Validity constraints for data analysis workflows

\ua9 2024Porting a scientific data analysis workflow (DAW) to a cluster infrastructure, a new software stack, or even only a new dataset with some notably different properties is often challenging. Despite the structured definition of the steps (tasks) and their interdependencies during a complex data analysis in the DAW specification, relevant assumptions may remain unspecified and implicit. Such hidden assumptions often lead to crashing tasks without a reasonable error message, poor performance in general, non-terminating executions, or silent wrong results of the DAW, to name only a few possible consequences. Searching for the causes of such errors and drawbacks in a distributed compute cluster managed by a complex infrastructure stack, where DAWs for large datasets typically are executed, can be tedious and time-consuming. We propose validity constraints (VCs) as a new concept for DAW languages to alleviate this situation. A VC is a constraint specifying logical conditions that must be fulfilled at certain times for DAW executions to be valid. When defined together with a DAW, VCs help to improve the portability, adaptability, and reusability of DAWs by making implicit assumptions explicit. Once specified, VCs can be controlled automatically by the DAW infrastructure, and violations can lead to meaningful error messages and graceful behavior (e.g., termination or invocation of repair mechanisms). We provide a broad list of possible VCs, classify them along multiple dimensions, and compare them to similar concepts one can find in related fields. We also provide a proof-of-concept implementation for the workflow system Nextflow

Validity constraints for data analysis workflows

Porting a scientific data analysis workflow (DAW) to a cluster infrastructure, a new software stack, or even only a new dataset with some notably different properties is often challenging. Despite the structured definition of the steps (tasks) and their interdependencies during a complex data analysis in the DAW specification, relevant assumptions may remain unspecified and implicit. Such hidden assumptions often lead to crashing tasks without a reasonable error message, poor performance in general, non-terminating executions, or silent wrong results of the DAW, to name only a few possible consequences. Searching for the causes of such errors and drawbacks in a distributed compute cluster managed by a complex infrastructure stack, where DAWs for large datasets typically are executed, can be tedious and time-consuming. We propose validity constraints (VCs) as a new concept for DAW languages to alleviate this situation. A VC is a constraint specifying logical conditions that must be fulfilled at certain times for DAW executions to be valid. When defined together with a DAW, VCs help to improve the portability, adaptability, and reusability of DAWs by making implicit assumptions explicit. Once specified, VCs can be controlled automatically by the DAW infrastructure, and violations can lead to meaningful error messages and graceful behavior (e.g., termination or invocation of repair mechanisms). We provide a broad list of possible VCs, classify them along multiple dimensions, and compare them to similar concepts one can find in related fields. We also provide a proof-of-concept implementation for the workflow system Nextflow

Comparative anatomy, phylogeny, and systematics of the Miocene giraffid Decennatherium pachecoi Crusafont, 1952 (Mammalia, Ruminantia, Pecora): State of the art

Program and Abstracts-70th Anniversary Meeting-Society of Vertebrate Paleontology. Deerfield 36 (2016)Decennatherium pachecoi Crusafont, 1952, is one of two giraffid species described from the Miocene of the Iberian Peninsula. This species is recovered exclusively from Vallesian faunas (MN9–10, late Miocene, 10–11 Ma). Despite being relatively well represented in the fossil record, except for the skull and ossicones, the complete vertebral column, and part of the upper dentition, its systematics and phylogenetic position among giraffids are the subject of debate. We update our knowledge of D. pachecoi, revising all Spanish material assigned to this species, as well as previously undescribed fossils. We reassess the systematics of Decennatherium, including its potential relationship with the second Iberian giraffid, the early Turolian Birgerbohlinia Crusafont, 1952, by means of the first cladistic analysis of the Giraffidae that includes Decennatherium together with the most relevant African and Eurasian taxa, both fossil and extant. Our results link Decennatherium with a ‘samothere’ clade, whereas Birgerbohlinia is nested within a ‘sivathere’ clade, thus refuting a previously assumed direct relationship between the two Spanish forms. Finally, we discuss some other possible finds of the genus Decennatherium in Greece, Turkey, and Iran. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Rios, M., I. M. Sánchez, and J. Morales. 2016. Comparative anatomy, phylogeny, and systematics of the Miocene giraffid Decennatherium pachecoi Crusafont, 1952 (Mammalia, Ruminantia, Pecora): State of the art. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1187624.M. Rios acknowledges support from the Ministerio de Economía y Competitividad for the pre-doctoral FPI grant BES-2012-052589, the FPI short-stay grant EEBB-I-14-07947, and the research project CGL2011-25754.Peer Reviewe