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DDBJ new system and service refactoring

Osamu Ogasawara, Jun Mashima, Yuichi Kodama, Eli Kaminuma, Yasukazu Nakamura, Kousaku Okubo, Toshihisa Takagi
2012 Nucleic Acids Research  
During this upgrade, it was considered crucial to replace and refactor substantial portions of the DDBJ software systems as well.  ...  Resources provided by the DDBJ include traditional nucleotide sequence data released in the form of 27 316 452 entries or 16 876 791 557 base pairs (as of June 2012), and raw reads of new generation sequencers  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of all members of the DDBJ for their assistance in data collection, annotation and release, and software development.  ... 
doi:10.1093/nar/gks1152 pmid:23180790 pmcid:PMC3531146 fatcat:yc6arcmponhpnkjkexwsjrul3i

Integrating biological research through Web services

H.T. Gao, J.H. Hayes, H. Cai
2005 Computer  
In 2003, for the DNA Data Bank of Japan (DDBJ), Hideaki Sugawara and colleagues defined DDBJ-XML and developed a DDBJ-SOAP server.  ...  To test the potential of a Web services solution, we implemented a microarray data-mining system that uses Web services in drug discovery-a research process that attempts to identify new avenues for developing  ... 
doi:10.1109/mc.2005.97 fatcat:pf7xaxiywjhlnki44smlbmd6x4

The European Nucleotide Archive in 2017

Nicole Silvester, Blaise Alako, Clara Amid, Ana Cerdeño-Tarrága, Laura Clarke, Iain Cleland, Peter W Harrison, Suran Jayathilaka, Simon Kay, Thomas Keane, Rasko Leinonen, Xin Liu (+11 others)
2017 Nucleic Acids Research  
Here, we outline ENA services and content in 2017 and provide insight into a selection of current key areas of development in ENA driven by challenges arising from the above growth.  ...  Advances in sequencing technology have driven exponential growth in the volume of data to be processed and stored and a substantial broadening of the user community.  ...  system to include all assembled and annotated sequences.  ... 
doi:10.1093/nar/gkx1125 pmid:29140475 pmcid:PMC5753375 fatcat:s2q7ka7s5nbufi7gnztodzyzym

Genenames.org: the HGNC resources in 2015

Kristian A. Gray, Bethan Yates, Ruth L. Seal, Mathew W. Wright, Elspeth A. Bruford
2014 Nucleic Acids Research  
more powerful search, a vastly improved HCOP tool and a REST service to increase the number of ways users can retrieve our data.  ...  As well as increasing the size of our database, we have continued redesigning our website http://www.genenames.org and have modified, updated and improved many aspects of the site including a faster and  ...  ACKNOWLEDGEMENT The authors would like to thank their former colleagues, specialist advisors and other researchers who have provided invaluable contributions to this project.  ... 
doi:10.1093/nar/gku1071 pmid:25361968 pmcid:PMC4383909 fatcat:6bgwdrhfizcmtfnls2i7s3iwly

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

Stephen A. Goff, Matthew Vaughn, Sheldon McKay, Eric Lyons, Ann E. Stapleton, Damian Gessler, Naim Matasci, Liya Wang, Matthew Hanlon, Andrew Lenards, Andy Muir, Nirav Merchant (+53 others)
2011 Frontiers in Plant Science  
plant biology research (PSCIC, 2006) . iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new  ...  in research and education.  ...  by code refactoring in HPC-friendly languages.  ... 
doi:10.3389/fpls.2011.00034 pmid:22645531 pmcid:PMC3355756 fatcat:nwkuqfhsorddrppjjzs6oz76ci

Visualizing conserved gene location across microbe genomes

Chris D. Shaw, Katy Börner, Jinah Park
2009 Visualization and Data Analysis 2009  
This paper describes the visualization and analysis steps, and presents a case study using a number of Rickettsia genomes.  ...  We have developed a visualization and analysis tool that enables the biologist to observe and examine gene organization among genomes, in the context of the primary sequence of interest.  ...  as new "organisms".  ... 
doi:10.1117/12.811912 dblp:conf/vda/Shaw09 fatcat:zrtc6hqztjcyxaqd7w5fympeiy

Strain-Level Diversity of Secondary Metabolism in Streptomyces albus

Ryan F. Seipke, Paul Hoskisson
2015 PLoS ONE  
Increased resistance to antibacterial agents and the lack of new antibiotics in the pipeline have led to a renaissance in natural product discovery.  ...  Streptomyces spp. are robust producers of medicinally-, industrially-and agriculturallyimportant small molecules.  ...  Acknowledgments I thank Matt Hutchings for his constructive comments of this work and two anonymous reviewers whose suggestions improved this manuscript.  ... 
doi:10.1371/journal.pone.0116457 pmid:25635820 pmcid:PMC4312078 fatcat:jze6zlvodjbcvmzmjqg6cuqgbm

Efforts Towards Accessible And Reliable Bioinformatics

Matúš Kalaš, Inge Jonassen
2015 Zenodo  
broad topic of integrative bioinformatics, in particular with respect to bioinformatics software and services.  ...  data format compatible with Web services and programmatic libraries, that is expressive enough to be usable as a common, canonical data model that serves tools, libraries, and users with convenient data  ...  Analysis Web Services, Troshin et al. 2011) , enabling deployment of new JABAWS-compatible Web services at users' sites, another example of smooth interoperability.  ... 
doi:10.5281/zenodo.33715 fatcat:2pxqpqu5yvat3ctdedqam3sjsi

Unlocking Big Data for better health

Steven Munevar
2017 Nature Biotechnology  
Following a transition period in which the old and new systems operate in parallel, all structure depositions will be handled with the new system.  ...  new search system, and an API, all scheduled for release in 2015; • Improved and extended the internal production process and data and database infrastructure to support the new website, search system  ... 
doi:10.1038/nbt.3918 pmid:28700551 fatcat:oqiurm5cgzec7lfenvjvlemxoy

Data Standards for Omics Data: The Basis of Data Sharing and Reuse [chapter]

Stephen A. Chervitz, Eric W. Deutsch, Dawn Field, Helen Parkinson, John Quackenbush, Phillipe Rocca-Serra, Susanna-Assunta Sansone, Christian J. Stoeckert, Chris F. Taylor, Ronald Taylor, Catherine A. Ball
2011 Msphere  
Here we provide a survey of existing and emerging standards that are intended to assist the free and open exchange of large-format data.  ...  The main components of data sharing standards are experiment description standards, data exchange standards, terminology standards, and experiment execution standards.  ...  storage systems.  ... 
doi:10.1007/978-1-61779-027-0_2 pmid:21370078 pmcid:PMC4152841 fatcat:5633yzznv5bijnxtw33dwtm7ne