Overview

VANESA is an open-source software project which aims to support scientist in the workflow of systems biology application cases. It provides a graphical user interface (GUI) and the general modeling approach is based on graphs. For Modeling, either biological networks or Petri nets can be chosen. Beside start the process of modeling from scratch, a biological network can be retrieved from a data warehouse via a web service. For the simulation of a biological network, it can be automatically transformed into a Petri net by a customizable set of transformation rules.

A Petri nets, either modeled directly or generated by the transformation, can be simulated can be simulated with the help of an OpenModelica installation. Simulation results are made available for further investigation during the process of simulation. They can be visualized, compared, and exported for further analyses.

Both, biological networks and Petri nets, can be analyzed by graph algorithms. Models are saved as SBML files, simulation results can be exported as CSV files, and graph pictures and charts can be saved as SVG, PNG, and PDF files.

Releases

The latest stable release is v.0.4 which requires a Java SE 11 (or newer) installation. It is compatible with OpenModelica 1.17.0.

The latest pre-release is v.0.5_pre. It is compatible with OpenModelica 1.23.1.

Requirements and Installation

VANESA requires a Java SE 11 (or newer) installation to execute the provided jare file. The simulation of Petri nets is based on OpenModelica and its Petri net library PNlib, and thus, an OpenModelica installation is required if the Petri net simulation is desired. A compatible OpenModelica version is given in the release notes, but in general the latest compatible stable release should be used instead of nightly builds.

The installation path must not contain any whitespaces!. The installation process will also set some environment variables which are needed for VANESA to detect the OpenModelica installation. A compatible version of PNlib is automatically downloaded and installed once the first simulation is executed.

Citation

If you use VANESA as part of your scientific work, please cite the following article:

C. Brinkrolf, C., S. J. Janowski, B. Kormeier, M. Lewinski, K. Hippe, D. Borck, R. Hofestädt VANESA - A Software Application for the Visualization and Analysis of Networks in Systems Biology Applications. Journal of Integrative Bioinformatics 11(2):239, 2014. DOI: 10.2390/biecoll-jib-2014-239

History

VANESA is an academic software project of the Bioinformatics / Medical Informatics Department of Faculty of Technology at Bielefeld University in Germany. Its success is the result of the contribution of various people: members of the Bioinformatics / Medical Informatics Department, their supervised students, and further collaborators.

Its development started as a student’s project, called network editor, before it was renamed to VANESA. In the following, a short project history with the key dates is given.

In 2009, VANESA was registered at SourceForge where the source code (as a CVS repository which is now deleted) and releases are managed.
In 2010, the first version, v.0.1, was released.
In 2012, the source code at SourceForge is managed as an SVN repository.
In 2013, C. Brinkrolf took over the lead development from S. J. Janowski and shifted the focus towards transformation and Petri net simulation. This change of focus is also reflected by a new SVN repository, called VANESA2. The last release of the old VANESA / VANESA 1 SVN repository is v.0.1.9 and requires Java 8. All following releases are based on the VANESA2 repository.
In 2021, the development moved from SourceForge to GitHub and the VANESA2 SVN was converted into a GIT repository.

Theses

Besides multiple Bachelor and Master theses, two dissertations shaped the direction of VANESA:

Janowski SJ. VANESA - A bioinformatics software application for the modeling, visualization, analysis, and simulation of biological networks in systems biology applications. Bielefeld: Bielefeld University; 2013.
Brinkrolf C. On Quantitative Modeling and Simulation of Biological Systems: An Open-Source Approach Using Biological Networks and Rule-Based Transformation to Hybrid Functional Petri Nets. Bielefeld: Universität Bielefeld; 2023.

Publications

VANESA was involved in the following publications:

S. Janowski, B. Kormeier, T. Töpel, K. Hippe, R. Hofestädt, N. Willassen, R. Friesen, S. Rubert, D. Borck, P. Haugen, M. Chen. Modeling of cell-to-cell communication processes with Petri nets using the example of quorum sensing. In Silico Biology 10:0003, 2010. Online Journal: https://doi.org/10.3233/isb-2010-0418
C. Klenke, S. Janowski, D. Borck, D. Widera, L. A. Ebmeyer, J. Kalinowski, A. Leichtle, R. Hofestädt, T. Upile, C. Kaltschmidt, B. Kaltschmidt, and H. Sudhoff Identification of Novel Cholesteatoma-related Gene Expression Signatures Using Full-genome Microarrays. PloS One, 2012. Online Journal: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0052718
Janowski SJ. VANESA - A bioinformatics software application for the modeling, visualization, analysis, and simulation of biological networks in systems biology applications. Bielefeld: Bielefeld University; 2013.
C. Brinkrolf, C., S. J. Janowski, B. Kormeier, M. Lewinski, K. Hippe, D. Borck, R. Hofestädt VANESA - A Software Application for the Visualization and Analysis of Networks in Systems Biology Applications. Journal of Integrative Bioinformatics 11(2):239, 2014. DOI: 10.2390/biecoll-jib-2014-239
S. J. Janowski, B. Kaltschmidt, C. Kaltschmidt Biological Netowrk Modeling and Analysis in M. Chen, R. Hofestädt (eds): Approaches in Integrative Bioinformatics - Towards the Virtual Cell, ISBN:3642412807, Springer Verlag, 203-244, 2014. DOI: 10.1007/978-3-642-41281-3_8
H. Hamzeiy, R. Suluyayla, C. Brinkrolf, S. Janowski, R. Hofestädt, J. Allmer Visualization and Analysis of Micro RNAs within KEGG Pathways using VANESA. Journal of Integrative Bioinformatics 14(1), 2017. DOI: 10.1515/jib-2016-0004
H. Hamzeiy, R. Suluyayla, C. Brinkrolf, S. J. Janowski, R. Hofestädt, J. Allmer Visualization and Analysis of miRNAs Implicated in Amyotrophic Lateral Sclerosis Within Gene Regulatory Pathways IOS Press in the Studies in Health Technologies and Informatics series 253:183-187, 2018. DOI: 10.3233/978-1-61499-896-9-183
C. Brinkrolf, N. A. Henke, L. Ochel, B. Pucker, O. Kruse, P. Lutter Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA Journal of Integrative Bioinformatics 15(3), 2018. DOI: 10.1515/jib-2018-0018
C. Brinkrolf, L. Ochel, R. Hofestädt VANESA: An open-source hybrid functional Petri net modeling and simulation environment in systems biology Biosystems, 2021;210:104531. DOI: 10.1016/j.biosystems.2021.104531
C. Brinkrolf, L. Ochel Comprehensive Open-Source Petri Net Toolchain for Modeling and Simulation in Systems Biology in M. Chen, R. Hofestädt (eds): Integrative Bioinformatics - History and Future, Springer Singapore, 2022. DOI: 10.1007/978-981-16-6795-4_13
Brinkrolf C. On Quantitative Modeling and Simulation of Biological Systems: An Open-Source Approach Using Biological Networks and Rule-Based Transformation to Hybrid Functional Petri Nets. Bielefeld: Universität Bielefeld; 2023.