SUMMARY We developed a Python package, ProDy, for structure-based analysis of protein dynamics. ProDy allows for quantitative characterization of structural variations in heterogeneous datasets of structures experimentally resolved for a given biomolecular system, and for comparison of these variations with the theoretically predicted equilibrium dynamics. Datasets include structural ensembles ...

Annotation graphs provide an efficient and expressive data model for linguistic annotations of time-series data. This technical report describes a complete software infrastructure supporting the rapid development of tools for transcribing and annotating time-series data. This general-purpose infrastructure uses annotation graphs as the underlying model, and allows developers to quickly create s...

We describe the design, development, and API of ODIN (Open Domain INformer), a domainindependent, rule-based event extraction (EE) framework. The proposed EE approach is: simple (most events are captured with simple lexico-syntactic patterns), powerful (the language can capture complex constructs, such as events taking other events as arguments, and regular expressions over syntactic graphs), r...

Whatever programming paradigm for data processing we choose, data has the tendency to live on the other side or to eventually end up there. The major paradigms for data processing are object, relational, XML and Cobol, while each paradigm offers many facets and many versions. Within object-oriented dataprocessing applications, each external or internal data model has the tendency to imply a hor...

Indian language WordNets have their individual web-based browsing interfaces along with a common interface for IndoWordNet. These interfaces prove to be useful for language learners and in an educational domain, however, they do not provide the functionality of connecting to them and browsing their data through a lucid application programming interface or an API. In this paper, we present our w...

We present Snap-SPARQL, which is a Java framework for working with SPARQL and OWL. The framework includes a parser, axiom template API, SPARQL algebra implementation, and graphical user interface components for reading, processing and executing SPARQL queries under the SPARQL 1.1 OWL Entailment Regime. While the framework was originally designed to support the implementation of a SPARQL teachin...

The objective of this paper is to present an optimal design for single-layer barrel vault frames via improved magnetic charged system search (IMCSS) and open application programming interface (OAPI). The IMCSS algorithm is utilized as the optimization algorithm and the OAPI is used as an interface tool between analysis software and the programming language. In the proposed algorithm, magnetic c...

A predominant (‘base’) scheme currently used in many circuit-switched LAN–WAN gateway applications is based on device-driver LAN redirections. Various functional and performance deficiencies associated with the LAN redirection (base) scheme and an RPC programming interface are described. This RPC definition supports the base scheme, as well as another (‘enhanced’) scheme. The enhanced scheme ov...

In this paper we describe an interface library IGOAAlib that supports the development of Open Agent Architecture (OAA) agents using the IndiGolog agent programming language. OAA is a multiagent infrastructure that supports facilitated communication. IndiGolog is a high-level agent programming language based on logic that supports planning and allows complex agent behaviours to be specified. Ful...

Large-scale pervasive public displays networks are becoming an emerging paradigm and represent a radical transformation in the way we think about information dissemination in public spaces. One of the features of pervasive public display systems is their ability to create experiences that span across multiple displays in a coordinated fashion. Proprietary single site display solutions exist but...