scholarly journals ELIMU-MDx: a web-based, open-source platform for storage, management and analysis of diagnostic qPCR data

BioTechniques ◽  
2020 ◽  
Vol 68 (1) ◽  
pp. 22-27 ◽  
Author(s):  
Silvan Krähenbühl ◽  
Fabian Studer ◽  
Etienne Guirou ◽  
Anna Deal ◽  
Philipp Mächler ◽  
...  
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Software Tool ◽  
Turnaround Time ◽  
Storage Management ◽  
Quantitative Real Time Pcr ◽  
Web Browser ◽  
Web Based ◽  
Data Standard ◽  
User Friendly

The Electronic Laboratory Information and Management Utensil for Molecular Diagnostics (ELIMU-MDx) is a user-friendly platform designed and built to accelerate the turnaround time of diagnostic qPCR assays. ELIMU-MDx is compliant with Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines and has extensive data-import capabilities for all major qPCR instruments by using the RDML data standard. This platform was designed as an open-source software tool and can be accessed through the web browser on all major operating systems.

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

Analysis of Free and Open Source Software (FOSS) Product in Web Based Client-Server Architecture

2018 ◽  
Vol 9 (3) ◽  
pp. 36-47
Author(s):  
Pushpa Singh ◽  
Narendra Singh
Keyword(s):  
Open Source ◽  
Market Share ◽  
Open Source Software ◽  
Analytical Study ◽  
Web Applications ◽  
Web Browser ◽  
Web Based ◽  
Client Server ◽  
Server Architecture ◽  
Client Server Architecture

Free and open source software (FOSS) differs from proprietary software. FOSS facilitates the design of various applications per the user's requirement. Web applications are not exceptional in this way. Web-based applications are mostly based on client server architecture. This article is an analytical study of FOSS products used in web-based client server architecture. This article will provide information about FOSS product such as FireFox (web browser), Apache (web server) and MySQL (RDBMS). These reveal that various FOSS products such as Apache server covers 65% of the market share, while MySQL covers 58.7% market share and hold the top-most rank.

A New Method for Morphometric Analysis of Opal Phytoliths from Plants

2014 ◽  
Vol 20 (6) ◽  
pp. 1876-1887 ◽  
Author(s):  
Welmoed A. Out ◽  
José F. Pertusa Grau ◽  
Marco Madella
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Standard Method ◽  
Morphometric Analysis ◽  
Software Tool ◽  
New Method ◽  
Phytolith Analysis ◽  
Opal Phytoliths ◽  
User Friendly ◽  
Comparability Of Results

AbstractMicro-morphometry has substantially gained ground in the field of phytolith analysis, but the comparability of results is limited due to the use of different methods. This paper presents a new, user-friendly method based on open-source software (FIJI) that is proposed as a step towards the introduction of a standard method. After obtaining a mask of a phytolith by making a digital drawing, 27 commonly used variables of size and shape are measured automatically. This method is not only useful for phytolith analysis, but may also be used for other fields of morphometric research. Users can furthermore customize the software tool when additional variables are required.

Analysis of Free and Open Source Software (FOSS) Product in Web Based Client-Server Architecture

2021 ◽  
pp. 96-108
Author(s):  
Pushpa Singh ◽  
Narendra Singh
Keyword(s):  
Open Source ◽  
Market Share ◽  
Open Source Software ◽  
Web Applications ◽  
Web Server ◽  
Web Browser ◽  
Web Based ◽  
Client Server ◽  
Server Architecture ◽  
Client Server Architecture

Free and open source software (FOSS) differs from proprietary software. FOSS facilitates the design of various applications per the user's requirement. Web applications are not exceptional in this way. Web-based applications are mostly based on client server architecture. This article is an analytical study of FOSS products used in web-based client server architecture. This article will provide information about FOSS product such as FireFox (web browser), Apache (web server) and MySQL (RDBMS). These reveal that various FOSS products such as Apache server covers 65% of the market share, while MySQL covers 58.7% market share and hold the top-most rank.

Evol2Circos: A Web-Based Tool for Genome Synteny and Collinearity Analysis and its Visualization in Fishes

2020 ◽  
Vol 111 (5) ◽  
pp. 486-490
Author(s):  
Manmohan Pandey ◽  
Basdeo Kushwaha ◽  
Ravindra Kumar ◽  
Prachi Srivastava ◽  
Suman Saroj ◽  
...  
Keyword(s):  
Large Scale ◽  
Software Tool ◽  
Web Browser ◽  
Web Based ◽  
Specific Data ◽  
Sequencing Technologies ◽  
Assembly Algorithms ◽  
User Friendly ◽  
Research Domains ◽  
Generation Sequencing

Abstract The advent of high throughput next-generation sequencing technologies and improved assembly algorithms have resulted in the accumulation of voluminous genomic data in public domains. These technologies have opened up entries for large scale comparative genome studies, especially the identification of conserved syntenic blocks among species, facilitating studies of the evolutionary importance of the conservation and variation in genomic organization. Synteny construction and visualization require computational and bioinformatics skills to prepare input files for the synteny analysis pipeline. The syntenic information for fishes is still in a juvenile stage and is scattered among different research domains. Here, we present a web-based tool “Evol2Circos” to provide a user-friendly graphical user interface (GUI) to analyze user-specific data for synteny construction and visualization, and to facilitate the browsing of syntenic information of different fishes using the Circos, bar, dual, and dot plots. The information generated from the tool can also be used for further downstream analyses. Evol2Circos software tool is tested under Ubuntu Linux. The web-browser, source code, documentation, user manual, example dataset and scripts are available online at 203.190.147.148/evole2circos/

Web Based GIS Application using Open Source Software for Sharing Geospatial Data

2015 ◽  
Vol 4 (1) ◽  
pp. 1224-1228 ◽  
Author(s):  
Debasish Chakraborty ◽  
◽  
Debanjan Sarkar ◽  
Shubham Agarwal ◽  
Dibyendu Dutta ◽  
...  
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Geospatial Data ◽  
Web Based ◽  
Gis Application

scholarly journals Cantera: an open source software tool for integrating complex thermo-chemistry into device-level simulations

2020 ◽  
Author(s):  
Richard West ◽  
Robert Kee ◽  
Kyle Niemeyer ◽  
Steven C. DeCaluwe ◽  
C. Goldsmith ◽  
...  
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Software Tool

scholarly journals An uncertainty-based protocol for the setup and measurement of soot/black carbon emissions from gas flares using sky-LOSA

2020 ◽  
Author(s):  
Bradley M. Conrad ◽  
Matthew R. Johnson
Keyword(s):  
Open Source ◽  
Black Carbon ◽  
Open Source Software ◽  
Carbon Emissions ◽  
Climate Models ◽  
Optical Measurement ◽  
Measurement Data ◽  
Software Tool ◽  
Measurement Protocol ◽  
Measurement Uncertainties

Abstract. Gas flaring is an important source of atmospheric soot/black carbon, especially in sensitive Arctic regions. However, emissions have traditionally been challenging to measure and remain poorly characterized, confounding international reporting requirements and adding uncertainty to climate models. The sky-LOSA optical measurement technique has emerged as a powerful means to quantify flare black carbon emissions in the field, but broader adoption has been hampered by the complexity of its deployment, where decisions during setup in the field can have profound, non-linear impacts on achievable measurement uncertainties. To address this challenge, this paper presents a prescriptive measurement protocol and associated open-source software tool that simplifies acquisition of sky-LOSA data in the field. Leveraging a comprehensive Monte Carlo-based General Uncertainty Analysis (GUA) to predict measurement uncertainties over the entire breadth of possible measurement conditions, general heuristics are identified to guide a sky-LOSA user toward optimal data collection. These are further extended in the open-source software utility, SetupSkyLOSA, which interprets the GUA results to provide detailed guidance for any specific combination of location, date/time, and flare, plume, and ambient conditions. Finally, a case study of a sky-LOSA measurement at an oil and gas facility in Mexico is used to demonstrate the utility of the software tool, where potentially small region(s) of optimal instrument setup are easily and quickly identified. It is hoped that this work will help increase the accessibility of the sky-LOSA technique and ultimately the availability of field measurement data for flare black carbon emissions.

Establishing Ethos on Proprietary and Open Source Software Websites

2014 ◽  
pp. 915-935
Author(s):  
Kevin Brock
Keyword(s):  
Operating System ◽  
Software Development ◽  
Open Source ◽  
Open Source Software ◽  
Image Manipulation ◽  
Public Acceptance ◽  
Web Browser ◽  
Software Products ◽  
Tremendous Amount ◽  
Rhetorical Appeals

The increasing prominence and variety of open source software (OSS) threaten to upset conventional approaches to software development and marketing. While a tremendous amount of scholarship has been published on the differences between proprietary and OSS development, little has been discussed regarding the effect of rhetorical appeals used to promote either type of software. This chapter offers just such an examination, focusing its scrutiny on the websites for three pairs of competitors (operating system, Web browser, and image manipulation program). The means by which the OSS websites promote their programs provide a significant set of insights into the potential trajectory of OSS development and its widespread public acceptance, in terms of both its initial philosophy and its perceived alternative nature to traditional software products and models.

Prospects of Open Source Software for Maximizing the User Expectations in Heterogeneous Network

2021 ◽  
pp. 257-271
Author(s):  
Pushpa Singh ◽  
Rajeev Agrawal
Keyword(s):  
Machine Learning ◽  
Open Source ◽  
Real Time ◽  
Open Source Software ◽  
Heterogeneous Networks ◽  
Heterogeneous Network ◽  
Research Work ◽  
Software Tool ◽  
Knn Classifier ◽  
User Expectations

This article focuses on the prospects of open source software and tools for maximizing the user expectations in heterogeneous networks. The open source software Python is used as a software tool in this research work for implementing machine learning technique for the categorization of the types of user in a heterogeneous network (HN). The KNN classifier available in Python defines the type of user category in real time to predict the available users in a particular category for maximizing profit for a business organization.

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