We are now over four decades into digitally managing the names of Earth's species. As the number of federating (i.e., software that brings together previously disparate projects under a common infrastructure, for example TaxonWorks) and aggregating (e.g., International Plant Name Index, Catalog of Life (CoL)) efforts increase, there remains an unmet need for both the migration forward of old data, and for the production of new, precise and comprehensive nomenclatural catalogs. Given this context, we provide an overview of how TaxonWorks seeks to contribute to this effort, and where it might evolve in the future. In TaxonWorks, when we talk about governed names and relationships, we mean it in the sense of existing international codes of nomenclature (e.g., the International Code of Zoological Nomenclature (ICZN)). More technically, nomenclature is defined as a set of objective assertions that describe the relationships between the names given to biological taxa and the rules that determine how those names are governed. It is critical to note that this is not the same thing as the relationship between a name and a biological entity, but rather nomenclature in TaxonWorks represents the details of the (governed) relationships between names. Rather than thinking of nomenclature as changing (a verb commonly used to express frustration with biological nomenclature), it is useful to think of nomenclature as a set of data points, which grows over time. For example, when synonymy happens, we do not erase the past, but rather record a new context for the name(s) in question. The biological concept changes, but the nomenclature (names) simply keeps adding up. Behind the scenes, nomenclature in TaxonWorks is represented by a set of nodes and edges, i.e., a mathematical graph, or network (e.g., Fig. 1). Most names (i.e., nodes in the network) are what TaxonWorks calls "protonyms," monomial epithets that are used to construct, for example, bionomial names (not to be confused with "protonym" sensu the ICZN). Protonyms are linked to other protonyms via relationships defined in NOMEN, an ontology that encodes governed rules of nomenclature. Within the system, all data, nodes and edges, can be cited, i.e., linked to a source and therefore anchored in time and tied to authorship, and annotated with a variety of annotation types (e.g., notes, confidence levels, tags). The actual building of the graphs is greatly simplified by multiple user-interfaces that allow scientists to review (e.g. Fig. 2), create, filter, and add to (again, not "change") the nomenclatural history. As in any complex knowledge-representation model, there are outlying scenarios, or edge cases that emerge, making certain human tasks more complex than others. TaxonWorks is no exception, it has limitations in terms of what and how some things can be represented. While many complex representations are hidden by simplified user-interfaces, some, for example, the handling of the ICZN's Family-group name, batch-loading of invalid relationships, and comparative syncing against external resources need more work to simplify the processes presently required to meet catalogers' needs. The depth at which TaxonWorks can capture nomenclature is only really valuable if it can be used by others. This is facilitated by the application programming interface (API) serving its data (https://api.taxonworks.org), serving text files, and by exports to standards like the emerging Catalog of Life Data Package. With reference to real-world problems, we illustrate different ways in which the API can be used, for example, as integrated into spreadsheets, through the use of command line scripts, and serve in the generation of public-facing websites. Behind all this effort are an increasing number of people recording help videos, developing documentation, and troubleshooting software and technical issues. Major contributions have come from developers at many skill levels, from high school to senior software engineers, illustrating that TaxonWorks leads in enabling both technical and domain-based contributions. The health and growth of this community is a key factor in TaxonWork's potential long-term impact in the effort to unify the names of Earth's species.
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On the scalability of Linux kernel maintainers' work
Open source software ecosystems evolve ways to balance the workload among groups of participants ranging from core groups to peripheral groups. As ecosystems grow, it is not clear whether the mechanisms that previously made them work will continue to be relevant or whether new mechanisms will need to evolve. The impact of failure for critical ecosystems such as Linux is enormous, yet the understanding of why they function and are effective is limited. We, therefore, aim to understand how the Linux kernel sustains its growth, how to characterize the workload of maintainers, and whether or not the existing mechanisms are scalable. We quantify maintainers’ work through the files that are maintained, and the change activity and the numbers of contributors in those files. We find systematic differences among modules; these differences are stable over time, which suggests that certain architectural features, commercial interests, or module-specific practices lead to distinct sustainable equilibria. We find that most of the modules have not grown appreciably over the last decade; most growth has been absorbed by a few modules. We also find that the effort per maintainer does not increase, even though the community has hypothesized that required effort might increase. However, the distribution of work among maintainers is highly unbalanced, suggesting that a few maintainers may experience increasing workload. We find that the practice of assigning multiple maintainers to a file yields only a power of 1/2 increase in productivity. We expect that our proposed framework to quantify maintainer practices will help clarify the factors that allow rapidly growing ecosystems to be sustainable.
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- Award ID(s):
- 1633437
- NSF-PAR ID:
- 10063576
- Date Published:
- Journal Name:
- ESEC/FSE 2018
- Page Range / eLocation ID:
- 27 to 37
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Complex structures, like the vertebrate skull, are composed of numerous elements or traits that must develop and evolve in a coordinated manner to achieve multiple functions. The strength of association among phenotypic traits (i.e., integration), and their organization into highly-correlated, semi-independent subunits termed modules, is a result of the pleiotropic and genetic correlations that generate traits. As such, patterns of integration and modularity are thought to be key factors constraining or facilitating the evolution of phenotypic disparity by influencing the patterns of variation upon which selection can act. It is often hypothesized that selection can reshape patterns of integration, parceling single structures into multiple modules or merging ancestrally semi-independent traits into a strongly correlated unit. However, evolutionary shifts in patterns of trait integration are seldom assessed in a unified quantitative framework. Here, we quantify patterns of evolutionary integration among regions of the archosaur skull to investigate whether patterns of cranial integration are conserved or variable across this diverse group. Using high-dimensional geometric morphometric data from 3D surface scans and computed tomography scans of modern birds (n = 352), fossil non-avian dinosaurs (n = 27), and modern and fossil mesoeucrocodylians (n = 38), we demonstrate that some aspects of cranial integration are conserved across these taxonomic groups, despite their major differences in cranial form, function, and development. All three groups are highly modular and consistently exhibit high integration within the occipital region. However, there are also substantial divergences in correlation patterns. Birds uniquely exhibit high correlation between the pterygoid and quadrate, components of the cranial kinesis apparatus, whereas the non-avian dinosaur quadrate is more closely associated with the jugal and quadratojugal. Mesoeucrocodylians exhibit a slightly more integrated facial skeleton overall than the other grades. Overall, patterns of trait integration are shown to be stable among archosaurs, which is surprising given the cranial diversity exhibited by the clade. At the same time, evolutionary innovations such as cranial kinesis that reorganize the structure and function of complex traits can result in modifications of trait correlations and modularity.
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Background: Open source requires participation of volunteer and commercial developers (users) in order to deliver functional high-quality components. Developers both contribute effort in the form of patches and demand effort from the component maintainers to resolve issues reported against it. Open source components depend on each other directly and transitively, and evidence suggests that more effort is required for reporting and resolving the issues reported further upstream in this supply chain. Aim: Identify and characterize patterns of effort contribution and demand throughout the open source supply chain and investigate if and how these patterns vary with developer activity; identify different groups of developers; and predict developers' company affiliation based on their participation patterns. Method: 1,376,946 issues and pull-requests created for 4433 NPM packages with over 10,000 monthly downloads and full (public) commit activity data of the 272,142 issue creators is obtained and analyzed and dependencies on NPM packages are identified. Fuzzy c-means clustering algorithm is used to find the groups among the users based on their effort contribution and demand patterns, and Random Forest is used as the predictive modeling technique to identify their company affiliations. Result: Users contribute and demand effort primarily from packages that they depend on directly with only a tiny fraction of contributions and demand going to transitive dependencies. A significant portion of demand goes into packages outside the users' respective supply chains (constructed based on publicly visible version control data). Three and two different groups of users are observed based on the effort demand and effort contribution patterns respectively. The Random Forest model used for identifying the company affiliation of the users gives a AUC-ROC value of 0.68, and variables representing aggregate participation patterns proved to be the important predictors. Conclusion: Our results give new insights into effort demand and supply at different parts of the supply chain of the NPM ecosystem and its users and suggests the need to increase visibility furthermore » « less
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Background: Open source requires participation of volunteer and commercial developers (users) in order to deliver functional high-quality components. Developers both contribute effort in the form of patches and demand effort from the component maintainers to resolve issues reported against it. Open source components depend on each other directly and transitively, and evidence suggests that more effort is required for reporting and resolving the issues reported further upstream in this supply chain. Aim: Identify and characterize patterns of effort contribution and demand throughout the open source supply chain and investigate if and how these patterns vary with developer activity; identify different groups of developers; and predict developers' company affiliation based on their participation patterns. Method: 1,376,946 issues and pull-requests created for 4433 NPM packages with over 10,000 monthly downloads and full (public) commit activity data of the 272,142 issue creators is obtained and analyzed and dependencies on NPM packages are identified. Fuzzy c-means clustering algorithm is used to find the groups among the users based on their effort contribution and demand patterns, and Random Forest is used as the predictive modeling technique to identify their company affiliations. Result: Users contribute and demand effort primarily from packages that they depend on directly with only a tiny fraction of contributions and demand going to transitive dependencies. A significant portion of demand goes into packages outside the users' respective supply chains (constructed based on publicly visible version control data). Three and two different groups of users are observed based on the effort demand and effort contribution patterns respectively. The Random Forest model used for identifying the company affiliation of the users gives a AUC-ROC value of 0.68, and variables representing aggregate participation patterns proved to be the important predictors. Conclusion: Our results give new insights into effort demand and supply at different parts of the supply chain of the NPM ecosystem and its users and suggests the need to increase visibility further upstream.more » « less
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We investigate the privacy practices of labor organizers in the computing technology industry and explore the changes in these practices as a response to remote work. Our study is situated at the intersection of two pivotal shifts in workplace dynamics: (a) the increase in online workplace communications due to remote work, and (b) the resurgence of the labor movement and an increase in collective action in workplaces— especially in the tech industry, where this phenomenon has been dubbed the tech worker movement. The shift of work-related communications to online digital platforms in response to an increase in remote work is creating new opportunities for and risks to the privacy of workers. These risks are especially significant for organizers of collective action, with several well-publicized instances of retaliation against labor organizers by companies. Through a series of qualitative interviews with 29 tech workers involved in collective action, we investigate how labor organizers assess and mitigate risks to privacy while engaging in these actions. Among the most common risks that organizers experienced are retaliation from their employer, lateral worker conflict, emotional burnout, and the possibility of information about the collective effort leaking to management. Depending on the nature and source of the risk, organizers use a blend of digital security practices and community-based mechanisms. We find that digital security practices are more relevant when the threat comes from management, while community management and moderation are central to protecting organizers from lateral worker conflict. Since labor organizing is a collective rather than individual project, individual privacy and collective privacy are intertwined, sometimes in conflict and often mutually constitutive. Notions of privacy that solely center individuals are often incompatible with the needs of organizers, who noted that safety in numbers could only be achieved when workers presented a united front to management. Based on our interviews, we identify key topics for future research, such as the growing prevalence of surveillance software and the needs of international and gig worker organizers. We conclude with design recommendations that can help create safer, more secure and more private tools to better address the risks that organizers face.more » « less
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.1145/3106237.3106287
