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BioDOM specifications


Unique identifier OMICS_14746
Name BioDOM
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data XML and non-XML files
Input format XML
Output data HOBIT files
Output format HOBIT
Operating system Unix/Linux, Mac OS, Windows
License Apache License version 2.0
Computer skills Advanced
Version 0.1
Stability Stable
Maintained Yes




No version available



  • person_outline Jan Krüger

Publication for BioDOM

BioDOM citations


Ubiquitous Monitoring of Electrical Household Appliances

PMCID: 3522958
PMID: 23202205
DOI: 10.3390/s121115159

[…] m. If we focus on standards and existing systems we will check that most of these systems are proprietary. If we desire a domotics system at home we will use these systems several times: Friend, GIV, Biodom, Hometronic, Cardio, Maior-Domo, Concelac, PLC, Dialoc, PlusControl, Dialogue, Simon VIS Domaike, Simon Vox Domolon, Starbox, DomoScope, Vantage, Domotel, VivimatPlus. Other standards, such as […]


BioXSD: the common data exchange format for everyday bioinformatics web services

PMCID: 2935419
PMID: 20823319
DOI: 10.1093/bioinformatics/btq391

[…] bioinformatics research institutes (Seibel et al., ). HOBIT XML defines a substantial number of types spread over multiple XSDs, which are programmatically accessible using a dedicated Java library (BioDOM). The ‘CBS Common Data Types’ have been in use among web services at the Center for Biological Sequence analysis (CBS) at the Technical University of Denmark and at EMBL, Heidelberg (http://www […]


Trends in modeling Biomedical Complex Systems

BMC Bioinformatics
PMCID: 2762057
PMID: 19828068
DOI: 10.1186/1471-2105-10-S12-I1

[…] ta interchange. In order to simplify interoperation between bioinformatics tools, the HOBIT XML schemas, that refers to some bioinformatics data types (sequence, RNA structure and alignment), and the BioDOM software library for their management were developed [].An ontology is the "specification of conceptualization" in a given domain of interest. It consists of a set of concepts in that specific […]


GeneFisher P: variations of GeneFisher as processes in Bio jETI

BMC Bioinformatics
PMCID: 2367627
PMID: 18460174
DOI: 10.1186/1471-2105-9-S4-S13

[…] cal modeling where subprocesses can be abstracted into so-called GraphSIBs, that enable viewing the process model at different levels of abstraction. Here the input file is read, checked by using the BioDOM web service as discussed earlier, and the number and type of the sequence(s) is entered by the user.• When the input and its classifications are available, the necessary steps preceding the act […]


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BioDOM institution(s)
Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany; Bioinformatics Group, Practical Computer Science Department, Faculty of Technology, Bielefeld University, Bielefeld, Germany; Department of Bioinformatics, UKG, University of Göttingen, Göttingen, Germany; Distributed Systems and Grid Computing, Central Institute for Applied Mathematics, Research Centre Jülich, Jülich, Germany
BioDOM funding source(s)
This work was supported by the "Impuls- und Vernetzungsfonds der Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.".

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