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The systems biology format converter

Nicolas Rodriguez, Jean-Baptiste Pettit, Piero Dalle Pezze, Lu Li, Arnaud Henry, Martijn P. van Iersel, Gael Jalowicki, Martina Kutmon, Kedar N. Natarajan, David Tolnay, Melanie I. Stefan, Chris T. Evelo (+1 others)
2016 BMC Bioinformatics  
Results: Here we present the System Biology Format Converter (SBFC), which provide a generic framework to potentially convert any format into another.  ...  Interoperability between formats is a recurring problem in systems biology research. Many tools have been developed to convert computational models from one format to another.  ...  To overcome these challenges, the Systems Biology Format Converter (SBFC) software provides an open source modular and extensible framework to potentially support conversion between any two formats using  ... 
doi:10.1186/s12859-016-1000-2 pmid:27044654 pmcid:PMC4820913 fatcat:hlfm36wroverfj5sazimwemt4i

SBFC – The Systems Biology Format Converter Framework

Martina Kutmon, Martina Kutmon, Nicolas Rodriguez
2011 Nature Precedings  
Context • Computational Modeling in Biology • Community with different goals -Descriptive models -Mathematical models • Different Formats -SBML, BioPAX, CellML, … -Octave, R, Matlab, Mathematica, … -SBGN  ...  get the file extension • GeneralConverter • input model and output model • convert method • method to set converter specific options • Often integrated in existing tools -not easy to reuse Goal •  ... 
doi:10.1038/npre.2011.6370 fatcat:u5duansktvgbzjyjmgqg5a7mze

SBFC – The Systems Biology Format Converter Framework

Martina Kutmon, Martina Kutmon, Nicolas Rodriguez
2011 Nature Precedings  
Context • Computational Modeling in Biology • Community with different goals -Descriptive models -Mathematical models • Different Formats -SBML, BioPAX, CellML, … -Octave, R, Matlab, Mathematica, … -SBGN  ...  get the file extension • GeneralConverter • input model and output model • convert method • method to set converter specific options • Often integrated in existing tools -not easy to reuse Goal •  ... 
doi:10.1038/npre.2011.6370.1 fatcat:ywc2ywnfwze7dauhnzqn3nx7su

cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats

2020 Bioinformatics  
However, the interoperability between the Systems Biology Graphical Notation (SBGN) Markup Language (SBGN-ML) and the CellDesigner's proprietary Systems Biology Markup Language (SBML) extension formats  ...  We discuss the functionality of the cd2sbgnml converter, which was successfully used for the translation of comprehensive large-scale diagrams such as the RECON Human Metabolic network (Noronha et al.,  ...  Acknowledgements We thank Marek Ostaszewski and Piotr Gawron for improving the CellDesigner version of ACSN. Funding  ... 
doi:10.1093/bioinformatics/btz969 pmid:31904823 fatcat:je3bo324hneefe3pkyxjcn6sze

An Implementation for Mapping SBML to BioSPI [chapter]

Zhupeng Dong, Xiaoju Dong, Xian Xu, Yuxi Fu, Zhizhou Zhang, Lin He
2005 Lecture Notes in Computer Science  
The Systems Biology Markup Language(SBML) is an XMLbased format for representing models of Systems Biology.  ...  Based on the previous research on modeling Systems Biology using process algebra, we propose a method to map SBML to BioSPI.  ...  Systems Biology is being developed to solve the problem. There exist many computational models and tools for studying Systems Biology.  ... 
doi:10.1007/11540007_145 fatcat:f6rrhkzdu5d3vmq7knsuipdshm

Trace2PS and FSA2PS: two software toolkits for converting trace and fsa files to PostScript format

Justina Krawczyk, Alexander Goesmann, Ralf Nolte, Martin Werber, Bernd Weisshaar
2009 Source Code for Biology and Medicine  
The converter modules support the commonly used file formats for storage of sequencing (ABI and SCF) and fragment analysis data (FSA).  ...  Conclusion: The software toolkits provide useful applications to convert sequencing and fragment analysis files from a proprietary into a more common, human-readable format.  ...  Acknowledgements The authors thank Prisca Viehoever and Daniela Holtgraewe for helping with questions concerning trace and fsa data as well as Peter Priess for technical support.  ... 
doi:10.1186/1751-0473-4-4 pmid:19622158 pmcid:PMC2722627 fatcat:5oufnrmilrbitidxfqj3pqkrnm

Closing the gap between formats for storing layout information in systems biology

David Hoksza, Piotr Gawron, Marek Ostaszewski, Jan Hasenauer, Reinhard Schneider
2020 Briefings in Bioinformatics  
Marek Ostaszewski is a scientist and a project manager at the LCSB, working on IT applied to knowledge management in systems biomedicine, in particular in Parkinson's disease, including clinical research  ...  Reinhard Schneider is the head of the Bioinformatics Core Facility at the LCSB.  ...  Another converter between the non-layout SBML and other systems biology formats is the Systems Biology Format Converter (SBFC) project (SFBC has SBML to SBGN-ML converter module that is 'in progress' as  ... 
doi:10.1093/bib/bbaa030 pmid:32083642 fatcat:s646ll2syfav3d2a2whusfjgjm

SMBLtoODEpy: A software program for converting SBML models into ODE models in Python

Steve Ruggiero, Ashlee Versypt
2019 Journal of Open Source Software  
Acknowledgments The research results discussed in this publication were made possible in part by funding through the award for project number HR17-057, from the Oklahoma Center for the Advancement of Science  ...  For example, the Systems Biology Format Converter (SBFC) is a suite of tools used to convert SBML models into scripts in multiple modeling and programming languages (Rodriguez et al., 2016) .  ...  Summary Systems Biology Markup Language (SBML) is a standard intermediate language for representing models of biological systems, particularly reaction networks Hucka et al., 2003) .  ... 
doi:10.21105/joss.01643 fatcat:ruvazqx3ezafjco2uyyja4r454

Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format

Ryan L Webb, Avi Ma'ayan
2011 Source Code for Biology and Medicine  
This problem is particularly of importance in the field of network systems biology where biochemical interactions between genes and their protein products are abstracted to networks.  ...  However, the overhead of converting datasets typically stored in data tables such as Excel, text or PDF into RDF or OWL formats is not trivial for nonspecialists and as such produces a barrier to seamless  ...  We would like to thank Emek Demir from MSKCC for assistance with the BioPAX specification.  ... 
doi:10.1186/1751-0473-6-5 pmid:21418653 pmcid:PMC3071313 fatcat:ni45vok2ojhpjmlhztdt6krchm

MOCCASIN: converting MATLAB ODE models to SBML

Harold F. Gómez, Michael Hucka, Sarah M. Keating, German Nudelman, Dagmar Iber, Stuart C. Sealfon
2016 Bioinformatics  
A community standard such as Systems Biology Markup Language (SBML) can serve as a neutral exchange format, but translating models from MATLAB to SBML can be challengingespecially for legacy models not  ...  We developed MOCCASIN (Model ODE Converter for Creating Automated SBML INteroperability) to help. MOCCASIN can convert ODEbased MATLAB models of biochemical reaction networks into the SBML format.  ...  Kepler), and by the Swiss Institute of Bioinformatics. Conflict of  ... 
doi:10.1093/bioinformatics/btw056 pmid:26861819 pmcid:PMC4908318 fatcat:fmafuqfxczbhvmmtkpkuejelnm

MFAML: a standard data structure for representing and exchanging metabolic flux models

H. Yun, D.-Y. Lee, J. Jeong, S. Lee, S. Y. Lee
2005 Bioinformatics  
It allows for the explicit description of stationary states of a metabolic system by defining environmental/genetic conditions of the system, e.g. flux measurements, balancing constraints and physiological  ...  In addition, a library of MFAML comprising a model parser and a converter provides an open framework for establishing the pipeline from metabolic modeling to metabolic flux analysis.  ...  ACKNOWLEDGEMENTS This work was supported by the Korean Systems Biology Research Program (M10309020000-03B5002-00000) of the MOST and by the BK21 project.  ... 
doi:10.1093/bioinformatics/bti502 pmid:15905275 fatcat:ngsxbysvcjhdxkvrcmrlutog7i

Constructing synthetic biology workflows in the cloud

Göksel Mısırlı, Curtis Madsen, Iñaki Sainz de Murieta, Matthieu Bultelle, Keith Flanagan, Matthew Pocock, Jennifer Hallinan, James Alastair McLaughlin, Justin Clark-Casey, Mike Lyne, Gos Micklem, Guy-Bart Stan (+2 others)
2017 Engineering Biology  
and ultimately to facilitate the synthetic biology life cycle for designing and implementing biological systems.  ...  Here, the authors present the Protocol for Linking External Nodes (POLEN), a Cloud-based system that facilitates synthetic biology design workflows that operate asynchronously.  ...  One of the limitations of many workflows is the need to provide a data conversion process to convert between data formats to allow processes to receive data in a format they can work with.  ... 
doi:10.1049/enb.2017.0001 fatcat:qi5dsmxnz5ggbg274o7ogjgufe

ODEbase: A Repository of ODE Systems for Systems Biology [article]

Christoph Lüders, Thomas Sturm, Ovidiu Radulescu
2022 arXiv   pre-print
Recently, symbolic computation and computer algebra systems have been successfully applied in systems biology, especially in chemical reaction network theory.  ...  Qualitative methods analyze dynamical input systems as formal objects, in contrast to investigating only part of the state space, as is the case with numerical simulation.  ...  Our student assistants Anna Meschede and Matthias Neidhardt at the University of Bonn supported us in the programming the web front-end.  ... 
arXiv:2201.08980v1 fatcat:m44ewmoh45dofel2qhvnvrlrji

In Silico Modeling of C1 Metabolism

Santhiya Kothandaram, Prabhakar Deonikar, Mrudhuula Mohan, Vyshali Venugopal, V. A. Shiva Ayyadurai
2015 American Journal of Plant Sciences  
Each of the three molecular pathway systems is individually modeled using the CytoSolve ® Collaboratory™, a proven and scalable computational systems biology platform for in silico modeling of complex  ...  The individual models predict the temporal behavior of formaldehyde, formate, sarcosine, glutathione (GSH), and many other key biomolecules involved in C1 metabolism, which may be hard to measure experimentally  ...  In this paper, the CytoSolve ® Collaboratory™, a proven and scalable computational systems biology approach [5] , is employed to convert the diagrammatic representations of the three molecular pathway  ... 
doi:10.4236/ajps.2015.69144 fatcat:iqmlzrukbnhsxknjltupbqhbxe

SBtab: a flexible table format for data exchange in systems biology

Timo Lubitz, Jens Hahn, Frank T. Bergmann, Elad Noor, Edda Klipp, Wolfram Liebermeister
2016 Bioinformatics  
SBtab is a table-based data format for Systems Biology, designed to support automated data integration and model building.  ...  The stand-alone Python code contains functions for file parsing, validation, conversion to SBML and HTML and an interface to SQLite databases, to be integrated into Systems Biology workflows.  ...  to the development of SBtab.  ... 
doi:10.1093/bioinformatics/btw179 pmid:27153616 pmcid:PMC4978929 fatcat:fzzxsohgp5bynik7iu3l54dp3i
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