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 Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software

GigaScience ◽  
2019 ◽  
Vol 8 (9) ◽  
Author(s):  
Peter Georgeson ◽  
Anna Syme ◽  
Clare Sloggett ◽  
Jessica Chung ◽  
Harriet Dashnow ◽  
...  
Keyword(s):  
Best Practices ◽  
Software Development ◽  
Open Source ◽  
Open Source Software ◽  
Command Line ◽  
Use Of Resources ◽  
Excellent Starting Point ◽  
Starting Point ◽  
Bioinformatics Software ◽  
Programming Practices

Abstract Background Bioinformatics software tools are often created ad hoc, frequently by people without extensive training in software development. In particular, for beginners, the barrier to entry in bioinformatics software development is high, especially if they want to adopt good programming practices. Even experienced developers do not always follow best practices. This results in the proliferation of poorer-quality bioinformatics software, leading to limited scalability and inefficient use of resources; lack of reproducibility, usability, adaptability, and interoperability; and erroneous or inaccurate results. Findings We have developed Bionitio, a tool that automates the process of starting new bioinformatics software projects following recommended best practices. With a single command, the user can create a new well-structured project in 1 of 12 programming languages. The resulting software is functional, carrying out a prototypical bioinformatics task, and thus serves as both a working example and a template for building new tools. Key features include command-line argument parsing, error handling, progress logging, defined exit status values, a test suite, a version number, standardized building and packaging, user documentation, code documentation, a standard open source software license, software revision control, and containerization. Conclusions Bionitio serves as a learning aid for beginner-to-intermediate bioinformatics programmers and provides an excellent starting point for new projects. This helps developers adopt good programming practices from the beginning of a project and encourages high-quality tools to be developed more rapidly. This also benefits users because tools are more easily installed and consistent in their usage. Bionitio is released as open source software under the MIT License and is available at https://github.com/bionitio-team/bionitio.

The context and state of open source software adoption in US academic libraries

2019 ◽  
Vol 37 (4) ◽  
pp. 641-659
Author(s):  
Namjoo Choi ◽  
Joseph A. Pruett
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Academic Libraries ◽  
Online Survey ◽  
Chief Information Officers ◽  
Content Type ◽  
Software Adoption ◽  
Current State ◽  
Funding Agencies ◽  
Low Levels

Purpose The purpose of this paper is to identify barriers and drivers to open source software (OSS) adoption, and measures awareness and adoption stages of OSS in US academic libraries. Design/methodology/approach An online survey of chief information officers, chief technology officers or heads for IT in US academic libraries was conducted. A total number of 179 responses were used for data analysis. Findings From the survey, the authors identify significant barriers and drivers that US academic libraries may consider before adopting OSS and found that awareness itself is not a barrier. While about half of respondents confirmed using OSS, the authors found surprisingly low levels of intent to adopt from current non-adopters. Practical implications This research offers insights for promoting OSS adoption. Also, it provides funding agencies and administrators with guidelines to encourage successful deployment of OSS in higher education. Originality/value While extant research is mostly anecdotal, this research draws from an online survey to snap-shot the current state of OSS adoption in US academic libraries and provides a baseline for practice and 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 OPEN SOURCE CLOUD-BASED TECHNOLOGIES FOR BIM

2018 ◽  
Vol XLII-2 ◽  
pp. 607-614 ◽  
Author(s):  
S. Logothetis ◽  
E. Karachaliou ◽  
E. Valari ◽  
E. Stylianidis
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Research Work ◽  
3D Models ◽  
Web Interface ◽  
Multiple Stakeholders ◽  
Architectural Engineering ◽  
Starting Point ◽  
Cloud Technologies ◽  
Survey Approach

This paper presents a Cloud-based open source system for storing and processing data from a 3D survey approach. More specifically, we provide an online service for viewing, storing and analysing BIM. Cloud technologies were used to develop a web interface as a BIM data centre, which can handle large BIM data using a server. The server can be accessed by many users through various electronic devices anytime and anywhere so they can view online 3D models using browsers. Nowadays, the Cloud computing is engaged progressively in facilitating BIM-based collaboration between the multiple stakeholders and disciplinary groups for complicated Architectural, Engineering and Construction (AEC) projects. Besides, the development of Open Source Software (OSS) has been rapidly growing and their use tends to be united. Although BIM and Cloud technologies are extensively known and used, there is a lack of integrated open source Cloud-based platforms able to support all stages of BIM processes. The present research aims to create an open source Cloud-based BIM system that is able to handle geospatial data. In this effort, only open source tools will be used; from the starting point of creating the 3D model with FreeCAD to its online presentation through BIMserver. Python plug-ins will be developed to link the two software which will be distributed and freely available to a large community of professional for their use. The research work will be completed by benchmarking four Cloud-based BIM systems: Autodesk BIM 360, BIMserver, Graphisoft BIMcloud and Onuma System, which present remarkable results.

scholarly journals Characterization and Classification of Collaborative Tools

2009 ◽  
pp. 361-370
Author(s):  
Javier Soriano ◽  
Rafael Fernández ◽  
Miguel Jiménez
Keyword(s):  
Software Development ◽  
Open Source ◽  
Open Source Software ◽  
Work Teams ◽  
Development Projects ◽  
Collaborative Effort ◽  
Open Source Software Development ◽  
Collaborative Tools ◽  
Software Product

Traditionally, collaboration has been a means for organizations to do their work. However, the context in which they do this work is changing, especially in regards to where the work is done, how the work is organized, who does the work, and with this the characteristics of collaboration. Software development is no exception; it is itself a collaborative effort that is likewise affected by these changes. In the context of both open source software development projects and communities and organizations that develop corporate products, more and more developers need to communicate and liaise with colleagues in geographically distant places about the software product they are conceiving, designing, building, testing, debugging, deploying and maintaining. Thus, work teams face sizeable collaborative challenges, for which they have need of tools that they can use to communicate and coordinate their work efficiently.

scholarly journals BioSig: The Free and Open Source Software Library for Biomedical Signal Processing

2011 ◽  
Vol 2011 ◽  
pp. 1-12 ◽  
Author(s):  
Carmen Vidaurre ◽  
Tilmann H. Sander ◽  
Alois Schlögl
Keyword(s):  
Signal Processing ◽  
Open Source ◽  
Open Source Software ◽  
Biomedical Signal Processing ◽  
Software Library ◽  
Biomedical Signal ◽  
Computer Interfaces ◽  
Relevant Element ◽  
Electrocardiogram Ecg ◽  
Electroencephalogram Eeg

BioSig is an open source software library for biomedical signal processing. The aim of the BioSig project is to foster research in biomedical signal processing by providing free and open source software tools for many different application areas. Some of the areas where BioSig can be employed are neuroinformatics, brain-computer interfaces, neurophysiology, psychology, cardiovascular systems, and sleep research. Moreover, the analysis of biosignals such as the electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), or respiration signals is a very relevant element of the BioSig project. Specifically, BioSig provides solutions for data acquisition, artifact processing, quality control, feature extraction, classification, modeling, and data visualization, to name a few. In this paper, we highlight several methods to help students and researchers to work more efficiently with biomedical signals.

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