ChimericSeq: An open-source, user-friendly interface for analyzing NGS data to identify and characterize viral-host chimeric sequences

Genome browsers play a vital role to provide visualisation for genomic data. It is often the case that bespoke genome browser customisations are required between different research groups, with an obvious necessity to update, upgrade and tailor tracks and features on a potentially frequent basis. However, most of the current genome browsers require highly curated data held in public repositories. Besides, these genome browsers often rely on particular dependencies, where writing plug-in or modifying existing code can be troublesome and resource expensive.We present TGAC Browser, a new open-source web-based genome browser designed to overcome shortcomings in available approaches. It uses a locally installed Ensembl Core Database schema and is also able to visualise data from well-known NGS data formats. We also added simple analysis functionality to perform BLAST searches within TGAC Browser. TGAC Browser also allows uploading your genomic data. TGAC Browser is an open-source, easy to set up, and user-friendly genome browser with minimal, lightweight configuration details.

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MackDroid - An Android based Application to monitor devices

Journal of Communications Technology Electronics and Computer Science ◽

10.22385/jctecs.v9i0.130 ◽

2016 ◽

Vol 9 ◽

pp. 1

Author(s):

Maaz Sirkhot ◽

Ekta Sirwani ◽

Aishwarya Kourani ◽

Akshit Batheja ◽

Kajal Jethanand Jewani

Keyword(s):

Operating System ◽

Open Source ◽

Vital Role ◽

Mobile Users ◽

Android Application ◽

Web Page ◽

Technological World ◽

Monitoring Service ◽

User Friendly

In this technological world, smartphones can be considered as one of the most far-reaching inventions. It plays a vital role in connecting people socially. The number of mobile users using an Android based smartphone has increased rapidly since last few years resulting in organizations, cyber cell departments, government authorities feeling the need to monitor the activities on certain targeted devices in order to maintain proper functionality of their respective jobs. Also with the advent of smartphones, Android became one of the most popular and widely used Operating System. Its highlighting features are that it is user friendly, smartly designed, flexible, highly customizable and supports latest technologies like IoT. One of the features that makes it exclusive is that it is based on Linux and is Open Source for all the developers. This is the reason why our project Mackdroid is an Android based application that collects data from the remote device, stores it and displays on a PHP based web page. It is primarily a monitoring service that analyzes the contents and distributes it in various categories like Call Logs, Chats, Key logs, etc. Our project aims at developing an Android application that can be used to track, monitor, store and grab data from the device and store it on a server which can be accessed by the handler of the application.

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An Interactive WebGIS Framework for Coastal Erosion Risk Management

Journal of Marine Science and Engineering ◽

10.3390/jmse9060567 ◽

2021 ◽

Vol 9 (6) ◽

pp. 567

Author(s):

Alessandra Capolupo ◽

Cristina Monterisi ◽

Alessandra Saponieri ◽

Fabio Addona ◽

Leonardo Damiani ◽

...

Keyword(s):

Open Source ◽

3D Visualization ◽

Erosion Risk ◽

Innovative Strategies ◽

Web Mapping ◽

Natural Processes ◽

Multi Scale ◽

Interactive Interface ◽

Multi Temporal ◽

User Friendly

The Italian coastline stretches over about 8350 km, with 3600 km of beaches, representing a significant resource for the country. Natural processes and anthropic interventions keep threatening its morphology, moulding its shape and triggering soil erosion phenomena. Thus, many scholars have been focusing their work on investigating and monitoring shoreline instability. Outcomes of such activities can be largely widespread and shared with expert and non-expert users through Web mapping. This paper describes the performances of a WebGIS prototype designed to disseminate the results of the Italian project Innovative Strategies for the Monitoring and Analysis of Erosion Risk, known as the STIMARE project. While aiming to include the entire national coastline, three study areas along the regional coasts of Puglia and Emilia Romagna have already been implemented as pilot cases. This WebGIS was generated using Free and Open-Source Software for Geographic information systems (FOSS4G). The platform was designed by combining Apache http server, Geoserver, as open-source server and PostgreSQL (with PostGIS extension) as database. Pure javascript libraries OpenLayers and Cesium were implemented to obtain a hybrid 2D and 3D visualization. A user-friendly interactive interface was programmed to help users visualize and download geospatial data in several formats (pdf, kml and shp), in accordance with the European INSPIRE directives, satisfying both multi-temporal and multi-scale perspectives.

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Microvessel Chaste: An Open Library for Spatial Modelling of Vascularized Tissues

10.1101/105692 ◽

2017 ◽

Cited By ~ 2

Author(s):

J.A. Grogan ◽

A.J. Connor ◽

B. Markelc ◽

R.J. Muschel ◽

P.K. Maini ◽

...

Keyword(s):

Open Source ◽

Tumour Growth ◽

Spatial Models ◽

3D Models ◽

Tissue Growth ◽

Coronary Perfusion ◽

Analysis Model ◽

User Friendly

AbstractSpatial models of vascularized tissues are widely used in computational physiology, to study for example, tumour growth, angiogenesis, osteogenesis, coronary perfusion and oxygen delivery. Composition of such models is time-consuming, with many researchers writing custom software for this purpose. Recent advances in imaging have produced detailed three-dimensional (3D) datasets of vascularized tissues at the scale of individual cells. To fully exploit such data there is an increasing need for software that allows user-friendly composition of efficient, 3D models of vascularized tissue growth, and comparison of predictions with in vivo or in vitro experiments and other models. Microvessel Chaste is a new open-source library for building spatial models of vascularized tissue growth. It can be used to simulate vessel growth and adaptation in response to mechanical and chemical stimuli, intra- and extra-vascular transport of nutrient, growth factor and drugs, and cell proliferation in complex 3D geometries. The library provides a comprehensive Python interface to solvers implemented in C++, allowing user-friendly model composition, and integration with experimental data. Such integration is facilitated by interoperability with a growing collection of scientific Python software for image processing, statistical analysis, model annotation and visualization. The library is available under an open-source Berkeley Software Distribution (BSD) licence at https://jmsgrogan.github.io/MicrovesselChaste. This article links to two reproducible example problems, showing how the library can be used to model tumour growth and angiogenesis with realistic vessel networks.

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RICOCHET: A quick-and-dirty approach to analyze μ-XRF synchrotron data using open-source utilities

HNPS Proceedings ◽

10.12681/hnps.1897 ◽

2019 ◽

Vol 23 ◽

pp. 162

Author(s):

E. Mitsi ◽

T. J. Mertzimekis

Keyword(s):

Open Source ◽

Online Analysis ◽

Synchrotron Facility ◽

User Friendly

A semi-automated procedure based on open-source utilities was designed and built to analyze spectra collected at a synchrotron accelerator using the μ-XRF technique. The software (RICOCHET) has a fast, efficient and user-friendly design aimed at performing online analysis. A few examples of its application using recent μ-XRF data from the SUL-X beamline at ANKA Synchrotron Facility (KIT) are presented.

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FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files

10.1101/393140 ◽

2018 ◽

Cited By ~ 1

Author(s):

Leandro Gabriel Roser ◽

Fernán Agüero ◽

Daniel Oscar Sánchez

Keyword(s):

Quality Control ◽

Data Analysis ◽

The Novel ◽

Web Environment ◽

Ngs Data Analysis ◽

Novel Concept ◽

Next Generation Sequencing Ngs ◽

User Friendly ◽

Ngs Data ◽

Analysis Platform

AbstractBackgroundExploration and processing of FASTQ files are the first steps in state-of-the-art data analysis workflows of Next Generation Sequencing (NGS) platforms. The large amount of data generated by these technologies has put a challenge in terms of rapid analysis and visualization of sequencing information. Recent integration of the R data analysis platform with web visual frameworks has stimulated the development of user-friendly, powerful, and dynamic NGS data analysis applications.ResultsThis paper presents FastqCleaner, a Bioconductor visual application for both quality-control (QC) and pre-processing of FASTQ files. The interface shows diagnostic information for the input and output data and allows to select a series of filtering and trimming operations in an interactive framework. FastqCleaner combines the technology of Bioconductor for NGS data analysis with the data visualization advantages of a web environment.ConclusionsFastqCleaner is an user-friendly, offline-capable tool that enables access to advanced Bioconductor infrastructure. The novel concept of a Bioconductor interactive application that can be used without the need for programming skills, makes FastqCleaner a valuable resource for NGS data analysis.

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Covid19Risk.ai: An open source repository and online calculator of prediction models for early diagnosis and prognosis of Covid-19

10.1101/2021.01.05.425384 ◽

2021 ◽

Author(s):

Iva Halilaj ◽

Avishek Chatterjee ◽

Yvonka van Wijk ◽

Guangyao Wu ◽

Brice van Eeckhout ◽

...

Keyword(s):

Open Source ◽

Predictive Models ◽

Prediction Models ◽

Patient Specific ◽

Diagnosis And Prognosis ◽

Online Calculator ◽

User Friendly ◽

Type 3 ◽

Proof Of Principle

AbstractObjectiveThe current pandemic has led to a proliferation of predictive models being developed to address various aspects of COVID-19 patient care. We aimed to develop an online platform that would serve as an open source repository for a curated subset of such models, and provide a simple interface for included models to allow for online calculation. This platform would support doctors during decision-making regarding diagnoses, prognoses, and follow-up of COVID-19 patients, expediting the models’ transition from research to clinical practice.MethodsIn this proof-of-principle study, we performed a literature search in PubMed and WHO database to find suitable models for implementation on our platform. All selected models were publicly available (peer reviewed publications or open source repository) and had been validated (TRIPOD type 3 or 2b). We created a method for obtaining the regression coefficients if only the nomogram was available in the original publication. All predictive models were transcribed on a practical graphical user interface using PHP 8.0.0, and published online together with supporting documentation and links to the associated articles.ResultsThe open source website https://covid19risk.ai/ currently incorporates nine models from six different research groups, evaluated on datasets from different countries. The website will continue to be populated with other models related to COVID-19 prediction as these become available. This dynamic platform allows COVID-19 researchers to contact us to have their model curated and included on our website, thereby increasing the reach and real-world impact of their work.ConclusionWe have successfully demonstrated in this proof-of-principle study that our website provides an inclusive platform for predictive models related to COVID-19. It enables doctors to supplement their judgment with patient-specific predictions from externally-validated models in a user-friendly format. Additionally, this platform supports researchers in showcasing their work, which will increase the visibility and use of their models.

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Secure Network Solutions for Enterprise Cloud Services

Cloud Technology ◽

10.4018/978-1-4666-6539-2.ch068 ◽

2015 ◽

pp. 1464-1486

Author(s):

Chengcheng Huang ◽

Phil Smith ◽

Zhaohao Sun

Keyword(s):

Cloud Computing ◽

Experimental Evidence ◽

Open Source ◽

Network Protocols ◽

Cloud Services ◽

Important Challenge ◽

Secure Network ◽

Cloud Network ◽

User Friendly ◽

Implementation Stage

Securing a cloud network is an important challenge for delivering cloud services to enterprise clouds. There are a number of secure network protocols, such as VPN protocols, currently available, to provide different secure network solutions for enterprise clouds. For example, PPTP, IPSec, and SSL/TLS are the most widely used VPN protocols in today's securing network solutions. However, there are some significant challenges in the implementation stage. For example, which VPN solution is easy to deploy in delivering cloud services? Which VPN solution is most user-friendly in enterprise clouds? This chapter explores these issues by implementing different VPNs in a virtual cloud network environment using open source software and tools. This chapter also reviews cloud computing and cloud services and looks at their relationships. The results not only provide experimental evidence but also facilitate the network implementers in deployment of secure network solutions for enterprise cloud services.

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Geopsy: A User-Friendly Open-Source Tool Set for Ambient Vibration Processing

Seismological Research Letters ◽

10.1785/0220190360 ◽

2020 ◽

Vol 91 (3) ◽

pp. 1878-1889 ◽

Cited By ~ 12

Author(s):

Marc Wathelet ◽

Jean-Luc Chatelain ◽

Cécile Cornou ◽

Giuseppe Di Giulio ◽

Bertrand Guillier ◽

...

Keyword(s):

Open Source ◽

User Interfaces ◽

Site Characterization ◽

Ambient Vibration ◽

The European Union ◽

Vibration Data ◽

Single Station ◽

Characterization Studies ◽

Single Trace ◽

User Friendly

Abstract Ambient vibrations are nowadays considerably used worldwide for numerous types of engineering applications and scientific research. Geopsy and its companion tools are part of that landscape. Since the first release of the program package in 2005, as outcome of the European Union project Site Effects aSsessment from AMbient noisE, Geopsy has become a mature multiplatform open-source package (released under GNU Public License version 3) that has already been recognized as a reference tool for analyzing ambient vibration data in the context of site characterization studies. The community of users has grown from a core group of researchers up to thousands of seismologists and engineers on every career level and on all continents. The versatility of geopsy allows for the processing of all kinds of data needed in site characterization studies, that is, from single station single trace to three-component array recordings. In all of the aforementioned cases, the steps from field acquisition to the production of publication-ready figures are covered and supported by user-friendly graphical user interfaces or corresponding command-line tools for the automation of the complete processing chain. To avoid black-box usage, a number of lower-level tools guarantee maximum flexibility in accessing and controlling processing results at any stage of the analysis.

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A43 Translational research: NGS metagenomics into clinical diagnostics

Virus Evolution ◽

10.1093/ve/vez002.042 ◽

2019 ◽

Vol 5 (Supplement_1) ◽

Author(s):

D Schmitz ◽

S Nooij ◽

T Janssens ◽

J Cremer ◽

H Vennema ◽

...

Keyword(s):

Clinical Diagnostics ◽

Patient Privacy ◽

User Friendliness ◽

Unique Identifier ◽

Audit Trail ◽

Long Term Storage ◽

Analysis Workflow ◽

User Friendly ◽

Ngs Data

Abstract As research next-generation sequencing (NGS) metagenomic pipelines transition to clinical diagnostics, the user-base changes from bioinformaticians to biologists, medical doctors, and lab-technicians. Besides the obvious need for benchmarking and assessment of diagnostic outcomes of the pipelines and tools, other focus points remain: reproducibility, data immutability, user-friendliness, portability/scalability, privacy, and a clear audit trail. We have a research metagenomics pipeline that takes raw fastq files and produces annotated contigs, but it is too complicated for non-bioinformaticians. Here, we present preliminary findings in adapting this pipeline for clinical diagnostics. We used information available on relevant fora (www.bioinfo-core.org) and experiences and publications from colleague bioinformaticians in other institutes (COMPARE, UBC, and LUMC). From this information, a robust and user-friendly storage and analysis workflow was designed for non-bioinformaticians in a clinical setting. Via Conda [https://conda.io] and Docker containers [http://www.docker.com], we made our disparate pipeline processes self-contained and reproducible. Furthermore, we moved all pipeline settings into a separate JSON file. After every analysis, the pipeline settings and virtual-environment recipes will be archived (immutably) under a persistent unique identifier. This allows long-term precise reproducibility. Likewise, after every run the raw data and final products will be automatically archived, complying with data retention laws/guidelines. All the disparate processes in the pipeline are parallelized and automated via Snakemake1 (i.e. end-users need no coding skills). In addition, interactive web-reports such as MultiQC [http://multiqc.info] and Krona2 are generated automatically. By combining Snakemake, Conda, and containers, our pipeline is highly portable and easily scaled up for outbreak situations, or scaled down to reduce costs. Since patient privacy is a concern, our pipeline automatically removes human genetic data. Moreover, all source code will be stored on an internal Gitlab server, and, combined with the archived data, ensures a clear audit trail. Nevertheless, challenges remain: (1) reproducible reference databases, e.g. being able to revert to an older version to reproduce old analyses. (2) A user-friendly GUI. (3) Connecting the pipeline and NGS data to in-house LIMS. (4) Efficient long-term storage, e.g. lossless compression algorithms. Nevertheless, this work represents a step forward in making user-friendly clinical diagnostic workflows.

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