A Dynamic Model for the Study and Simulation of the Pantograph–Rigid Catenary Interaction with an Overlapping Span

In this paper, the authors present a mathematical and engineering model to optimally calculate the dynamic equation on the pantograph–catenary interaction when considering a rigid catenary with an overlapping span. The model starts from well-known methods adapted to the special features of rigid catenary. As a result, an algorithm for the integration of a dynamic equation based on explicit methods is provided. Moreover, from this algorithm, a reliable, efficient, and user-friendly software tool called RICATI is developed in order to approach the model to railway-based companies. The results show the usefulness of an application. such as RICATI, to check the behavior of the configuration initially established for a catenary, allowing solutions to be obtained for the problems encountered when simulating the passage of the pantograph (or pantographs), not only for the overlapping span but also for the entire catenary. That encourages us to continue future works.

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CHR: An Integrated Software Tool for chilling requirements

10.21203/rs.3.rs-34169/v1 ◽

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.

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

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.163-167.4564 ◽

2010 ◽

Vol 163-167 ◽

pp. 4564-4569 ◽

Cited By ~ 2

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.

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

Scientific Reports ◽

10.1038/s41598-019-52451-8 ◽

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.

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

ACS Synthetic Biology ◽

10.1021/acssynbio.5b00284 ◽

2016 ◽

Vol 5 (7) ◽

pp. 774-780 ◽

Cited By ~ 46

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

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CellTracker (not only) for dummies

Bioinformatics ◽

10.1093/bioinformatics/btv686 ◽

2015 ◽

Vol 32 (6) ◽

pp. 955-957 ◽

Cited By ~ 46

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.

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SoccerEye: A Software Solution to Observe and Record Behaviours in Sport Settings

The Open Sports Sciences Journal ◽

10.2174/1875399x01306010047 ◽

2013 ◽

Vol 6 (1) ◽

pp. 47-55 ◽

Cited By ~ 9

Author(s):

Daniel Barreira ◽

Julio Garganta ◽

Julen Castellano ◽

M. Teresa Anguera

Keyword(s):

Ad Hoc ◽

Software Tool ◽

Visual Basic ◽

Soccer Players ◽

Natural Setting ◽

Starting Time ◽

Technological Advances ◽

Diachronic Analysis ◽

User Friendly ◽

Quality Recording

In soccer, the need for direct observation of tactical behaviour has led to continuous technological advances in motion recording software. Here we present SoccerEye, a sports-specific software tool to observe and record the behaviour of soccer players in their natural setting and in real time. The software was written in Visual Basic Express 2010 and includes the following features: computerised coding, improved-quality recording, episodic sampling, the measurement of time, and diachronic analysis. Its configuration is well defined but allows for incorporation of ad hoc categories. Data can be exported in multiple generic formats, including the SDIS format for the analysis of interaction sequences with GSEQ software. However, by considering time and sequential decisions, SoccerEye itself tracks activity profiles and the dynamics of play. The greatest advantage of SoccerEye is the possibility to conduct diachronic analysis, which regards an event or multi event sequence in terms of change over time. This type of analysis takes into account the behaviour of a player and his or her team when facing the opponent, the space (pitch area) and time (starting time and duration) of each event, and other factors such as match status, match time, and competition stage. SoccerEye is a freeaccess user-friendly application that can be used to observe a single player or an entire team while controlling over the environment in which the observation takes place. This tool will hopefully contribute to the better understanding of the dynamics of soccer play.

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DBSCAN-SWA: an integrated tool for rapid prophage detection and annotation

10.1101/2020.07.12.199018 ◽

2020 ◽

Author(s):

Rui Gan ◽

Fengxia Zhou ◽

Yu Si ◽

Han Yang ◽

Chuangeng Chen ◽

...

Keyword(s):

Dna Sequences ◽

Bacterial Infections ◽

Software Tool ◽

High Specificity ◽

Bacterial Genomes ◽

Bacterial Host ◽

Accurate Identification ◽

Bacterial Dna ◽

Intracellular Form ◽

User Friendly

AbstractSummaryAs an intracellular form of a bacteriophage in the bacterial host genome, a prophage is usually integrated into bacterial DNA with high specificity and contributes to horizontal gene transfer (HGT). Phage therapy has been widely applied, for example, using phages to kill bacteria to treat pathogenic and resistant bacterial infections. Therefore, it is necessary to develop effective tools for the fast and accurate identification of prophages. Here, we introduce DBSCAN-SWA, a command line software tool developed to predict prophage regions of bacterial genomes. DBSCAN-SWA runs faster than any previous tool. Importantly, it has great detection power based on analysis using 184 manually curated prophages, with a recall of 85% compared with Phage_Finder (63%), VirSorter (74%) and PHASTER (82%) for raw DNA sequences. DBSCAN-SWA also provides user-friendly visualizations including a circular prophage viewer and interactive DataTables.Availability and implementationDBSCAN-SWA is implemented in Python3 and is freely available under an open source GPLv2 license from https://github.com/HIT-ImmunologyLab/DBSCAN-SWA/.

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MPTHub: an open-source software for characterizing the transport of particles in biorelevant media

10.1101/2021.09.15.460434 ◽

2021 ◽

Author(s):

Leandro Gabriel ◽

Helena Almeida ◽

Marta Avelar ◽

Bruno Sarmento ◽

Jose das Neves

Keyword(s):

Effective Diffusivity ◽

Software Tool ◽

Trajectory Data ◽

Polystyrene Nanoparticles ◽

Biorelevant Media ◽

Time Resolved ◽

Fundamental Biology ◽

Living Organisms ◽

Memory Resources ◽

User Friendly

The study of the transport of particles in different environments plays an essential role in understanding interactions with humans and other living organisms. Importantly, obtained data can be directly used for multiple applications in fields such as fundamental biology, toxicology or medicine. Particle movement in biorelevant media can be readily monitored using microscopy and converted into time-resolved trajectories using freely available tracking software. However, translation into tangible and meaningful parameters is time-consuming and not always intuitive. Thus, we developed a new software - MPTHub - as an open-access, stand-alone, user-friendly tool for the rapid and reliable analysis of particle trajectories extracted from video microscopy. The software was programmed using Python and allowed to import and analyze trajectory data, and export relevant data such as individual and ensemble time-averaged mean square displacements and effective diffusivity, and anomalous transport exponent. Data processing was reliable, fast (total processing time of less than 10 sec) and required minimal memory resources (up to a maximum of around 150 MB in RAM). Demonstration of software applicability was conducted by studying the transport of different polystyrene nanoparticles (100-200 nm) in mucus surrogates. Overall, MPTHub represents a freely available software tool that can be used even by unexperienced users for studying the transport of particles in biorelevant media.

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AmpUMI: Design and analysis of unique molecular identifiers for deep amplicon sequencing

10.1101/288118 ◽

2018 ◽

Author(s):

Kendell Clement ◽

Rick Farouni ◽

Daniel E. Bauer ◽

Luca Pinello

Keyword(s):

Allelic Diversity ◽

Pcr Amplification ◽

Software Tool ◽

Amplicon Sequencing ◽

Dna Fragments ◽

Genomic Locus ◽

Sequencing Studies ◽

High Allelic Diversity ◽

Downstream Analysis ◽

User Friendly

AbstractMotivationUnique molecular identifiers (UMIs) are added to DNA fragments before PCR amplification to discriminate between alleles arising from the same genomic locus and sequencing reads produced by PCR amplification. While computational methods have been developed to take into account UMI information in genome-wide and single-cell sequencing studies, they are not designed for modern amplicon based sequencing experiments, especially in cases of high allelic diversity. Importantly, no guidelines are provided for the design of optimal UMI length for amplicon-based sequencing experiments.ResultsBased on the total number of DNA fragments and the distribution of allele frequencies, we present a model for the determination of the minimum UMI length required to prevent UMI collisions and reduce allelic distortion. We also introduce a user-friendly software tool called AmpUMI to assist in the design and the analysis of UMI-based amplicon sequencing studies. AmpUMI provides quality control metrics on frequency and quality of UMIs, and trims and deduplicates amplicon sequences with user specified parameters for use in downstream analysis. AmpUMI is open-source and freely available at http://github.com/pinellolab/[email protected]

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Immunopeptidomics for Dummies: Detailed Experimental Protocols and Rapid, User-Friendly Visualization of MHC I and II Ligand Datasets with MhcVizPipe

10.1101/2020.11.02.360958 ◽

2020 ◽

Author(s):

Kevin A. Kovalchik ◽

Laura Wessling ◽

Frederic Saab ◽

Qing Ma ◽

Jérôme Despault ◽

...

Keyword(s):

Mhc Class I ◽

Software Tool ◽

Class I ◽

Mhc I ◽

Binding Motifs ◽

Histocompatibility Complex ◽

Starting Point ◽

Technical Report ◽

Experimental Protocols ◽

User Friendly

ABSTRACTImmunopeptidomics refers to the science of investigating the composition and dynamics of peptides presented by major histocompatibility complex (MHC) class I and class II molecules using mass spectrometry (MS). Here, we aim to provide a technical report to any non-expert in the field wishing to establish and/or optimize an immunopeptidomic workflow with relatively limited computational knowledge and resources. To this end, we thoroughly describe step-by-step instructions to isolate MHC class I and II-associated peptides from various biological sources, including mouse and human biospecimens. Most notably, we created MhcVizPipe (MVP) (https://github.com/CaronLab/MhcVizPipe), a new and easy-to-use open-source software tool to rapidly assess the quality and the specific enrichment of immunopeptidomic datasets upon the establishment of new workflows. In fact, MVP enables intuitive visualization of multiple immunopeptidomic datasets upon testing sample preparation protocols and new antibodies for the isolation of MHC class I and II peptides. In addition, MVP enables the identification of unexpected binding motifs and facilitates the analysis of non-canonical MHC peptides. We anticipate that the experimental and bioinformatic resources provided herein will represent a great starting point for any non-expert and will therefore foster the accessibility and expansion of the field to ultimately boost its maturity and impact.

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