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Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient
2013
BMC Bioinformatics
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Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great "Tree of Life" (ToL). ...
While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. ...
Such a system will not replace the time-consuming generation of robust phylogenies by experts, but aims to make those hard-won results conveniently accessible to everyone else. ...
doi:10.1186/1471-2105-14-158
pmid:23668630
pmcid:PMC3669619
fatcat:5gj4e7u4vjbkrcbrappwoqq3aq
The Shape of Trees – Limits of Current Diversification Models
[article]
2021
bioRxiv
pre-print
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Patterns of adequacy are described across trees and models and causes for inadequacy – particularly if all models are inadequate – are explored. ...
Using a large set of empirical phylogenies, and a new approach to test models using aspects of tree shape, we test how a set of staple models performs with regards to adequacy. ...
. & Jordan, G. (2013) Phylotastic! Making tree-of-life knowledge accessible, 407 reusable and convenient. ...
doi:10.1101/2021.01.26.428344
fatcat:dif5ldr6f5gsfbb7mlcpoeni6u
BioHackathon 2015: Semantics of data for life sciences and reproducible research
2020
F1000Research
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the reusability of biological data. ...
We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences ...
) and the Database Center for Life Science (DBCLS). ...
doi:10.12688/f1000research.18236.1
pmid:32308977
pmcid:PMC7141167
fatcat:oaglnztjrrhpvgluujl3reudoe
Patent Conflicts in User-Driven Biotechnology: Examining Knowledge Management Strategies for Patentable Research Resources to Stimulate DIY Bio and Other Social Production in Biotechnology
2021
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The proliferation of patents and related rights protecting upstream research can be detrimental to progress and citizens' welfare because they can increase the cost of R&D, interfere with access to upstream ...
Many DIYers depend on self-funding and community resources to experiment with biotechnology. Proprietary research tools and equipment are harder to access. ...
Making tree-of-life knowledge accessible, reusable, and convenient" (2013), 14 BMC Bioinformatics 158); Peter B Nichol "Hacking the future of health at Yale", CIO Magazine (26 January 2017) online: CIO ...
doi:10.20381/ruor-25839
fatcat:jshlqcc7gzbpzjzhhaa6aibgle
OASIcs, Volume 64, ICLP'18, Complete Volume
[article]
2018
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The availability of efficient answer set solvers (e.g., clasp and its descendants [8, 2]) gave Answer set programming (ASP) a leading role in languages for knowledge representation and reasoning. ...
ASP is regarded as the computational embodiment of non-monotonic reasoning because of its simple syntax and elegant non-monotonic semantics. ...
Introduction The Phylotastic 1 project is an attempt for making use of phylogeny trees in education or for researching in biology. ...
doi:10.4230/oasics.iclp.2018
fatcat:exbunzcx7rgrhg32iguyfxca7u