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Phylotastic: An Experiment in Creating, Manipulating, and Evolving Phylogenetic Biology Workflows Using Logic Programming

2018 Theory and Practice of Logic Programming  
This paper illustrates how Phylotastic has addressed the challenges of creating and refining phylogenetic analysis workflows using logic programming technology and how such solutions have been used within  ...  An evolutionary biology workflow can be viewed as a plan which composes web services that can retrieve, manipulate, and produce phylogenetic trees.  ...  Phylogenies are useful in all areas of biology, to provide a hierarchical framework for classification and for process-based models that allow scientists to make robust inferences from comparisons of evolved  ... 
doi:10.1017/s1471068418000236 fatcat:jer6pjr45nbe7iwm7eq4rno4mq

Introduction to the 34-th international conference on logic programming special issue

2018 Theory and Practice of Logic Programming  
This special issue of Theory and Practice of Logic Programming (TPLP) contains the regular papers accepted for presentation at the 34-th International Conference on Logic Programming (ICLP 2018), held  ...  in Oxford, United Kingdom, from July 14th to July 17th, 2018.  ...  designed the web pages; Paul Fodor and Neda Saeedloei, who jointly chaired the Doctoral Program of ICLP; and  ... 
doi:10.1017/s1471068418000352 fatcat:npib57qunzgzvhp4grx2fsavae

BioHackathon 2015: Semantics of data for life sciences and reproducible research

Rutger A. Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano, Shuichi Kawashima, Jin-Dong Kim, Yuki Moriya, Toshiaki Tokimatsu, Atsuko Yamaguchi, Yasunori Yamamoto, Hongyan Wu, Peter Amstutz (+65 others)
2020 F1000Research  
We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote  ...  , including chemistry, genotypes and phenotypes, orthology and phylogeny, proteomics, genomics, glycomics, and metabolomics.  ...  ) and the Database Center for Life Science (DBCLS).  ... 
doi:10.12688/f1000research.18236.1 pmid:32308977 pmcid:PMC7141167 fatcat:oaglnztjrrhpvgluujl3reudoe

OASIcs, Volume 64, ICLP'18, Complete Volume [article]

Alessandro Dal Palu', Paul Tarau, Neda Saeedloei, Paul Fodor
The popularity of ASP is demonstrated by the increasing number of authors publishing ASP-based research work in artificial intelligence as well as non-logic programming venues, and its use as a natural  ...  ., clasp and its descendants [8, 2]) gave Answer set programming (ASP) a leading role in languages for knowledge representation and reasoning.  ...  Web Service Ontology (WSO) Phylotastic uses web service composition to generate workflows for the extraction/construction of phylogenetic trees. It makes use of two ontologies: WSO and PO.  ... 
doi:10.4230/oasics.iclp.2018 fatcat:exbunzcx7rgrhg32iguyfxca7u