

Notes for the Linux version

Some extra notes for the Linux platform:

If the R shell is opened from the R menu a path with a load command for the workspace is copied
to the clipboard. If you want to work with you favourite GUI you can then simply paste
the command from the clipboard to work with the stored workspace.

The Space view fullscreen comand didn't work on my platform with the latest JRE but with
the beta version of Java 1.6.10. If you have this problem, too simply rename the shipped
JRE and copy the 1.6.10 version to that folder and rename it to “jre” (not necessary if
this version is on your system path as default!)... read more

Posted by Bio7 2008-07-11

Bio7 1.2 for Linux released

Finally a Linux version of Bio7 1.2 has been released. It comes with all the new features of
the Windows version.
Please install R correctly with all the dependencies to use the new features.
This version is shipped with Java 1.6.07
For an installation simply unzip the file.

Please select the "Always run in background" option to hide the dialogs
if a job is running.
Additionally adjust the paths to R (Rserve package
is expected!)and to OpenOffice for a full functional Bio7.
For the new import scripts the "rgdal" package has
to be installed, too.
The scripts are able to import different grid
types (arcgrid, *.hgt etc.) and shapefiles
which are loaded in R and visualized (grids!)in ImageJ.
For the new image methods with R i added a new tab
in the R shell with examples to demonstrate how to work efficiently with big (image) matrices.... read more

Posted by Bio7 2008-07-10

Stable Linux version will be released soon!

A Linux version of Bio7 1.2 will be released soon with an improved and stable ImageJ version.

Posted by Bio7 2008-07-01

Bio7 1.2 for Windows released!

Today i released Bio7 1.2 for Windows:

Important to know:

Because Windows Vista is very sensitive to user rights etc. i reorganized the package installation
for installable add-on packages inside of Bio7. The default add-on packages location is now Rhome/site-library.
At this location inside Bio7 the packages will be installed by default (if not changed).

When starting the Rgui by means of Bio7 the default path to available packages is determined over the registry (Rhome with the Rhome/etc/.Rprofile file).
To synchronize the package location (Bio7 and Rgui) please start Bio7 with the enabled „Install path at startup“ once to set the registry path to the bundled R location.
By default this option is disabled (Not to harm an existing user installation!).... read more

Posted by Bio7 2008-05-20

New Flash tutorials available!

Today i uploaded three new Flash tutorials
on the main site of Bio7 which demonstrate
some of the new features of Bio7 1.2.
Finally after some delay i hope to release Bio7 1.2
the next week.

Posted by Bio7 2008-05-17

A few weeks more needed for the next release!

The planned 1.2 release of Bio7
needs a few weeks more work. The release
is now scheduled for April.

Reasons:
The new features have to be tested and
improved for a reliable platform and more
examples have to be
created.

Posted by Bio7 2008-03-28

Linux: No flickering Swing panels with Java 1.6.04

With the new release of Java 1.6.04 the Swing panels
are drawn without the disturbing flickerings on Linux. Install the new Java version if you want to see the difference.
Simply rename the embedded jre folder of the Bio7 release to start Bio7 with the new Java Runtime.

Posted by Bio7 2008-01-17

Plans for the next release

The next release of Bio7 will come with some
new features and also some improvements.

Improvements to come:

On Windows the embedded R editor will be more stable
if the interpreted source hasn't
got the right syntax and also prints errors
to the Bio7 console without the need to open
the OS console (The Rserve app. will not crash!).
Additionally the print() method will work too
(output to the Bio7 console).... read more

Posted by Bio7 2008-01-10

New useful script!

I created a new and very simple BeanShell script
for Bio7 and R (source template from the R mailing!).

It is very useful because it executes copied text from the clipboard.
On Windows a good possibility to test a R script in Bio7 without an exit of the Rserve application(I wrapped it in a try statement!).

Simply copy an RScript to the clipboard (e.g. from the RScript editor in Bio7 or from the Internet!) and then execute
the Script(Put this script in the Scripts->Statistic-Scripts menu).
The script is available in the download location.... read more

Posted by Bio7 2007-12-05

Shapefile exporter script available!

I released the first version of the Shapefile
exporter script. For this script the R package
'maptools' has to be installed.
Simply drop the script in the Export_Scripts folder. Open the Image perspective
and then execute the script.
The script uses the R package 'maptools' ('sp')
to export ImageJ selections from the Roi manager
to a shapefile. For a successful execution the
ROI Manager has to be active and one shape type has to be selected for the export.
For the line shapes only use the segmented and
freehand selection tools!... read more

Posted by Bio7 2007-10-25

Shapefile exporter will be soon available!

I've developed a shapefile exporter script which uses the R packages "sp" and "maptools" to export points, lines and polygons (seperately) from the ROI Manager of the embedded ImageJ. This means that you can use the embedded ImageJ with all the selection capabilities (e.g. combined with a
particle analysis) to export a shapefile which then can be loaded in a Gis Software (e.g. Quantum Gis, Grass, Saga). The script will be soon available.

Posted by Bio7 2007-10-24

Updated Examples!

I've added a few new examples to the old examples (Examples1.1) for the Bio7 application.
They can be found in Bio7_Examples(Extra_Snippets)
and Ecological Modelling/Random (CreateImageStack_RandomWalk.java).
Two of the examples demonstrate how to plot
images in R and automatically load and add this images to a stack in ImageJ. Only one image is used as a temporary container for the plots(in the same directory->use Refresh!). This examples can easily be changed to any plot R offers for example to render simulations with the help of R plots.
The simulations then can be stored as an *.avi,
*.gif (ImageJ default methods) or converted to an *.swf file for a presentation.... read more

Posted by Bio7 2007-10-15