The software CARMEN was developed to support functional and comparative genome analysis. CARMEN provides the visualization of automatically obtained metabolic networks based on KEGG database information and stores the generated data in standardized SBML format. SBML is an open source XML-based format that facilitates the description of models and their exchange between various simulation and analysis tools (Hucka, 2003).
The reconstruction procedures of CARMEN allow users to quickly gain insights into metabolic networks of published or unpublished genome sequences and offer a user-friendly way to visualize and adapt automatically generated metabolic networks. The combination of biochemical reactions and genome annotation data facilitates the rapid detection of metabolic features. Furthermore, the generated pathways provide automated access to modeling and simulation tools that are compliant to the SBML standard.
CARMEN provides two main applications:
- The generation of KGML-based models based on KEGG database information
- The generation of SBML(template)-based models for comparative genomics
Both model generations can be run on this webserver ('Online Reconstruction'). You can download and run all programs and modules locally ('Downloads').
Further information can be found in the documentation section, which is divided into KGML- and SBML-based model generation. All displayed pathways are stored in SBML. You may download these SBML files by right clicking ('Save as...') on the download links. They can be visualized using the CellDesigner software.
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2016/03/29 - SBML reconstruction online available and recent KEGG maps incorporatedA web-based version of the SBML-based reconstruction is available online ("SBML BASED RECONSTRUCION => ONLINE RECONSTRUCTION"). It supports the mapping of core genome file to an SBML file as well as the mapping of an organism to one annotated in the SBML using two Genbank files. There is also an option for the recently implemented mapping of a pan genome file to the SBML file.
The KGML based reconstruction now uses a more recent version of the KEGG maps (January 2016).
2016/01/21 - Update of the SBML versionSeveral minor bugs in the SBML version have been fixed. A new command-line option is available for the use of pan genome files exported from EDGAR:
-p EDGAR pan genome file, max number of genomes can be set with parameter -n or the number is derived from the file -n number of genomes (for EDGAR pan genome file)Genes in the input SBML are colored with a gradient according to the number of orthologous genes. Colors can be changed in the Config file.
A web-based version of the SBML reconstruction is on the way.
2015/07/22 - Update of website and KGML versionThe CARMEN website received a general overhaul. In addition, a new version of the KGML-based reconstruction has been made available for download. Several problems with reaction-edges that got lost during creation of SBML have been fixed. Two new command-line options are available for the selection of the output format as well as exclusion/inclusion of links to other KEGG-maps :
-f output format, 1=SBML 2.1 (for CellDesigner), 2=SBML2.4; 3=SBML 2.4 (for CellDesigner); 4=SBML 3.1; A=all (default = 3) -m include maplinks, add T for true (default = F)The new version is used within the webinterface and now relies on more recent KEGG-maps (November 2014). In addition to yeast and bacteria, published fungi, protozoa, and virus genomes are now available for reconstruction. A new version of the SBML-based reconstruction is in preparation and will be made available soon.