Networking beyond the software code? an explorative examination of the development of an open source car project

Functional, usable, and maintainable open-source software is increasingly essential to scientific research, but there is a large variation in formal training for software development and maintainability. Here, we propose 10 “rules” centered on 2 best practice components: clean code and testing. These 2 areas are relatively straightforward and provide substantial utility relative to the learning investment. Adopting clean code practices helps to standardize and organize software code in order to enhance readability and reduce cognitive load for both the initial developer and subsequent contributors; this allows developers to concentrate on core functionality and reduce errors. Clean coding styles make software code more amenable to testing, including unit tests that work best with modular and consistent software code. Unit tests interrogate specific and isolated coding behavior to reduce coding errors and ensure intended functionality, especially as code increases in complexity; unit tests also implicitly provide example usages of code. Other forms of testing are geared to discover erroneous behavior arising from unexpected inputs or emerging from the interaction of complex codebases. Although conforming to coding styles and designing tests can add time to the software development project in the short term, these foundational tools can help to improve the correctness, quality, usability, and maintainability of open-source scientific software code. They also advance the principal point of scientific research: producing accurate results in a reproducible way. In addition to suggesting several tips for getting started with clean code and testing practices, we recommend numerous tools for the popular open-source scientific software languages Python, R, and Julia.

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Investigation of the Software Code Vulnerabilities' Impact on the Popularity of Open Source Software Projects

Journal of Information Technology Research ◽

10.4018/jitr.2021070104 ◽

2021 ◽

Vol 14 (3) ◽

pp. 58-69

Author(s):

Madanjit Singh ◽

Munish Saini ◽

Manevpreet Kaur

Keyword(s):

Open Source ◽

Open Source Software ◽

Software Evolution ◽

Source Code ◽

Project Managers ◽

Software Projects ◽

Software Vulnerabilities ◽

Software Code ◽

Change Requests ◽

Increasing Trends

This paper has statically investigated the source code of open source software (OSS) projects to uncover the presence of vulnerabilities in the code. The conducted research emphasizes that the presence of vulnerabilities has adverse effects on the overall software quality. The authors found the increasing trends in the vulnerabilities as the lines of code (LOC) increases during the software evolution. This signifies the fact that the addition of new features or change requests into the OSS project may cause an increase in vulnerability. Further, the relation between software vulnerabilities and popularity is also examined. This research does not find the existence of any relationship among software vulnerabilities and popularity. This research will provide significant implications to the developers and project managers to better understand the present state of the software.

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Identifying Conserved Genomic Elements and Designing Universal Probe Sets To Enrich Them

10.1101/077172 ◽

2016 ◽

Cited By ~ 4

Author(s):

Brant C. Faircloth

Keyword(s):

Open Source ◽

Sequence Data ◽

Genomic Information ◽

Genetic Studies ◽

Software Code ◽

Genomic Regions ◽

Probe Set ◽

Conserved Genomic Regions ◽

Targeted Enrichment

AbstractTargeted enrichment of conserved genomic regions is a popular method for collecting large amounts of sequence data from non-model taxa for phylogenetic, phylogeographic, and population genetic studies. Yet, few open-source workflows are available to identify conserved genomic elements shared among divergent taxa and to design enrichment baits targeting these regions. These shortcomings limit the application of targeted enrichment methods to many organismal groups. Here, I describe a universal workflow for identifying conserved genomic regions in available genomic data and for designing targeted enrichment baits to collect data from these conserved regions. I demonstrate how this computational approach can be applied to diverse organismal groups by identifying sets of conserved loci and designing enrichment baits targeting thousands of these loci in the understudied arthropod groups Arachnida, Coleoptera, Diptera, Hemiptera, or Lepidoptera. I then use in silico analyses to demonstrate that these conserved loci reconstruct the accepted relationships among genome sequences from the focal arthropod orders, and we perform in vitro validation of the Arachnid probe set as part of a separate manuscript (Starrett et al. Submitted). All of the documentation, design steps, software code, and probe sets developed here are available under an open-source license for restriction-free testing and use by any research group, and although the examples in this manuscript focus on understudied and exceptionally diverse arthropod groups, the software workflow is applicable to all organismal groups having some form of pre-existing genomic information.

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Following the Code: Spillovers and Knowledge Transfer

Review of Network Economics ◽

10.1515/rne-2017-0056 ◽

2017 ◽

Vol 16 (3) ◽

pp. 243-267

Author(s):

Neil Gandal ◽

Peter Naftaliev ◽

Uriel Stettner

Keyword(s):

Knowledge Transfer ◽

Open Source ◽

Open Source Software ◽

Software Reuse ◽

Knowledge Spillovers ◽

Micro Level ◽

Software Code

Abstract Knowledge spillovers in Open Source Software (OSS) can occur via two channels: In the first channel, programmers take knowledge and experience gained from one OSS project they work on and employ it in another OSS project they work on. In the second channel, programmers reuse software code by taking code from an OSS project and employing it in another. We develop a methodology to measure software reuse in a large OSS network at the micro level and show that projects that reuse code from other projects have higher success. We also demonstrate knowledge spillovers from projects connected via common programmers.

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Digitizing ECG image: new fully automated method and open-source software code

10.1101/2021.07.13.21260461 ◽

2021 ◽

Author(s):

Julian Fortune ◽

Natalie Coppa ◽

Kazi T Haq ◽

Hetal Patel ◽

Larisa G Tereshchenko

Keyword(s):

Open Source ◽

Open Source Software ◽

Primary Source ◽

Software Tool ◽

Altman Analysis ◽

Limits Of Agreement ◽

Automated Method ◽

High Area ◽

Software Code ◽

Ecg Leads

Background: We aimed to develop and validate an automated, open-source code ECG-digitizing tool and assess agreements of ECG measurements across three types of median beats, comprised of digitally recorded, simultaneous and asynchronous ECG leads, and digitized asynchronous ECG leads. Methods: We used the data of clinical studies participants (n=230; mean age 30 ± 15 y; 25% female; 52% had the cardiovascular disease) with available both digitally recorded and printed on paper and then scanned ECGs, split into development (n=150) and validation (n=80) datasets. The agreement between ECG and VCG measurements on the digitally recorded time-coherent median beat, representative asynchronous digitized, and digitally recorded beats was assessed by Bland-Altman analysis. Results: Agreement between digitally recorded and digitized representative beat was high [area spatial ventricular gradient (SVG) elevation bias 2.5(95% limits of agreement [LOA] -7.9-13.0) degrees; precision 96.8%; inter-class correlation [ICC] 0.988; Lin concordance coefficient ρc 0.97(95% confidence interval [CI] 0.95-0.98)]. Agreement between digitally recorded asynchronous and time-coherent median beats was moderate for area-based VCG metrics (spatial QRS-T angle bias 1.4(95%LOA -33.2-30.3) degrees; precision 94.8%; ICC 0.95; Lin concordance coefficient ρc 0.90(95%CI 0.82-0.95)], but poor for peak-based VCG metrics of global electrical heterogeneity. Conclusions: We developed and validated an open-source software tool for paper-ECG digitization. Asynchronous ECG leads are the primary source of disagreement in measurements on digitally recorded and digitized ECGs.

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O PAPEL DOS DESENVOLVEDORES NOS CODE SMELLS EM PROJETOS OPEN SOURCE

Anais dos Seminários de Iniciação Científica ◽

10.13102/semic.v0i23.6558 ◽

2021 ◽

Author(s):

Bernardo Oliveira Rosa

Keyword(s):

Open Source ◽

Code Smells ◽

Software Code ◽

Para Determinar

Este trabalho visa contribuir com evidências experimentais para a discussão sobre CodeSmell (FOWLER, 1999) e a utilidade real de sua identificação e estudo para a indústriade software. Code smells, ou, numa tradução literal, “mal cheiros de código”, é umconceito utilizado na Programação Orientada a Objetos para determinar se um projetopode vir a ter problemas no sua evolução.

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DESIGN, IMPLEMENTATION AND VERIFICATION OF SOFTWARE CODE FOR RADIATION DOSE ASSESSMENT BASED ON SIMPLE GENERIC ENVIRONMENTAL MODEL

JURNAL TEKNOLOGI REAKTOR NUKLIR TRI DASA MEGA ◽

10.17146/tdm.2017.19.2.3536 ◽

2017 ◽

Vol 19 (2) ◽

pp. 103

Author(s):

I Putu Susila ◽

Arif Yuniarto

Keyword(s):

Radiation Dose ◽

Open Source ◽

International Atomic Energy Agency ◽

Atomic Energy ◽

Dose Assessment ◽

Energy Agency ◽

Safety Report ◽

Significant Difference ◽

Radiation Dose Assessment ◽

Software Code

Radiation dose assessment to determine the potential of radiological impacts of various installations within nuclear facility complex is necessary to ensure evironmental and public safety. A simple generic model-based method for calculating radiation doses caused by the release of radioactive substances into the environment has been published by the International Atomic Energy Agency (IAEA) as the Safety Report Series No. 19 (SRS-19). In order to assist the application of the assessment method and a basis for the development of more complex assessment methods, an open-source based software code has been designed and implemented. The software comes with maps and is very easy to be used because assessment scenarios can be done through diagrams. Software verification was performed by comparing its result to SRS-19 and CROM software calculation results. Dose estimated by SRS-19 are higher compared to the result of developed software. However, these are still acceptable since dose estimation in SRS-19 is based on conservative approach. On the other hand, compared to CROM software, the same results for three scenarios and a non-significant difference of 2.25% in another scenario were obtained. These results indicate the correctness of our implementation and implies that the developed software is ready for use in real scenario. In the future, the addition of various features and development of new model need to be done to improve the capability of software that has been developed.Keywords: Radiation dose assessment, software code, radioactive discharge, environment, IAEA SRS-19. PERANCANGAN, IMPLEMENTASI DAN VERIFIKASI PERANGKAT LUNAK UNTUK KAJIAN DOSIS RADIASI BERBASIS MODEL LINGKUNGAN GENERIK SEDERHANA. Kajian dosis radiasi untuk mengetahui potensi dampak radiologi akibat pengoperasian berbagai instalasi yang ada di dalam kawasan instalasi nuklir sangat diperlukan untuk menjamin keselamatan masyarakat dan lingkungan. Metode sederhana berbasis model lingkungan generik untuk menghitung dosis radiasi yang disebabkan oleh pelepasan zat radioaktif ke lingkungan telah diterbitkan oleh International Atomic Energy Agency (IAEA) sebagai Safety Report Series No. 19 (SRS-19). Untuk lebih memudahkan penerapan metode tersebut, maupun sebagai dasar kajian serta pengembangan metode yang lebih kompleks, maka dilakukan perancangan dan implementasi perangkat lunak terkait berbasis open-source. Perangkat lunak yang dibuat telah dilengkapi dengan peta serta sangat mudah digunakan karena skenario kajian dosis radiasi dapat dibuat melalui diagram. Verifikasi melalui komparasi dengan nilai hasil perhitungan di SRS-19 serta hasil perhitungan perangkat lunak CROM. Hasil komparasi dengan SRS-19 menunjukkan adanya perbedaan pada empat skenario yang diuji. Hal ini wajar karena pada SRS-19 perhitungan dilakukan dengan pendekatan konservatif sehingga nilai dosis yang dihasilkan lebih besar jika dibandingkan dengan perangkat lunak yang dikembangkan. Selanjutnya, pada komparasi dengan perangkat lunak CROM, keduanya menunjukkan hasil yang sama pada tiga skenario serta perbedaan yang tidak siginifikan yaitu sebesar 2,25% pada satu skenario. Hasil tersebut menunjukkan bahwa implementasi perangkat lunak telah berhasil dan perangkat lunak tersebut dapat digunakan untuk kajian yang nyata. Kedepannya, penambahan berbagai fitur serta pengembangan model kajian perlu dilakukan untuk meningkatkan kemampuan perangkat lunak yang telah dibuat. Kata kunci: Kajian dosis radiasi, perangkat lunak, lepasan zat radioaktif, lingkungan, IAEA SRS-19

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Analisa Pemanfaatan Dan Peran Software Open-source Bagi Mahasiswa Universitas Abdurrab

Jurnal Buana Informatika ◽

10.24002/jbi.v12i1.4145 ◽

2021 ◽

Vol 12 (1) ◽

pp. 49

Author(s):

Salamun Salamun ◽

Sukri Sukri

Keyword(s):

University Students ◽

Open Source ◽

Open Source Software ◽

The Internet ◽

Student Interest ◽

Software Application ◽

The Public ◽

Internet Users ◽

Software Code

Abstract. Analysis of Software Utilization and the Role of Open-source for Abdurrab University Students. Open-source software can be acquired by downloading it for free from the internet, where the software code is published to the public or internet users. Generally, people will fix the software weaknesses and modify its display or language. Then, the repaired software is uploaded and published back to the internet. At the same time, other people will also download this open-source software application and fix other flaws. The purpose of this study was to determine the benefits and roles of open-source software for Abdurrab University students. The results of this study indicate an increase in student interest in using open-source applications and the influence, utilization, and role of open-source software for Abdurrab University students. The conclusion in this study is that open-source software still plays an important role for students because it is very helpful in various aspects to support learning.Keywords: Internet, Software, University of Abdurrab, open-sourceAbstrak.Open-source software dapat dimiliki dengan cara mengunduh secara gratis dari internet, yang mana kode software dipublikasikan ke publik atau pengguna internet. Umumnya, orang akan memperbaiki kelemahan-kelemahan software tersebut dan memodifikasi tampilan atau bahasanya. Lalu, software yang diperbaiki tersebut diunggah dan dipublikasikan kembali ke internet. Pada saat yang sama, orang lain juga akan mengunduh aplikasi software open-source ini dan memperbaiki kelemahan-kelemahan lain. Tujuan dari penelitian ini adalah mengetahui manfaat dan peran open-source software bagi mahasiswa Universitas Abdurrab. Hasil penelitian ini memperlihatkan adanya peningkatan minat mahasiswa dalam menggunakan aplikasi open-source dan pengaruh, pemanfaatan, serta peran software open-source bagi mahasiswa Universitas Abdurrab. Kesimpulan pada penelitian ini ialah open-source software masih berperan penting bagi mahasiswa karena sangat membantu dalam berbagai aspek untuk mendukung pembelajaran.Kata Kunci: Internet, Software, Universitas Abdurrab, open-source

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EviAtlas: a tool for visualising evidence synthesis databases

10.31219/osf.io/jwr87 ◽

2019 ◽

Author(s):

Neal Robert Haddaway ◽

Andrew Feierman ◽

Matthew Grainger ◽

Charles T. Gray ◽

Ezgi Tanriver Ayder ◽

...

Keyword(s):

Open Source ◽

Open Source Software ◽

Evidence Synthesis ◽

Synthesis Method ◽

Evidence Base ◽

Geographical Information ◽

Spatially Explicit ◽

Systematic Map ◽

Systematic Mapping ◽

Software Code

Systematic mapping assesses the nature of an evidence base, answering how much evidence exists on a particular topic. Perhaps the most useful outputs of a systematic map are an interactive database of studies and their meta-data, along with visualisations of this database. Despite the rapid increase in systematic mapping as an evidence synthesis method, there is currently a lack of Open Source software for producing interactive visualisations of systematic map databases. In April 2018, as attendees at and coordinators of the first ever Evidence Synthesis Hackathon in Stockholm, we decided to address this issue by developing an R-based tool called EviAtlas, an Open Access (i.e. free to use) and Open Source (i.e. software code is freely accessible and reproducible) tool for producing interactive, attractive tables and figures that summarise the evidence base. Here, we present our tool which includes the ability to generate vital visualisations for systematic maps and reviews as follows: a complete data table; a spatially explicit geographical information system (Evidence Atlas); Heat Maps that cross-tabulate two or more variables and display the number of studies belonging to multiple categories; and standard descriptive plots showing the nature of the evidence base, for example the number of studies published per year or number of studies per country. We believe that EviAtlas will provide a stimulus for the development of other exciting tools to facilitate evidence synthesis.

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