[{"id":616,"title":"The Growing Need for Domain-Driven Languages","sha":"d216d707e6077f0c53aabf8cb1751bd9","user_id":null,"state":"published","body":"With computer science permeating every research disciple such that even rudimentary computational skills are now required for most research careers, it should not be the case that one needs advanced knowledge of computer science to be effective in their field.\r\n\r\nIf we take Bioinformatics as an example, the non-computational biologist practitioner should be able to express theories in a truncated form of how they already speak of biology -- a Domain-Driven Language (DDL) which can then be computationally processed. Tools such as Nextflow and Snakemake, as workflow managers, make progress in this direction, but as they do not abstract away the data flow model they rely upon, do not go far enough.\r\n\r\nI posit that unified domain-driven grammars are possible consisting of: verbs which define the action to be done (e.g., align); adjectives which define how the verb is to be done (e.g., local); nouns which define what the verb acts upon (e.g., sequence 1 and sequence 2); intents which define manner of action (e.g., longest match); and helpers which are meant to clarify intent (e.g., sequence 1 is reference, sequence 2 is query). An executed DDL should be able to use the same grammar to describe what was run in terms the executor understands.","created_at":"2019-09-05T00:26:51.488Z","updated_at":"2020-06-16T16:30:37.128Z","zenodo_id":3445545,"doi":"https://doi.org/10.5281/zenodo.3445545","subject":null,"tags":["dsl","bioinformatics","abstraction"],"vote_count":5,"view_count":1,"score":5.1,"deleted":false,"muted":false,"tweeted":false,"attachment_file_name":null,"attachment_content_type":null,"attachment_file_size":null,"attachment_updated_at":null},{"id":617,"title":"Solitary Ecological Dominance Consensus","sha":"3c146a83ef7dbf87f8eb4eae6a9e278e","user_id":null,"state":"published","body":"Is it possible to model the distributed dominance hierarchy of solitary species via a modified Byzantine fault problem? Traditionally used in distributed computing where the network consists of some unreliable actors, meanwhile a concerted strategy must be agreed upon, the Byzantine fault problem allows for erroneous communication of some global consensus under sparse pairwise communication. Under the assumption that solitary species individuals have some internal understanding of their own place in a dominance hierarchy (e.g., they know how aggressive they are compared to others), could we use the framework presented by the Byzantine fault problem to find a consensus of the hierarchy itself? In the traditional model, the Byzantine general must agree upon whether to attack a city or not -- under the solitary ecological dominance consensus this binary attack choice could be replaced with another binary choice such as entering another individual's range or not.\r\n\r\nThe genesis of this idea was in attempting to find some manner to determine the dominance hierarchy of the elusive, solitary Aye-aye of Madagascar. We can slice tracking and nesting data in a variety of binary manners, but the lack of clear contests between individuals led to a failure to construct a ecological dominance hierarchy by known methods.","created_at":"2019-09-05T01:24:45.699Z","updated_at":"2019-11-20T05:50:13.912Z","zenodo_id":3445547,"doi":"https://doi.org/10.5281/zenodo.3445547","subject":null,"tags":["ecology","distributed","aye-aye","sparse"],"vote_count":2,"view_count":1,"score":2.1,"deleted":false,"muted":false,"tweeted":true,"attachment_file_name":null,"attachment_content_type":null,"attachment_file_size":null,"attachment_updated_at":null}]