METIS (Metabolic Information Input System)

The METIS (Metabolic Information Input System) Editor is a user-friendly open-source application designed for the storage and input of information on metabolism and degradation reactions in the database employed by the Chemical Reactivity and Fate Tool (CRAFT) software. The METIS Editor allows the user to:

    • input, inspect, and modify chemical reactions organised in pathways, so that these reactions can later on be used as example reactions in CRAFT [1]
    • draw, edit and manipulate reactions, including the addition of atom-atom mapping information, by using a graphical reaction editor module based on MOSES, a proprietary chemoinformatics platform of Molecular Networks GmbH [2]. The editor module is integrated within METIS as a specially crafted binary module (MOSES.ReactionEditorEmbedded)
    • annotate each reaction with arbitrary properties
    • supply the reactions to CRAFT with the option to revoke these example reactions, if necessary
    • store reactions and metabolic pathways independent of CRAFT
    • edit, browse, print out, and annotate reactions and metabolic pathways independent of CRAFT
    • exchange reactions and metabolic pathways (using the RD file format), either with CRAFT or other applications

The METIS editor was developed by Molecular Networks GmbH (Erlangen, Germany) under the terms of a JRC contract. The software is made freely available as a service to scientific researchers and anyone with an interest in the application of computational tools in the assessment of chemical reactivity and metabolism, which are important considerations in the risk assessment of chemicals.
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METIS (Version 1.0) - Download area (June 2010 release)


The METIS Editor 1.0 software can be downloaded (free of charge) from this web site.

The METIS Editor 1.0 requires:
    • a minimum of 512 MB of operating memory (RAM); it is recommended, however, to have at least 1 GB of memory
    • a minimum of 70 MB of free hard disc space for the program and data files
    • the Java(TM) runtime environment (JRE) version 1.6 or newer, available for download at the Java home page
    • a MySQL database which is used to store the reaction information. Typically, METIS is used as a supplement to CRAFT applications, therefore, if CRAFT applications are already installed and configured, the same MySQL database instance will automatically be used by METIS. A local installation of a MySQL database on the same PC where METIS and CRAFT are installed is advisable if it is intended to work offline with METIS and CRAFT. Otherwise several users can simultaneously access a common MySQL database within their LAN. The MySQL server setup program can be downloaded from the MySQL home page.
The source code files are integrated within the setup package and can be optionally installed by the user.

 

Contact persons

Please send any comments, enquiries or bug reports to Molecular Networks with copy to the Computational Toxicology Group.

 

Key features


    • Easy to install.
    • Easy-to-follow manual provided with example biodegradation metabolic pathway.
    • Capability to import and export whole biodegradation pathways as well as single reactions (MDL RXN and MDL RD(F) file formats supported).
    • Capability to import structures of single molecules (e.g. reaction substrates/products/enzymes) to MOSES.ReactionEditorEmbedded (Chemical Structure Files, i.e. *.SDF, *.MOL, *.CTX formats supported).
    • Capability to attach, manage and modify specified reaction properties (e.g. name, references, URLs, data values).

 

Copyright and Disclaimer Notice


The METIS Editor 1.0 is open source software licensed under the terms of the EUPL licence version 1.1 only. You may not use this work except in compliance with this Licence. The file license.txt in the installation directory contains the Licence text. For more details, please consult the web-site of IDABC - European Union Public Licence - EUPL v.1.1 . The METIS Editor 1.0 employs also a graphical reaction editor module based on MOSES, a proprietary chemoinformatics system developed earlier by Molecular Networks GmbH [2]. The MOSES system, its modules and MOSES.ReactionEditorEmbedded co-distributed with METIS are licensed for the use in conjunction with METIS software only. The detailed license information is included and can be found in the file license.txt in the METIS installation directory.

We request that proper credit is given to the copyright and authorship for METIS. This includes adding the following copyright notice to the beginning of your source code files, and to any copyright notice that you may distribute with programs based on this work:
    Developed by Molecular Networks GmbH on behalf of the Joint Research Centre (JRC). Copyright European Union (2010).
The METIS Editor tool is made available by the JRC as a service to the worldwide scientific and regulatory communities. The JRC provides no technical support, warranties or remedies for this software. It does not imply any endorsement or acceptance by the JRC or by the European Union of the algorithms encoded in the software. The European Union shall not be liable to the User or any third party for any direct or indirect, special, incidental, punitive, cover or consequential damages, arising out of the use of, or inability to use, the METIS Editor 1.0.

 

References

  1. Chemical Reactivity and Fate Tool, Molecular Networks GmbH
  2. MOSES - Extensive Chemoinformatics platform, Molecular Networks GmbH
  3. CTfile Formats, Version: November 2007