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...CCO is a mid-level extension of Basic Formal Ontology (BFO), an upper-level ontology framework widely used to structure and integrate ontologies in the biomedical domain (Arp, et al., 2015). BFO aims to represent the most generic categories of entity and the most generic types of relations that hold between them, by defining a small number of classes and relations. CCO then extends from BFO in the sense that every class in CCO is asserted to be a subclass of some class in BFO, and that CCO adopts the generic relations defined in BFO (e.g., has_part) (Smith and Grenon, 2004). ...

nichenetr: the R implementation of the NicheNet method. The goal of NicheNet is to study intercellular communication from a computational perspective. NicheNet uses human or mouse gene expression data of interacting cells as input and combines this with a prior model that integrates existing knowledge on ligand-to-target signaling paths. This allows to predict ligand-receptor interactions that might drive gene expression changes in cells of interest. This model of prior information on...

...Thel Virtual Machine (VMware) is a 64 bit Ubuntu Server 14.04, with MySQL (Percona Server) and PostgreSQL 9.4 as the database flavours and PDI version 5.2 CE. NB: Directory version_2.4 contains the most recent Virtual Machine. The readme.txt contains info about that VM.

SnapLogic is an Open Source Data Integration framework that combines the power of state-of-the-art dynamic programming languages with standard Web interfaces to solve today's most pressing problems in data integration.