scholarly journals The Open Source Seed Licence: A novel approach to safeguarding access to plant germplasm

PLoS Biology ◽  
2018 ◽  
Vol 16 (10) ◽  
pp. e3000023 ◽  
Author(s):  
Johannes Kotschi ◽  
Bernd Horneburg
Keyword(s):  
Open Source ◽  
Plant Germplasm ◽  
Novel Approach

scholarly journals Design of a Didactical Activity for the Analysis of Uncertainties in Thermography through the Use of Robust Statistics as Teacher-Oriented Approach

2021 ◽  
Vol 13 (3) ◽  
pp. 402
Author(s):  
Pablo Rodríguez-Gonzálvez ◽  
Manuel Rodríguez-Martín
Keyword(s):  
Open Source ◽  
Robust Statistics ◽  
Three Dimensional ◽  
Learning Material ◽  
Novel Approach ◽  
Learning Programs ◽  
Institutional Learning ◽  
Thermographic Image ◽  
Visualization Techniques ◽  
Free Open Source

The thermography as a methodology to quantitative data acquisition is not usually addressed in the degrees of university programs. The present manuscript proposes a novel approach for the acquisition of advanced competences in engineering courses associated with the use of thermographic images via free/open-source software solutions. This strategy is established from a research based on the statistical and three-dimensional visualization techniques over thermographic imagery to improve the interpretation and comprehension of the different sources of error affecting the measurements and, thereby, the conclusions and analysis arising from them. The novelty is focused on the detection of non-normalities in thermographic images, which is illustrates in the experimental section. Additionally, the specific workflow for the generation of learning material related with this aim is raised for asynchronous and e-learning programs. These virtual materials can be easily deployed in an institutional learning management system, allowing the students to work with the models by means of free/open-source solutions easily. Subsequently, the present approach will give new tools to improve the application of professional techniques, will improve the students’ critical sense to know how to interpret the uncertainties in thermography using a single thermographic image, therefore they will be better prepared to face future challenges with more critical thinking.

Poster 158: Open-Source Rehabilitation Reference Mobile Web Application: A Novel Approach to Creating Collaborative Resources for Physiatrists in Training

PM&R ◽  
2017 ◽  
Vol 9 ◽  
pp. S182-S183
Author(s):  
George E. Marzloff ◽  
Tariq Z. Rajnarine ◽  
Andrew Abdou ◽  
Anokhi Mehta ◽  
Miguel X. Escalon
Keyword(s):  
Open Source ◽  
Web Application ◽  
Mobile Web ◽  
Novel Approach

scholarly journals Disambiguate: An open-source application for disambiguating two species in next generation sequencing data from grafted samples

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 2741 ◽  
Author(s):  
Miika J. Ahdesmäki ◽  
Simon R. Gray ◽  
Justin H. Johnson ◽  
Zhongwu Lai
Keyword(s):  
Open Source ◽  
Variant Calling ◽  
High Sensitivity ◽  
Next Generation Sequencing Data ◽  
Sequencing Data ◽  
Novel Approach ◽  
Gene Expression Quantification ◽  
Closed Source ◽  
Generation Sequencing ◽  
Bioinformatics Community

Grafting of cell lines and primary tumours is a crucial step in the drug development process between cell line studies and clinical trials. Disambiguate is a program for computationally separating the sequencing reads of two species derived from grafted samples. Disambiguate operates on alignments to the two species and separates the components at very high sensitivity and specificity as illustrated in artificially mixed human-mouse samples. This allows for maximum recovery of data from target tumours for more accurate variant calling and gene expression quantification. Given that no general use open source algorithm accessible to the bioinformatics community exists for the purposes of separating the two species data, the proposed Disambiguate tool presents a novel approach and improvement to performing sequence analysis of grafted samples. Both Python and C++ implementations are available and they are integrated into several open and closed source pipelines. Disambiguate is open source and is freely available at https://github.com/AstraZeneca-NGS/disambiguate.

A Topic Modeling Based Approach for Enhancing Corpus Querying

2019 ◽  
Vol 10 (3) ◽  
pp. 38-50
Author(s):  
Nouh Talal Alhindawi ◽  
Belal Abu Ata ◽  
Lana Mahmoud Obeidat ◽  
Mohammad Subhi Al-Batah ◽  
Muad Abu-Ata
Keyword(s):  
Information Retrieval ◽  
Open Source ◽  
Topic Modeling ◽  
Retrieval Process ◽  
New Novel ◽  
Novel Approach ◽  
Open Source Systems

In information retrieval, the accuracy of the retrieval process is mainly dependent on query terms selection; therefore, the user must choose the needed terms carefully and selectively. Traditionally, the process of selecting query terms is done manually. However, in the last two decades, a lot of research has been directed towards automating the process of choosing and enhancing query terms. In this article, a new novel approach is presented, which relies on topic modeling in query building and expansion. Two open source systems were selected to perform the experiments, results show that adding the topic's term to the user's query clearly improves its quality and thus, improves the ranking results.

An Approach to Detect Similar Script Functions in Web Applications Based on Calling Information

2012 ◽  
Vol 263-266 ◽  
pp. 1593-1599 ◽  
Author(s):  
Jung Il Kim ◽  
Eun Joo Lee
Keyword(s):  
Open Source ◽  
System Performance ◽  
Web Applications ◽  
Structural Similarity ◽  
The Other ◽  
Novel Approach ◽  
System Maintenance ◽  
Key Issues ◽  
Function Code ◽  
Maintenance Problem

Cloned code might exacerbate a system maintenance problem, so it is important to remove duplicate code to improve system performance. In web development, script code can often be duplicated as a unit of a script function. Previous research for detecting similar script functions forecasted candidates of similar script functions based on the name of the function and classified the detected candidates into four similarity levels by comparing factors contained within the script functions. There are two key issues that need to be considered to detect similar script functions when using that method. One was that a pair of similar script functions needs to have the same name to be detected. The other was that some modifications particularly such as adding or removing calling statements were not identified after detecting. Adding or removing calling statements might prevent identification for duplicate script function. In this paper, we propose a novel approach to detect similar script functions that can determine the similarity of a script function by evaluating the structural similarity of function code and the calling structure. The evaluation for detecting the structural similarity of code and the calling structure is performed based on a similarity metric, FSIM, which we have defined. We showed the usefulness of FSIM by applying it to three open source projects.

scholarly journals Exploring the Relation Between Co-changes and Architectural Smells

2020 ◽  
Vol 2 (1) ◽  
Author(s):  
Darius Sas ◽  
Paris Avgeriou ◽  
Ronald Kruizinga ◽  
Ruben Scheedler
Keyword(s):  
Open Source ◽  
State Of The Art ◽  
Statistical Tests ◽  
Trade Offs ◽  
Novel Approach ◽  
Multiple Case ◽  
Research Questions ◽  
Low Levels ◽  
The Times

AbstractThe interplay between Maintainability and Reliability can be particularly complex and different kinds of trade-offs may arise when developers try to optimise for either one of these two qualities. To further understand how Maintainability and Reliability influence each other, we perform an empirical study using architectural smells and source code file co-changes as proxies for these two qualities, respectively. The study is designed using an exploratory multiple-case case study following well-know guidelines and using fourteen open source Java projects. Three different research questions are identified and investigated through statistical analysis. Co-changes are detected by using both a state-of-the-art algorithm and a novel approach. The three architectural smells selected are among the most important from the literature and are detected using open source tools. The results show that 50% of co-changes eventually end up taking part in an architectural smell. Moreover, statistical tests indicate that in 50% of the projects, files and packages taking part in smells are more likely to co-change than non-smelly files. Finally, co-changes were also found to appear before smells 90% of the times a smell and a co-change appear in the same file pair. Our findings show that Reliability is indirectly affected by low levels of Maintainability even at the architectural level. This is because low-quality components require more frequent changes by the developers, increasing chances to eventually introduce faults.

scholarly journals Citizen-Centered, Auditable, and Privacy-Preserving Population Genomics

2019 ◽  
Author(s):  
Dennis Grishin ◽  
Jean Louis Raisaro ◽  
Juan Ramón Troncoso-Pastoriza ◽  
Kamal Obbad ◽  
Kevin Quinn ◽  
...  
Keyword(s):  
Open Source ◽  
Population Genomics ◽  
Homomorphic Encryption ◽  
Genomic Data ◽  
Data Access ◽  
Privacy Preserving ◽  
Genomic Databases ◽  
Privacy Concerns ◽  
Novel Approach ◽  
Security Guarantees

AbstractThe growing number of health-data breaches, the use of genomic databases for law enforcement purposes and the lack of transparency of personal-genomics companies are raising unprecedented privacy concerns. To enable a secure exploration of genomic datasets with controlled and transparent data access, we propose a novel approach that combines cryptographic privacy-preserving technologies, such as homomorphic encryption and secure multi-party computation, with the auditability of blockchains. This approach provides strong security guarantees against realistic threat models by empowering individual citizens to decide who can query and access their genomic data and by ensuring end-to-end data confidentiality. Our open-source implementation supports queries on the encrypted genomic data of hundreds of thousands of individuals, with minimal overhead. Our work opens a path towards multi-functional, privacy-preserving genomic-data analysis.One Sentence SummaryA citizen-centered open-source response to the privacy concerns that hinder population genomics, based on modern cryptography.

scholarly journals Supporting Unit Test Generation via Automated Isolation

2017 ◽  
Vol 61 (2) ◽  
pp. 116 ◽  
Author(s):  
Dávid Honfi ◽  
Zoltán Micskei
Keyword(s):  
Open Source ◽  
Test Generation ◽  
Symbolic Execution ◽  
Source Code ◽  
Unit Test ◽  
Prototype Implementation ◽  
Code Coverage ◽  
Novel Approach ◽  
Dynamic Symbolic Execution

Testing is a significantly time-consuming, yet commonly employed activity to improve the quality of software. Thus, techniques like dynamic symbolic execution were proposed for generating tests only from source code. However, current approaches usually could not create thorough tests for software units with dependencies (e.g. calls to file system or external services). In this paper, we present a novel approach that synthesizes an isolation sandbox, which interacts with the test generator to increase the covered behaviour in the unit under test. The approach automatically transforms the code of the unit under test, and lets the test generator choose values for parameters in the calls to dependencies. The paper presents a prototype implementation that collaborates with the IntelliTest test generator. The automated isolation is evaluated on source code from open-source projects. The results show that the approach can significantly increase the code coverage achieved by the generated tests.

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