scholarly journals MLDSP-GUI: An alignment-free standalone tool with an interactive graphical user interface for DNA sequence comparison and analysis

2019 ◽  
Author(s):  
Gurjit S. Randhawa ◽  
Kathleen A. Hill ◽  
Lila Kari
Keyword(s):  
User Interface ◽  
Open Source ◽  
Graphical User Interface ◽  
Dna Sequences ◽  
Disease Classification ◽  
Supplementary Information ◽  
Link Type ◽  
Alignment Free ◽  
Comparison And Analysis ◽  
Interactive Graphical User Interface

AbstractSummaryMLDSP-GUI (Machine Learning with Digital Signal Processing) is an open-source, alignment-free, ultrafast, computationally lightweight, standalone software tool with an interactive Graphical User Interface (GUI) for comparison and analysis of DNA sequences. MLDSP-GUI is a general-purpose tool that can be used for a variety of applications such as taxonomic classification, disease classification, virus subtype classification, evolutionary analyses, among others.AvailabilityMLDSP-GUI is open-source, cross-platform compatible, and is available under the terms of the Creative Commons Attribution 4.0 International license (http://creativecommons.org/licenses/by/4.0/). The executable and dataset files are available at https://sourceforge.net/projects/mldsp-gui/[email protected] informationSupplementary data are available online.

scholarly journals MLDSP-GUI: an alignment-free standalone tool with an interactive graphical user interface for DNA sequence comparison and analysis

2019 ◽  
Vol 36 (7) ◽  
pp. 2258-2259 ◽  
Author(s):  
Gurjit S Randhawa ◽  
Kathleen A Hill ◽  
Lila Kari
Keyword(s):  
User Interface ◽  
Open Source ◽  
Graphical User Interface ◽  
Dna Sequences ◽  
Software Tool ◽  
Digital Signal ◽  
Disease Classification ◽  
Supplementary Information ◽  
Alignment Free ◽  
Comparison And Analysis

Abstract Summary Machine Learning with Digital Signal Processing and Graphical User Interface (MLDSP-GUI) is an open-source, alignment-free, ultrafast, computationally lightweight, and standalone software tool with an interactive GUI for comparison and analysis of DNA sequences. MLDSP-GUI is a general-purpose tool that can be used for a variety of applications such as taxonomic classification, disease classification, virus subtype classification, evolutionary analyses, among others. Availability and implementation MLDSP-GUI is open-source, cross-platform compatible, and is available under the terms of the Creative Commons Attribution 4.0 International license (http://creativecommons.org/licenses/by/4.0/). The executable and dataset files are available at https://sourceforge.net/projects/mldsp-gui/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Open source tools for geographic analysis in transport planning

2021 ◽  
Author(s):  
Robin Lovelace
Keyword(s):  
User Interface ◽  
Open Source ◽  
Citizen Participation ◽  
Simulation Software ◽  
First Century ◽  
Transport Planning ◽  
Geographic Analysis ◽  
Link Type ◽  
Twenty First Century ◽  
Interactive Map

AbstractGeographic analysis has long supported transport plans that are appropriate to local contexts. Many incumbent ‘tools of the trade’ are proprietary and were developed to support growth in motor traffic, limiting their utility for transport planners who have been tasked with twenty-first century objectives such as enabling citizen participation, reducing pollution, and increasing levels of physical activity by getting more people walking and cycling. Geographic techniques—such as route analysis, network editing, localised impact assessment and interactive map visualisation—have great potential to support modern transport planning priorities. The aim of this paper is to explore emerging open source tools for geographic analysis in transport planning, with reference to the literature and a review of open source tools that are already being used. A key finding is that a growing number of options exist, challenging the current landscape of proprietary tools. These can be classified as command-line interface, graphical user interface or web-based user interface tools and by the framework in which they were implemented, with numerous tools released as R, Python and JavaScript packages, and QGIS plugins. The review found a diverse and rapidly evolving ‘ecosystem’ tools, with 25 tools that were designed for geographic analysis to support transport planning outlined in terms of their popularity and functionality based on online documentation. They ranged in size from single-purpose tools such as the QGIS plugin AwaP to sophisticated stand-alone multi-modal traffic simulation software such as MATSim, SUMO and Veins. Building on their ability to re-use the most effective components from other open source projects, developers of open source transport planning tools can avoid ‘reinventing the wheel’ and focus on innovation, the ‘gamified’ A/B Street https://github.com/dabreegster/abstreet/#abstreet simulation software, based on OpenStreetMap, a case in point. The paper, the source code of which can be found at https://github.com/robinlovelace/open-gat, concludes that, although many of the tools reviewed are still evolving and further research is needed to understand their relative strengths and barriers to uptake, open source tools for geographic analysis in transport planning already hold great potential to help generate the strategic visions of change and evidence that is needed by transport planners in the twenty-first century.

A New Paradigm for Ship Design Calculations

2015 ◽  
Author(s):  
Stephen M. Hollister
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Ship Design ◽  
New Paradigm ◽  
New Model ◽  
Analysis Tools ◽  
Cross Platform ◽  
Open Code ◽  
Design Calculations ◽  
Interactive Graphical User Interface

A new model for ship design calculations is presented that separates the graphical user interface (GUI) from the calculations (CALC). Design programs can now be defined as more than one interactive graphical user interface tied to one calculation. Several different GUIs can be created for one CALC engine and one GUI can be created to launch several CALC engines in sequence. The GUI of choice is a spreadsheet due to its availability, programmable customization, powerful analysis tools, cross-platform capability, and open code environment.

scholarly journals The DNA walk and its demonstration of deterministic chaos—relevance to genomic alterations in lung cancer

2019 ◽  
Vol 35 (16) ◽  
pp. 2738-2748 ◽  
Author(s):  
Blake Hewelt ◽  
Haiqing Li ◽  
Mohit Kumar Jolly ◽  
Prakash Kulkarni ◽  
Isa Mambetsariev ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Open Source ◽  
Fractal Analysis ◽  
Dna Sequences ◽  
Chaotic Behavior ◽  
Supplementary Information ◽  
Wild Type ◽  
Genomic Alterations ◽  
Turtle Graphics ◽  
Dna Walk

AbstractMotivationAdvancements in cancer genetics have facilitated the development of therapies with actionable mutations. Although mutated genes have been studied extensively, their chaotic behavior has not been appreciated. Thus, in contrast to naïve DNA, mutated DNA sequences can display characteristics of unpredictability and sensitivity to the initial conditions that may be dictated by the environment, expression patterns and presence of other genomic alterations. Employing a DNA walk as a form of 2D analysis of the nucleotide sequence, we demonstrate that chaotic behavior in the sequence of a mutated gene can be predicted.ResultsUsing fractal analysis for these DNA walks, we have determined the complexity and nucleotide variance of commonly observed mutated genes in non-small cell lung cancer, and their wild-type counterparts. DNA walks for wild-type genes demonstrate varying levels of chaos, with BRAF, NTRK1 and MET exhibiting greater levels of chaos than KRAS, paxillin and EGFR. Analyzing changes in chaotic properties, such as changes in periodicity and linearity, reveal that while deletion mutations indicate a notable disruption in fractal ‘self-similarity’, fusion mutations demonstrate bifurcations between the two genes. Our results suggest that the fractals generated by DNA walks can yield important insights into potential consequences of these mutated genes.Availability and implementationIntroduction to Turtle graphics in Python is an open source article on learning to develop a script for Turtle graphics in Python, freely available on the web at https://docs.python.org/2/library/turtle.html. cDNA sequences were obtained through NCBI RefSeq database, an open source database that contains information on a large array of genes, such as their nucleotide and amino acid sequences, freely available at https://www.ncbi.nlm.nih.gov/refseq/. FracLac plugin for Fractal analysis in ImageJ is an open source plugin for the ImageJ program to perform fractal analysis, free to download at https://imagej.nih.gov/ij/plugins/fraclac/FLHelp/Introduction.html.Supplementary informationSupplementary data are available at Bioinformatics online.

Development of an Interactive Graphical User Interface (GUI) for EnergyPlus

2010 ◽  
Author(s):  
Yiqun Pan ◽  
Qiqiang Li ◽  
Hui Zhou ◽  
Joe Huang ◽  
Sen Huang ◽  
...  
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Visualization Tool ◽  
Hvac System ◽  
Modeling Tools ◽  
Building Geometry ◽  
System Module ◽  
Further Development ◽  
Space Conditions ◽  
Interactive Graphical User Interface

In order to make EnergyPlus easier to use in China, VisualEPlus, a Chinese graphical user interface for the program, has been developed. VisualEPlus is designed to be generic, so that it can be used in any country, as well as be linked to other modeling tools and interfaces for EnergyPlus. VisualEPlus has three main modules: (1) a Building Loads Module for defining the building geometry, envelope, and space conditions that has been adapted from an existing DOE-2 interface (DOE2IN); (2) a HVAC System Module with a drag-and-drop feature for defining the HVAC system; and (3) a View Report Module with a reporting and visualization tool for EnergyPlus reports and outputs. This paper presents the background and development of VisualEPlus, describes its main functions and features as compared to other existing interfaces for EnergyPlus, and discusses plans for the further development of VisualEPlus.

scholarly journals CRAFT: Compact genome Representation towards large-scale Alignment-Free daTabase

2020 ◽  
Author(s):  
Yang Young Lu ◽  
Jiaxing Bai ◽  
Yiwen Wang ◽  
Ying Wang ◽  
Fengzhu Sun
Keyword(s):  
Dna Sequences ◽  
Sequence Comparison ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Practical Interest ◽  
Supplementary Information ◽  
Computationally Efficient ◽  
Sequencing Technologies ◽  
Alignment Free

AbstractMotivationRapid developments in sequencing technologies have boosted generating high volumes of sequence data. To archive and analyze those data, one primary step is sequence comparison. Alignment-free sequence comparison based on k-mer frequencies offers a computationally efficient solution, yet in practice, the k-mer frequency vectors for large k of practical interest lead to excessive memory and storage consumption.ResultsWe report CRAFT, a general genomic/metagenomic search engine to learn compact representations of sequences and perform fast comparison between DNA sequences. Specifically, given genome or high throughput sequencing (HTS) data as input, CRAFT maps the data into a much smaller embedding space and locates the best matching genome in the archived massive sequence repositories. With 102 – 104-fold reduction of storage space, CRAFT performs fast query for gigabytes of data within seconds or minutes, achieving comparable performance as six state-of-the-art alignment-free measures.AvailabilityCRAFT offers a user-friendly graphical user interface with one-click installation on Windows and Linux operating systems, freely available at https://github.com/jiaxingbai/[email protected]; [email protected] informationSupplementary data are available at Bioinformatics online.

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