scholarly journals AnFiSA: An open-source computational platform for the analysis of sequencing data for rare genetic disease

2021 ◽  
Author(s):  
Michael Bouzinier ◽  
Dmitry Etin ◽  
Sergey I. Trifonov ◽  
Viktoria Evdokimova ◽  
Vladimir Ulitin ◽  
...  
Keyword(s):  
Open Source ◽  
Genomic Analysis ◽  
Database Management System ◽  
Genetic Diagnostics ◽  
Sequencing Data ◽  
Software Developers ◽  
Software Packages ◽  
Architectural Principles ◽  
Clinical Rules ◽  
Computational Platform

Despite genomic sequencing rapidly transforming from being a bench-side tool to a routine procedure in a hospital, there is a noticeable lack of genomic analysis software that supports both clinical and research workflows as well as crowdsourcing. Furthermore, most existing software packages are not forward-compatible in regards to supporting ever-changing diagnostic rules adopted by the genetics community. Regular updates of genomics databases make reproducible and traceable automated genetic diagnostics to be a challenge. Lastly, most of the software tools score low on explainability amongst clinicians. We have created a fully open-source variant curation tool, AnFiSA, with the intention to invite and accept contributions from clinicians, researchers and professional software developers. The design of AnFiSA addresses the aforementioned issues with current genomics software via the following architectural principles: using a multidimensional database management system (DBMS) for genomic data to address reproducibility, curated decision trees adaptable to changing clinical rules, and a crowdsourcing-friendly interface to address difficult-to-diagnose cases. We discuss how we have chosen our technology stack and describe the design and implementation of the software. Finally, we show in detail how selected workflows can be implemented using the current version of AnFiSA by a medical geneticist.

Social Status in an Open-Source Community

2005 ◽  
Vol 70 (5) ◽  
pp. 823-842 ◽  
Author(s):  
Daniel Stewart
Keyword(s):  
Open Source ◽  
Online Community ◽  
Large Scale ◽  
Social Cues ◽  
Natural Setting ◽  
Laboratory Setting ◽  
Community Members ◽  
Software Developers ◽  
Status Mobility ◽  
The Status

Despite a fair amount of conjecture regarding the circumstances that lead to the generation of status orders, most of the previous literature in this area typically has studied the effects of social cues within a laboratory setting. This article analyzes the evolution of the status hierarchy within a large-scale, natural setting. The results of empirical analyses assessing a large online community of software developers show that in the process of status attainment, community members tend to evaluate a focal actor's reputation according to publicly available social references. Ironically, these same social references also work to constrain an actor's status mobility.

Selection of Plagiarism Detection Software and Its Integration Into Moodle for Universities

2019 ◽  
pp. 200-215 ◽  
Author(s):  
Mehmet Bilge Kağan Önaçan ◽  
Mesut Uluağ ◽  
Tolga Önel ◽  
Tunç Durmuş Medeni
Keyword(s):  
Higher Education ◽  
Open Source ◽  
Selection Criteria ◽  
Nominal Group Technique ◽  
Education Institution ◽  
Nominal Group ◽  
Plagiarism Detection ◽  
Software Packages ◽  
Detection Software ◽  
Selection Of

Plagiarism detection software packages have an important role in detection of plagiarism in exams, assignments, projects, and scientific researches. The main goal of this chapter is the selection of plagiarism detection software (PDS) and its integration into Moodle, an open source learning management system (LMS), for the use of a higher education institution. For this reason, first, the selection criteria are determined by nominal group technique (NGT) and then the most appropriate PDS is selected. At the end of the study, Crot, an open source PDS, is determined and integrated into Moodle. The suggested selection criteria would be useful for other higher education institutions in Turkey and other countries that rely on open software.

Selection of Plagiarism Detection Software and Its Integration Into Moodle for Universities

2018 ◽  
pp. 239-258
Author(s):  
Mehmet Bilge Kağan Önaçan ◽  
Mesut Uluağ ◽  
Tolga Önel ◽  
Tunç Durmuş Medeni
Keyword(s):  
Higher Education ◽  
Open Source ◽  
Selection Criteria ◽  
Nominal Group Technique ◽  
Education Institution ◽  
Nominal Group ◽  
Plagiarism Detection ◽  
Software Packages ◽  
Detection Software ◽  
Selection Of

Plagiarism detection software packages have an important role in detection of plagiarism in exams, assignments, projects, and scientific researches. The main goal of this chapter is the selection of plagiarism detection software (PDS) and its integration into Moodle, an open source learning management system (LMS), for the use of a higher education institution. For this reason, first, the selection criteria are determined by nominal group technique (NGT) and then the most appropriate PDS is selected. At the end of the study, Crot, an open source PDS, is determined and integrated into Moodle. The suggested selection criteria would be useful for other higher education institutions in Turkey and other countries that rely on open software.

Development of Assessment Criteria for Various Open Sources GIS Software Packages

2021 ◽  
pp. 398-412
Author(s):  
Shahriar Shams
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Assessment Criteria ◽  
Significant Development ◽  
Analysis And Design ◽  
Advantages And Disadvantages ◽  
Software Packages ◽  
Open Source Gis ◽  
Gis Software

There has been a significant development in the area of free and open source geospatial software. Research has flourished over the decades from vendor-dependent software to open source software where researchers are paying increasing attention to maximize the value of their data. It is often a difficult task to choose particular open source GIS (OGIS) software among a number of emerging OGIS software. It is important to characterise the projects according to some unified criteria. Each software has certain advantages and disadvantages and it is always time consuming to identify exactly which software to select for a specific purpose. This chapter focuses on the assessment criteria enabling developers, researchers, and GIS users to select suitable OGIS software to meet their requirements for analysis and design of geospatial application in multidisciplinary fields. This chapter highlights the importance of assessment criteria, followed by an explanation of each criteria and their significance with examples from existing OGIS software.

scholarly journals Genomic Landscape of Early-stage Colorectal Neoplasia Developing From the Ulcerative Colitis Mucosa in the Japanese Population

2020 ◽  
Author(s):  
Kenta Matsumoto ◽  
Yuji Urabe ◽  
Shiro Oka ◽  
Katsuaki Inagaki ◽  
Hidenori Tanaka ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Early Stage ◽  
Colorectal Neoplasia ◽  
Genomic Analysis ◽  
The Cancer Genome Atlas ◽  
Sequencing Data ◽  
Kras Mutations ◽  
Tp53 Mutations ◽  
Amino Terminal ◽  
Cancer Genome Atlas

Abstract Backgrounds Colorectal neoplasias (CRN)s developing from the ulcerative colitis (UC) mucosa include both colitic and sporadic neoplasias. Although several genomic analyses of advanced colitis-associated cancer are available, such studies do not distinguish between colitic and sporadic cases, and the early-stage genomic alterations involved in the onset of colitic cancer remain unclear. To address this, we performed a genomic analysis of early-stage CRN developing from the UC mucosa (CRNUC). Methods We extracted DNA from 36 early-stage CRNUCs (T1 cancer, 10; dysplasia, 26) from 32 UC patients and performed targeted sequencing of 43 genes commonly associated with colitis-associated cancer and compared the results with sequencing data from the Japanese invasive colitis-associated cancer. Results The most frequently mutated gene in the CRNUC cohort was APC (mutated in 47.2% of the cases), followed by TP53 (44.4%), KRAS (27.8%), and PRKDC (27.8%). None of the TP53 mutations occurred at any of the hotspot codons. Although the TP53 mutations in The Cancer Genome Atlas of Colorectal Cancer were dispersed throughout the gene, those detected here in CRNUC cases were concentrated in the amino terminal part of the DNA-binding domain. Interestingly, the mutations in KRAS and TP53 were mutually exclusive in CRNUC, and CRNUCs with KRAS mutations had histologically serrated lesions in the gland duct. Mayo endoscopic subscore was higher in TP53-mutated CRNUCs and lower in KRAS-mutated CRNUCs. Conclusions Our findings suggest that early-stage CRNUC can be classified into 2 groups: those developing through the carcinogenic pathway via TP53 mutations and those developing through the carcinogenic pathway via KRAS mutations.

Evidence-Based Assurance to Support Process Quality in the F/OSS Community

2007 ◽  
pp. 120-146
Author(s):  
Anas Tawileh ◽  
Omer F. Rana ◽  
Wendy Ivins ◽  
Stephen McIntosh
Keyword(s):  
Quality Assurance ◽  
Open Source ◽  
Open Source Software ◽  
Growth Rates ◽  
Development Process ◽  
End Users ◽  
Evidence Based ◽  
Software Developers ◽  
Substantial Growth ◽  
Development Processes

This chapter investigates the quality issues of the free and open source software (F/OSS) development processes. It argues that software developed within the F/OSS paradigm has witnessed substantial growth rates within the software developers’ community. However, end users from outside the community are still sceptical about adopting F/OSS because of the perceived lack of quality assurance mechanisms within the F/OSS development process. The authors aim to promote higher adoption of F/OSS artefacts outside the developers’ community by exploring possibilities to provide appropriate evidence based assurances that F/OSS artefacts will meet the quality levels expected by users.

scholarly journals Evaluation and selection of open-source EMR software packages based on integrated AHP and TOPSIS

2015 ◽  
Vol 53 ◽  
pp. 390-404 ◽  
Author(s):  
A.A. Zaidan ◽  
B.B. Zaidan ◽  
Ahmed Al-Haiqi ◽  
M.L.M. Kiah ◽  
Muzammil Hussain ◽  
...  
Keyword(s):  
Open Source ◽  
Software Packages ◽  
Selection Of
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