scholarly journals Advances in decomposing complex metabolite mixtures using substructure- and network-based computational metabolomics approaches

2021 ◽  
Author(s):  
Mehdi A. Beniddir ◽  
Kyo Bin Kang ◽  
Grégory Genta-Jouve ◽  
Florian Huber ◽  
Simon Rogers ◽  
...  
Keyword(s):  
Natural Product ◽  
Large Scale ◽  
Scale Analysis ◽  
Computational Tools ◽  
Natural Product Discovery ◽  
Large Scale Analysis ◽  
Metabolite Annotation

This review highlights the key computational tools and emerging strategies for metabolite annotation, and discusses how these advances will enable integrated large-scale analysis to accelerate natural product discovery.

scholarly journals REVA as a Well-curated Database for Human Expression-modulating Variants

2021 ◽  
Author(s):  
Yu Wang ◽  
Fang-Yuan Shi ◽  
Yu Liang ◽  
Ge Gao
Keyword(s):  
Large Scale ◽  
Regulatory Mechanism ◽  
State Of The Art ◽  
Scale Analysis ◽  
Computational Tools ◽  
Functional Annotations ◽  
Link Type ◽  
Large Scale Analysis ◽  
Multiple State ◽  
Limited Sensitivity

AbstractMore than 80% of disease- and trait-associated human variants are noncoding. By systematically screening multiple large-scale studies, we compiled REVA, a manually curated database for over 11.8 million experimentally tested noncoding variants with expression-modulating potentials. We provided 2424 functional annotations that could be used to pinpoint plausible regulatory mechanism of these variants. We further benchmarked multiple state-of-the-art computational tools and found their limited sensitivity remains a serious challenge for effective large-scale analysis. REVA provides high-qualify experimentally tested expression-modulating variants with extensive functional annotations, which will be useful for users in the noncoding variants community. REVA is available at http://reva.gao-lab.org.

scholarly journals CellProfiler 4: Improvements in Speed, Utility and Usability

2021 ◽  
Author(s):  
David R Stirling ◽  
Madison J Swain-Bowden ◽  
Alice M Lucas ◽  
Anne E. Carpenter ◽  
Beth A Cimini ◽  
...  
Keyword(s):  
Image Analysis ◽  
User Interface ◽  
Large Scale ◽  
Source Image ◽  
Scale Analysis ◽  
Analysis Program ◽  
Computational Tools ◽  
Large Scale Analysis ◽  
Free Open Source ◽  
Microscopy Images

CellProfiler is a free, open source image analysis program which enables researchers to generate modular pipelines with which to process microscopy images into interpretable measurements. Here we describe CellProfiler 4, a new version of this software which has been ported to the Python 3 language. Based on user feedback, we have made several user interface refinements to improve the usability of the software. We introduced new modules to expand the capabilities of the software. We also evaluated performance and made targeted optimisations to reduce the time and cost associated with running common large-scale analysis pipelines. This release will ensure that researchers will have continued access to CellProfilers powerful computational tools in the coming years.

scholarly journals CellProfiler 4: improvements in speed, utility and usability

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
David R. Stirling ◽  
Madison J. Swain-Bowden ◽  
Alice M. Lucas ◽  
Anne E. Carpenter ◽  
Beth A. Cimini ◽  
...  
Keyword(s):  
Large Scale ◽  
Biological Information ◽  
Source Image ◽  
Scale Analysis ◽  
Imaging Data ◽  
Computational Tools ◽  
Large Scale Analysis ◽  
Improved Performance ◽  
Free Open Source ◽  
Microscopy Images

Abstract Background Imaging data contains a substantial amount of information which can be difficult to evaluate by eye. With the expansion of high throughput microscopy methodologies producing increasingly large datasets, automated and objective analysis of the resulting images is essential to effectively extract biological information from this data. CellProfiler is a free, open source image analysis program which enables researchers to generate modular pipelines with which to process microscopy images into interpretable measurements. Results Herein we describe CellProfiler 4, a new version of this software with expanded functionality. Based on user feedback, we have made several user interface refinements to improve the usability of the software. We introduced new modules to expand the capabilities of the software. We also evaluated performance and made targeted optimizations to reduce the time and cost associated with running common large-scale analysis pipelines. Conclusions CellProfiler 4 provides significantly improved performance in complex workflows compared to previous versions. This release will ensure that researchers will have continued access to CellProfiler’s powerful computational tools in the coming years.

scholarly journals Identifying draught cattle in the past: Lessons from large-scale analysis of archaeological datasets

2021 ◽  
Vol 33 ◽  
pp. 258-269
Author(s):  
Matilda Holmes ◽  
Richard Thomas ◽  
Helena Hamerow
Keyword(s):  
Large Scale ◽  
Scale Analysis ◽  
The Past ◽  
Large Scale Analysis
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