scholarly journals Mesh Generation and Flexible Shape Comparisons for Bio-Molecules

2016 ◽  
Vol 4 (1) ◽  
Author(s):  
Zhanheng Gao ◽  
Reihaneh Rostami ◽  
Xiaoli Pang ◽  
Zhicheng Fu ◽  
Zeyun Yu
Keyword(s):  
Software Tool ◽  
Shape Descriptor ◽  
Beltrami Operator ◽  
Molecular Surface ◽  
Modeling Tools ◽  
Generating Method ◽  
Small Set ◽  
User Friendly ◽  
Invariant Shape ◽  
Memory Efficient

AbstractNovel approaches for generating and comparing flexible (non-rigid) molecular surface meshes are developed. The mesh-generating method is fast and memory-efficient. The resulting meshes are smooth and accurate, and possess high mesh quality. An isometric-invariant shape descriptor based on the Laplace- Beltrami operator is then explored for mesh comparing. The new shape descriptor is more powerful in discriminating different surface shapes but rely only on a small set of signature values. The shape descriptor is applied to shape comparison between molecules with deformed structures. The proposed methods are implemented into a program that can be used as a stand-alone software tool or as a plug-in to other existing molecular modeling tools. Particularly, the code is encapsulated into a software toolkit with a user-friendly graphical interface developed by the authors.

scholarly journals CHR: An Integrated Software Tool for chilling requirements

2020 ◽  
Author(s):  
Chen Chen ◽  
Wanyu Xu ◽  
Ningning Gou ◽  
Lasu Bai ◽  
Lin Wang ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
Software Tool ◽  
Fruit Trees ◽  
Cold Weather ◽  
Chilling Requirements ◽  
Deciduous Fruit ◽  
Heat Requirement ◽  
Integrated Software ◽  
User Friendly ◽  
Analyze Data

Abstract Background Bud dormancy in deciduous fruit trees enables plants to survive cold weather. The buds adopt dormant state and resume growth after satisfying the chilling requirements. Chilling requirements play a key role in flowering time. So far, several chilling models, including ≤ 7.2 °C model, the 0–7.2 °C model, Utah model, and Dynamic Model, have been developed; however, it is still time-consuming to determine the chilling requirements employing any model. This calls for efficient tools that can analyze data. Results In this study, we developed novel software Chilling and Heat Requirement (CHR), by flexibly integrating data conversions, model selection, calculations, statistical analysis, and plotting. Conclusion CHR is a tool for chilling requirements estimation, which will be very useful to researchers. It is very simple, easy, and user-friendly.

Quantification Methods for Construction Waste Generation at Construction Sites: A Review

2010 ◽  
Vol 163-167 ◽  
pp. 4564-4569 ◽  
Author(s):  
Ahmad Firman Masudi ◽  
Che Rosmani Che Hassan ◽  
Noor Zalina Mahmood ◽  
Siti Nazziera Mokhtar ◽  
Nik Meriam Sulaiman
Keyword(s):  
Construction Projects ◽  
Software Tool ◽  
Waste Reduction ◽  
Building Construction ◽  
Civil Infrastructure ◽  
Waste Generation ◽  
Construction Sites ◽  
Construction Waste ◽  
Future Direction ◽  
User Friendly

Estimation of construction and demolition (C&D) waste amount is crucial for implementing waste minimization program. Estimation of C&D waste amount generated is a mean in assessing the potential for waste reduction. Thus, a better understanding of C&D waste generation in terms of causes and sources can be achieved. The aim of this paper is to conduct a review on available construction waste quantification methods from previous studies, which have been utilized in certain countries, while attempting to choose the most suitable and applicable method, and to direct future studies for better quantification methods. This review is applicable only for building construction projects and did not include civil/infrastructure, demolition, renovation, and excavation projects. Six quantification methods and/or waste audit tool available from literatures are discussed, which include their limitation and future direction for this study. It is believed that some combination of these quantification methods could make a good impact in accurate numerical estimation of construction waste amount generated in building construction projects. A strong and accurate database as presented by Soliz-Guzman, combined with effective, vital, and resourceful estimation suggested by Jalali’s Global Index (GI), also with the aid of user-friendly software tool like the SMARTAudit could provide an effective and reliable waste quantification.

scholarly journals EVR: reconstruction of bacterial chromosome 3D structure models using error-vector resultant algorithm

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Kang-Jian Hua ◽  
Bin-Guang Ma
Keyword(s):  
Parallel Implementation ◽  
3D Structure ◽  
Software Tool ◽  
Structural Features ◽  
Bacterial Chromosome ◽  
Modeling Tools ◽  
Computing Power ◽  
Error Vector ◽  
Contact Frequency ◽  
Simple Error

Abstract Background More and more 3C/Hi-C experiments on prokaryotes have been published. However, most of the published modeling tools for chromosome 3D structures are targeting at eukaryotes. How to transform prokaryotic experimental chromosome interaction data into spatial structure models is an important task and in great need. Results We have developed a new reconstruction program for bacterial chromosome 3D structure models called EVR that exploits a simple Error-Vector Resultant (EVR) algorithm. This software tool is particularly optimized for the closed-loop structural features of prokaryotic chromosomes. The parallel implementation of the program can utilize the computing power of both multi-core CPUs and GPUs. Conclusions EVR can be used to reconstruct the bacterial 3D chromosome structure based on the contact frequency matrix derived from 3C/Hi-C experimental data quickly and precisely.

scholarly journals NmrLineGuru: Standalone and User-Friendly GUIs for Fast 1D NMR Lineshape Simulation and Analysis of Multi-State Equilibrium Binding Models

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Chao Feng ◽  
Evgenii L. Kovrigin ◽  
Carol Beth Post
Keyword(s):  
Kinetic Model ◽  
Molecular Interactions ◽  
Rate Constants ◽  
Nmr Spectra ◽  
Equilibrium Constants ◽  
Software Tool ◽  
Biological Interactions ◽  
Equilibrium Binding ◽  
Accurate Quantitative Analysis ◽  
User Friendly

Abstract The ability of high-resolution NMR spectroscopy to readout the response of molecular interactions at multiple atomic sites presents a unique capability to define thermodynamic equilibrium constants and kinetic rate constants for complex, multiple-step biological interactions. Nonetheless, the extraction of the relevant equilibrium binding and rate constants requires the appropriate analysis of not only a readout that follows the equilibrium concentrations of typical binding titration curves, but also the lineshapes of NMR spectra. To best take advantage of NMR data for characterizing molecular interactions, we developed NmrLineGuru, a software tool with a user-friendly graphical user interface (GUI) to model two-state, three-state, and four-state binding processes. Application of NmrLineGuru is through stand-alone GUIs, with no dependency on other software and no scripted input. NMR spectra can be fitted or simulated starting with user-specified input parameters and a chosen kinetic model. The ability to both simulate and fit NMR spectra provides the user the opportunity to not only determine the binding parameters that best reproduce the measured NMR spectra for the selected kinetic model, but to also query the possibility that alternative models agree with the data. NmrLineGuru is shown to provide an accurate, quantitative analysis of complex molecular interactions.

The function analysis diagram: Intended benefits and coexistence with other functional models

2013 ◽  
Vol 27 (3) ◽  
pp. 249-257 ◽  
Author(s):  
Marco Aurisicchio ◽  
Rob Bracewell ◽  
Gareth Armstrong
Keyword(s):  
Adaptive Design ◽  
Research Collaboration ◽  
Function Analysis ◽  
Software Tool ◽  
Major Power ◽  
Modeling Tools ◽  
Diagram Method ◽  
Functional Models ◽  
Simple Notation

AbstractUnderstanding product functions is a key aspect of the work undertaken by engineers involved in complex system design. The support offered to these engineers by existing modeling tools such as the function tree and the function structure is limited because they are not intuitive and do not scale well to deal with real-world engineering problems. A research collaboration between two universities and a major power system company in the aerospace domain has allowed the authors to further develop a method for function analysis known as function analysis diagram that was already in use by line engineers. The capability to generate and edit these diagrams was implemented in the Decision Rationale editor, a software tool for capturing design rationale. This article presents the intended benefits of the method and justifies them using an engineering case study. The results of the research have shown that the function analysis diagram method has a simple notation, permits the modeling of product functions together with structure, allows the generation of rich and accurate descriptions of product functionality, is useful to work with variant and adaptive design tasks, and can coexist with other functional modeling methods.

scholarly journals FlowCal: A User-Friendly, Open Source Software Tool for Automatically Converting Flow Cytometry Data from Arbitrary to Calibrated Units

2016 ◽  
Vol 5 (7) ◽  
pp. 774-780 ◽  
Author(s):  
Sebastian M. Castillo-Hair ◽  
John T. Sexton ◽  
Brian P. Landry ◽  
Evan J. Olson ◽  
Oleg A. Igoshin ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Open Source ◽  
Open Source Software ◽  
Software Tool ◽  
Flow Cytometry Data ◽  
User Friendly

CellTracker (not only) for dummies

2015 ◽  
Vol 32 (6) ◽  
pp. 955-957 ◽  
Author(s):  
Filippo Piccinini ◽  
Alexa Kiss ◽  
Peter Horvath
Keyword(s):  
Graphical User Interface ◽  
Open Source Software ◽  
Phase Contrast ◽  
Cell Tracking ◽  
Source Code ◽  
Software Tool ◽  
Time Lapse ◽  
Supplementary Information ◽  
Differential Interference Contrast ◽  
User Friendly

Abstract Motivation: Time-lapse experiments play a key role in studying the dynamic behavior of cells. Single-cell tracking is one of the fundamental tools for such analyses. The vast majority of the recently introduced cell tracking methods are limited to fluorescently labeled cells. An equally important limitation is that most software cannot be effectively used by biologists without reasonable expertise in image processing. Here we present CellTracker, a user-friendly open-source software tool for tracking cells imaged with various imaging modalities, including fluorescent, phase contrast and differential interference contrast (DIC) techniques. Availability and implementation: CellTracker is written in MATLAB (The MathWorks, Inc., USA). It works with Windows, Macintosh and UNIX-based systems. Source code and graphical user interface (GUI) are freely available at: http://celltracker.website/. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

Sign in / Sign up

Export Citation Format

Share Document