Bioinformatics Workflows and Web Services in Systems Biology Made Easy for Experimentalists

2013 ◽  
pp. 299-310 ◽  
Author(s):  
Rafael C. Jimenez ◽  
Manuel Corpas
Keyword(s):  
Systems Biology ◽  
Web Services ◽  
Bioinformatics Workflows

scholarly journals Combination of a data warehouse concept with web services for the establishment of the Pseudomonas systems biology database SYSTOMONAS

2007 ◽  
Vol 4 (1) ◽  
pp. 12-21 ◽  
Author(s):  
Claudia Choi ◽  
Richard Münch ◽  
Boyke Bunk ◽  
Jens Barthelmes ◽  
Christian Ebeling ◽  
...  
Keyword(s):  
Systems Biology ◽  
Web Services ◽  
Data Warehouse ◽  
Regulatory Networks ◽  
Hybrid Approach ◽  
Structural Diversity ◽  
Heterogeneous Data ◽  
Data Consistency ◽  
Biological Databases ◽  
Genome Database

Summary Systems biology requires the integration of data from various sources and their combined interpretation using different bioinformatics tools. Integration of different biological databases, however, is often problematic due to their semantic and structural diversity. Moreover, necessary continuous updates of both the structure and content of a database provide further challenges for an integration process. We established the novel database SYSTOMONAS for SYSTems biology of pseudOMONAS by integrating heterogeneous data from highly different external resources including BioCyc, BRENDA, ENZYME, Pseudomonas Genome Database v2, KEGG, and PRODORIC. For this purpose we combined a data warehouse concept with the advantages of web services. This hybrid approach benefits from the fast performance and data consistency provided by the data warehouse system and from the up-to-dateness ensured by use of dynamic web services. The data warehouse part is realized by ETL processes (Extract, Transform, Load), during which data are checked for consistency and standardized to ensure their integrity. While accessing SYSTOMONAS via the internet, parts of the data warehouse content are dynamically enriched using the web service part of the system via SOAP (originally for Simple Object Access Protocol) interfaces with BRENDA, KEGG and PRODORIC. SYSTOMONAS is designed to integrate in-house experimental high-throughput data with up-to-date information available in the mentioned public databases. SYSTOMONAS also serves as a repository for the prediction of metabolic and regulatory networks. SYSTOMONAS is accessible at http://www.systomonas.de.

scholarly journals A Metabolic Reaction Balancing Web Service for Computational Systems Biology

2017 ◽  
Author(s):  
Paul D. Dobson ◽  
Pedro Mendes ◽  
Douglas B. Kell ◽  
Neil Swainston
Keyword(s):  
Systems Biology ◽  
Web Services ◽  
Web Service ◽  
Chinese Hamster ◽  
Ovary Cell ◽  
Mixed Integer ◽  
Metabolic Reconstruction ◽  
Metabolic Reaction ◽  
Computational Systems Biology ◽  
Computational Systems

AbstractBackgroundIn metabolic network reconstruction the stoichiometric balancing of reactions is essential to create realistic constraint-based models. At the genome scale, balancing is a repetitive task that consumes valuable curator resource that could be deployed elsewhere. Automatic reaction balancing is possible and could be useful across computational systems biology, but widespread use of the appropriate code has been limited by the diversity of non-interoperable programming languages used in the field. RESTful web services offer a language-agnostic way of binding services together.ResultsReaction balancing can be posed as a mixed integer linear programming problem to identify stoichiometric coefficients and infer commonly missing components. This functionality has been exposed as a web service that consumes a list of reactions as JSON or SBML. The reaction balancing web service has been deployed at http://www.nactem.ac.uk/balancer. Code is available via Github. By way of demonstration the service has been applied to a Chinese hamster ovary cell metabolic reconstruction to bring a further 219 reactions into balance.ConclusionsThe majority of systems biology software cannot access existing automatic reaction balancing tools due to a lack of language-specific bindings. Web services bridge different languages by using widely-spoken web communication protocols, meaning that one binding works for almost all languages. Automatic reaction balancing can now be consumed by any systems biology software via a RESTful web service.

Combining integrated systems-biology approaches with intervention-based experimental design provides a higher-resolution path forward for microbiome research

2019 ◽  
Vol 42 ◽  
Author(s):  
J. Alfredo Blakeley-Ruiz ◽  
Carlee S. McClintock ◽  
Ralph Lydic ◽  
Helen A. Baghdoyan ◽  
James J. Choo ◽  
...  
Keyword(s):  
Systems Biology ◽  
High Resolution ◽  
Experimental Design ◽  
Integrated Systems ◽  
Microbiome Research ◽  
Constructive Criticism

Abstract The Hooks et al. review of microbiota-gut-brain (MGB) literature provides a constructive criticism of the general approaches encompassing MGB research. This commentary extends their review by: (a) highlighting capabilities of advanced systems-biology “-omics” techniques for microbiome research and (b) recommending that combining these high-resolution techniques with intervention-based experimental design may be the path forward for future MGB research.

Systems Biology

2009 ◽  
Author(s):  
Bernhard O. Palsson ◽  
Marc Abrams
Keyword(s):  
Systems Biology

WS-Security on PRODML

2014 ◽  
Vol 1 (1) ◽  
pp. 9-34
Author(s):  
Bobby Suryajaya
Keyword(s):  
Web Services ◽  
Digital Signature ◽  
Data Transfer ◽  
Web Services Security ◽  
Soap Message ◽  
Simulation Results ◽  
End To End

SKK Migas plans to apply end-to-end security based on Web Services Security (WS-Security) for Sistem Operasi Terpadu (SOT). However, there are no prototype or simulation results that can support the plan that has already been communicated to many parties. This paper proposes an experiment that performs PRODML data transfer using WS-Security by altering the WSDL to include encryption and digital signature. The experiment utilizes SoapUI, and successfully loaded PRODML WSDL that had been altered with WSP-Policy based on X.509 to transfer a SOAP message.

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