scholarly journals Data Sharing in the High-throughput University - Mobility and Precarity

2021 ◽  
Author(s):  
Stefan Reichmann

The nascent field of data science and the expansion of the higher education sector share surprising affinities. The emergence of the “entrepreneurial university” has brought increasing differentiation of the work roles of academics in addition to increased mobility and, for some, precarity. At the same time, researchers are dealing with unprecedented amounts of data. The present article describes how policies and infrastructures implemented to support researchers with data curation tasks might be repurposed by research administrators to tackle problems of academic mobility rooted in increasing precarity of non-tenured research staff. Findings suggest that the organizational benefit of research data management (RDM) is not increased efficiency or reusability of research, but rather increased control over data left behind by non-tenured staff. Recent interest in data mobility needs to be understood by reference to increased researcher mobility. While the view of data as context-independent evidence has been challenged by reference to the investments necessary to mobilize data as evidence in the first place, the material presented here suggests that RDM is repurposed by universities as a strategy to manage, not data, but rather increasing rates of staff turnover. The mobility of data producers and the immobility of data are frequently in tension. Handing over data is problematic irrespective of domain, data type, and funding source. The term “high-throughput university” is introduced in opposition to “high-throughput” data production techniques to suggest that findability and reusability of data need to be recontextualized with reference to increased academic mobility.

2018 ◽  
Vol 106 (4) ◽  
Author(s):  
Jean-Paul Courneya ◽  
Alexa Mayo

Despite having an ideal setup in their labs for wet work, researchers often lack the computational infrastructure to analyze the magnitude of data that result from “-omics” experiments. In this innovative project, the library supports analysis of high-throughput data from global molecular profiling experiments by offering a high-performance computer with open source software along with expert bioinformationist support. The audience for this new service is faculty, staff, and students for whom using the university’s large scale, CORE computational resources is not warranted because these resources exceed the needs of smaller projects. In the library’s approach, users are empowered to analyze high-throughput data that they otherwise would not be able to on their own computers. To develop the project, the library’s bioinformationist identified the ideal computing hardware and a group of open source bioinformatics software to provide analysis options for experimental data such as scientific images, sequence reads, and flow cytometry files. To close the loop between learning and practice, the bioinformationist developed self-guided learning materials and workshops or consultations on topics such as the National Center for Biotechnology Information’s BLAST, Bioinformatics on the Cloud, and ImageJ. Researchers apply the data analysis techniques that they learned in the classroom in an ideal computing environment.


Author(s):  
Yongjoo Kim ◽  
Jongeun Lee ◽  
A. Shrivastava ◽  
J. W. Yoon ◽  
Doosan Cho ◽  
...  

Amino Acids ◽  
2008 ◽  
Vol 35 (3) ◽  
pp. 517-530 ◽  
Author(s):  
Xing-Ming Zhao ◽  
Luonan Chen ◽  
Kazuyuki Aihara

Cell Cycle ◽  
2021 ◽  
pp. 1-15
Author(s):  
Lian Duan ◽  
Zhendong Wang ◽  
Xin Zheng ◽  
Junjian Li ◽  
Huamin Yin ◽  
...  

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ali Rohani ◽  
Jennifer A. Kashatus ◽  
Dane T. Sessions ◽  
Salma Sharmin ◽  
David F. Kashatus

Abstract Mitochondria are highly dynamic organelles that can exhibit a wide range of morphologies. Mitochondrial morphology can differ significantly across cell types, reflecting different physiological needs, but can also change rapidly in response to stress or the activation of signaling pathways. Understanding both the cause and consequences of these morphological changes is critical to fully understanding how mitochondrial function contributes to both normal and pathological physiology. However, while robust and quantitative analysis of mitochondrial morphology has become increasingly accessible, there is a need for new tools to generate and analyze large data sets of mitochondrial images in high throughput. The generation of such datasets is critical to fully benefit from rapidly evolving methods in data science, such as neural networks, that have shown tremendous value in extracting novel biological insights and generating new hypotheses. Here we describe a set of three computational tools, Cell Catcher, Mito Catcher and MiA, that we have developed to extract extensive mitochondrial network data on a single-cell level from multi-cell fluorescence images. Cell Catcher automatically separates and isolates individual cells from multi-cell images; Mito Catcher uses the statistical distribution of pixel intensities across the mitochondrial network to detect and remove background noise from the cell and segment the mitochondrial network; MiA uses the binarized mitochondrial network to perform more than 100 mitochondria-level and cell-level morphometric measurements. To validate the utility of this set of tools, we generated a database of morphological features for 630 individual cells that encode 0, 1 or 2 alleles of the mitochondrial fission GTPase Drp1 and demonstrate that these mitochondrial data could be used to predict Drp1 genotype with 87% accuracy. Together, this suite of tools enables the high-throughput and automated collection of detailed and quantitative mitochondrial structural information at a single-cell level. Furthermore, the data generated with these tools, when combined with advanced data science approaches, can be used to generate novel biological insights.


2011 ◽  
Vol 71 (2) ◽  
pp. 266-279 ◽  
Author(s):  
Ezra Kissel ◽  
Martin Swany ◽  
Aaron Brown

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