scholarly journals PolyAlign: A Versatile LC-MS Data Alignment Tool for Landmark-Selected and -Automated Use

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
Heidi Vähämaa ◽  
Ville R. Koskinen ◽  
Waltteri Hosia ◽  
Robert Moulder ◽  
Olli S. Nevalainen ◽  
...  
Keyword(s):  
Software Tool ◽  
Substantial Improvement ◽  
Peak Alignment ◽  
Data Alignment ◽  
Alignment Tool ◽  
Polynomial Transformation ◽  
Hermite Transformation ◽  
Reference Map ◽  
User Friendly ◽  
Automated Alignment

We present a versatile user-friendly software tool, PolyAlign, for the alignment of multiple LC-MS signal maps with the option of manual landmark setting or automated alignment. One of the spectral images is selected as a reference map, and after manually setting the landmarks, the program warps the images using either polynomial or Hermite transformation. The software provides an option for automated landmark finding. The software includes a very fast zoom-in function synchronized between the images, which facilitate detecting correspondences between the adjacent images. Such an interactive visual process enables the analyst to decide when the alignment is satisfactory and to correct known irregularities. We demonstrate that the software provides significant improvements in the alignment of LC-MALDI data, with 10–15 landmark pairs, and it is also applicable to correcting electrospray LC-MS data. The results with practical data show substantial improvement in peak alignment compared to MZmine, which was among the best analysis packages in a recent assessment. The PolyAlign software is freely available and easily accessible as an integrated component of the popular MZmine software, and also as a simpler stand-alone Perl implementation to preview data and apply landmark directed polynomial transformation.

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 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.

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

scholarly journals COPAR: A ChIP-Seq Optimal Peak Analyzer

2017 ◽  
Vol 2017 ◽  
pp. 1-4
Author(s):  
Binhua Tang ◽  
Xihan Wang ◽  
Victor X. Jin
Keyword(s):  
High Throughput ◽  
Genomic Feature ◽  
Data Sets ◽  
Sequencing Data ◽  
Genomic Features ◽  
Peak Alignment ◽  
Chip Sequencing ◽  
Quality Check ◽  
User Friendly ◽  
High Throughput Experiments

Sequencing data quality and peak alignment efficiency of ChIP-sequencing profiles are directly related to the reliability and reproducibility of NGS experiments. Till now, there is no tool specifically designed for optimal peak alignment estimation and quality-related genomic feature extraction for ChIP-sequencing profiles. We developed open-sourced COPAR, a user-friendly package, to statistically investigate, quantify, and visualize the optimal peak alignment and inherent genomic features using ChIP-seq data from NGS experiments. It provides a versatile perspective for biologists to perform quality-check for high-throughput experiments and optimize their experiment design. The package COPAR can process mapped ChIP-seq read file in BED format and output statistically sound results for multiple high-throughput experiments. Together with three public ChIP-seq data sets verified with the developed package, we have deposited COPAR on GitHub under a GNU GPL license.

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.

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

2013 ◽  
Vol 6 (1) ◽  
pp. 47-55 ◽  
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.

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

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/.

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

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.

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

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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