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- Andam, Berima, 1986, et al.
(author)
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Florida: Feature LOcatIon DAshboard for extracting and visualizing feature traces
- 2017
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In: Proceedings of the Eleventh International Workshop on Variability Modelling of Software-intensive Systems, VaMoS 2017. - New York, NY, USA : ACM. ; Part F126227, s. 100-107
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Conference paper (peer-reviewed)abstract
- © 2017 Copyright held by the owner/author(s). Features are high-level, domain-specific abstractions over implementation artifacts. Developers use them to communicate and reason about a system, in order to maintain and evolve it. These activities, however, require knowing the locations of features - a common challenge when a system has many developers, many (cloned) variants, or a long lifespan. We believe that embedding feature-location information into software artifacts via annotations eases typical feature-related engineering tasks, such as modifying and removing features, or merging cloned features into a product line. However, regardless of where such annotations stem from - whether embedded by developers when writing code, or retroactively recovered using a feature-location technique - tool support is needed for developers to exploit such annotations. In this tool demonstration, we present a lightweight tool that extracts annotations from software artifacts, aggregates and processes them, and visualizes feature-related information for developers. Views, such as which files implement a specific feature, are presented on different levels of abstraction. Feature metrics, such as feature size, feature scattering, feature tangling, and numbers of feature authors, are also presented. Our tool also incorporates an information-retrieval-based feature-location technique to retroactively recover feature locations.
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| 29. |
- Ayllón, Daniel, et al.
(author)
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Keeping modelling notebooks with TRACE : Good for you and good for environmental research and management support
- 2021
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In: Environmental Modelling & Software. - : Elsevier BV. - 1364-8152 .- 1873-6726. ; 136
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Journal article (peer-reviewed)abstract
- The acceptance and usefulness of simulation models are often limited by the efficiency, transparency, reproducibility, and reliability of the modelling process. We address these issues by suggesting that modellers (1) “trace” the iterative modelling process by keeping a modelling notebook corresponding to the laboratory notebooks used by empirical researchers, (2) use a standardized notebook structure and terminology based on the existing TRACE documentation framework, and (3) use their notebooks to compile TRACE documents that supplement publications and reports. These practices have benefits for model developers, users, and stakeholders: improved and efficient model design, analysis, testing, and application; increased model acceptance and reuse; and replicability and reproducibility of the model and the simulation experiments. Using TRACE terminology and structure in modelling notebooks facilitates production of TRACE documents. We explain the rationale of TRACE, provide example TRACE documents, and suggest strategies for keeping “TRACE Modelling Notebooks.”
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| 30. |
- Ballantyne, Kaye N., et al.
(author)
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Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats
- 2014
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In: Human Mutation. - : John Wiley & Sons. - 1059-7794 .- 1098-1004. ; 35:8, s. 1021-1032
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Journal article (peer-reviewed)abstract
- Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, greater than99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836-0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father-son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RMY-STRs in identifying and separating unrelated and related males and provides a reference database.
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