Bio7

Bio7
Developer(s)	Marcel Austenfeld
Initial release	2007
Stable release	3.5 / May, 2023
Repository	github.com/Bio7/bio7 ;
Operating system	Windows, Linux, Macintosh
License	Eclipse Public License
Website	https://bio7.org/

The open-source application Bio7 is a software for ecological simulation models, image analysis and statistical analysis.^[1] Built upon the RCP framework of Eclipse it embeds several tools and programming languages for the analysis of complex ecological systems. Several Java based scripting languages (Groovy, BeanShell, Python/Jython, JavaScript, ImageJ Macro) and the Java language can be used from within Bio7 for the creation of simulation models and analysis tasks.

In addition, Bio7 also contains a complete graphical user interface for the statistical R programming language^[2] and the scientific image analysis tool ImageJ^[3] with special functions to send image data from ImageJ to R or R data to ImageJ. It is considered a diverging fork of ImageJ to improve the UI integration.^[4]

References

^ Guiet, Romain; Burri, Olivier; Seitz, Arne (2019), Rebollo, Elena; Bosch, Manel (eds.), "Open Source Tools for Biological Image Analysis", Computer Optimized Microscopy: Methods and Protocols, vol. 2040, New York, NY: Springer, pp. 23–37, doi:10.1007/978-1-4939-9686-5_2, ISBN 978-1-4939-9686-5, PMID 31432473
^ Austenfeld, Marcel, und Wolfram Beyschlag. „A Graphical User Interface for R in a Rich Client Platform for Ecological Modeling". Journal of Statistical Software 49, Nr. 4 (2012): 1–19. doi:10.18637/jss.v049.i04
^ Austenfeld M, Beyschlag W: The Use of ImageJ within an Ecological Modeling Platform, ImageJ User and Developer Conference 2010, Luxembourg, Conference Proceedings, 211–216.
^ Schindelin, Johannes; Rueden, Curtis T.; Hiner, Mark C.; Eliceiri, Kevin W. (2015). "The ImageJ ecosystem: An open platform for biomedical image analysis". Molecular Reproduction and Development. 82 (7–8): 518–529. doi:10.1002/mrd.22489. PMC 5428984. PMID 26153368.

External links

Bio7 on GitHub
Bio7 on SourceForge

[1] Guiet, Romain; Burri, Olivier; Seitz, Arne (2019), Rebollo, Elena; Bosch, Manel (eds.), "Open Source Tools for Biological Image Analysis", Computer Optimized Microscopy: Methods and Protocols, vol. 2040, New York, NY: Springer, pp. 23–37, doi:10.1007/978-1-4939-9686-5_2, ISBN 978-1-4939-9686-5, PMID 31432473

[2] Austenfeld, Marcel, und Wolfram Beyschlag. „A Graphical User Interface for R in a Rich Client Platform for Ecological Modeling". Journal of Statistical Software 49, Nr. 4 (2012): 1–19. doi:10.18637/jss.v049.i04

[3] Austenfeld M, Beyschlag W: The Use of ImageJ within an Ecological Modeling Platform, ImageJ User and Developer Conference 2010, Luxembourg, Conference Proceedings, 211–216.

[4] Schindelin, Johannes; Rueden, Curtis T.; Hiner, Mark C.; Eliceiri, Kevin W. (2015). "The ImageJ ecosystem: An open platform for biomedical image analysis". Molecular Reproduction and Development. 82 (7–8): 518–529. doi:10.1002/mrd.22489. PMC 5428984. PMID 26153368.

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v t e R (programming language)
Features	Sweave
Implementations	Distributed R Microsoft R Open (Revolution R Open) Renjin
Packages	Bibliometrix easystats qdap lumi RGtk2 Rhea Rmetrics rnn RQDA Shiny SimpleITK Statcheck tidyverse ggplot2 dplyr knitr
Interfaces	Bio7 Emacs Speaks Statistics Java GUI for R KH Coder Rattle GUI R Commander RExcel RKWard RStudio
People	Roger Bivand Jenny Bryan John Chambers Peter Dalgaard Dirk Eddelbuettel Robert Gentleman Ross Ihaka Thomas Lumley Brian D. Ripley Julia Silge Luke Tierney Hadley Wickham Yihui Xie
Organisations	R Consortium Revolution Analytics R-Ladies Posit PBC (formerly RStudio PBC)
Publications	The R Journal