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Qualitative translation of relations from BioPAX to SBML qual

Finja Büchel, Clemens Wrzodek, Florian Mittag, Andreas Dräger, Johannes Eichner, Nicolas Rodriguez, Nicolas Le Novère, Andreas Zell
2012 Computer applications in the biosciences : CABIOS  
Before the development of SBML qual, relations could not be properly translated into SBML.  ...  Until now, there exists no BioPAX to SBML converter that is fully capable of translating both reactions and relations.  ...  ACKNOWLEDGEMENTS We wish to acknowledge the Qualitative Models and JSBML teams. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/bts508 pmid:22923304 pmcid:PMC3467751 fatcat:e437jgyzyvhzdk2zucgoy6s5ai

Precise generation of systems biology models from KEGG pathways

Clemens Wrzodek, Finja Büchel, Manuel Ruff, Andreas Dräger, Andreas Zell
2013 BMC Systems Biology  
Finally, we compare several existing conversion tools for KEGG pathways and show that the conversion from KEGG to BioPAX does not involve a loss of information, whilst lossless translations to SBML can  ...  The drawback of many of those converters is that even for creating initial models, a basic translation of a KGML document to an SBML or BioPAX document is not sufficient.  ...  We acknowledge support by Deutsche Forschungsgemeinschaft and Open Access Publishing Fund of Tuebingen University.  ... 
doi:10.1186/1752-0509-7-15 pmid:23433509 pmcid:PMC3623889 fatcat:wcyr44lh5zeubgryetbreouzua

ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis

Michael Römer, Johannes Eichner, Andreas Dräger, Clemens Wrzodek, Finja Wrzodek, Andreas Zell, Bin Liu
2016 PLoS ONE  
Currently, the collection encompasses software for conversion and processing of community standards SBML and BioPAX, transcription factor analysis, and analysis of microarray data from transcriptomics  ...  Users only need a web browser and an active internet connection in order to benefit from this service.  ...  BioPAX2SBML converts BioPAX models into SBML. This program was the first converter that properly translated qualitative relations [11] .  ... 
doi:10.1371/journal.pone.0149263 pmid:26882475 pmcid:PMC4801062 fatcat:ast2kevfivab7hsxgxrxdj643i

Path2Models: large-scale generation of computational models from biochemical pathway maps

Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn van Iersel, Sarah Keating (+14 others)
2013 BMC Systems Biology  
All models are encoded using SBML Core and Qual packages, and available through BioModels Database.  ...  Results: To increase the efficiency with which such models can be created, we automatically generated mathematical models from pathway representations using a suite of freely available software.  ...  Each KGML entry was translated to an SBML Level 3 Qualitative Species (qual package) and each KGML relation was translated in an SBML Transition (qual package).  ... 
doi:10.1186/1752-0509-7-116 pmid:24180668 pmcid:PMC4228421 fatcat:xihw5mql45gpzmiuc4svlr23nm

Improving Collaboration by Standardization Efforts in Systems Biology

Andreas Dräger, Bernhard Ø. Palsson
2014 Frontiers in Bioengineering and Biotechnology  
Thereby, the mathematical description of systems and approaches for their (repeated) simulation are clearly separated from each other and also from their graphical representation.  ...  Central database infrastructures have been established that provide the scientific community with persistent links from model annotations to online resources.  ...  Health grant for the continued development of essential SBML software support (NIH, United States, award number GM070923).  ... 
doi:10.3389/fbioe.2014.00061 pmid:25538939 pmcid:PMC4259112 fatcat:yvsizmtklreanfa6oybwaifccm

SBML Level 3: an extensible format for the exchange and reuse of biological models

Sarah M Keating, Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger, Claudine Chaouiya, Frank T Bergmann, Andrew Finney, Colin S Gillespie, Tomáš Helikar, Stefan Hoops, Rahuman S Malik‐Sheriff (+130 others)
2020 Molecular Systems Biology  
A community of modelers and software authors developed SBML Level 3 over the past decade.  ...  We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose.  ...  The "qual" package introduces SBML elements to allow the definition of qualitative species, which are used to associate discrete levels of activities with entity pools, as well as transitions, which define  ... 
doi:10.15252/msb.20199110 pmid:32845085 fatcat:srpqfrpjx5hcpa7nztuifqpgfm

The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling

Vasundra Touré, Åsmund Flobak, Anna Niarakis, Steven Vercruysse, Martin Kuiper
2020 Briefings in Bioinformatics  
However, different visions, based on distinct biological interests, have led to the development of multiple ways to describe and annotate causal molecular interactions.  ...  It can therefore be challenging to efficiently explore various resources of causal interaction and maintain an overview of recorded contextual information that ensures valid use of the data.  ...  Acknowledgements The authors would like to thank Charles Tapley Hoyt for providing feedback on the manuscript. Conf lict of interest None declared.  ... 
doi:10.1093/bib/bbaa390 pmid:33378765 pmcid:PMC8294520 fatcat:tevslhoc2rgarjhzrcxdljzaea

Modelling techniques for biomolecular networks [article]

Gerhard Mayer
2020 arXiv   pre-print
Then follows an overlook about connections between different kinds of models and how they can be converted to each other.  ...  In the end we give a short review about the difference between quantitative and qualitative models and describe the mathematics that specifically deals with qualitative modelling.  ...  They defined the SBML qual format [128] , allowing the representation of multivalued logical models.  ... 
arXiv:2003.00327v1 fatcat:ldcslhpgdrhfpavwypbx2c6qxu

Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems

Stéphanie Boué, Marja Talikka, Jurjen Willem Westra, William Hayes, Anselmo Di Fabio, Jennifer Park, Walter K. Schlage, Alain Sewer, Brett Fields, Sam Ansari, Florian Martin, Emilija Veljkovic (+3 others)
2015 Database: The Journal of Biological Databases and Curation  
descriptions to retrieve biological networks of interest.  ...  This comprehensive collection of networks is now freely available to the scientific community in a centralized web-based repository, the Causal Biological Network database, which is composed of over 120  ...  Acknowledgements We would like to thank Jean Binder, David Page, Michael Maria, Andrea Matthews and Susan Patel for project management and support with preparation of this manuscript, all contributors  ... 
doi:10.1093/database/bav030 pmid:25887162 pmcid:PMC4401337 fatcat:ugmdyd4uvrddbkt3dyc2xwv63i

Discrete modeling for integration and analysis of large-scale signaling networks

Pierre Vignet, Jean Coquet, Sébastien Auber, Matéo Boudet, Anne Siegel, Nathalie Théret
2022
The method can be applied to every BioPAX (large-scale) model thanks to a specific package which automatically generates Cadbiom models from BioPAX files.  ...  Here we developed an integrated approach to build large-scale dynamic networks from BioPAX knowledge databases in order to analyse trajectories and to identify sets of biological entities that control  ...  Acknowledgments The authors thank Olivier Collin and the excellent support of the GenOuest bioinformatics core facility and Dr C Lavau (Inserm U1085, University of Rennes 1) for proofreading the manuscript  ... 
doi:10.1371/journal.pcbi.1010175 pmid:35696426 pmcid:PMC9232147 fatcat:5ofbwza2xrb63jjcgebsvufmki

Methoden und Algorithmen für die Systems Biology Graphical Notation [article]

Tobias Czauderna, Universitäts- Und Landesbibliothek Sachsen-Anhalt, Martin-Luther Universität, Schreiber, Falk, Prof. Dr., Kummer, Ursula, Prof. Dr.
2018
In particular it discusses problems such as the translation of pathway maps from the KEGG database into SBGN PD maps including automatic layout and the conversion of SBGN PD maps into SBGN AF maps.  ...  Three SBGN languages (PD, ER, and AF) allow for the representation of different aspects of biological systems at different levels of detail as SBGN maps.  ...  4), der Umwandlung von SBGN PD-Karten in SBGN AF-Karten ("Translate PD to AF", siehe auch Kapitel 5) und zusätzlich der Übersetzung von SBML in SBGN ("Translate SBML to SBGN") zu sehen.  ... 
doi:10.25673/1416 fatcat:cehoeh37evcthgodz623jyiyue