scholarly journals Connecting the dots between computational tools to analyse soil–root water relations

2018 ◽  
Vol 70 (9) ◽  
pp. 2345-2357 ◽  
Author(s):  
Sixtine Passot ◽  
Valentin Couvreur ◽  
Félicien Meunier ◽  
Xavier Draye ◽  
Mathieu Javaux ◽  
...  
2018 ◽  
Author(s):  
Sixtine Passot ◽  
Valentin Couvreur ◽  
Félicien Meunier ◽  
Xavier Draye ◽  
Mathieu Javaux ◽  
...  

AbstractIn the recent years, many computational tools, such as image analysis, data management, process-based simulation and upscaling tools, were developed to help quantify and understand water flow in the soil-root system, at multiple scales (tissue, organ, plant and population). Several of these tools work together or, at least, are compatible. However, for the un-informed researcher, they might seem disconnected, forming a unclear and disorganised succession of tools.In this article, we present how different pieces of work can be further developed by connecting them to analyse soil-root-water relations in a comprehensive and structured network. This “explicit network of soil-root computational tools” informs the reader about existing tools and help them understand how their data (past and future) might fit within the network. We also demonstrate the novel possibilities of scale-consistent parameterizations made possible by the network with a set of case studies from the literature. Finally, we discuss existing gaps in the network and how we can move forward to fill them.HighlightsMany computational tools exist to quantify water flow in the soil-root system. These tools can be arranged in a comprehensive network that can be leveraged to better interpret experimental data.


2019 ◽  
Author(s):  
Brian C. Ross ◽  
Fabio Anaclerio ◽  
Nicola Lorusso ◽  
Mario Ventura ◽  
Jim Costello

AbstractMeasurement of in-vivo chromosome conformations (structures) in single cells is a major technological goal of structural biology. If one could identify many genetic loci in a microscope image despite the limited palette of fluorescent colors used to label them, then the conformation could be solved at some resolution by ‘connecting the dots’. Computational tools for making this reconstruction are expected to produce near-perfect reconstructions when the number of fluorescent colors is high enough, irrespective of the number of loci assayed. Here we report the first experimental test of the performance of these reconstruction algorithms and check their ability to reconstruct experimentally-measured conformations. We also demonstrate the experimental metrics needed to assess reconstruction quality. Our results indicate that current sequential FISH experiments may be close to the point where the reconstructions are nearly flawless at some distance scales.


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