Difference between revisions of "Template:Article of the week"

From LIMSWiki
Jump to navigationJump to search
(Updated article of the week text.)
(Updated article of the week text.)
Line 1: Line 1:
<div style="float: left; margin: 0.5em 0.9em 0.4em 0em;">[[File:Fig5 Lukauskas BMCBioinformatics2016 17-Supp16.gif|240px]]</div>
<div style="float: left; margin: 0.5em 0.9em 0.4em 0em;">[[File:Fig2 Harvey JoCheminformatics2017 9.gif|240px]]</div>
'''"[[Journal:DGW: An exploratory data analysis tool for clustering and visualisation of epigenomic marks|DGW: An exploratory data analysis tool for clustering and visualisation of epigenomic marks]]"'''
'''"[[Journal:A metadata-driven approach to data repository design|A metadata-driven approach to data repository design]]"'''


Functional [[Genomics|genomic]] and epigenomic research relies fundamentally on [[sequencing]]-based methods like ChIP-seq for the detection of DNA-protein interactions. These techniques return large, high-dimensional data sets with visually complex structures, such as multi-modal peaks extended over large genomic regions. Current tools for visualisation and data exploration represent and leverage these complex features only to a limited extent.
The design and use of a metadata-driven data repository for research data management is described. Metadata is collected automatically during the submission process whenever possible and is registered with DataCite in accordance with their current metadata schema, in exchange for a persistent digital object identifier. Two examples of data preview are illustrated, including the demonstration of a method for integration with commercial software that confers rich domain-specific [[data analysis|data analytics]] without introducing customization into the repository itself. ('''[[Journal:A metadata-driven approach to data repository design|Full article...]]''')<br />
 
We present DGW (Dynamic Gene Warping), an open-source software package for simultaneous alignment and clustering of multiple epigenomic marks. DGW uses dynamic time warping to adaptively rescale and align genomic distances which allows to group regions of interest with similar shapes, thereby capturing the structure of epigenomic marks. We demonstrate the effectiveness of the approach in a simulation study and on a real epigenomic data set from the ENCODE project. ('''[[Journal:DGW: An exploratory data analysis tool for clustering and visualisation of epigenomic marks|Full article...]]''')<br />
<br />
<br />
''Recently featured'':  
''Recently featured'':  
: ▪ [[Journal:DGW: An exploratory data analysis tool for clustering and visualisation of epigenomic marks|DGW: An exploratory data analysis tool for clustering and visualisation of epigenomic marks]]
: ▪ [[Journal:SCIFIO: An extensible framework to support scientific image formats|SCIFIO: An extensible framework to support scientific image formats]]
: ▪ [[Journal:SCIFIO: An extensible framework to support scientific image formats|SCIFIO: An extensible framework to support scientific image formats]]
: ▪ [[Journal:Use of application containers and workflows for genomic data analysis|Use of application containers and workflows for genomic data analysis]]
: ▪ [[Journal:Use of application containers and workflows for genomic data analysis|Use of application containers and workflows for genomic data analysis]]
: ▪ [[Journal:Informatics metrics and measures for a smart public health systems approach: Information science perspective|Informatics metrics and measures for a smart public health systems approach: Information science perspective]]

Revision as of 19:15, 3 April 2017

Fig2 Harvey JoCheminformatics2017 9.gif

"A metadata-driven approach to data repository design"

The design and use of a metadata-driven data repository for research data management is described. Metadata is collected automatically during the submission process whenever possible and is registered with DataCite in accordance with their current metadata schema, in exchange for a persistent digital object identifier. Two examples of data preview are illustrated, including the demonstration of a method for integration with commercial software that confers rich domain-specific data analytics without introducing customization into the repository itself. (Full article...)

Recently featured:

▪ DGW: An exploratory data analysis tool for clustering and visualisation of epigenomic marks
▪ SCIFIO: An extensible framework to support scientific image formats
▪ Use of application containers and workflows for genomic data analysis
Retrieved from "https://www.limswiki.org/index.php?title=Template:Article_of_the_week&oldid=29716"