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

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(Updated article of the week text.)
(Updated article of the week text.)
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<div style="float: left; margin: 0.5em 0.9em 0.4em 0em;">[[File:Fig2 Heo BMCBioinformatics2017 18.gif|240px]]</div>
<div style="float: left; margin: 0.5em 0.9em 0.4em 0em;">[[File:Fig1 Grigis FInNeuroinformatics2017 11.jpg|240px]]</div>
'''"[[Journal:Analyzing the field of bioinformatics with the multi-faceted topic modeling technique|Analyzing the field of bioinformatics with the multi-faceted topic modeling technique]]"'''
'''"[[Journal:Neuroimaging, genetics, and clinical data sharing in Python using the CubicWeb framework|Neuroimaging, genetics, and clinical data sharing in Python using the CubicWeb framework]]"'''


[[Bioinformatics]] is an interdisciplinary field at the intersection of molecular biology and computing technology. To characterize the field as a convergent domain, researchers have used bibliometrics, augmented with text-mining techniques for content analysis. In previous studies, Latent Dirichlet Allocation (LDA) was the most representative topic modeling technique for identifying topic structure of subject areas. However, as opposed to revealing the topic structure in relation to metadata such as authors, publication date, and journals, LDA only displays the simple topic structure.
In neurosciences or psychiatry, the emergence of large multi-center population imaging studies raises numerous technological challenges. From distributed data collection, across different institutions and countries, to final data publication service, one must handle the massive, heterogeneous, and complex data from genetics, imaging, demographics, or clinical scores. These data must be both efficiently obtained and downloadable. We present a Python solution, based on the CubicWeb open-source semantic framework, aimed at building population imaging study repositories. In addition, we focus on the tools developed around this framework to overcome the challenges associated with data sharing and collaborative requirements. We describe a set of three highly adaptive web services that transform the CubicWeb framework into a (1) multi-center upload platform, (2) collaborative quality assessment platform, and (3) publication platform endowed with massive-download capabilities. Two major European projects, IMAGEN and EU-AIMS, are currently supported by the described framework. We also present a Python package that enables end users to remotely query neuroimaging, genetics, and clinical data from scripts. ('''[[Journal:Neuroimaging, genetics, and clinical data sharing in Python using the CubicWeb framework|Full article...]]''')<br />
 
In this paper, we adopt the Author-Conference-Topic (ACT) model of Tang ''et al.'' to study the field of bioinformatics from the perspective of keyphrases, authors, and journals. The ACT model is capable of incorporating the paper, author, and conference into the topic distribution simultaneously. To obtain more meaningful results, we used journals and keyphrases instead of conferences and the bag-of-words. For analysis, we used PubMed to collect forty-six bioinformatics journals from the MEDLINE database. We conducted time series topic analysis over four periods from 1996 to 2015 to further examine the interdisciplinary nature of bioinformatics. ('''[[Journal:Analyzing the field of bioinformatics with the multi-faceted topic modeling technique|Full article...]]''')<br />
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''Recently featured'':  
''Recently featured'':  
: ▪ [[Journal:Analyzing the field of bioinformatics with the multi-faceted topic modeling technique|Analyzing the field of bioinformatics with the multi-faceted topic modeling technique]]
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: ▪ [[Journal:Intervene: A tool for intersection and visualization of multiple gene or genomic region sets|Intervene: A tool for intersection and visualization of multiple gene or genomic region sets]]
: ▪ [[Journal:Users’ perspectives on a picture archiving and communication system (PACS): An in-depth study in a teaching hospital in Kuwait|Users’ perspectives on a picture archiving and communication system (PACS): An in-depth study in a teaching hospital in Kuwait]]
: ▪ [[Journal:Users’ perspectives on a picture archiving and communication system (PACS): An in-depth study in a teaching hospital in Kuwait|Users’ perspectives on a picture archiving and communication system (PACS): An in-depth study in a teaching hospital in Kuwait]]
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Revision as of 17:35, 14 August 2017

Fig1 Grigis FInNeuroinformatics2017 11.jpg

"Neuroimaging, genetics, and clinical data sharing in Python using the CubicWeb framework"

In neurosciences or psychiatry, the emergence of large multi-center population imaging studies raises numerous technological challenges. From distributed data collection, across different institutions and countries, to final data publication service, one must handle the massive, heterogeneous, and complex data from genetics, imaging, demographics, or clinical scores. These data must be both efficiently obtained and downloadable. We present a Python solution, based on the CubicWeb open-source semantic framework, aimed at building population imaging study repositories. In addition, we focus on the tools developed around this framework to overcome the challenges associated with data sharing and collaborative requirements. We describe a set of three highly adaptive web services that transform the CubicWeb framework into a (1) multi-center upload platform, (2) collaborative quality assessment platform, and (3) publication platform endowed with massive-download capabilities. Two major European projects, IMAGEN and EU-AIMS, are currently supported by the described framework. We also present a Python package that enables end users to remotely query neuroimaging, genetics, and clinical data from scripts. (Full article...)

Recently featured:

Analyzing the field of bioinformatics with the multi-faceted topic modeling technique
Intervene: A tool for intersection and visualization of multiple gene or genomic region sets
Users’ perspectives on a picture archiving and communication system (PACS): An in-depth study in a teaching hospital in Kuwait