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

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<div style="float: left; margin: 0.5em 0.9em 0.4em 0em;">[[File:Fig1 Grigis FInNeuroinformatics2017 11.jpg|240px]]</div>
'''"[[Journal:Global data quality assessment and the situated nature of “best” research practices in biology|Global data quality assessment and the situated nature of “best” research practices in biology]]"'''
'''"[[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]]"'''


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 />
This paper reflects on the relation between international debates around data quality assessment and the diversity characterizing research practices, goals and environments within the life sciences. Since the emergence of molecular approaches, many biologists have focused their research, and related methods and instruments for data production, on the study of genes and genomes. While this trend is now shifting, prominent institutions and companies with stakes in molecular biology continue to set standards for what counts as "good science" worldwide, resulting in the use of specific data production technologies as proxy for assessing data quality. This is problematic considering (1) the variability in research cultures, goals and the very characteristics of biological systems, which can give rise to countless different approaches to knowledge production; and (2) the existence of research environments that produce high-quality, significant datasets despite not availing themselves of the latest technologies. Ethnographic research carried out in such environments evidences a widespread fear among researchers that providing extensive information about their experimental set-up will affect the perceived quality of their data, making their findings vulnerable to criticisms by better-resourced peers. These fears can make scientists resistant to sharing data or describing their provenance. ('''[[Journal:Global data quality assessment and the situated nature of “best” research practices in biology|Full article...]]''')<br />
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''Recently featured'':  
''Recently featured'':  
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Revision as of 15:46, 22 August 2017

"Global data quality assessment and the situated nature of “best” research practices in biology"

This paper reflects on the relation between international debates around data quality assessment and the diversity characterizing research practices, goals and environments within the life sciences. Since the emergence of molecular approaches, many biologists have focused their research, and related methods and instruments for data production, on the study of genes and genomes. While this trend is now shifting, prominent institutions and companies with stakes in molecular biology continue to set standards for what counts as "good science" worldwide, resulting in the use of specific data production technologies as proxy for assessing data quality. This is problematic considering (1) the variability in research cultures, goals and the very characteristics of biological systems, which can give rise to countless different approaches to knowledge production; and (2) the existence of research environments that produce high-quality, significant datasets despite not availing themselves of the latest technologies. Ethnographic research carried out in such environments evidences a widespread fear among researchers that providing extensive information about their experimental set-up will affect the perceived quality of their data, making their findings vulnerable to criticisms by better-resourced peers. These fears can make scientists resistant to sharing data or describing their provenance. (Full article...)

Recently featured:

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