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.

scholarly journals The Encyclopedia of Proteome Dynamics: the KinoViewer

2018 ◽  
Vol 35 (8) ◽  
pp. 1441-1442 ◽  
Author(s):  
Alejandro Brenes ◽  
Angus I Lamond
Keyword(s):  
Open Access ◽  
Supplementary Information ◽  
Analysis Tool ◽  
Graphical Display ◽  
Visualization Tool ◽  
Dynamic Visualization ◽  
Graphical Interface ◽  
Mouse Cells ◽  
Interactive Data ◽  
User Friendly

Abstract Summary The Encyclopedia of Proteome Dynamics (EPD) ‘KinoViewer’ is an interactive data visualization tool designed for analysis and exploration of both protein and transcript data, showing expression of kinase genes in either human or mouse cells and tissues. The KinoViewer provides a comprehensive, updated graphical display of all human/mouse kinases and an open access analysis tool for the community with a user-friendly graphical interface. Availability and implementation The KinoViewer is based on a manually drawn SVG, which is utilized with D3.js to create a dynamic visualization. It can be accessed at: https://peptracker.com/epd/analytics/. The KinoViewer is currently only accessible through the EPD, it is open access and can be used either to view internal datasets, or used to upload and visualize external user datasets. Supplementary information Supplementary data are available at Bioinformatics online.

Enhancement of Angiogenic Efficacy of Human Cord Blood Cell Transplantation

2006 ◽  
Vol 12 (6) ◽  
pp. 1651-1661 ◽  
Author(s):  
Seung-Woo Cho ◽  
So-Jung Gwak ◽  
Sun-Woong Kang ◽  
Suk Ho Bhang ◽  
Kang Won Song ◽  
...  
Keyword(s):  
Blood Cell ◽  
Cord Blood ◽  
Cell Transplantation ◽  
Human Cord Blood ◽  
Cord Blood Cell

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.

scholarly journals CrosstalkNet: mining large-scale bipartite co-expression networks to characterize epi-stroma crosstalk

2017 ◽  
Author(s):  
Venkata Manem ◽  
George Adam ◽  
Tina Gruosso ◽  
Mathieu Gigoux ◽  
Nicholas Bertos ◽  
...  
Keyword(s):  
Stromal Cells ◽  
Large Scale ◽  
Network Visualization ◽  
Visualization Tool ◽  
Biological Processes ◽  
Web Based ◽  
Link Type ◽  
A Cell ◽  
Large Scale Networks ◽  
User Friendly

ABSTRACTBackground:Over the last several years, we have witnessed the metamorphosis of network biology from being a mere representation of molecular interactions to models enabling inference of complex biological processes. Networks provide promising tools to elucidate intercellular interactions that contribute to the functioning of key biological pathways in a cell. However, the exploration of these large-scale networks remains a challenge due to their high-dimensionality.Results:CrosstalkNet is a user friendly, web-based network visualization tool to retrieve and mine interactions in large-scale bipartite co-expression networks. In this study, we discuss the use of gene co-expression networks to explore the rewiring of interactions between tumor epithelial and stromal cells. We show how CrosstalkNet can be used to efficiently visualize, mine, and interpret large co-expression networks representing the crosstalk occurring between the tumour and its microenvironment.Conclusion:CrosstalkNet serves as a tool to assist biologists and clinicians in exploring complex, large interaction graphs to obtain insights into the biological processes that govern the tumor epithelial-stromal crosstalk. A comprehensive tutorial along with case studies are provided with the application.Availability:The web-based application is available at the following location: http://epistroma.pmgenomics.ca/app/. The code is open-source and freely available from http://github.com/bhklab/EpiStroma-webapp.Contact:[email protected]

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 QualitySNPng: a user-friendly SNP detection and visualization tool

2013 ◽  
Vol 41 (W1) ◽  
pp. W587-W590 ◽  
Author(s):  
Harm Nijveen ◽  
Martijn van Kaauwen ◽  
Danny G. Esselink ◽  
Brechtje Hoegen ◽  
Ben Vosman
Keyword(s):  
Visualization Tool ◽  
Snp Detection ◽  
User Friendly

Enhancement of Angiogenic Efficacy of Human Cord Blood Cell Transplantation

2006 ◽  
Vol 0 (0) ◽  
pp. 060706073730045
Author(s):  
Seung-Woo Cho ◽  
So-Jung Gwak ◽  
Sun-Woong Kang ◽  
Suk Ho Bhang ◽  
Kang Won Song ◽  
...  
Keyword(s):  
Blood Cell ◽  
Cord Blood ◽  
Cell Transplantation ◽  
Human Cord Blood ◽  
Cord Blood Cell

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.

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.

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