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BioPAX support in CellDesigner

Huaiyu Mi, Anushya Muruganujan, Emek Demir, Yukiko Matsuoka, Akira Funahashi, Hiroaki Kitano, Paul D. Thomas
2011 Computer applications in the biosciences : CABIOS  
save the pathway data in BioPAX Level 3 format.  ...  In order to encourage formal representation of pathways, we describe a software package that allows users to create pathway diagrams using CellDesigner, a user-friendly graphical pathway-editing tool and  ...  ACKNOWLEDGEMENTS We thank Susan Paley and Peter Karp for their input in the initial map between BioPAX and CellDesigner, and Igor Rodchenkov for his continuous help to our understanding of BioPAX and Paxtools  ... 
doi:10.1093/bioinformatics/btr586 pmid:22021903 pmcid:PMC3232372 fatcat:grlz6widijhgbiouxjxzxyszqu

BiNoM Cytoscape Plugin for constructing, querying and analyzing biological networks, using systems biology standards

Andrei Zinovyev, Andrei Zinovyev
2010 Nature Precedings  
, SBML and CellDesigner formats after user manipulations Network clipboard Conversion between standards (CellDesigner->BioPAX, BioPAX->SBML) Full support of BioPAX information (reaction network, interaction  ...  a BioPAX file from simple factsheet (managing families, implicit reactions) 8) Index huge BioPAX file (i.e., whole Reactome), make a query, save facilitates model building in the bottom-up approach Some  ... 
doi:10.1038/npre.2010.5120.1 fatcat:hrohwvjdhvahxl7ulmkj5b6nr4

BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks

A. Zinovyev, E. Viara, L. Calzone, E. Barillot
2007 Bioinformatics  
In addition, BiNoM allows the analysis of networks created with CellDesigner software and their conversion into BioPAX format.  ...  BiNoM (Biological Network Manager) is a new bioinformatics software that significantly facilitates the usage and the analysis of biological networks in standard systems biology formats (SBML, SBGN, BioPAX  ...  In addition, BiNoM supports conversion of CellDesigner to BioPAX and BioPAX to SBML formats.  ... 
doi:10.1093/bioinformatics/btm553 pmid:18024474 fatcat:x7bqkdjb6zhyrkwo575ginrasi

BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats

Eric Bonnet, Laurence Calzone, Daniel Rovera, Gautier Stoll, Emmanuel Barillot, Andrei Zinovyev
2013 BMC Systems Biology  
Conclusions: Here, we provide an in-depth overview of the BiNoM functions, and we also detail novel aspects such as the support of the BioPAX Level 3 format and the implementation of a new algorithm for  ...  , BioPAX Level 3 and CSML; export to SBML, CellDesigner and BioPAX Level 3), and a set of algorithms to analyze and reduce the complexity of biological networks.  ...  Import from Export (from / to) CellDesigner v3.x, 4.1, 4.2 BioPAX Level 3 / BioPAX Level 3 BioPAX Level 3 BioPAX Level 3 / SBML Level 2 SBML Level 2 CellDesigner v3.x, 4.1, 4.2 / CellDesigner  ... 
doi:10.1186/1752-0509-7-18 pmid:23453054 pmcid:PMC3646686 fatcat:kurxbxlhwnfchh4l3cr5lviufi

From Pathways to Biomolecular Events: Opportunities and Challenges

Tomoko Ohta, Sampo Pyysalo, Jun'ichi Tsujii
2011 Workshop on Biomedical Natural Language Processing  
annotation support.  ...  Until recently, few information extraction approaches were capable of resolving the level of detail in text required to support the annotation of such pathway representations.  ...  This work was partially supported by Grant-in-Aid for Specially Promoted Research (MEXT, Japan).  ... 
dblp:conf/bionlp/OhtaPT11 fatcat:ceq622po4nadvpf5aoff2yvtta

LibSBGN: current status and future plans

Alice Villeger, Alice Villeger
2010 Nature Precedings  
Growing SBGN soKware support • Ready for developer adopPon • Arcadia • Athena • BiNoM • BioModels Database • BioPAX • BioUML • ByoDyn • CellDesigner • Dunnart • Edinburgh Pathway Editor • JWS Online •  ...  SBML -BioPAX + layout extension -CellML + layout informaHon?  ... 
doi:10.1038/npre.2010.5304.1 fatcat:y7zbs64b2jaevisty7qlek5mge

LibSBGN Status Update

Martijn van Iersel, Martijn van Iersel, Tobias Czauderna, Alice Villeger
2011 Nature Precedings  
Many tools support SBGN • Arcadia • Athena • BiNoM • BioModels Database • BioPAX • BioUML • ByoDyn • CellDesigner • Dunnart • Edinburgh Pathway Editor • JWS Online • Mayday • Netbuilder (Apostrophe) •  ...  ) -Hiroaki Kitano (CellDesigner) -Nicolas Le Novère (BioModels Database) -Augustin Luna (MIM) -Yukiko Matsuoka ( • Better handling of submaps CellDesigner) -Huaiyu Mi (PANTHER Pathway) -Stuart Moodie (  ...  -Use the library and support the schema -Take part in online discussions -Contribute content to the SourceForge project  ... 
doi:10.1038/npre.2011.6373 fatcat:lrdycsoobrcq3p7cwmyohorgfi

LibSBGN Status Update

Martijn van Iersel, Martijn van Iersel, Tobias Czauderna, Alice Villeger
2011 Nature Precedings  
Many tools support SBGN • Arcadia • Athena • BiNoM • BioModels Database • BioPAX • BioUML • ByoDyn • CellDesigner • Dunnart • Edinburgh Pathway Editor • JWS Online • Mayday • Netbuilder (Apostrophe) •  ...  ) -Hiroaki Kitano (CellDesigner) -Nicolas Le Novère (BioModels Database) -Augustin Luna (MIM) -Yukiko Matsuoka ( • Better handling of submaps CellDesigner) -Huaiyu Mi (PANTHER Pathway) -Stuart Moodie (  ...  -Use the library and support the schema -Take part in online discussions -Contribute content to the SourceForge project  ... 
doi:10.1038/npre.2011.6373.1 fatcat:r3a3elg3mzbc3oydayyf3ktofq

Celldesigner: A Modeling Tool for Biochemical Networks

Akira Funahashi, Yukiko Matsuoka, Akiya Jouraku, Hiroaki Kitano, Norihiro Kikuchi
2006 Proceedings of the 2006 Winter Simulation Conference  
CellDesigner is implemented in Java, thus it runs on various platforms such as Windows, Linux, and MacOS X. CellDesigner is freely available via the Web.  ...  CellDesigner also supports simulation and parameter search, which is supported by integration with SBML ODE Solver, enabling us to simulate through our sophisticated graphical user interface.  ...  This research is in part supported by the ERATO-SORST program (Japan Science and Technology Agency), the International Standard Development area of the International Joint Research Grant (NEDO, Japanese  ... 
doi:10.1109/wsc.2006.322946 dblp:conf/wsc/FunahashiMJKK06 fatcat:j7xm46qjlzhxndwfxmos5zjue4

Extracting Biological Pathway Models From NLP Event Representations

Michael Spranger, Sucheendra Palaniappan, Samik Ghosh
2015 Proceedings of BioNLP 15  
This paper describes an an open-source software system for the automatic conversion of NLP event representations to system biology structured data interchange formats such as SBML and BioPAX.  ...  Cellular components SBML has graphical editing tool support through, for example, CellDesigner.  ...  Popular software like CellDesigner add a layer of custom XML annotations to resolve this. For our tools to be used in CellDesigner we have to add such information in the conversion process.  ... 
doi:10.18653/v1/w15-3805 dblp:conf/bionlp/SprangerPG15 fatcat:2qccccwkr5fvlpkxfdj2lomeky

Extracting Biological Pathway Models From NLP Event Representations [article]

Michael Spranger and Sucheendra K. Palaniappan and Samik Ghosh
2016 arXiv   pre-print
This paper describes an an open-source software system for the automatic conversion of NLP event representations to system biology structured data interchange formats such as SBML and BioPAX.  ...  Cellular components SBML has graphical editing tool support through, for example, CellDesigner.  ...  Popular software like CellDesigner add a layer of custom XML annotations to resolve this. For our tools to be used in CellDesigner we have to add such information in the conversion process.  ... 
arXiv:1608.03764v1 fatcat:jyjp4tubsndhng4lp3ady6xafq

cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats

2020 Bioinformatics  
CellDesigner is a well-established biological map editor used in many large-scale scientific efforts (Funahashi et al., 2007).  ...  CellDesigner files.  ...  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

AlzPathway: a comprehensive map of signaling pathways of Alzheimer's disease

Satoshi Mizuno, Risa Iijima, Soichi Ogishima, Masataka Kikuchi, Yukiko Matsuoka, Samik Ghosh, Tadashi Miyamoto, Akinori Miyashita, Ryozo Kuwano, Hiroshi Tanaka
2012 BMC Systems Biology  
We have collected and manually curated over 100 review articles related to AD, and have built an AD pathway map using CellDesigner.  ...  AlzPathway is available as both the SBML (Systems Biology Markup Language) map for CellDesigner and the high resolution image map.  ...  Funding: This work was supported by Grant-in-Aid for Scientific Research (22700311) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan.  ... 
doi:10.1186/1752-0509-6-52 pmid:22647208 pmcid:PMC3411424 fatcat:cl5lvl7izvgbnovoka52pivzn4

Getting Started in Biological Pathway Construction and Analysis

Ganesh A Viswanathan, Jeremy Seto, Sonali Patil, German Nudelman, Stuart C Sealfon, Olga Troyanskaya
2008 PLoS Computational Biology  
Our pathway research is supported by US National Institutes of Health NIAID contract HHSN2662000500021C.  ...  Cytoscape can also access large databases containing protein and gene interactions with additional support for PSI-MI and BioPAX formats.  ...  Pathway Analysis Tools for Integration and Knowledgebase (PATIKA) provides a Web-based interface to public databases, such as Reactome, HPRD, and IntAct through supporting both SBML and BioPAX formats.  ... 
doi:10.1371/journal.pcbi.0040016 pmid:18463709 pmcid:PMC2323403 fatcat:dldyxs5cdbabpbf23srfddtbye

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  ...  In this category of software tools, only MINERVA [16] supports layout encoded in SBML, CellDesigner SBML or SBGN-ML. NaviCell [39] platform supports only import from CellDesigner.  ...  BioUML [40] supports CellDesigner SBML and is supposed to support SBGN-ML.  ... 
doi:10.1093/bib/bbaa030 pmid:32083642 fatcat:s646ll2syfav3d2a2whusfjgjm
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