(publication, available)
    Dynamic visualisation of constraint-based metabolic models

FBA-SimVis is a VANTED Add-on for the constraint-based analysis of metabolic models with special focus on the dynamic and visual exploration of metabolic flux data resulting from model analysis.
Screenshot of the DBE website, the new DBE2 system is fully integrated into VANTED, available as an Add-on. Click here to access DBE2.
(publication, available)
    DBE2 - Database for Biological Experiments

The database system "DBE2", is an extension of the original DBE system, which also supported data presentation in the web (example). The improved version of this system, DBE2 may now be used to easily store biological experiment data in a central and save place at our institute. It can be accessed directly from within the VANTED tool by installing a VANTED Add-on (link). Your experiment data can be easily shared and combined with different datasets using the VANTED and DBE2 systems.

(publication, available)
  HIVE - Handy Integration and Visualisation of multimodal Experimental Data

In the frame of the SysSEED project, HIVE combines network-focused Systems Biology approaches with spatio-temporal information. It extends the functionality of VANTED by adding the handling of volumes and images, together with a workspace approach, allowing one to integrate data of different biological data domains. HIVE is written in Java and Java3D and the main tasks are:
  • handling of omics data, networks, images and volumes
  • integration of different data types using a graph-based workspace
  • combining biological data in different ways and
  • manifold visualisations of combined data

(publication, available)
  SBGN-ED - Editing, Translating and Validating of SBGN Maps

SBGN-ED is a VANTED Add-on which allows to create and edit all three types of SBGN maps, that is Process Description, Entity Relationship and Activity Flow, to validate these maps according to the SBGN specifications, to translate maps from the KEGG and MetaCrop pathway databases into SBGN, and to export SBGN maps into several file and image formats.
SBGN (Systems Biology Graphical Notation) is an emerging standard for graphical representations of biochemical and cellular processes studied in systems biology.

  CentiLib - Computation of network centralities

CentiLib is an Add-on for the computation and investigation of weighted and unweighted centralities in biological networks. Even though CentiLib was developed to integrate the computation of centralities into as many tools for the visualisation and analysis of biological networks as possible, it can be used for other types of networks, too.

  FluxMap - visual exploration of flux distributions in biological networks

FluxMap is an easy to use tool for the advanced visualization of simulated or measured flux data in biological networks. Flux data import is achieved via a structured template basing on intuitive reaction equations. Flux data is mapped onto any network and visualized using edge thickness. Various visualization options and interaction possibilities enable comparison and visual analysis of complex experimental setups in an interactive way.

  MetaCrop - Browsing and working with information from the MetaCrop database

MetaCrop is an Add-on to enable browsing of the content of the handcurated Metacrop database. Users can directly load hand-layouted pathway maps or metabolic network models to use for browsing, pathway exploration, data-mapping and analysis or use them for metabolic modelling. The user can also filter the pathway for species specific information, which will be visually highlighted.

  PetriNet - Reconstruction, Simulation, and Analysis of biological networks using Petri nets

PetriNet is an Add-on to handle discrete and continuous place-transition nets of varying complexity. The editing of Petri nets and the transformation of biological networks into Petri nets is possible in an interactive way. Simulation and analysis are supported by different visualization and interaction techniques to capture the properties and behaviour of Petri nets quickly (e. g. interactive animation of the switching behavior, interactive exploration of invariants and the reachability graph).

(poster, available)
  GLIEP - Navigation and exploration of interconnected pathway visualization

GLIEP stands for "Glyph-based Link Exploration of Pathways" and helps to guide the navigation and exploration process of interconnected pathway visualization as well as providing insight into the overall interconnectivity.
  Navigation Addon

This addon adds navigational functionality by providing a view with an overview graph, that shows the current pane of the graph and allows users to move that pane. This addon also supports navigation using an extra frame outside of vanted, so that users still can use the functions embedded in the tabs without loosing the navigation feature.

  View Data Addon

An addon to view heatmap experimental data in detail. This is usefull if multiple mappings appear on a node element. The addon helps users to distinguish single heatmap elements and their values.