Medical Systems Biology

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1. Installation

The software requires the Java runtime environment >=1.5.0 (JRE 5.0) which can be downloaded from oracle.

  1. Install JRE 5.0 (1.5.0) or higher if it is not available on your system.
  2. Download the current VennMaster version and unpack the file into a directory.
  3. Start VennMaster by
    • Windows: Double click on venn.bat in the installation directory.
    • Unix/Linux/MacOS X: Call venn.sh from the command line (ensure that your java executable is in the search path) in the installation directory.
    Hint: It is not recommended to call VennMaster by a direct click on the venn.jar file since the standard memory assignment is too low for the most Euler arrangements.

VennMaster is packed into a single zip archive which must be unzipped into the desired directory (e.g. "C:\Program Files\" or your home directory). Call venn.sh in the VennMaster directory from the command line (Linux or Mac OS X) or double click venn.bat under Microsoft Windows in the file explorer.
When using many categories VennMaster may report an out of memory error. In these cases reduce the number of categories by specifying other import filter settings or open venn.sh (Linux or Mac OS X) or venn.bat (Windows) with a text editor (e.g. vi or notepad) and change the memory size by editing the two -X options of the java call. The -X options specify the memory size (in MB) assigned to the software. These can be adapted depending on the available memory and the problem size (number of categories/elements). The standard settings are usually too small for the most problems (2MB for Sun Java 1.5 on linux and 1MBon win).

Download

VennMaster_0.38.0.zip (Version 0.37.5)

Version history

VennMaster-0.37.5.zip (Version 0.37.5)
VennMaster-0.37.4.zip (Version 0.37.4)
VennMaster-0.37.3.zip (Version 0.37.3)
VennMaster-src-0.37.3-20080219.zip (Source code version 0.37.3)
VennMaster-0.37.2.zip (Version 0.37.2)
VennMaster-src-0.37.2-20080110.zip (Source code version 0.37.2)
VennMaster-0.37.0.zip (Version 0.37.0)
VennMaster-src-0.37.0-20071119.zip (Sour ce code version 0.37.0)
VennMaster-0.36.0.zip (Version 0.36.0)
VennMaster-src-0.36.0-20070907.zip (Source code version 0.36.0)
VennMaster-0.35.0.zip (Version 0.35.0)

VennMaster-src-0.35.0-20070806.zip (Source code version 0.35.0)

Sources

VennMaster sources are maintained at GitHub. Visit the groups development page at https://github.com/sysbio-ulm/

License

VennMaster and the VennMaster source code are licensed under a

Creative Commons License 
This work is licensed under a Creative Commons Attribution-Noncommercial 3.0 License.

 

Job Openings

Wissenschaftlicher Mitarbeiter (m/w/d) 

 

Latest News

 

  1. Our paper "Prediction of resistance to bevacizumab plus FOLFOX in metastatic colorectal cancer-Results of the prospective multicenter PERMAD trial" has been published in PLoS One.

     

  2. "Introducing a machine learning algorithm for delirium prediction—the Supporting SURgery with GEriatric Co-Management and AI project (SURGE-Ahead)has been published in Age and Ageing.

Our paper "Segmentation-based cardiomegaly detection based on semi-supervised estimation of cardiothoracic ratio" has been published in Scientific Reports.

 

"Prospective study validating a multidimensional treatment decision score predicting the 24-month outcome in untreated patients with clinically isolated syndrome and early relapsing–remitting multiple sclerosis, the ProVal-MS study" has been published in Neurological Research and Practice.

 

Our paper "GatekeepR: an R shiny application for the identification of nodes with high dynamic impact in boolean networks" has been published online first in Bioinformatics.

 

Our paper "The Necessity of Interoperability to Uncover the Full Potential of Digital Health Devices" has been published in JMIR Medical Informatics.

 

"Multicentric pilot study to standardize clinical whole exome sequencing (WES) for cancer patients" has been published in npj Precision Oncology.

 

Our paper "AMBAR-interactive alteration annotations for molecular tumor boards" has been published in Computer Methods and Programs in Biomedicine.

 

"A protocol for the use of cloud-based quantum computers for logical network analysis of biological systems" has been published in STAR Protocols.

 

Our paper "A systems biology approach to define mechanisms, phenotypes, and drivers in PanNETs with a personalized perspective" has been published in npj systems biology and applications.

 

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"Self-Assessment of Having COVID-19 With the Corona Check Mhealth App" has been published in IEEE Journal of Biomedical and Health Informatics.


Our first quantum computing paper "Leveraging quantum computing for dynamic analyses of logical networks in systems biology" has been published in Patterns.