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An automated infrastructure to support high-throughput bioinformatics

Gianmauro Cuccuru, Simone Leo, Luca Lianas, Michele Muggiri, Andrea Pinna, Luca Pireddu, Paolo Uva, Andrea Angius, Giorgio Fotia, Gianluigi Zanetti
<span title="">2014</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qbcyvrkrbbdcfb65juklunsa44" style="color: black;">2014 International Conference on High Performance Computing &amp; Simulation (HPCS)</a> </i> &nbsp;
The challenge of scaling Efficient data processing challenges are perhaps the most evident: high throughput storage capacity tracking data provenance reliably documenting analysis procedures  ...  specific data flow pattern luca.pireddu@crs4.it (CRS4) Automation in bio July 23, 2014 13 / 29 Example: part of the traceability graph produced by an exome processing workflow.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/hpcsim.2014.6903742">doi:10.1109/hpcsim.2014.6903742</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/hpcs/CuccuruLLMPPUAFZ14.html">dblp:conf/hpcs/CuccuruLLMPPUAFZ14</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fymhmvi3qvfpretrjfkhhwexx4">fatcat:fymhmvi3qvfpretrjfkhhwexx4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170829025636/http://publications.crs4.it/pubdocs/2014/CLLMPPUAFZ14/hpcs_2014_bologna_global_view_automation.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b4/bb/b4bb3267bbaa876f876a1bf80a3d5057b9e31510.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/hpcsim.2014.6903742"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

BioBlend: automating pipeline analyses within Galaxy and CloudMan

C. Sloggett, N. Goonasekera, E. Afgan
<span title="2013-04-28">2013</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
infrastructure, and automate complex analyses over large data sets within the familiar Galaxy environment.  ...  BioBlend makes it easy for bioinformaticians to automate endto-end large-data analysis, from scratch, in a way that is highly accessible to collaborators, by allowing them to both provision the required  ...  Funding: This work was, in part, supported by the Genomics Virtual Laboratory (GVL) grant from the National eResearch Collaboration Tools and Resources (NeCTAR). Conflict of interest: None declared.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btt199">doi:10.1093/bioinformatics/btt199</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23630176">pmid:23630176</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4288140/">pmcid:PMC4288140</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wzs5buyyrjd57pr5txrx3pwa7i">fatcat:wzs5buyyrjd57pr5txrx3pwa7i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170811181526/http://bib.irb.hr/datoteka/627609.PUBLISHED_BioBlend.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/43/2c/432c199bcb76ad321ccdf6f2d41bbb4102af9c8b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btt199"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4288140" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Creating reusable tools from scripts: the Galaxy Tool Factory

R. Lazarus, A. Kaspi, M. Ziemann
<span title="2012-09-28">2012</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Availability and implementation: The Galaxy administrative interface supports automated installation from the main GTS.  ...  Source code and support are available at the project website, https://bitbucket.org/ fubar/galaxytoolfactory. The Tool Factory is implemented as an installable Galaxy  ...  bioinformatics analysis packages in an integrated and persistent framework, designed to support biologist users performing reproducible analyses.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bts573">doi:10.1093/bioinformatics/bts573</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23024011">pmid:23024011</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3509488/">pmcid:PMC3509488</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6q3y5zkntrgbvf2nn2c4cols34">fatcat:6q3y5zkntrgbvf2nn2c4cols34</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180730071846/https://watermark.silverchair.com/bts573.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAcAwggG8BgkqhkiG9w0BBwagggGtMIIBqQIBADCCAaIGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM-5Iz3FmKSSijBgiSAgEQgIIBc9zw6Nv2FptV55OjzJRGOpr3ybOa2P_lVsCSLTkpypBshF4aZV1VE9AQmpOyOW6i_u9ItSCehU8phml7Ep6gWixx3AjaS1BDKJf0Vbpcy1eurNJYXoIRTGkRCE71isZfaYS4h8ZMeX2g4LOsmdOPJfHYqQgFVg2c_Jf_xoOZbpDqvDcT1GmC25qtWNWKsnhuXMoERPNc3gomPeNylR_TVX7_71BMbq3yZBe4VrTQG7MAvfPemz0oQmkKfL8CjeAZPXZ3V0_tE3raoXGE3KBPCe2oSQbCpYK-6WOyRCUZZ6rKmawxFmcp3idKrI0ScPLj-3x6BWeW_tVq04bnY09OlzJfGrY0YGp86GkOXyMUWJh3VGdmh5_Fe9MonZ_D-jM0knD5pzKwTjoFpwY-OY7_LELS8YT2TmZHyr5HKSLsUL3HJ1smsXuVJYo-0RYjAnvncinFK5Ru9r3NnzvkGBXJ_XAgPWJqFHaA5ERx7CULHbVPvybO" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/dc/eb/dceb035257a024e3e2a4b90757214558ec56406c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bts573"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3509488" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

PUMA2--grid-based high-throughput analysis of genomes and metabolic pathways

N. Maltsev
<span title="2006-01-01">2006</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The PUMA2 system (available at http://compbio.mcs. 10 anl.gov/puma2) is an interactive, integrated bioinformatics environment for high-throughput genetic sequence analysis and metabolic reconstructions  ...  PUMA2 supports both 25 automated and interactive expert-driven annotation of genomes, using a variety of publicly available bioinformatics tools.  ...  for high-throughput analysis High-throughput computations in PUMA2 are performed by an automated Genome Analysis and Database Update (GADU) server with a grid-based distributed computational 60  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkj095">doi:10.1093/nar/gkj095</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16381888">pmid:16381888</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1347457/">pmcid:PMC1347457</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mgv7alb7cfapnl55exjkgs2ru4">fatcat:mgv7alb7cfapnl55exjkgs2ru4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170810095736/http://www.mcs.anl.gov/uploads/cels/papers/P1296.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/71/06/71066f6b5bcad94a9dabaa4b3cfd10fd6dfd7436.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkj095"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347457" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Recommendations on e-infrastructures for next-generation sequencing

Ola Spjuth, Erik Bongcam-Rudloff, Johan Dahlberg, Martin Dahlö, Aleksi Kallio, Luca Pireddu, Francesco Vezzi, Eija Korpelainen
<span title="2016-06-07">2016</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/apde6vbe7vfoxkfibp7n4mzonm" style="color: black;">GigaScience</a> </i> &nbsp;
both processing capacity and e-infrastructure flexibility when making strategic decisions to support the data analysis demands of tomorrow.  ...  With ever-increasing amounts of data being produced by next-generation sequencing (NGS) experiments, the requirements placed on supporting e-infrastructures have grown.  ...  to the recommendations presented in this manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13742-016-0132-7">doi:10.1186/s13742-016-0132-7</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27267963">pmid:27267963</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4897895/">pmcid:PMC4897895</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vwt5p5p6q5gpdkzt5ezdsyebsy">fatcat:vwt5p5p6q5gpdkzt5ezdsyebsy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171016033705/http://publisher-connector.core.ac.uk/resourcesync/data/Springer-OA/pdf/915/aHR0cDovL2xpbmsuc3ByaW5nZXIuY29tLzEwLjExODYvczEzNzQyLTAxNi0wMTMyLTcucGRm.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/08/bf/08bf0d0a1de6af11610dfc7f086be703276c5fc6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13742-016-0132-7"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4897895" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A Robust And Extensible Framework For Tracking Biodata Provenance, Analysis Workflows And Results

Gianmauro Cuccuru, Rossano Atzeni, Luca Lianas, Ricardo Medda, Luca Pireddu, Paolo Uva, Ilenia Zara, Gianluigi Zanetti, Giorgio Fotia
<span title="2016-10-26">2016</span> <i title="Zenodo"> Zenodo </i> &nbsp;
Reference: Cuccuru G. et al. (2014) An Automated Infrastructure to Support High-troughput Bioinformatics. In: Smari, Waleed W. and Zeljkovic V (ed) Proc. IEEE Int. Conf. High Perform. Comput. Simul.  ...  Figure 1 . 1 Main components of the automated CRS4 infrastructure to support end-to-end analysis of sequencing data(Cuccuru et al., 2014).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.164837">doi:10.5281/zenodo.164837</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/e5c55yxccfdvfb4mivmnc3nwi4">fatcat:e5c55yxccfdvfb4mivmnc3nwi4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201222160241/https://zenodo.org/record/164837/files/NETTAB_2016_poster_Cuccuru.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/72/a0/72a0028e2aa0d361265358b93df7ad6f8e026148.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.164837"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> zenodo.org </button> </a>

Using multiple grid resources for bioinformatics applications in GADU

D. Sulakhe, A. Rodriguez, M. Wilde, I. Foster, N. Maltsev
<span title="">2006</span> <i title="IEEE"> Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGRID&#39;06) </i> &nbsp;
GADU is a high-throughput computational system developed to automate the steps involved in accessing the Grid resources for running bioinformatics applications.  ...  This paper describes the requirements for building an automated scalable system such as GADU that can run a job simultaneously on different Grids.  ...  Acknowledgments We extend special thanks to the following individuals who contributed valuable advice and support: Elizabeth Glass, Mark D'Souza, Jens Voeckler, Miron Livny, Alain Roy, Susan Coghlan, and  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/ccgrid.2006.1630934">doi:10.1109/ccgrid.2006.1630934</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ujrq565bajb7xfz2rdnfoawxtu">fatcat:ujrq565bajb7xfz2rdnfoawxtu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170829214600/http://swift-lang.org/papers/pdfs/GridResourcesForGADU.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/de/f3/def32f96767fea59ecae291841d3593df8213b6f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/ccgrid.2006.1630934"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Bioinformatics clouds for big data manipulation

Lin Dai, Xin Gao, Yan Guo, Jingfa Xiao, Zhang Zhang
<span title="">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/m5tyg6kdofe7db2hdtm2zxndi4" style="color: black;">Biology Direct</a> </i> &nbsp;
computing infrastructure into utility-supplied cloud computing delivered over the Internet, in order to handle the vast quantities of biological data generated by high-throughput experimental technologies  ...  As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house  ...  This work was supported by grants from King Abdullah University of Science and Technology (a start-up grant to XG), the National Natural Science Foundation of China (60803050 and 61132009 to LD), the "  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1745-6150-7-43">doi:10.1186/1745-6150-7-43</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23190475">pmid:23190475</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3533974/">pmcid:PMC3533974</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/plt5x7aqpbcofiddfyk23fl4gm">fatcat:plt5x7aqpbcofiddfyk23fl4gm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809075141/https://biologydirect.biomedcentral.com/track/pdf/10.1186/1745-6150-7-43?site=biologydirect.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fd/df/fddfd9f34d972df7b48d23f43fd0ad4d578052a6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1745-6150-7-43"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3533974" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

<span title="2015-11-28">2015</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The SIB Swiss Institute of Bioinformatics (www. isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia  ...  These solutions allow life scientists to turn the exponentially growing amount of data into knowledge.  ...  Acknowledgements to Additional SIB Members (non-coauthors) The authors would like to explicitly thank the following SIB members not mentioned in the co-author list above:  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkv1310">doi:10.1093/nar/gkv1310</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26615188">pmid:26615188</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4702916/">pmcid:PMC4702916</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/oxgje3pvj5hv5mqgjcvm4w2xiy">fatcat:oxgje3pvj5hv5mqgjcvm4w2xiy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190428025647/https://www.research-collection.ethz.ch/bitstream/handle/20.500.11850/114269/gkv1310.pdf;jsessionid=63FFF7CED63EA4F971F70934B4A23D25?sequence=2" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/91/53/9153dab3f27eef8b6a06504dde724eb47d530201.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkv1310"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702916" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences

Nirav Merchant, Eric Lyons, Stephen Goff, Matthew Vaughn, Doreen Ware, David Micklos, Parker Antin
<span title="2016-01-11">2016</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tsaumnzpkvdmvdi3blhl5clb24" style="color: black;">PLoS Biology</a> </i> &nbsp;
tools; and cloud, high-performance, high-throughput computing. iPlant provides training, learning material, and best practice resources to help all researchers make the best use of their data, expand their  ...  The iPlant Collaborative provides life science research communities access to comprehensive, scalable, and cohesive computational infrastructure for data management; identity management; collaboration  ...  These projects have allowed iPlant to rapidly deploy and extend its cyberinfrastructure.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pbio.1002342">doi:10.1371/journal.pbio.1002342</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26752627">pmid:26752627</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4709069/">pmcid:PMC4709069</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uwhpaj2ryvewlgfyljkx2sjdzm">fatcat:uwhpaj2ryvewlgfyljkx2sjdzm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180721053033/http://repository.cshl.edu/32225/1/Ware%20and%20Micklos%20PLoS%20Biol%202016.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/06/d2/06d2a3fde80c5644f14f743b29a57f6b02e850d9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pbio.1002342"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4709069" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Analysis of high-throughput plant image data with the information system IAP

Christian Klukas, Jean-Michel Pape, Alexander Entzian
<span title="2012-06-01">2012</span> <i title="Walter de Gruyter GmbH"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fvl4m6o2tre4pcvl4ljymxu4ly" style="color: black;">Journal of Integrative Bioinformatics</a> </i> &nbsp;
work, cover the complete end-to-end pipeline, starting with the image transfer from the imaging infrastructure, (grid distributed) image analysis, data management for raw data and analysis results, to  ...  SummaryThis work presents a sophisticated information system, the Integrated Analysis Platform (IAP), an approach supporting large-scale image analysis for different species and imaging systems.  ...  As the Oracle database requires special and complicated setup, handling and operation in addition to high licensing fees, for IAP it was desired to switch to an open source alternative.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1515/jib-2012-191">doi:10.1515/jib-2012-191</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/v3l6l5wlpfhydhvuqk4xw3ggsy">fatcat:v3l6l5wlpfhydhvuqk4xw3ggsy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201124083757/https://www.degruyter.com/downloadpdf/journals/jib/9/2/article-p16.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3b/4b/3b4b6cc17cad0ba28bf174d97c673ce5c85bd240.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1515/jib-2012-191"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> degruyter.com </button> </a>

Experiences with workflows for automating data-intensive bioinformatics

Ola Spjuth, Erik Bongcam-Rudloff, Guillermo Carrasco Hernández, Lukas Forer, Mario Giovacchini, Roman Valls Guimera, Aleksi Kallio, Eija Korpelainen, Maciej M Kańduła, Milko Krachunov, David P Kreil, Ognyan Kulev (+6 others)
<span title="2015-08-19">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/m5tyg6kdofe7db2hdtm2zxndi4" style="color: black;">Biology Direct</a> </i> &nbsp;
High-throughput technologies, such as next-generation sequencing, have turned molecular biology into a data-intensive discipline, requiring bioinformaticians to use high-performance computing resources  ...  Workflow systems can be useful to simplify construction of analysis pipelines that automate tasks, support reproducibility and provide measures for fault-tolerance.  ...  Acknowledgements The hackathons and workshops leading to this compilation were supported by COST Action BM1006 Next Generation Sequencing Data Analysis Network SeqAhead.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13062-015-0071-8">doi:10.1186/s13062-015-0071-8</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26282399">pmid:26282399</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4539931/">pmcid:PMC4539931</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cxotvdjwrndblm7gvu5myegsrq">fatcat:cxotvdjwrndblm7gvu5myegsrq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170912050520/https://link.springer.com/content/pdf/10.1186%2Fs13062-015-0071-8.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/85/d5/85d5da9e5122d3b4088ed1cbfd5d1dbaaa8610bf.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13062-015-0071-8"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4539931" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Interoperability of GADU in Using Heterogeneous Grid Resources for Bioinformatics Applications

D. Sulakhe, A. Rodriguez, M. Wilde, I. Foster, N. Maltsev
<span title="">2008</span> <i title="Institute of Electrical and Electronics Engineers (IEEE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/opxxmwcvy5fnnhqoc4wtvb4etm" style="color: black;">IEEE Transactions on Information Technology in Biomedicine</a> </i> &nbsp;
GADU is a highthroughput computational system developed to automate the steps involved in accessing the Grid resources for running bioinformatics applications.  ...  This paper describes the requirements for building an automated scalable system such as GADU that can run jobs on different Grids.  ...  Acknowledgments We extend special thanks to the following individuals who contributed valuable advice and support: Elizabeth Glass, Mark D'Souza, Jens Voeckler, Miron Livny, Alain Roy, Susan Coghlan, and  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/titb.2007.897783">doi:10.1109/titb.2007.897783</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18348953">pmid:18348953</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3dmhxt2j2rcjfcfeacah2yr25e">fatcat:3dmhxt2j2rcjfcfeacah2yr25e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20161221114334/http://www.mcs.anl.gov/uploads/cels/papers/P1403.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/29/7f/297fc69937f7bc1ac0d39e0ddc791d73f4f05253.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/titb.2007.897783"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

H. Parkinson, U. Sarkans, N. Kolesnikov, N. Abeygunawardena, T. Burdett, M. Dylag, I. Emam, A. Farne, E. Hastings, E. Holloway, N. Kurbatova, M. Lukk (+10 others)
<span title="2010-11-10">2010</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The ArrayExpress Archive is closely integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute.  ...  The ArrayExpress Archive (http://www.ebi.ac.uk/ arrayexpress) is one of the three international public repositories of functional genomics data supporting publications.  ...  Work is in progress to develop an automated BioConductor (7) package to identify, extract and reprocess RNA-Seq data for inclusion in the GXA.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkq1040">doi:10.1093/nar/gkq1040</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21071405">pmid:21071405</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3013660/">pmcid:PMC3013660</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4rn24k5lvzhajj4huiufljvsgy">fatcat:4rn24k5lvzhajj4huiufljvsgy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190228170853/http://pdfs.semanticscholar.org/a6bf/e1fa00d80a2ac69c27f3e5fde49d72bdf226.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a6/bf/a6bfe1fa00d80a2ac69c27f3e5fde49d72bdf226.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkq1040"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013660" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Towards a Modeling Infrastructure for Studying Plant Cells

T. Girke
<span title="2003-05-08">2003</span> <i title="American Society of Plant Biologists (ASPB)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lyouqq67dncvxgcbflq26svwta" style="color: black;">Plant Physiology</a> </i> &nbsp;
miniaturized high-throughput instrumentation.  ...  An important question in this endeavor remains whether the current bioinformatics infrastructure is sufficiently prepared for the new requirement of systems-based approaches in plant biology because the  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1104/pp.103.022103">doi:10.1104/pp.103.022103</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12805570">pmid:12805570</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/k5d6v7zwrjektns3fftzxzieyi">fatcat:k5d6v7zwrjektns3fftzxzieyi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190503181656/http://www.plantphysiol.org/content/plantphysiol/132/2/410.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6d/fd/6dfde889ce93c292b2b48722cfe54cb203f62923.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1104/pp.103.022103"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>
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