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.

scholarly journals Validating cohesion metrics by mining open source software data with association rules

2008 ◽  
Author(s):  
◽  
Pariksha Singh
Keyword(s):  
Software Development ◽  
Open Source ◽  
Association Rules ◽  
Open Source Software ◽  
Object Oriented ◽  
Software Measurement ◽  
Object Oriented Design ◽  
Starting Point ◽  
Measurement Science ◽  
Open Source Software Package

Competitive pressure on the software industry encourages organizations to examine the effectiveness of their software development and evolutionary processes. Therefore it is important that software is measured in order to improve the quality. The question is not whether we should measure software but how it should be measured. Software measurement has been in existence for over three decades and it is still in the process of becoming a mature science. The many influences of new software development technologies have led to a diverse growth in software measurement technologies which have resulted in various definitions and validation techniques. An important aspect of software measurement is the measurement of the design, which nowadays often means the measurement of object oriented design. Chidamer and Kemerer (1994) designed a metric suite for object oriented design, which has provided a new foundation for metrics and acts as a starting point for further development of the software measurement science. This study documents theoretical object oriented cohesion metrics and calculates those metrics for classes extracted from a sample of open source software packages. For each open source software package, the following data is recorded: software size, age, domain, number of developers, number of bugs, support requests, feature requests, etc. The study then tests by means of association rules which theoretical cohesion metrics are validated hypothesis: that older software is more cohesive than younger software, bigger packages is less cohesive than smaller packages, and the smaller the software program the more maintainable it is. This study attempts to validate existing theoretical object oriented cohesion metrics by mining open source software data with association rules.

scholarly journals The 2017 Bioinformatics Open Source Conference (BOSC)

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 1858
Author(s):  
Nomi L. Harris ◽  
Peter J.A. Cock ◽  
Brad Chapman ◽  
Christopher J. Fields ◽  
Karsten Hokamp ◽  
...  
Keyword(s):  
Software Development ◽  
Open Source ◽  
Open Source Software ◽  
Open Data ◽  
Open Science ◽  
Research Community ◽  
Biological Research ◽  
Non Profit ◽  
Bioinformatics Software ◽  
Bioinformatics Community

The Bioinformatics Open Source Conference (BOSC) is a meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. The 18th annual BOSC (http://www.open-bio.org/wiki/BOSC_2017) took place in Prague, Czech Republic in July 2017. The conference brought together nearly 250 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, open and reproducible science, and this year’s theme, open data. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community, called the OBF Codefest.

scholarly journals The Divergent Anarcho-utopian Discourses of the Open Source Software Movement

2006 ◽  
Vol 30 (4) ◽  
Author(s):  
Dale A. Bradley
Keyword(s):  
Software Development ◽  
Open Source ◽  
Open Source Software ◽  
Free Software ◽  
Open Source Software Development ◽  
Programming Practices ◽  
Free Software Foundation ◽  
The Way

Abstract: The discourse informing open source programming is important for many reasons, not the least of which is the way in which its ideological positions are translated into practical actions. It is argued that the initial anarcho-utopian move initiated by Richard Stallman’s GNU Project and Free Software Foundation is currently being transformed into an organizational utopia in the form of the largely Linux-based open source movement. The utopian impulse evident in open source software development is therefore addressed from the perspective that the promises of liberation that inform its anarchy-inspired politics may be undermined by efforts to integrate its communal programming practices into existing market hegemonies. Résumé : Le discours sur la programmation libre est important à plusieurs égards, notamment dans la manière dont ses positions idéologiques se transforment en actions concrètes. Cet article soutient que le mouvement anarcho-utopique lancé par Richard Stallman avec son projet GNU et la Fondation pour le logiciel libre se transforme actuellement en une utopie organisationnelle prenant la forme d’un Mouvement du logiciel libre qui se fonde en grande partie sur le système Linux. Cet article adopte la perspective qu’on risque aujourd’hui de perdre de vue l'impulsion utopique qui était évidente dans le développement initial de logiciels libres. On risque en outre d’oublier les promesses de liberté qui sous

scholarly journals The 2016 Bioinformatics Open Source Conference (BOSC)

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 2464
Author(s):  
Nomi L. Harris ◽  
Peter J.A. Cock ◽  
Brad Chapman ◽  
Christopher J. Fields ◽  
Karsten Hokamp ◽  
...  
Keyword(s):  
Software Development ◽  
Open Source ◽  
Open Source Software ◽  
Open Science ◽  
Research Community ◽  
Biological Research ◽  
Non Profit ◽  
Link Type ◽  
Bioinformatics Software ◽  
Bioinformatics Community

Message from the ISCB: The Bioinformatics Open Source Conference (BOSC) is a yearly meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. BOSC has been run since 2000 as a two-day Special Interest Group (SIG) before the annual ISMB conference. The 17th annual BOSC (http://www.open-bio.org/wiki/BOSC_2016) took place in Orlando, Florida in July 2016. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community. The conference brought together nearly 100 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, and open and reproducible science.

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.

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