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Domain-specific languages for composing signature discovery workflows

Ferosh Jacob, Jeff Gray, Adam Wynne, Yan Liu, Nathan Baker
2012 Proceedings of the 2012 workshop on Domain-specific modeling - DSM '12  
This raises an engineering issue on how to generate web service wrappers for these heterogeneous executables and to compose them into a scientific workflow environment (e.g., Taverna).  ...  We demonstrate our approach with a real-world workflow composed of services wrapping remote executables.  ...  Creating workflows using WDL A WDL file generates a Taverna workflow based on the descriptions specified by the user.  ... 
doi:10.1145/2420918.2420934 fatcat:nxiu4z4itzg6jnxahspdujqrta

Classification of the state-of-the-art dynamic web services composition techniques

Atif Alamri, Mohamad Eid, Abdulmotaleb El Saddik
2006 International Journal of Web and Grid Services  
The proposed taxonomy of these techniques is derived based on a comprehensive survey of what has been done so far in dynamic web service composition.  ...  Finally, we summarise our findings and present a vision for future research work in this area.  ...  A semantic context-based approach for composing web services is proposed in Mrissa et al. (2005) .  ... 
doi:10.1504/ijwgs.2006.010805 fatcat:e2rooan6unfxbpbnywewrqrowm

A Service-Oriented Framework for Real-Time and Distributed Geoprocessing [chapter]

Bastian Schaeffer, Bastian Baranski, Theodor Foerster, Johannes Brauner
2011 Lecture Notes in Geoinformation and Cartography  
As a result, web-based geoinformation is generated, which supports in particular spatial decision making.  ...  Moreover, an approach will be introduced to improve complex and large-scale geoprocesses in two dimensions: On the vertical scale, by significantly increasing the performance of single processes by means  ...  Even though in our case only WPS instances are incorporated, the presented approach for establishing workflows can be applied to any type of Web Service interface because the approach is based on the mainstream  ... 
doi:10.1007/978-3-642-10595-1_1 fatcat:n64j6lhegbflthhaln7j7oghiy

Wrappers – A Mechanism to Support State-Based Authorization in Web Applications [chapter]

Martin S Olivier, Ehud Gudes
2002 IFIP International Federation for Information Processing  
The solution presented in this paper is an approach referred to as wrappers: a wrapper is a simple program that has enough knowledge about a specific application's potential states and the actions that  ...  The paper presents its concepts in a World-wide Web environment that renders it immediately useful.  ...  (such as many current online stores) or to create a tool that will automatically derive a specification from others such as those used for workflow systems in general.  ... 
doi:10.1007/0-306-47008-x_14 fatcat:okkzafbv4jaobpxg6k2vzykmy4

Querying multiple bioinformatics information sources

David Buttler, Matthew Coleman, Terence Critchlow, Renato Fileto, Wei Han, Calton Pu, Daniel Rocco, Li Xiong
2002 SIGMOD record  
Second, most of the queries required by Genomics researchers involve complex data extraction, and sophisticated workflows that implement the complex associative access.  ...  Advances in Semantic Web and Ontologies have pushed the role of semantics to a new frontier: Semantic Composition of Web Services.  ...  Figure 1 represents the workflow that a genomics research has created to gather the data required for this analysis.  ... 
doi:10.1145/637411.637421 fatcat:h6zbfiidtvh6viewdek2ubwr6e

A semantic grid-based data access and integration service for bioinformatics

G. Aloisio, M. Cafaro, I. Epicoco, S. Fiore, M. Mirto
2005 CCGrid 2005. IEEE International Symposium on Cluster Computing and the Grid, 2005.  
Blast and Rasmol) available as Web Services, into a workflow.  ...  Given the heterogeneous nature of biological data and their intensive use in many tools, in this paper we propose a semantic data access and integration (DAI) service, based on the Grid paradigm, for the  ...  ProGenGrid is based on the following key approaches: web/grid services, workflow, ontologies and data integration through the Grid.  ... 
doi:10.1109/ccgrid.2005.1558554 dblp:conf/ccgrid/AloisioCEFM05 fatcat:ei3cjwgtvfdazpjms2kr2fzk3u

An Architecture of a Workflow System for Integrated Asset Management in the Smart Oil Field Domain

Ramakrishna Soma, Amol Bakshi, Viktor K Prasanna
2007 2007 IEEE Congress on Services (Services 2007)  
We then propose an architecture for the system based on the three key goals of the system: support for integrating legacy tools and analysis modules, support for audit trails and data quality indicators  ...  Integrated Asset Management (IAM) is the vision of IT-enabled transformation of oilfield operations where information integration from a variety of tools for reservoir modeling, simulation, and performance  ...  ACKNOWLEDGMENT This research was funded by CiSoft a joint USC-Chevron Center of Excellence for Research and Academic Training on Interactive Smart Oilfield Technologies.  ... 
doi:10.1109/services.2007.15 dblp:conf/IEEEscc/SomaBP07 fatcat:6drn6nlqgzfyfiterhyvqcnqbm

Using Mediation to Achieve Provenance Interoperability

Tommy Ellqvist, David Koop, Juliana Freire, Cláudio Silva, Lena Strömbäck
2009 2009 Congress on Services - I  
In this paper, we describe a mediator-based architecture for integrating provenance information from multiple sources.  ...  API that is general and able to express complex queries over provenance information from different sources.  ...  Specifically, we plan to develop automatic mechanisms for translating highlevel provenance queries into calls to the API, for example: queries defined through a query-by-example interface [21] ; and through  ... 
doi:10.1109/services-i.2009.68 dblp:conf/services/EllqvistKFSS09 fatcat:brdioxkodvdxtbaoxrtyqvlhdy

Integrating light-weight workflow management systems within existing business environments

P. Muth, J. Weissenfels, M. Gillmann, G. Weikum
1999 Proceedings 15th International Conference on Data Engineering (Cat. No.99CB36337)  
This approach is powerful cf the control flow is specified and implemented from scratch, but it has severe drawbacks if a workflow management system is to be integrated within environments with existing  ...  solutions for implementing control flow.  ...  For each application program, a proxy object identifying its wrapper has to be created.  ... 
doi:10.1109/icde.1999.754944 dblp:conf/icde/MuthWGW99 fatcat:wpphkmxggzgs3jmbtnz5ezxb24

Wrappers––a mechanism to support state-based authorisation in Web applications

M.S. Olivier, Ehud Gudes
2002 Data & Knowledge Engineering  
This paper proposes the use of a simple program (a "wrapper") that has enough knowledge about a specific application's potential states and the actions that are permissible in each state.  ...  The premises of this paper are 1) security is application dependent because application semantics directly influence proper protection; but 2) applications are generally too complex to be trusted to implement  ...  (such as many current online stores) or to create a tool that will automatically derive a specification from others such as those used for workflow systems in general.  ... 
doi:10.1016/s0169-023x(02)00129-5 fatcat:jm23egjlvrfyffkm3awmsol2aq

Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system

Todd H Oakley, Markos A Alexandrou, Roger Ngo, M Pankey, Celia K C Churchill, William Chen, Karl B Lopker
2014 BMC Bioinformatics  
Osiris and Galaxy provide a sharable, standardized, modular user interface, and the ability to easily create complex workflows using a graphical interface.  ...  Results: We developed a suite of wrappers for new and existing phylogenetics tools for the Galaxy workflow management system that we call Osiris.  ...  Weakliem and the Life Sciences Computing Group (LSCG) for extensive technical assistance. Thanks to P. Cruz for developing some tool wrappers in Osiris.  ... 
doi:10.1186/1471-2105-15-230 pmid:24990571 pmcid:PMC4227113 fatcat:stzllhl2zzh3znlpinrafnwxea

VLAM-G: Interactive Data Driven Workflow Engine for Grid-Enabled Resources

Vladimir Korkhov, Dmitry Vasyunin, Adianto Wibisono, Adam S.Z. Belloum, Márcia A. Inda, Marco Roos, Timo M. Breit, L.O. Hertzberger
2007 Scientific Programming  
The RTS is a dataflow driven workflow engine which utilizes Grid resources, hiding the complexity of the Grid from a scientist.  ...  In turn, workflow management systems provide a high-level environment for rapid prototyping of experimental computing systems.  ...  Marcel van Batenburg for fruitful discussions and the bioinformatics group of Dr. Antoine van Kampen for making the human transcriptome map data available to us.  ... 
doi:10.1155/2007/812036 fatcat:hsjiixrifrbqfcgznu2h3qkfva

An agent-based approach to tool integration

Flavio Corradini, Leonardo Mariani, Emanuela Merelli
2004 International Journal on Software Tools for Technology Transfer (STTT)  
We noticed that the agent paradigm provided a suitable technology for abstraction in tool integration. Throughout the paper, the discussion refers to a case study in the bioinformatics domain.  ...  In this paper we analyze the tool-integration problem at different abstraction levels and discuss different views on a layered software architecture that we have designed specifically for a middleware  ...  We would like to thank Alessandro Ricci for valuable comments on a preliminary version of this paper.  ... 
doi:10.1007/s10009-004-0158-5 fatcat:5j4cwhb62vhrlf2nxbyrzgm77a

Triana: a graphical Web service composition and execution toolkit

S. Majithia, M. Shields, I. Taylor, I. Wang
2004 Proceedings. IEEE International Conference on Web Services, 2004.  
Here, we newly extend this functionality to create a Web services binding for the GAP, which allows users to graphically and transparently create Web services workflows.  ...  Triana uses a peer to peer subset of the GridLab GAT interface, that we have labeled the GAP Interface.  ...  The Triana system is an ongoing project based at Cardiff University; the latest version can be downloaded at http://www.trianacode.org/. 5.0  ... 
doi:10.1109/icws.2004.1314777 dblp:conf/icws/MajithiaSTW04 fatcat:jks745swfjbl7jbo5mgxvqev7u

Semantic Annotation of Maps Through Knowledge Provenance [chapter]

Nicholas Del Rio, Paulo Pinheiro da Silva, Ann Q. Gates, Leonardo Salayandia
2007 Lecture Notes in Computer Science  
As a result, complex metadata may be required to describe maps semantically. This paper presents an approach to describe maps by annotating associated provenance.  ...  For example, a user study is presented showing that scientists with different levels of expertise and background are able to evaluate the quality of maps by analyzing their knowledge provenance information  ...  PML Service Wrapper (PSW) is a general-purpose Web service wrapper that logs knowledge provenance associated with workflow execution as PML documents.  ... 
doi:10.1007/978-3-540-76876-0_2 fatcat:rza4lj2v6re67ik7b6ogckuazm
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