scholarly journals Precise measurements of chromatin diffusion dynamics by modeling using Gaussian processes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Guilherme M. Oliveira ◽  
Attila Oravecz ◽  
Dominique Kobi ◽  
Manon Maroquenne ◽  
Kerstin Bystricky ◽  
...  
Keyword(s):  
Gaussian Processes ◽  
Embryonic Stem ◽  
Graphical Interface ◽  
Computational Framework ◽  
Chromatin Dynamics ◽  
Temporal Correlations ◽  
Diffusion Dynamics ◽  
User Friendly ◽  
Nuclear Processes ◽  
Diffusion Properties

AbstractThe spatiotemporal organization of chromatin influences many nuclear processes: from chromosome segregation to transcriptional regulation. To get a deeper understanding of these processes, it is essential to go beyond static viewpoints of chromosome structures, to accurately characterize chromatin’s diffusion properties. We present GP-FBM: a computational framework based on Gaussian processes and fractional Brownian motion to extract diffusion properties from stochastic trajectories of labeled chromatin loci. GP-FBM uses higher-order temporal correlations present in the data, therefore, outperforming existing methods. Furthermore, GP-FBM allows to interpolate incomplete trajectories and account for substrate movement when two or more particles are present. Using our method, we show that average chromatin diffusion properties are surprisingly similar in interphase and mitosis in mouse embryonic stem cells. We observe surprising heterogeneity in local chromatin dynamics, correlating with potential regulatory activity. We also present GP-Tool, a user-friendly graphical interface to facilitate usage of GP-FBM by the research community.

scholarly journals Precise measurements of chromatin diffusion dynamics by modeling using Gaussian processes

2021 ◽  
Author(s):  
Guilherme M Oliveira ◽  
Attila Oravecz ◽  
Dominique Kobi ◽  
Manon Maroquenne ◽  
Kerstin Bystricky ◽  
...  
Keyword(s):  
Gaussian Processes ◽  
Embryonic Stem ◽  
Graphical Interface ◽  
Nuclear Dynamics ◽  
Computational Framework ◽  
Chromatin Dynamics ◽  
Diffusion Dynamics ◽  
User Friendly ◽  
Nuclear Processes ◽  
Diffusion Properties

The spatiotemporal organization of chromatin influences many nuclear processes: from chromosome segregation to transcriptional regulation. To get a deeper understanding of these processes it is essential to go beyond static viewpoints of chromosome structures, and to accurately characterize chromatin mobility and its diffusion properties. Here, we present GP-FBM: a new computational framework based on Gaussian processes and fractional Brownian motion to analyze and extract diffusion properties from stochastic trajectories of labeled chromatin loci. GP-FBM is able to optimally use the higher-order correlations present in the data and therefore outperforms existing methods. Furthermore, GP-FBM is able to extrapolate trajectories from missing data and account for substrate movement automatically. Using our method we show that diffusive chromatin diffusion properties are surprisingly similar in interphase and mitosis in mouse embryonic stem cells. Moreover, we observe surprising heterogeneity in local chromatin dynamics, which correlates with transcriptional activity. We also present GP-Tool, a user-friendly graphical interface to facilitate the use of GP FBM by the research community for future studies of nuclear dynamics.

scholarly journals Ribo-ODDR: Oligo design pipeline for experiment-specific rRNA depletion in ribo-seq

2021 ◽  
Author(s):  
Ferhat Alkan ◽  
Joana Silva ◽  
Eric Pintó Barberà ◽  
William J Faller
Keyword(s):  
Ribosome Profiling ◽  
Supplementary Information ◽  
Experimental Conditions ◽  
Computational Framework ◽  
Rna Translation ◽  
Rrna Depletion ◽  
Selection For ◽  
Nucleotide Resolution ◽  
User Friendly ◽  
Oligo Design

Abstract Motivation Ribosome Profiling (Ribo-seq) has revolutionized the study of RNA translation by providing information on ribosome positions across all translated RNAs with nucleotide-resolution. Yet several technical limitations restrict the sequencing depth of such experiments, the most common of which is the overabundance of rRNA fragments. Various strategies can be employed to tackle this issue, including the use of commercial rRNA depletion kits. However, as they are designed for more standardized RNAseq experiments, they may perform suboptimally in Ribo-seq. In order to overcome this, it is possible to use custom biotinylated oligos complementary to the most abundant rRNA fragments, however currently no computational framework exists to aid the design of optimal oligos. Results Here, we first show that a major confounding issue is that the rRNA fragments generated via Ribo-seq vary significantly with differing experimental conditions, suggesting that a “one-size-fits-all” approach may be inefficient. Therefore we developed Ribo-ODDR, an oligo design pipeline integrated with a user-friendly interface that assists in oligo selection for efficient experiment-specific rRNA depletion. Ribo-ODDR uses preliminary data to identify the most abundant rRNA fragments, and calculates the rRNA depletion efficiency of potential oligos. We experimentally show that Ribo-ODDR designed oligos outperform commercially available kits and lead to a significant increase in rRNA depletion in Ribo-seq. Availability Ribo-ODDR is freely accessible at https://github.com/fallerlab/Ribo-ODDR Supplementary information Supplementary data are available at Bioinformatics online.

SIR2004: an improved tool for crystal structure determination and refinement

2005 ◽  
Vol 38 (2) ◽  
pp. 381-388 ◽  
Author(s):  
Maria C. Burla ◽  
Rocco Caliandro ◽  
Mercedes Camalli ◽  
Benedetta Carrozzini ◽  
Giovanni L. Cascarano ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Ab Initio ◽  
Structure Determination ◽  
Protein Structures ◽  
Medium Size ◽  
Graphical Interface ◽  
Asymmetric Unit ◽  
Density Maps ◽  
Data Resolution ◽  
User Friendly

SIR2004is the evolution of theSIR2002program [Burla, Camalli, Carrozzini, Cascarano, Giacovazzo, Polidori & Spagna (2003).J. Appl. Cryst.36, 1103]. It is devoted to the solution of crystal structures by direct and Patterson methods. Several new features implemented inSIR2004make this program efficient: it is able to solveab initioboth small/medium-size structures as well as macromolecules (up to 2000 atoms in the asymmetric unit). In favourable circumstances, the program is also able to solve protein structures with data resolution up to 1.4–1.5 Å, and to provide interpretable electron density maps. A powerful user-friendly graphical interface is provided.

RES2INS: a graphical interface for theSHELXprogram suite

1998 ◽  
Vol 31 (6) ◽  
pp. 963-964
Author(s):  
Leonard J. Barbour ◽  
Jerry L. Atwood
Keyword(s):  
Operating System ◽  
Structural Model ◽  
Graphical Interface ◽  
Structure Solution ◽  
User Friendly

RES2INSruns under the MS-DOS operating system and allows the user to view graphically the results of successiveSHELXstructure solution and refinement runs. In addition, the structural model can be edited in a user-friendly manner and these changes can be carried through to a newSHELXinstruction file. The program is menu driven and extensive use is made of the mouse for the facilitation of operations on individual atoms.

scholarly journals Visualizing hematopoiesis as a stochastic process

2018 ◽  
Vol 2 (20) ◽  
pp. 2637-2645
Author(s):  
Jason Xu ◽  
Yiwen Wang ◽  
Peter Guttorp ◽  
Janis L. Abkowitz
Keyword(s):  
Stochastic Process ◽  
Cell Expansion ◽  
Visualization Tool ◽  
Graphical Interface ◽  
Human Cord Blood ◽  
Virtual Experiments ◽  
Clonal Hematopoiesis ◽  
Cord Blood Cell ◽  
Statistical Background ◽  
User Friendly

Abstract Stochastic simulation has played an important role in understanding hematopoiesis, but implementing and interpreting mathematical models requires a strong statistical background, often preventing their use by many clinical and translational researchers. Here, we introduce a user-friendly graphical interface with capabilities for visualizing hematopoiesis as a stochastic process, applicable to a variety of mammal systems and experimental designs. We describe the visualization tool and underlying mathematical model, and then use this to simulate serial transplantations in mice, human cord blood cell expansion, and clonal hematopoiesis of indeterminate potential. The outcomes of these virtual experiments challenge previous assumptions and provide examples of the flexible range of hypotheses easily testable via the visualization tool.

PreDICT: a graphical user interface to the DICVOL14 indexing software program for powder diffraction data

2019 ◽  
Vol 34 (3) ◽  
pp. 233-241 ◽  
Author(s):  
Justin R. Blanton ◽  
Robert J. Papoular ◽  
Daniel Louër
Keyword(s):  
Powder Diffraction ◽  
Laboratory Data ◽  
Graphical Interface ◽  
Powder Diffraction Data ◽  
X Ray ◽  
Moderate Number ◽  
Diffraction Patterns ◽  
User Friendly ◽  
Recent Version ◽  
Selection Of

A straightforward intuitive user-friendly compact graphical interface, PreDICT (Premier DICVOL Tool) has been developed to take full advantage of the new capabilities of the most recent version of the DICVOL14 Indexing Software. The latter, an updated version of DICVOL04, includes optimizations, e.g. for monoclinic and triclinic cases, a detailed review of the input data from the indexing solutions, cell centering tests, as well as the handling of a moderate number of impurity peaks. Among the most salient features of PreDICT, one can mention the ability (1) to use 2θ non-equistepped input 1D X-ray powder diffraction patterns as can be obtained from 2D detectors, (2) to strip laboratory data from its Kα2 contribution when present, (3) to generate 2θ equistepped output 1D X-ray powder diffraction patterns in both the “.XY” and “.GSA” formats. In addition, PreDICT allows for the following features: (1) full access to the native DICVOL14 input/output ASCII file system is retained, (2) for any selection of a DICVOL14 suggested unit cell, all predicted Bragg peaks up to a certain 2θMAX value are clearly displayed and indicated, thereby emphasizing the contribution of the unaccounted peaks (if any) to the 1D X-ray powder diffraction pattern under current investigation.

Review. Fluorescence Microscopy Studies of Porous Silica Materials

2013 ◽  
Vol 68 (5-6) ◽  
pp. 423-444 ◽  
Author(s):  
Bastian Rühle ◽  
Melari Davies ◽  
Thomas Bein ◽  
Christoph Bräuchle
Keyword(s):  
Drug Delivery ◽  
Fluorescence Microscopy ◽  
Single Molecule ◽  
Catalyst Deactivation ◽  
Porous Silica ◽  
Diffusion Dynamics ◽  
Silica Materials ◽  
Microscopy Techniques ◽  
And Diffusion ◽  
Diffusion Properties

In this article, we discuss how fluorescence microscopy techniques are used to investigate important characteristics of porous silica materials. We start with a discussion of the synthesis, formation mechanism and functionalization of these materials. We then give an introduction to single molecule microscopy and show how this technique can be used to gain deeper insights into some defining properties of porous silica, such as pore structure, host-guest interactions and diffusion dynamics. We also provide examples from the literature demonstrating how fluorescence microscopy is used for elucidating important aspects of porous silica materials and heterogeneous catalysis, e. g. diffusion properties, reactivity, morphology, intergrowth, accessibility, and catalyst deactivation. Finally, a short outlook on the scope of porous silica hosts in drug delivery applications is given

Design of a Platform for Safety Justification of Safety-Critical Software

2017 ◽  
Author(s):  
Guo Jia ◽  
Yang Ming
Keyword(s):  
Software Reliability ◽  
Nuclear Power ◽  
Power Plants ◽  
Graphical Interface ◽  
Key Factors ◽  
Safety Critical ◽  
Software Products ◽  
Software Product ◽  
Quality And Reliability ◽  
User Friendly

Since safety-critical software is crucial to nuclear safety in the occurrence of accident, it is required to have rather higher requirements in both reliability and safety than the non-safety one. However, since the complexity of a software product, how to ensure the reliability and safety of a software product is still a challenging work. The paper presents a design of a platform for safety justification of safety-critical software of nuclear power plants. A syllogism referred as to Claim, Argument and Evidence (CAE) is applied to clarify the key factors that will affect software reliability and the dependencies between them. The proposed safety justification platform offers a user-friendly graphical interface to help construct a CAE model by a drag and drop way. The proposed safety justification platform could be used for the rigorous argument of various factors that may affect the reliability of a safety-critical software product during different phases of its life cycle and establishing their causalities. In this way, it could greatly improve its creditability and applicability and lowering the uncertainties in software development and application, and therefore has a significant engineering values in ensuring and improving the quality and reliability of nuclear software products.

A development of user-friendly graphical interface for a blanket simulator

2010 ◽  
Vol 85 (10-12) ◽  
pp. 1957-1965
Author(s):  
Young-Seok Lee ◽  
Seok-Heun Yoon ◽  
Jung-Hoon Han
Keyword(s):  
Graphical Interface ◽  
User Friendly
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