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An integration platform for heterogeneous bioinformatics software components
2001
IBM Systems Journal
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In this paper, we describe an approach to the problem of integration of heterogeneous bioinformatics resources that relies on a generalized software platform, written in the Java TM language, that we call ...
The platform is not restricted in its utility to bioinformatics, and could be useful for any rapidly changing field in which the integration of heterogeneous legacy components is important. ...
to make the project possible; and to the National Center for Genome Resources for funding and support. ...
doi:10.1147/sj.402.0570
fatcat:nxtwkjfzfnburjvihwgqtfjrzy
Graphically-enabled integration of bioinformatics tools allowing parallel execution
2000
Proceedings. AMIA Symposium
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TurboGenomics, which is a software package currently in its alpha-testing phase, allows integration of heterogeneous software components to be done graphically. ...
In addition, the tool is capable of making the integrated components run in parallel. ...
unified application from a number of heterogeneous software components. ...
pmid:11079861
pmcid:PMC2243957
fatcat:zjwfdkc5xzesbecy7gvjgejfaa
Platform for EpiGenomic Research (PEGR): A flexible management platform for reproducible epigenomic and genomic research
2021
Zenodo
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., Pegasus, Galaxy), these platforms are generally limited to reproducing software workflows [15, 16]. ...
To our knowledge, there are no free open-source platforms that manage entire experimental pipelines, from wet-bench experiments to bioinformatic analyses. ...
We developed the Platform for Epigenomic and Genomic Research (PEGR), a web-based project management platform that integrates wet-bench sample tracking with downstream bioinformatic workflows (managed ...
doi:10.5281/zenodo.5570116
fatcat:owpo7qbgxnfb7bh4hlmid2bvdy
Cyclone: A Platform For Data Intensive Scientific Applications In Heterogeneous Multi-Cloud/Multi-Provider Environment
2016
Zenodo
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This paper presents results of the ongoing development of the CYCLONE as a platform for scientific applications in heterogeneous multi-cloud/multi-provider environment. ...
to the CYCLONE infrastructure components. ...
We are thankful to our colleagues who collaborate with us to deploy selected bioinformatics applications in the CYCLONE testbed: Christian Baudet (Centre Léon Bérard, Lyon, France) and Thomas Lacroix ( ...
doi:10.5281/zenodo.243122
fatcat:3u4evra2dffepfuqf7coblakqi
Cyclone: A Platform For Data Intensive Scientific Applications In Heterogeneous Multi-Cloud/Multi-Provider Environment
2016
Zenodo
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This paper presents results of the ongoing development of the CYCLONE as a platform for scientific applications in heterogeneous multi-cloud/multi-provider environment. ...
to the CYCLONE infrastructure components. ...
We are thankful to our colleagues who collaborate with us to deploy selected bioinformatics applications in the CYCLONE testbed: Christian Baudet (Centre Léon Bérard, Lyon, France) and Thomas Lacroix ( ...
doi:10.5281/zenodo.59160
fatcat:dxjh7l6ih5cvbhe5aweq3b5wfu
ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources
2001
Bioinformatics
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Results: We present a component-based approach that relies on a generalized platform for component integration. ...
Motivation: Heterogeneity of databases and software resources continues to hamper the integration of biological information. ...
ACKNOWLEDGEMENTS The authors are grateful to Faye Schilkey, Tom Cartner, David Hanley, and Dawn Perry for contributions in prototype development and documentation, to Allan Dickerman for insights on integration-intensive ...
doi:10.1093/bioinformatics/17.1.83
pmid:11222265
fatcat:yiqxnsvsazh3zeksbvxttfk2di
A semantic grid-based data access and integration service for bioinformatics
2005
CCGrid 2005. IEEE International Symposium on Cluster Computing and the Grid, 2005.
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The main goal of the DAI is to provide bioinformatics tools with advanced functionalities and data integration services for heterogeneous biological data banks, such as PDB and Swiss-Prot. ...
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 ...
A Computational Grid could be a solution to many bioinformatics issues because it allows the deployment, distribution and management of needed biological software components, the harmonized standard integration ...
doi:10.1109/ccgrid.2005.1558554
dblp:conf/ccgrid/AloisioCEFM05
fatcat:ei3cjwgtvfdazpjms2kr2fzk3u
Bringing Web 2.0 to bioinformatics
2008
Briefings in Bioinformatics
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Enabling deft data integration from numerous, voluminous and heterogeneous data sources is a major bioinformatic challenge. ...
In addition to its research potential, we also describe its potential role as an e-learning platform in education. ...
Acknowledgements We thank two anonymous reviewers for their constructive comments on this article, Prof. ...
doi:10.1093/bib/bbn041
pmid:18842678
pmcid:PMC2638627
fatcat:cjpbzmxuzjcvhhekmykgisj5zi
Research on data integration of bioinformatics database based on web services
2009
2009 First International Conference on Networked Digital Technologies
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In this paper, we present a data integration program based on Web Services of heterogeneous bioinformatics databases. ...
How to unify the bioinformatics database from different countries has become an important issue in Bioinformatics. ...
Conclusion We can use Web Services technology to realize the integration of the bioinformatics database and set up a unifi ed platform for the users. ...
doi:10.1109/ndt.2009.5272808
fatcat:ugo34fm3ijdtbem5swbgld5vyy
BioDWH: a data warehouse kit for life science data integration
2008
Journal of Integrative Bioinformatics
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This open source software can be used as a general infrastructure for integrative bioinformatics research and development. ...
This paper presents a novel bioinformatics data warehouse software kit that integrates biological information from multiple public life science data sources into a local database management system. ...
Acknowledgements This work is supported by Sixth Framework Programme Priority 1 Life Sciences, Genomics and Biotechnology for Health: "CardioWorkBench -Drug Design for Cardiovascular Diseases: Integration ...
doi:10.2390/biecoll-jib-2008-93
pmid:20134070
fatcat:6znf76ylf5ht7pbo3dxjpysz4u
BioDWH: A Data Warehouse Kit for Life Science Data Integration
2008
Journal of Integrative Bioinformatics
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This open source software can be used as a general infrastructure for integrative bioinformatics research and development. ...
Finally, a practical application of the system is presented within the emerging area of medical bioinformatics to show the usefulness of the approach.The BioDWH data warehouse software is available for ...
Acknowledgements This work is supported by Sixth Framework Programme Priority 1 Life Sciences, Genomics and Biotechnology for Health: "CardioWorkBench -Drug Design for Cardiovascular Diseases: Integration ...
doi:10.1515/jib-2008-93
fatcat:f7pd2hs37jbj7d2yg6fsaj5jpq
ChinaGrid: Making Grid Computing a Reality
[chapter]
2004
Lecture Notes in Computer Science
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integrate widespread computational resources into super, ubiquitous and transparent aggregation. ...
The purpose of this paper is to introduce this great grid project to the world completely for the first time. ...
Acknowledgement Special thanks to following people providing materials for this paper of each ChinaGrid application platform: Professor Weiming Zheng from Tsinghua University, Professor Xiaoming Li from ...
doi:10.1007/978-3-540-30544-6_2
fatcat:x7wfsimiifeqfoqjjly2ln7uiy
CYCLONE: A Multi-cloud Federation Platform for Complex Bioinformatics and Energy Applications (Short Paper)
2016
2016 5th IEEE International Conference on Cloud Networking (Cloudnet)
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Some real-life use-cases in the scientific area of energy optimization and bioinformatics are in use to validate the CYCLONE architecture and integrated platform, from the viewpoints of service deployment ...
Multi-cloud applications delivered across heterogeneous public cloud service providers poses different technical and operational challenges in terms of resource brokering, integration, implementation of ...
Bioinformatics software is characterized by a high degree of fragmentation: literally hundreds of different software packages are regularly used for scientific analyses with an incompatible variety of ...
doi:10.1109/cloudnet.2016.44
dblp:conf/cloudnet/GallicoBBBGAHK16
fatcat:yuy4n42p7jbunc5aylx57pt3z4
Data modeling: the key to biological data integration
2012
EMBnet journal
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The association of the software module dedicated to genome annotation and comparison with the microbial database results in a powerful easy-to-use integrated bioinformatics platform. ...
In this context, explicit and formal data modeling provides very appropriate tools for integrating heterogeneous data, for properly connecting methods and data, and for allowing computer scientists, bioinformaticians ...
doi:10.14806/ej.18.b.550
fatcat:lyhirzxb2zeipbswpncljejawq
Enabling high-throughput data management for systems biology: The Bioinformatics Resource Manager
2007
Bioinformatics
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The Bioinformatics Resource Manager (BRM) is a software environment that provides the user with data management, retrieval and integration capabilities. ...
Designed in collaboration with biologists, BRM simplifies mundane analysis tasks of merging microarray and proteomic data across platforms, facilitates integration of users' data with functional annotation ...
ACKNOWLEDGEMENTS The research described in this article was conducted under the LDRD Program at the Pacific Northwest National Laboratory, a multiprogram national laboratory operated by Battelle for the ...
doi:10.1093/bioinformatics/btm031
pmid:17324940
fatcat:6zcslqw2avgy3ag26dnqus7gji
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