Software tools for manipulating fe mesh, virtual surgery and post-processing

This paper describes a set of software tools which we developed for the calculation of fluid flow through cardiovascular organs. Our tools work with medical data from a CT scanner, but could be used with any other 3D input data. For meshing we used a Tetgen tetrahedral mesh generator, as well as a mesh re-generator that we have developed for conversion of tetrahedral elements into bricks. After adequate meshing we used our PAKF solver for calculation of fluid flow. For human-friendly presentation of results we developed a set of post-processing software tools. With modification of 2D mesh (boundary of cardiovascular organ) it is possible to do virtual surgery, so in a case of an aorta with aneurism, which we had received from University Clinical center in Heidelberg from a multi-slice 64-CT scanner, we removed the aneurism and ran calculations on both geometrical models afterwards. The main idea of this methodology is creating a system that could be used in clinics

Overview of architectures with arduino boards as building blocks for data acquisition and control systems

Standard SBCs (Single Board Computer) with number of standard shields and sensors can be used as building blocks for rapid development of network of intelligent devices with sensing, control and Internet access. Arduino family of boards having high popularity and large number of sold units featuring open access, reliability, robustness, standard connections and low prices, possesses large potential for implementation of autonomous remote measurement and control systems of various levels of complexity. As Arduino boards can function independently, they are complete small computer platforms that can perform various tasks requiring some kind of interaction with the outer world. Arduino boards can be used and programmed in various ways, and can be arranged in various combinations forming some typical implementation architectures that this paper discusses. Starting from basic and simple configurations, more advanced are gradually considered from the aspects of chosen way of programming and combining with other boards. Special attention is devoted to NodeJS as programming platform for Arduino boards and considerations of libraries used with Arduino boards like Johnny-Five, Galileo-io firmata equivalent, mraa library and other ways of program access to GPIO like Linux Sysfs. As typical representatives of Arduino boards' family, the Arduino Uno, Arduino Due and Arduino Galileo were selected, with justification that all other not mentioned boards are somewhere between those selected, according to official hardware specifications

PIBAS FedSPARQL: A web-based platform for integration and exploration of bioinformatics datasets

© 2017 The Author(s). Background: There are a huge variety of data sources relevant to chemical, biological and pharmacological research, but these data sources are highly siloed and cannot be queried together in a straightforward way. Semantic technologies offer the ability to create links and mappings across datasets and manage them as a single, linked network so that searching can be carried out across datasets, independently of the source. We have developed an application called PIBAS FedSPARQL that uses semantic technologies to allow researchers to carry out such searching across a vast array of data sources. Results: PIBAS FedSPARQL is a web-based query builder and result set visualizer of bioinformatics data. As an advanced feature, our system can detect similar data items identified by different Uniform Resource Identifiers (URIs), using a text-mining algorithm based on the processing of named entities to be used in Vector Space Model and Cosine Similarity Measures. According to our knowledge, PIBAS FedSPARQL was unique among the systems that we found in that it allows detecting of similar data items. As a query builder, our system allows researchers to intuitively construct and run Federated SPARQL queries across multiple data sources, including global initiatives, such as Bio2RDF, Chem2Bio2RDF, EMBL-EBI, and one local initiative called CPCTAS, as well as additional user-specified data source. From the input topic, subtopic, template and keyword, a corresponding initial Federated SPARQL query is created and executed. Based on the data obtained, end users have the ability to choose the most appropriate data sources in their area of interest and exploit their Resource Description Framework (RDF) structure, which allows users to select certain properties of data to enhance query results. Conclusions: The developed system is flexible and allows intuitive creation and execution of queries for an extensive range of bioinformatics topics. Also, the novel similar data items detection algorithm can be particularly useful for suggesting new data sources and cost optimization for new experiments. PIBAS FedSPARQL can be expanded with new topics, subtopics and templates on demand, rendering information retrieval more robust