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An integration platform for heterogeneous bioinformatics software components

A. C. Siepel, A. N. Tolopko, A. D. Farmer, P. A. Steadman, F. D. Schilkey, B. D. Perry, W. D. Beavis
2001 IBM Systems Journal  
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

K H Cheung, P Miller, A Sherman, S Weston, E Stratmann, M Schultz, M Snyder, A Kumar
2000 Proceedings. AMIA Symposium  
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

Danying Shao, Gretta Kellogg, Ali Nematbakhsh, Prashant Kuntala, Shaun Mahony, B Frank Pugh, William Lai
2021 Zenodo  
., 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

Yuri Demchenko, Miroslav Zivkiovic, Cees De Laat, Christophe Blanchet, Mohamed Bedri, Jean-François Gibrat, Oleg Lodygensky, Mathias Slawik, Ilke Zilci, Rob Branchat, Charles Loomis
2016 Zenodo  
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

Yuri Demchenko, Miroslav Zikovich, Cess de Laat, Christophe Blanchet, Mohamed Bedri, Jean-François Gibrat, Oleg Lodygensky, Mathias Slawik, Ilke Zilci, Rob Branchat, Charles Loomis
2016 Zenodo  
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

A. Siepel, A. Farmer, A. Tolopko, M. Zhuang, P. Mendes, W. Beavis, B. Sobral
2001 Bioinformatics  
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

G. Aloisio, M. Cafaro, I. Epicoco, S. Fiore, M. Mirto
2005 CCGrid 2005. IEEE International Symposium on Cluster Computing and the Grid, 2005.  
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

Z. Zhang, K.-H. Cheung, J. P. Townsend
2008 Briefings in Bioinformatics  
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

Yuelan Liu, Jianhua Wang, Yuefan Liu, Zhenwu Tan
2009 2009 First International Conference on Networked Digital Technologies  
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

Thoralf Töpel, Benjamin Kormeier, Andreas Klassen, Ralf Hofestädt
2008 Journal of Integrative Bioinformatics  
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

Thoralf Töpel, Benjamin Kormeier, Andreas Klassen, Ralf Hofestädt
2008 Journal of Integrative Bioinformatics  
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]

Hai Jin
2004 Lecture Notes in Computer Science  
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)

D. Gallico, M. Biancani, C. Blanchet, M. Bedri, J.-F. Gibrat, J. I. A. Baranda, D. Hacker, M. Kourkouli
2016 2016 5th IEEE International Conference on Cloud Networking (Cloudnet)  
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

François Rechenmann
2012 EMBnet journal  
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

A. R. Shah, M. Singhal, K. R. Klicker, E. G. Stephan, H. S. Wiley, K. M. Waters
2007 Bioinformatics  
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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