scholarly journals RcdMathLib: An Open Source Software Library for Computing on Resource-Limited Devices

Sensors ◽  
2021 ◽  
Vol 21 (5) ◽  
pp. 1689
Author(s):  
Zakaria Kasmi ◽  
Abdelmoumen Norrdine ◽  
Jochen Schiller ◽  
Mesut Güneş ◽  
Christoph Motzko
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Low Cost ◽  
Optimization Methods ◽  
Software Library ◽  
Matrix Operations ◽  
Resource Limited ◽  
Linear And Nonlinear ◽  
Iot Devices ◽  
Value Decomposition

We developped an open source library called RcdMathLib for solving multivariate linear and nonlinear systems. RcdMathLib supports on-the-fly computing on low-cost and resource-constrained devices, e.g., microcontrollers. The decentralized processing is a step towards ubiquitous computing enabling the implementation of Internet of Things (IoT) applications. RcdMathLib is modular- and layer-based, whereby different modules allow for algebraic operations such as vector and matrix operations or decompositions. RcdMathLib also comprises a utilities-module providing sorting and filtering algorithms as well as methods generating random variables. It enables solving linear and nonlinear equations based on efficient decomposition approaches such as the Singular Value Decomposition (SVD) algorithm. The open source library also provides optimization methods such as Gauss–Newton and Levenberg–Marquardt algorithms for solving problems of regression smoothing and curve fitting. Furthermore, a positioning module permits computing positions of IoT devices using algorithms for instance trilateration. This module also enables the optimization of the position by performing a method to reduce multipath errors on the mobile device. The library is implemented and tested on resource-limited IoT as well as on full-fledged operating systems. The open source software library is hosted on a GitLab repository.

scholarly journals Advancing HIV Vaccine Research With Low-Cost High-Performance Computing Infrastructure: An Alternative Approach for Resource-Limited Settings

2019 ◽  
Vol 13 ◽  
pp. 117793221988234
Author(s):  
Batsirai M Mabvakure ◽  
Raymond Rott ◽  
Leslie Dobrowsky ◽  
Peter Van Heusden ◽  
Lynn Morris ◽  
...  
Keyword(s):  
Open Source ◽  
High Performance Computing ◽  
Open Source Software ◽  
High Performance ◽  
Low Cost ◽  
Resource Limited Settings ◽  
Resource Limited ◽  
Desktop Computers ◽  
Performance Computing ◽  
Generation Sequencing

Next-generation sequencing (NGS) technologies have revolutionized biological research by generating genomic data that were once unaffordable by traditional first-generation sequencing technologies. These sequencing methodologies provide an opportunity for in-depth analyses of host and pathogen genomes as they are able to sequence millions of templates at a time. However, these large datasets can only be efficiently explored using bioinformatics analyses requiring huge data storage and computational resources adapted for high-performance processing. High-performance computing allows for efficient handling of large data and tasks that may require multi-threading and prolonged computational times, which is not feasible with ordinary computers. However, high-performance computing resources are costly and therefore not always readily available in low-income settings. We describe the establishment of an affordable high-performance computing bioinformatics cluster consisting of 3 nodes, constructed using ordinary desktop computers and open-source software including Linux Fedora, SLURM Workload Manager, and the Conda package manager. For the analysis of large antibody sequence datasets and for complex viral phylodynamic analyses, the cluster out-performed desktop computers. This has demonstrated that it is possible to construct high-performance computing capacity capable of analyzing large NGS data from relatively low-cost hardware and entirely free (open-source) software, even in resource-limited settings. Such a cluster design has broad utility beyond bioinformatics to other studies that require high-performance computing.

scholarly journals SynBiopython: an open-source software library for Synthetic Biology

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Jing Wui Yeoh ◽  
Neil Swainston ◽  
Peter Vegh ◽  
Valentin Zulkower ◽  
Pablo Carbonell ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Open Source ◽  
Open Source Software ◽  
Development Projects ◽  
Software Library ◽  
Current State ◽  
Starting Point ◽  
Common Problems ◽  
Data Tracking ◽  
Python Package

Abstract Advances in hardware automation in synthetic biology laboratories are not yet fully matched by those of their software counterparts. Such automated laboratories, now commonly called biofoundries, require software solutions that would help with many specialized tasks such as batch DNA design, sample and data tracking, and data analysis, among others. Typically, many of the challenges facing biofoundries are shared, yet there is frequent wheel-reinvention where many labs develop similar software solutions in parallel. In this article, we present the first attempt at creating a standardized, open-source Python package. A number of tools will be integrated and developed that we envisage will become the obvious starting point for software development projects within biofoundries globally. Specifically, we describe the current state of available software, present usage scenarios and case studies for common problems, and finally describe plans for future development. SynBiopython is publicly available at the following address: http://synbiopython.org.

scholarly journals Merging a Remote Microscope and Virtual Worlds: Teaching Kingdom Plantae on Basic Education

2016 ◽  
Vol 12 (04) ◽  
pp. 27 ◽  
Author(s):  
Caroline Porto Antonio ◽  
João Paulo Lima ◽  
João Bosco Alves ◽  
Juarez Bento Silva ◽  
José Pedro Simão
Keyword(s):  
Learning Environment ◽  
Open Source ◽  
Science Teaching ◽  
Open Source Software ◽  
Virtual Worlds ◽  
Basic Education ◽  
Low Cost ◽  
Virtual Learning Environment ◽  
Educational Tool ◽  
Plant Parts

This paper presents an educational tool based on open source software and low cost hardware to supplement science teaching, merging concepts of remote experiment, virtual worlds and virtual learning environment. Using an avatar, students can move around in an enriched environment and access a remote microscope that enables visualization of plant parts and interaction with the available samples.

Review of Open Source Software (OSS)

2012 ◽  
pp. 26-40
Author(s):  
Bhasker Mukerji ◽  
Ramaraj Palanisamy
Keyword(s):  
Developing Countries ◽  
Public Sector ◽  
Open Source ◽  
Open Source Software ◽  
Low Cost ◽  
Source Code ◽  
Developed Countries ◽  
Economic Resources ◽  
Large Pool ◽  
Public Sector Organizations

The popularity of Open Source Software (OSS) in developing countries is quiet evident from its widespread adoption across government departments and public sector organizations. The use of OSS saves economic resources of cash starved countries, provides an opportunity to promote e-government, and to utilize their resources in other sectors. Many developing countries have a large pool of skilled developers who can modify the source code of the OSS at a very low cost. Many governments in developing and developed countries have switched to OSS which probably encourages others to follow the trend. It was not possible to follow the adoption trend in all the developing countries but the usage of OSS in countries like India, Brazil, and Venezuela provides us an insight. The successful adoption of OSS requires thorough analysis of its advantages as well as the issues associated with it. This chapter will provide an overview of OSS, characteristics of OSS developers, and their motivation to volunteer by contributing in OSS projects, followed by the advantages and issues associated with OSS.

scholarly journals Software-Based Three-Dimensional Deconvolution Microscopy of Cytoskeletal Proteins in Cultured Fibroblast Using Open-Source Software and Open Hardware

2019 ◽  
Vol 5 (12) ◽  
pp. 88
Author(s):  
Kazuo Katoh
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Laser Scanning ◽  
Low Cost ◽  
Three Dimensional ◽  
Cytoskeletal Proteins ◽  
Laser Scanning Microscopy ◽  
Confocal Laser ◽  
Actual Measurement ◽  
Open Hardware

As conventional fluorescence microscopy and confocal laser scanning microscopy generally produce images with blurring at the upper and lower planes along the z-axis due to non-focal plane image information, the observation of biological images requires “deconvolution.” Therefore, a microscope system’s individual blur function (point spread function) is determined theoretically or by actual measurement of microbeads and processed mathematically to reduce noise and eliminate blurring as much as possible. Here the author describes the use of open-source software and open hardware design to build a deconvolution microscope at low cost, using readily available software and hardware. The advantage of this method is its cost-effectiveness and ability to construct a microscope system using commercially available optical components and open-source software. Although this system does not utilize expensive equipment, such as confocal and total internal reflection fluorescence microscopes, decent images can be obtained even without previous experience in electronics and optics.

scholarly journals Use of Free and Open-Source Software (FOSS) in the U.S. Department of Defense

2003 ◽  
Vol 2003 (01) ◽  
pp. 0102
Author(s):  
Terry Bollinger
Keyword(s):  
Software Development ◽  
Open Source ◽  
Open Source Software ◽  
Department Of Defense ◽  
Low Cost ◽  
Source Code ◽  
Leading Edge ◽  
Cyber Attacks ◽  
Software Analysis ◽  
The U.S

This report documents the results of a study by The MITRE Corporation on the use of free and open-source software (FOSS) in the U.S. Department of Defense (DoD). FOSS gives users the right to run, copy, distribute, study, change, and improve it as they see fit, without asking permission or making fiscal payments to any external group or person. The study showed that FOSS provides substantial benefits to DoD security, infrastructure support, software development, and research. Given the openness of its source code, the finding that FOSS profoundly benefits security was both counterintuitive and instructive. Banning FOSS in DoD would remove access to exceptionally well-verified infrastructure components such as OpenBSD and robust network and software analysis tools needed to detect and respond to cyber-attacks. Finally, losing the hands-on source code accessibility of FOSS source code would reduce DoD’s ability to respond rapidly to cyberattacks. In short, banning FOSS would have immediate, broad, and strongly negative impacts on the DoD’s ability to defend the U.S. against cyberattacks. For infrastructure support, the deep historical ties between FOSS and the emergence of the Internet mean that removing FOSS applications would strongly negatively impact the DoD’s ability to support web and Internet-based applications. Software development would be hit especially hard due to many leading-edge and broadly used tools being FOSS. Finally, the loss of access to low-cost data processing tools and the inability to share results in the more potent form of executable FOSS software would seriously and negatively impact nearly all forms of scientific and data-driven research.

scholarly journals Development of framework for detecting smoking scene in video clips

2019 ◽  
Vol 13 (1) ◽  
pp. 22
Author(s):  
Poonam Ghuli ◽  
Shashank B N ◽  
Athri G Rao
Keyword(s):  
Machine Learning ◽  
Object Detection ◽  
Open Source ◽  
Image Recognition ◽  
Open Source Software ◽  
Software Library ◽  
Accurate Model ◽  
Video Clips ◽  
Warning Messages ◽  
Warning Message

<p>According to Global Adult Tobacco Survey 2016-17, 61.9% of people quitting tobacco the reason was the warnings displayed on the product covers. The focus of this paper is to automatically display warning messages in video clips. This paper explains the development of a system to automatically detect the smoking scenes using image recognition approach in video clips and then add the warning message to the viewer.  The approach aims to detect the cigarette object using Tensorflow’s object detection API. Tensorflow is an open source software library for machine learning provided by Google which is broadly used in the field image recognition. At present, Faster R-CNN with Inception ResNet is theTensorflow’s slowest but most accurate model. Faster R-CNN with Inception Resnet v2 model is used to detect smoking scenes by training the model with cigarette as an object.</p><p><em><br /></em></p>

scholarly journals Communicating with (Some) Canadians: Communication Rights and Government Online in Canada

2009 ◽  
Vol 34 (3) ◽  
Author(s):  
Michael Felczak ◽  
Richard Smith ◽  
Geoffrey Glass
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Public Libraries ◽  
Low Cost ◽  
The Internet ◽  
Policy Recommendations ◽  
Government Information ◽  
Government Programs ◽  
Online Programs ◽  
Government Websites

Abstract: A communication rights framework is used to evaluate recent government online initiatives in Canada. Through an analysis of policy documents, government websites, user experiences, and the existing and evolving computing environment, the authors argue that government online programs fail to adequately ensure the communication rights of Canadians who use free and open source software, including Canadians who seek alternatives to proprietary software, Canadians who require low-cost computing, and Canadians who access the Internet via public libraries and community centres that use free and open source software. Existing government programs also fail to ensure the communication rights of Canadians without access to the Internet, including Canadians who do not use or plan to use the Internet. The authors identify specific problem areas in the provision of government information, services, and consultations and suggest policy recommendations that address the identified shortcomings.Résumé : Dans cet article, les auteurs utilisent une perspective fondée sur le droit à la communication pour évaluer des initiatives en ligne de la part du gouvernement canadien. Au moyen de l’analyse de documents de politique générale, de sites gouvernementaux, d’expériences d’utilisateurs et de l’environnement informatique actuel dans son évolution constante, les auteurs soutiennent que les programmes gouvernementaux en ligne ne réussissent pas à protéger de manière adéquate les droits de communication des Canadiens qui utilisent des logiciels libres gratuits, y compris ceux qui désirent une alternative aux logiciels propriétaires, ceux qui dépendent de services informatiques à bas prix et ceux qui accèdent à Internet dans les bibliothèques et centres communautaires équipés de logiciels libres gratuits. En outre, les programmes gouvernementaux actuels sont incapables de protéger les droits de communication de ces Canadiens qui n’ont pas accès à Internet, c’est-à-dire ceux qui ne l’utilisent pas présentement ainsi que ceux qui n’ont pas l’intention de l’utiliser. Les auteurs identifient des problèmes spécifiques reliés à la fourniture d’informations, de services et de consultations de la part du gouvernement et recommandent des politiques qui s’adressent aux défauts identifiés.

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