Welcome to VANTED at SourceForge!
This is the homepage of VANTED at SourceForge. VANTED is a data and network visualization software which is based on GRAVISTO. VANTED and its derivates DBE-Gravisto and KGML-ED extend this functionality as outlined below. Click here for contact information.
Click here to proceed to the SourceForge page for VANTED. You will find information on recent developments and information on how to download the source code of the system. You may easily start any of the binary versions of these applications by clicking on the table-headers in the features comparison table, below. Extended documentation and further information on VANTED is available here and for KGML-ED here.
By using any of the software available from this site you acknowledge and agree that the use of KGML-ED/VANTED/DBE-Gravisto is at your sole risk and the the entire risk as to satisfactory quality, performance, accuracy and effort is with you. It can not be guaranteed, that the functions contained in these software systems will meet your requirements, that the operation will be uninterrupted or error-free, or that defects in the software will be corrected.
| KGML-ED | VANTED 1.0 | VANTED 1.5 | DBE-Gravisto | |
|---|---|---|---|---|
| Program Focus | Editing and exploration of KEGG pathways. | Visualization and basic statistical analysis of experimental data in the context of networks. | Visualization and extended analysis of experimental data in the context of networks or hierarchies. | ←; Additionally the representation of metabolic data in the DBE-Database. Integrated connectivity to the DBE-Database and to the FLAREX system, managing expression data at the IPK. |
| Main File Format | KGML | GML | ← | ← |
| Input Formats | KGML, GML in KGML-ED format | KGML (limited), GML, DOT, Pajek .NET, SBML 2 | KGML, GML, DOT, Pajek .NET, SBML 2, graphML | ← |
| Output Formats | KGML, GML, XWG, Pajek .NET, DOT | GML, DOT | GML, XWG, Pajek .NET, DOT, SBML→PNT, graphML | ←; PovRay (limited) |
| Database Connections | KEGG Pathway, KEGG Orthology (KO), KEGG Compound, SIB Enzyme | KEGG Pathway (limited), KEGG Compound, SIB Enzyme | KEGG Pathway, KEGG Orthology (KO), KEGG Compound, SIB Enzyme | ←; DBE-Database (Metabolic Data), FLAREX (Expression Data), eventually additional pathway DBs |
| Statistic Functions | not available | t-Test (2 variants), U-Test, Pearson- and Spearman correlation of samples and for time series | ←, histogram functions for traversing graph hierarchies, histogram of any numeric network element attribute | ← |
| Data Mapping | not available | possible (mapping to nodes) | ←, additionally data mapping for graph edges | ← |
| Data Mapping Input Templates | not applicable | XLS Format: two template formats | ←; additional transposed version of one template; KEGG Expression Format; general tabular format. All files in XLS or CSV format. Additional support of a application specific XML based import and export format for mapping data. | ← |
| Data Mapping Functions | not applicable | Support for alternative enzyme and compound identifiers. | ←; additional support for mapping gene identifiers, listed in the KEGG KO database. Support for alternative user-provided identifers and mapping tables. | ← |
| Advanced Graph Manipulation | KEGG Pathway exploration and layout functions | Cluster layout functions | ←; Processing of hierarchies (Gene Ontology, KEGG Pathway hierarchy or user provided), relevant to experimental data. | ←, Subgraph-Search and improved Subgraph layout functions |
| Reference Literature | [1] Klukas and Schreiber: Dynamic exploration and editing of KEGG pathway diagrams. Bioinformatics. 2006 |
[2] Junker, Klukas and Schreiber: VANTED: A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics. 2006 [3] Klukas, Junker und Schreiber: VANTED: Datenauswertung im Netzwerk-Kontext. GENOMXPRESS. 1.06 [4] Klukas, Junker and Schreiber: The VANTED software system for transcriptomics, proteomics and metabolomics analysis. Journal of Pesticide Science. 2006 |
[5] Borisjuk, Hajirezaei, Klukas, Rolletschek and Schreiber: Integrating data from biological experiments into metabolic networks with the DBE information system. In Silico Biology. 2004 [6] Klukas, Schreiber, Koschützki: Graph Pattern Analysis with PatternGravisto. Journal of Graph Algorithms and Applications. 2005 [7] Klukas, Schreiber and Schwöbbermeyer: Coordinated Perspectives and Enhanced Force-Directed Layout for the Analysis of Network Motifs. APVIS 2006 | |
| Selected publications which used these systems for data visualization | [8] Rolletschek, Radchuk, Klukas, Schreiber and Borisjuk (2005): Regulation of lipid biosynthesis in soybean seeds: evidence for a key role of photosynthetic oxygen release. New Phytologist |
[9] Junker, Koschützki and Schreiber (2006): Kinetic Modelling with the Systems Biology Modelling Environment SyBME. Journal of Integrative Bioinformatics (0018) [10] Weise, Grosse, Klukas, Koschützki, Scholz, Schreiber and Junker (2006): Meta-All: a system for managing metabolic pathway information. BMC Bioinformatics (7:465) [11] Tognetti, Zurbriggen, Morandi, Fillat, Valle, Hajirezaei and Carillo (2007): Enhanced plant tolerance to iron starvation by functional substitution of chloroplast ferredoxin with a bacterial flavodoxin. Proc. Natl. Acad. Sci. USA [12] R. Radchuk, V. Radchuk, Götz, Weichert, Richter, Emery, Weschke and Weber (2007): Ectopic expression of phosphoenolpyruvate carboxylase in Vicia narbonensis seeds: effects of improved nutrient status on seed maturation and transcriptional regulatory networks. The Plant Journal (51, 819-839) (supplementary material figures) |
Development Timeline
A simplified overview of the time course for development of some of the systems, which have been developed at the Network Analysis Group at the IPK. Starting point of this overview is June 2003, the time I finished my studies at the Otto-von-Guericke University of Magdeburg and joined the group at IPK Gatersleben. Development is based on the extensive work on the general network editor and development platform Gravisto, which took place at the University of Passau. Different team members participated in the following in the development of the shown systems: Development is supervised by Dr. Falk Schreiber, lead of Network Analysis Group. Development of Pattern-Gravisto is a joint-effort with my colleage Dirk Koschützki. The VANTED system and the DBE information system is mainly developed by myself, with small contributions of student interns, which partly implemented functions like the printing code and the tree layouts. Additional external libraries and algorithms have been used, too, which are listed in the About dialog of these systems. The pattern layout functionality of Pattern-Gravisto is now part of the MAVisto application, a further improved version is included in DBE-Gravisto.It is expected, that further developments are based on further discussions or contributions, based on the now public source code.