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Network portal: a database for storage, analysis and visualization of biological networks

Serdar Turkarslan, Elisabeth J. Wurtmann, Wei-Ju Wu, Ning Jiang, J. Christopher Bare, Karen Foley, David J. Reiss, Pavel Novichkov, Nitin S. Baliga
2013 Nucleic Acids Research  
storage, visualization and analysis of biological networks.  ...  We have designed the network portal (http://networks.systemsbiology.net) to serve as a modular database for the integration of user uploaded and public data, with inference algorithms and tools for the  ...  ACKNOWLEDGEMENTS We thank Christopher Plaisier and Aaron Brooks for critical reading of the manuscript and helpful suggestions. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkt1190 pmid:24271392 pmcid:PMC3964938 fatcat:ffzkuvfxvjft5mmtfuwbbcvcuu

DroPNet: a web portal for integrated analysis of Drosophila protein-protein interaction networks

Y. Renaud, A. Baillif, J.-B. Perez, M. Agier, E. Mephu Nguifo, V. Mirouse
2012 Nucleic Acids Research  
DroPNet (Drosophila Protein Network) is a Drosophila-dedicated web portal for generating and analyzing protein-protein interaction (PPI) networks.  ...  DroPNet, therefore, provides an essential basis for further biological analysis by linking functional and physical interactions and reinforcing the relevance of each.  ...  ACKNOWLEDGEMENTS We thank Jordan Raff for the permission of using data from their RNAi screen as a sample. We thank Finley lab for DroID database, which is really helpful for us.  ... 
doi:10.1093/nar/gks434 pmid:22641854 pmcid:PMC3394298 fatcat:ptbob76l2fbu7kb6o75va2itmu

canEvolve: A Web Portal for Integrative Oncogenomics

Mehmet Kemal Samur, Zhenyu Yan, Xujun Wang, Qingyi Cao, Nikhil C. Munshi, Cheng Li, Parantu K. Shah, Dilek Colak
2013 PLoS ONE  
The network analysis capability includes storage and visualization of gene co-expression, inferred gene regulatory networks and protein-protein interaction information.  ...  2013. canEvolve: A web portal for integrative oncogenomics. PLoS ONE 8(2): e56228.  ...  We thank the CaSNP database team and Shirley Liu for sharing the data of CaSNP. Author Contributions  ... 
doi:10.1371/journal.pone.0056228 pmid:23418540 pmcid:PMC3572035 fatcat:txb4e546bna3fhcu4h6xkmi6i4

The Telescience Portal for advanced tomography applications

Steven T. Peltier, Abel W. Lin, David Lee, Stephen Mock, Stephan Lamont, Tomas Molina, Mona Wong, Lu Dai, Maryann E. Martone, Mark H. Ellisman
2003 Journal of Parallel and Distributed Computing  
instrumentation, advanced image processing and visualization, access to distributed/federated databases, and network-enabled data management and archival are tightly coupled within a secure environment  ...  More than just a collection of individual applications, the Portal provides a transparent workflow, where simple intuitive interfaces for grid-enabled parallel computation, resource scheduling, remote  ...  Acknowledgments This work was supported in part by grants from the National Science Foundation (DBI 9318180 and ASC 975249) and the National Institutes of Health (RR 04050 and DC 03192).  ... 
doi:10.1016/s0743-7315(03)00061-3 fatcat:gwfvj66xpbhtrgixbihjjmz6xq

Comprehensive Screening of Gene Function and Networks by DNA Microarray Analysis in Japanese Patients with Idiopathic Portal Hypertension

Kohei Kotani, Joji Kawabe, Hiroyasu Morikawa, Tomohiko Akahoshi, Makoto Hashizume, Susumu Shiomi
2015 Mediators of Inflammation  
In functional annotation analysis using the Database for Annotation Visualization and Integrated Discovery tool, clusters showing dysfunction in patients with IPH involved gene terms related to the immune  ...  The functions of genes involved in idiopathic portal hypertension (IPH) remain unidentified.  ...  Yoshiyuki Takahara for his assistance of constructive discussion.  ... 
doi:10.1155/2015/349215 pmid:26549939 pmcid:PMC4609492 fatcat:p3dq7iitbfchhl6zy2yrzuj64q

African Genomic Medicine Portal: A Web Portal for Biomedical Applications

Houcemeddine Othman, Lyndon Zass, Jorge E. B. da Rocha, Fouzia Radouani, Chaimae Samtal, Ichrak Benamri, Judit Kumuthini, Yasmina J. Fakim, Yosr Hamdi, Nessrine Mezzi, Maroua Boujemaa, Chiamaka Jessica Okeke (+24 others)
2022 Journal of Personalized Medicine  
To overcome these challenges, we developed the African Genomic Medicine Portal (AGMP), a database that contains metadata on genomic medicine studies conducted on African-ancestry populations.  ...  This information is typically segmented across several different biomedical data repositories, which often lack sufficient fine-grained structure and annotation to account for the diversity of African  ...  The number of biological and biomedical databases have increased over the last two decades, with resources for diverse organisms, molecules, interactions and pathways.  ... 
doi:10.3390/jpm12020265 pmid:35207753 pmcid:PMC8879570 fatcat:s6fu5apwpbgzvmhcpa4i6rtz2m

EOSC Portal Profiles v4.00

Sanchez-P. Jorge-A.
2021 Zenodo  
They contribute to the unified framework for describing and offering EOSC Resources to end-users in a harmonized way, guaranteeing the interoperability of resources metadata with open APIs.  ...  EOSC Profiles are specifications that define common data models for EOSC entities (Providers, Resources, etc.) and related Code Lists, Taxonomies and Classifications.  ...  The facilities are relevant for Biological-and development for storage, retrieval, and analysis of the data. all the related factors impacting behaviours.  ... 
doi:10.5281/zenodo.5726889 fatcat:dhwylcbtdjd4vjlfiglvu755vu

PlantMetabolomics.org: A Web Portal for Plant Metabolomics Experiments

P. Bais, S. M. Moon, K. He, R. Leitao, K. Dreher, T. Walk, Y. Sucaet, L. Barkan, G. Wohlgemuth, M. R. Roth, E. S. Wurtele, P. Dixon (+8 others)
2010 Plant Physiology  
PlantMetabolomics.org (PM) is a web portal and database for exploring, visualizing, and downloading plant metabolomics data.  ...  The database tries to capture a complete annotation of the experiment metadata along with the metabolite abundance databased on the evolving Metabolomics Standards Initiative.  ...  ACKNOWLEDGMENTS This work was performed at the Virtual Reality Application Center, Iowa State University, with the assistance of the Bioinformatics Laboratory of the Bioinformatics and Computational Biology  ... 
doi:10.1104/pp.109.151027 pmid:20147492 pmcid:PMC2850039 fatcat:6eoz5y4gxbesrhd75cvmaviboa

Prometheus: omics portals for interkingdom comparative genomic analyses [article]

Gunhwan Ko, Insu Jang, Namjin Koo, Seong-Jin Park, Sang-Ho Oh, Min-Seo Kim, Jin-Hyuk Choi, Hyeongmin Kim, Young Mi Sim, Iksu Byeon, Pan-Gyu Kim, Kye Young Kim (+8 others)
2017 bioRxiv   pre-print
Functional analyses of genes are crucial for unveiling biological responses, for genetic engineering, and for developing new medicines.  ...  Prometheus suggests a new paradigm for comparative analyses with large amounts of genomic information.  ...  Indeed, the accessibility of bioinformatics 22 analysis is currently a major hurdle for ongoing biologic research.  ... 
doi:10.1101/232298 fatcat:kvvtaodyqfbx3iiefrru4vcffu

The Natural History Museum Data Portal

2019 Database: The Journal of Biological Databases and Curation  
This paper describes the technical development of the data portal, from its inception to beta launch in December 2015, its first 2 years of operation, and future plans for the project.  ...  The Natural History Museum, London (NHM), generates and holds some of the largest global data sets relating to the biological and geological diversity of the natural world.  ...  Finally, we would like to thank staff from across the NHM who have embraced the data portal as a repository for their data sets. Funding Natural History Museum Science Group. Conflict of interest.  ... 
doi:10.1093/database/baz038 pmid:30985890 pmcid:PMC6459053 fatcat:fh3nh6uesndkvcggk377ao6dua

Prometheus, an omics portal for interkingdom comparative genomic analyses

Gunhwan Ko, Insu Jang, Namjin Koo, Seong-Jin Park, Sang-Ho Oh, Min-Seo Kim, Jin-Hyuk Choi, Hyeongmin Kim, Young Mi Sim, Iksu Byeon, Pan-Gyu Kim, Kye Young Kim (+6 others)
2020 PLoS ONE  
Functional analyses of genes are crucial for unveiling biological responses, genetic engineering, and developing new medicines.  ...  Prometheus is a new paradigm for comparative analyses of large amounts of genomic information.  ...  Indeed, the accessibility of bioinformatics analysis is currently a major hurdle for ongoing biologic research.  ... 
doi:10.1371/journal.pone.0240191 pmid:33112870 fatcat:wk65d4lcdbdarhscbtucidqwre

The Virtual Kidney: an eScience interface and Grid portal

P. J. Harris, R. Buyya, X. Chu, T. Kobialka, E. Kazmierczak, R. Moss, W. Appelbe, P. J. Hunter, S. R. Thomas
2009 Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences  
This initiative exploits high-bandwidth communication networks for collaborative research and for shared access to knowledge resources.  ...  Models are run locally or remotely with a Grid resource broker managing scheduling, monitoring and visualization of simulation results and application, credential and resource allocation.  ...  , followed by a statistical analysis tool followed by a link to a database tool for genetic information).  ... 
doi:10.1098/rsta.2008.0291 pmid:19414450 fatcat:xjb23pj7onfutae6xcabcknofy

OverCOVID: an integrative web portal for SARS-CoV-2 bioinformatics resources

Md. Asif Ahsan, Yongjing Liu, Cong Feng, Ralf Hofestädt, Ming Chen
2021 Journal of Integrative Bioinformatics  
In addition, a network view of the resources is provided to display the scope of the research.  ...  Other information like SARS-CoV-2 strains is visualized and various layers of interaction resources is listed in distinct pages of the web portal.  ...  Resources Network In the 'resources network' page, an additional network view of the resources ( Figure 2C ) is provided to visually indicate the scope of research for each database/tool and to intuitively  ... 
doi:10.1515/jib-2020-0046 pmid:33735949 fatcat:mpzrhuxfvbcsdntjzvagpz3mt4

LungMAP Portal Ecosystem: Systems-Level Exploration of the Lung [article]

Nathan Gaddis, Joshua Fortriede, Minzhe Guo, Eric E Bardes, Michal Kouril, Scott Tabar, Kevin Burns, Maryanne E Ardini-Poleske, Stephanie Loos, Daniel Schnell, Kang Jin, Balaji Iyer (+21 others)
2021 bioRxiv   pre-print
This portal connects a broad-spectrum of research networks, bulk and single-cell multi-omics data and a diverse collection of image data that span mammalian lung development and disease.  ...  To centralize and standardize information across broad lung research efforts we expanded the LungMAP.net website into a gateway portal.  ...  We would like to thank the Cincinnati Children's Research Foundation for their additional support and the Data and Technology Services and Research IT Services in the Division of Biomedical Informatics  ... 
doi:10.1101/2021.12.05.471312 fatcat:ufvimh2dsvfqjors2lxj55sciy

Application portals: practice and experience

Mary Thomas, Maytal Dahan, Kurt Mueller, Steve Mock, Cathie Mills, Ray Regno
2002 Concurrency and Computation  
The implementation of multiple Grid computing portals has led us to develop a methodology for Grid portal development that facilitates rapid prototyping and building of portals.  ...  In this paper, we describe our experiences gained in building Grid portals and developing software for the Grid.  ...  In addition, The authors would like to acknowledge the San Diego Supercomputer Center and the NSF funded NPACI program for their support (both with resources and staff) and for allowing the portals project  ... 
doi:10.1002/cpe.694 fatcat:pfjlwdzrx5avnhgflhyizuxfra
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