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DDBJ new system and service refactoring
2012
Nucleic Acids Research
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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
2005
Computer
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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
2017
Nucleic Acids Research
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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
2014
Nucleic Acids Research
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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
2011
Frontiers in Plant Science
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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
2009
Visualization and Data Analysis 2009
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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
2015
PLoS ONE
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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
2015
Zenodo
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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
2017
Nature Biotechnology
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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]
2011
Msphere
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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