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Reactome: a database of reactions, pathways and biological processes

D. Croft, G. O'Kelly, G. Wu, R. Haw, M. Gillespie, L. Matthews, M. Caudy, P. Garapati, G. Gopinath, B. Jassal, S. Jupe, I. Kalatskaya (+10 others)
2010 Nucleic Acids Research  
Reactome (http://www.reactome.org) is a collaboration among groups at the  ...  Development of the Reactome data model and fly and chicken databases is a collaborative project and this work benefited greatly from our interactions with Carl Schmidt, Mark Williams and Michael Ashburner  ...  ACKNOWLEDGEMENTS We are grateful to the many researchers who have volunteered to be external authors and reviewers.  ... 
doi:10.1093/nar/gkq1018 pmid:21067998 pmcid:PMC3013646 fatcat:yu7wdrauubeyji53uzmbqjmz5m

BiologicalNetworks: visualization and analysis tool for systems biology

M. Baitaluk, M. Sedova, A. Ray, A. Gupta
2006 Nucleic Acids Research  
database objects as well as for complex network level properties, for the analysis and modelling of complex biological processes.  ...  on to regulatory, metabolic and cellular networks.  ...  ACKNOWLEDGEMENTS Part of this work was funded by the National Science Foundation grants EIA-0205061 and EIA-0130059 to A.G. and A.R.  ... 
doi:10.1093/nar/gkl308 pmid:16845051 pmcid:PMC1538788 fatcat:zaxskckjlzbdni2gbk3ytgz2sa

Computational tools for metabolic engineering

Wilbert B. Copeland, Bryan A. Bartley, Deepak Chandran, Michal Galdzicki, Kyung H. Kim, Sean C. Sleight, Costas D. Maranas, Herbert M. Sauro
2012 Metabolic Engineering  
In this review, we present a number of tools that can assist in modifying and understanding cellular metabolic networks. The review covers seven areas of relevance to metabolic engineers.  ...  Computational tools are utilized throughout the metabolic engineering workflow to extract and interpret relevant information from large data sets, to present complex models in a more manageable form, and  ...  DC; NHGRI (R42HG006737) and NLM (R41LM010745) to MG; BEACON: NSF Center for the Study of Evolution in Action (0939454) to SCS; and NIH/NIGMS (GM081070) and NSF (no. 0827592) to HMS.  ... 
doi:10.1016/j.ymben.2012.03.001 pmid:22629572 pmcid:PMC3361690 fatcat:xqnmydnnejcupp2ujup45krwnm

VisANT: an online visualization and analysis tool for biological interaction data

Zhenjun Hu, Joseph Mellor, Jie Wu, Charles DeLisi
2004 BMC Bioinformatics  
This networked view of biology brings the potential for systematic understanding of living molecular systems.  ...  The new software provides a general tool for mining and visualizing such data in the context of sequence, pathway, structure, and associated annotations.  ...  Results Design One of the major design goals is flexibility -both with respect to the assimilation of new types of data, and the need for evolving a graphical interface that can fit new techniques for  ... 
doi:10.1186/1471-2105-5-17 pmid:15028117 pmcid:PMC368431 fatcat:vbdb5yh7lnbqvjt2rd7mnuaegu

A Newborn Screening System Based on Service-Oriented Architecture Embedded Support Vector Machine

Kai-Ping Hsu, Sung-Huai Hsieh, Sheau-Ling Hsieh, Po-Hsun Cheng, Yung-Ching Weng, Jang-Hung Wu, Feipei Lai
2009 Journal of medical systems  
By evaluating metabolic substances data collected from tandem mass spectrometry (MS/MS), we can interpret and determine whether a newborn has a metabolic disorder.  ...  The clinical symptoms of metabolic disorders are rarely apparent during the neonatal period, and if they are not treated earlier, irreversible damages, such as mental retardation or even death, may occur  ...  Acknowledgments The authors would like to acknowledge members of the Pediatrics and Medical Genetics Office, the Information Systems Office at NTUH for their assistance.  ... 
doi:10.1007/s10916-009-9305-6 pmid:20703618 fatcat:qphn5625xnhzlf6w5eezoof6di

A Scalable and Integrative System for Pathway Bioinformatics and Systems Biology [chapter]

Behnam Compani, Trent Su, Ivan Chang, Jianlin Cheng, Kandarp H. Shah, Thomas Whisenant, Yimeng Dou, Adriel Bergmann, Raymond Cheong, Barbara Wold, Lee Bardwell, Andre Levchenko (+2 others)
2010 Advances in Experimental Medicine and Biology  
The Sigmoid modeling system is a three-tier architecture comprising distributed modules that implement pathway/cell model generation and simulation (xCellerator/Mathematica), a pathway modeling database  ...  (Sigmoid proper), a Web service-oriented middleware, a graphical user interface, and in the future, parameter optimization and other datamining technologies.  ...  NASA Intelligent Systems Program support of EM, and by the Institute for Genomics and Bioinformatics at UCI.  ... 
doi:10.1007/978-1-4419-5913-3_58 pmid:20865537 pmcid:PMC3021415 fatcat:yu3q2xltrzf7ziadpenwufatta

Neural systems language: A formal modeling language for the systematic description, unambiguous communication, and automated digital curation of neural connectivity

Ramsay A. Brown, Larry W. Swanson
2013 Journal of Comparative Neurology  
Furthermore, the accelerating volume of novel data generated on neural connectivity outpaces the rate at which this data is curated into neuroinformatics databases to synthesize digitally systems-level  ...  Systematic description and the unambiguous communication of findings and models remain among the unresolved fundamental challenges in systems neuroscience.  ...  Burns, Joel Hahn, and Richard H. Thompson and Mr. T. Dalton Combs for their valuable discussions and assistance.  ... 
doi:10.1002/cne.23348 pmid:23787962 pmcid:PMC4760645 fatcat:5uvc6uij6rglfoemehpzd2isju

Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models

Méziane Aite, Marie Chevallier, Clémence Frioux, Camille Trottier, Jeanne Got, María Paz Cortés, Sebastián N. Mendoza, Grégory Carrier, Olivier Dameron, Nicolas Guillaudeux, Mauricio Latorre, Nicolás Loira (+4 others)
2018 PLoS Computational Biology  
Data Availability Statement: The complete datasets used for the reconstruction of the four metabolic networks (genome, proteome, metabolic network and proteome for the template models, seeds and targets  ...  Genome-scale metabolic models have become the tool of choice for the global analysis of microorganism metabolism, and their reconstruction has attained high standards of quality and reliability.  ...  Dittami (Station Biologique de Roscoff) for the expertise and analysis support in the reconstruction process of Ectocarpus siliculosus metabolic network and Caroline Baroukh, Elodie Nicolau and Bruno Saint-Jean  ... 
doi:10.1371/journal.pcbi.1006146 pmid:29791443 pmcid:PMC5988327 fatcat:6tpm6fqgqbcubinvhrlvqso5u4

PathMe: Merging and exploring mechanistic pathway knowledge [article]

Daniel Domingo-Fernández, Sarah Mubeen, Josep Marín-Llaó, Charles Tapley Hoyt, Martin Hofmann-Apitius
2018 bioRxiv   pre-print
A number of pathway databases have facilitated pathway-centric approaches that assist in the interpretation of molecular signatures yielded by these experiments.  ...  We demonstrate the utility of the PathMe framework in: i) integrating pathway landscapes at the database level, ii) comparing the degree of consensus at the pathway level, and iii) exploring pathway crosstalk  ...  For instance, Systems Biology Markup Language (SBML) is a standard for the representation of computational models of systems biology, Systems Biology Graphical Notation (SBGN) facilitates the storage and  ... 
doi:10.1101/451625 fatcat:b3qz2wooy5gx5k4wi3whd2mqgi

GenMAPP 2: new features and resources for pathway analysis

Nathan Salomonis, Kristina Hanspers, Alexander C Zambon, Karen Vranizan, Steven C Lawlor, Kam D Dahlquist, Scott W Doniger, Josh Stuart, Bruce R Conklin, Alexander R Pico
2007 BMC Bioinformatics  
We have redesigned the GenMAPP database to support multiple gene annotations and species as well as custom species database creation for a potentially unlimited number of species.  ...  Results: To address the growing needs of the microarray community we have released version 2 of Gene Map Annotator and Pathway Profiler (GenMAPP), a new GenMAPP database schema, and integrated resources  ...  We thank Jeff C Lawlor for his work on GenMAPP installer and downloader and Stephen Ordway and Gary Howard for editorial assistance. This work was supported by the J.  ... 
doi:10.1186/1471-2105-8-217 pmid:17588266 pmcid:PMC1924866 fatcat:xxrpnzcivreobfrgte3lzn3kce

MicroScope-an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data

2017 Briefings in Bioinformatics  
It combines tools and graphical interfaces to analyze genomes and to perform the manual curation of gene function in a comparative genomics and metabolic context.  ...  In this article, we describe the free-of-charge MicroScope services for the annotation and analysis of microbial (meta)genomes, transcriptomic and re-sequencing data.  ...  Acknowledgements The authors would like to thank all MicroScope users for their feedback, which helped greatly in optimizing and improving many functionalities of the system.  ... 
doi:10.1093/bib/bbx113 pmid:28968784 pmcid:PMC6931091 fatcat:3kbei6onubhe3cobdiuk72xt4a

Pathway Tools version 24.0: Integrated Software for Pathway/Genome Informatics and Systems Biology [article]

Peter D. Karp, Suzanne M. Paley, Peter E. Midford, Markus Krummenacker, Richard Billington, Anamika Kothari, Wai Kit Ong, Pallavi Subhraveti, Ingrid M. Keseler, Ron Caspi
2020 arXiv   pre-print
Scientists around the world have created more than 9,800 PGDBs by using Pathway Tools, many of which are curated databases for important model organisms.  ...  It offers metabolic-informatics tools, such as metabolic reconstruction, quantitative metabolic modeling, prediction of reaction atom mappings, and metabolic route search.  ...  Christos Ouzounis was a co-developer of the original metabolic pathway prediction algorithm, contributed an early version of the import/export system, and has been a source of much sound advice.  ... 
arXiv:1510.03964v4 fatcat:3plt5gcqmvg33pi6vd2mhufsda

The Pathway Editor: A tool for managing complex biological networks

A. Sorokin, K. Paliy, A. Selkov, O. V. Demin, S. Dronov, P. Ghazal, I. Goryanin
2006 IBM Journal of Research and Development  
Acknowledgments We thank Eugene Selkov and Eugene Selkov, Jr., as well as GlaxoSmithKline, Hugh Spence, and Frank Tobin in particular for ideas, support, useful comments and feedback during the initial  ...  Experts Group, The Open Group, and BioCarta, Inc. in the United States, other countries, or both.  ...  The flexible visualization strategy allows researchers to tune the visual representation of a map for a variety of desired graphical notations.  ... 
doi:10.1147/rd.506.0561 fatcat:dduxd735a5aatlxqiyffofdeti

BioSilicoSystems – A Multipronged Approach Towards Analysis and Representation of Biological Data (PhD Thesis)

Sridhar Hariharaputran, Sridhar Hariharaputran
2010 Nature Precedings  
For a more accurate representation of the real systems and to obtain the best agreement with the experimental data the parameters of such models can be modified.  ...  Further, the parsers written for the transfer will assist for converting the source files supplied by the databases and then for transferring and integrating the data into VINEdb.  ...  Appendix I Appendix III As explained in the SBML web pages the following enzymatic reaction will be represented by SBML as <?xml version="1.0" encoding="UTF-8"?  ... 
doi:10.1038/npre.2010.5164.1 fatcat:bo3ri2crajb5xk7kukxhe6affa

BioSilicoSystems – A Multipronged Approach Towards Analysis and Representation of Biological Data (PhD Thesis)

Sridhar Hariharaputran, Sridhar Hariharaputran
2010 Nature Precedings  
For a more accurate representation of the real systems and to obtain the best agreement with the experimental data the parameters of such models can be modified.  ...  Further, the parsers written for the transfer will assist for converting the source files supplied by the databases and then for transferring and integrating the data into VINEdb.  ...  Appendix I Appendix III As explained in the SBML web pages the following enzymatic reaction will be represented by SBML as <?xml version="1.0" encoding="UTF-8"?  ... 
doi:10.1038/npre.2010.5164 fatcat:72ufu6ycfba55gi6bvhatcld3e
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