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eXframe: reusable framework for storage, analysis and visualization of genomics experiments

Amit U Sinha, Emily Merrill, Scott A Armstrong, Tim W Clark, Sudeshna Das
<span title="">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Results: We have developed eXframe -a reusable web-based framework for genomics experiments that provides 1) the ability to publish structured data compliant with accepted standards 2) support for multiple  ...  Conclusion: The web-based framework eXframe offers structured annotation of experiments as well as uniform processing and storage of molecular data from microarray and next generation sequencing platforms  ...  Clemens Scherzer for helpful discussions and for providing requirements.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-12-452">doi:10.1186/1471-2105-12-452</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22103807">pmid:22103807</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3235155/">pmcid:PMC3235155</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/w4xj72om4rcttnhrnxzbxkwyze">fatcat:w4xj72om4rcttnhrnxzbxkwyze</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830115531/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-12-452?site=http://bmcbioinformatics.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/44/26/44263e0649753cdeca40cd9a0865eeb577f7e58c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-12-452"> <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/PMC3235155" 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 eGenVar data management system—cataloguing and sharing sensitive data and metadata for the life sciences

Sabry Razick, Rok Močnik, Laurent F. Thomas, Einar Ryeng, Finn Drabløs, Pål Sætrom
<span title="2014-01-01">2014</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ejkvir3kzbdojf5kygupkidsca" style="color: black;">Database: The Journal of Biological Databases and Curation</a> </i> &nbsp;
Our system and software suite thereby provide a common framework for cataloguing and sharing both public and private data.  ...  Instead, we describe a metadata cataloguing system and a software suite for reporting the presence of data from the life sciences domain.  ...  Similarly, the eXframe (31) system can provide a good visualization platform for collected data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bau027">doi:10.1093/database/bau027</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24682735">pmid:24682735</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4030636/">pmcid:PMC4030636</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vmtos4lognhcjkt6bwfc6abtvu">fatcat:vmtos4lognhcjkt6bwfc6abtvu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190430153155/https://ntnuopen.ntnu.no/ntnu-xmlui/bitstream/handle/11250/2389641/Database-2014-Razick-database-bau027.pdf?sequence=3" 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/0d/3f/0d3f7167257a8c0df7a7cea4ae5db89f358c106d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bau027"> <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/PMC4030636" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Harnessing Big Data for Systems Pharmacology [article]

Lei Xie, Eli Draizen, Philip Bourne
<span title="2016-09-23">2016</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
It will allow systems pharmacology modeling to be findable, accessible, interoperable, reusable, reliable, interpretable, and actionable.  ...  interplay of biological networks, and is dependent on pharmacokinetics.  ...  Acknowledgement This research was supported by the National Library of Medicine of the National Institute of Health under the award number R01LM011986 (LX) References  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/077115">doi:10.1101/077115</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/owkyissq65agrdovh2vdgux24m">fatcat:owkyissq65agrdovh2vdgux24m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190502020624/https://www.biorxiv.org/content/biorxiv/early/2016/09/23/077115.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/3f/b9/3fb97caad04f163b2310b404ebbe3c077f15d2c1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/077115"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Harnessing Big Data for Systems Pharmacology

Lei Xie, Eli J. Draizen, Philip E. Bourne
<span title="2017-01-06">2017</span> <i title="Annual Reviews"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jxqqgho7bncrvgfyfznramju3q" style="color: black;">Annual Review of Pharmacology and Toxicology</a> </i> &nbsp;
It will allow systems pharmacology modeling to be findable, accessible, interoperable, reusable, reliable, interpretable, and actionable. the integration of genome-wide, heterogeneous, and dynamic data  ...  MD generates millions of conformations for further analysis -ten times more than all the structures deposited in the Protein Data Bank (PDB) (28) to date.  ...  Acknowledgement This research was supported by the National Library of Medicine of the National Institute of Health under the award number R01LM011986 (LX) References  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1146/annurev-pharmtox-010716-104659">doi:10.1146/annurev-pharmtox-010716-104659</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27814027">pmid:27814027</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5626567/">pmcid:PMC5626567</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/oajwecyapvbghjgft2wizxoeze">fatcat:oajwecyapvbghjgft2wizxoeze</a> </span>
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