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 Schulz JofPathInformatics2016 7.jpg|240px]]</div>
<div style="float: left; margin: 0.5em 0.9em 0.4em 0em;">[[File:Fig1 Schulz JofPathInformatics2016 7.jpg|240px]]</div>
'''"[[Journal:Use of application containers and workflows for genomic data analysis|Use of application containers and workflows for genomic data analysis]]"'''
'''"[[Journal:SCIFIO: An extensible framework to support scientific image formats|SCIFIO: An extensible framework to support scientific image formats]]"'''


The rapid acquisition of biological data and development of computationally intensive analyses has led to a need for novel approaches to software deployment. In particular, the complexity of common analytic tools for [[genomics]] makes them difficult to deploy and decreases the reproducibility of computational experiments. Recent technologies that allow for application virtualization, such as Docker, allow developers and bioinformaticians to isolate these applications and deploy secure, scalable platforms that have the potential to dramatically increase the efficiency of big data processing. While limitations exist, this study demonstrates a successful implementation of a pipeline with several discrete software applications for the analysis of next-generation sequencing (NGS) data. ('''[[Journal:Use of application containers and workflows for genomic data analysis|Full article...]]''')<br />
No gold standard exists in the world of scientific image acquisition; a proliferation of instruments each with its own proprietary data format has made out-of-the-box sharing of that data nearly impossible. In the field of light microscopy, the Bio-Formats library was designed to translate such proprietary data formats to a common, open-source schema, enabling sharing and reproduction of scientific results. While Bio-Formats has proved successful for microscopy images, the greater scientific community was lacking a domain-independent framework for format translation.
 
SCIFIO (SCientific Image Format Input and Output) is presented as a freely available, open-source library unifying the mechanisms of reading and writing image data. The core of SCIFIO is its modular definition of formats, the design of which clearly outlines the components of image I/O to encourage extensibility, facilitated by the dynamic discovery of the SciJava plugin framework. SCIFIO is structured to support coexistence of multiple domain-specific open exchange formats, such as Bio-Formats’ OME-TIFF, within a unified environment. ('''[[Journal:SCIFIO: An extensible framework to support scientific image formats|Full article...]]''')<br />
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Revision as of 18:52, 21 March 2017

Fig1 Schulz JofPathInformatics2016 7.jpg

"SCIFIO: An extensible framework to support scientific image formats"

No gold standard exists in the world of scientific image acquisition; a proliferation of instruments each with its own proprietary data format has made out-of-the-box sharing of that data nearly impossible. In the field of light microscopy, the Bio-Formats library was designed to translate such proprietary data formats to a common, open-source schema, enabling sharing and reproduction of scientific results. While Bio-Formats has proved successful for microscopy images, the greater scientific community was lacking a domain-independent framework for format translation.

SCIFIO (SCientific Image Format Input and Output) is presented as a freely available, open-source library unifying the mechanisms of reading and writing image data. The core of SCIFIO is its modular definition of formats, the design of which clearly outlines the components of image I/O to encourage extensibility, facilitated by the dynamic discovery of the SciJava plugin framework. SCIFIO is structured to support coexistence of multiple domain-specific open exchange formats, such as Bio-Formats’ OME-TIFF, within a unified environment. (Full article...)

Recently featured:

Use of application containers and workflows for genomic data analysis
Informatics metrics and measures for a smart public health systems approach: Information science perspective
Deployment of analytics into the healthcare safety net: Lessons learned