Protection of Intellectual Property Rights in Ukraine in the Light of European Integration Processes

The article provides an assessment of the state of legislation of Ukraine on the protection of intellectual property at the present stage. The most important problematic aspects and prospects of improving the legal regulation of intellectual property protection on the way to European integration are described in detail. The experience of foreign countries in ensuring the protection of intellectual property is analyzed. Particular attention is paid to the features of computer program protection, which is especially relevant nowadays. Features of the use of license agreements by the owner of computer programs, namely BSD License, Apache License, GNU General Public License, GNU Lesser General Public License, were analyzed. The conclusion is drawn that a system of continuous analysis of decisions made by European countries in the field of intellectual property law, as well as on issues related to general state policy on the administration of intellectual property, in order to implement developed approaches to legislation and law enforcement practice, could improve the protection of intellectual property rights in Ukraine.

cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats

Motivation CellDesigner is a well-established biological map editor used in many large-scale scientific efforts. However, the interoperability between the Systems Biology Graphical Notation (SBGN) Markup Language (SBGN-ML) and the CellDesigner’s proprietary Systems Biology Markup Language (SBML) extension formats remains a challenge due to the proprietary extensions used in CellDesigner files. Results We introduce a library named cd2sbgnml and an associated web service for bidirectional conversion between CellDesigner’s proprietary SBML extension and SBGN-ML formats. We discuss the functionality of the cd2sbgnml converter, which was successfully used for the translation of comprehensive large-scale diagrams such as the RECON Human Metabolic network and the complete Atlas of Cancer Signalling Network, from the CellDesigner file format into SBGN-ML. Availability and implementation The cd2sbgnml conversion library and the web service were developed in Java, and distributed under the GNU Lesser General Public License v3.0. The sources along with a set of examples are available on GitHub (https://github.com/sbgn/cd2sbgnml and https://github.com/sbgn/cd2sbgnml-webservice, respectively). Supplementary information Supplementary data are available at Bioinformatics online.

A portable general-purpose application programming interface for CIF 2.0

The CIF API is an application programming interface and accompanying reference implementation for reading and writing CIFs and manipulating CIF data, with support for all versions of CIF through CIF 2.0. It features full support for Unicode in data block and save frame codes, data names, and data values; flexible character encoding; CIF 2.0 List and Table data types; CIF version auto-detection; event-based parsing; and arbitrary-precision numeric values. The interface and implementation are written in portable C, and they have been successfully built and tested on Linux, OS X and Windows. The CIF API is open-source software, available for use under the GNU Lesser General Public License.

Overview and Assessment of Unity Toolkits for Rapid Development of an Educational VR Application

As the interest in Virtual Reality (VR) increases, so does the number of software toolkits available for various VR applications. Given that more games are being made with the Unity game engine than any other game technology, several of these toolkits are developed to be directly imported into Unity. A feature and interaction comparison of the toolkits is needed by Unity developers to properly suit one for a specific application. This paper presents an overview and comparison of several virtual reality toolkits available for developers using the Unity game engine. getReal3D, MiddleVR, and Reality-based User Interface System (RUIS) are analysed for VR interaction and display on multi-projection immersive environments like Cave Automatic Virtual Environments (CAVE)s. MiddleVR was found to have the highest performance and most versatile toolkit for CAVE display and interaction. However, taking cost into account, RUIS is the clear winner as it is available for free under the Lesser General Public License (LGPL) Version 3 license.

PaxtoolsR: Pathway Analysis in R Using Pathway Commons

Purpose: PaxtoolsR package enables access to pathway data represented in the BioPAX format and made available through the Pathway Commons webservice for users of the R language. Features include the extraction, merging, and validation of pathway data represented in the BioPAX format. This package also provides novel pathway datasets and advanced querying features for R users through the Pathway Commons webservice allowing users to query, extract, and retrieve data and integrate this data with local BioPAX datasets. Availability: The PaxtoolsR package is compatible with R 3.1.1 on Windows, Mac OS X, and Linux using Bioconductor 3.0 and is available through the Bioconductor R package repository along with source code and a tutorial vignette describing common tasks, such as data visualization and gene set enrichment analysis. Source code and documentation are at http://bioconductor.org/packages/release/bioc/html/paxtoolsr.html. This plugin is free, open-source and licensed under the GNU Lesser General Public License (LGPL) v3.0.

The GL Service: Web Service to Exchange GL String Encoded HLA & KIR Genotypes With Complete and Accurate Allele and Genotype Ambiguity

Genotype List (GL) Strings use a set of hierarchical character delimiters to represent allele and genotype ambiguity in HLA and KIR genotypes in a complete and accurate fashion. A RESTful web service called Genotype List Service was created to allow users to register a GL String and receive a unique identifier for that string in the form of a URI. By exchanging URIs and dereferencing them through the GL Service, users can easily transmit HLA genotypes in a variety of useful formats. The GL Service was developed to be secure, scalable, and persistent. An instance of the GL Service is configured with a nomenclature and can be run in strict or non-strict modes. Strict mode requires alleles used in the GL String to be present in the allele database using the fully qualified nomenclature. Non-strict mode allows any GL String to be registered as long as it is syntactically correct. The GL Service source code is free and open source software, distributed under the GNU Lesser General Public License (LGPL) version 3 or later.

Advances in Technology Project Management

As organizations must continually drive down costs of software-driven projects, they need to evaluate the Systems Development Life Cycle (SDLC) and other software-based design methodologies. These methodologies include looking at software-based alternatives that could save a significant amount of money by reducing the amount of proprietary software. This chapter explores the use and integration of Open Source Software (OSS) in software-driven projects to include in enterprise organizations. Additionally, the legalities of the GNU General Public License (GPL), Lesser General Public License (LGPL), Berkeley Software Distribution (BSD), and Creative Commons are explored with the integration of these OSS solutions into organizations. Lastly, the chapter covers the software assurance and cyber security controls to associate with OSS to deploy a hardened product that meets the needs of today's dynamically evolving global business enterprise.

Advances in Technology Project Management

As organizations must continually drive down costs of software-driven projects, they need to evaluate the Systems Development Life Cycle (SDLC) and other software-based design methodologies. These methodologies include looking at software-based alternatives that could save a significant amount of money by reducing the amount of proprietary software. This chapter explores the use and integration of Open Source Software (OSS) in software-driven projects to include in enterprise organizations. Additionally, the legalities of the GNU General Public License (GPL), Lesser General Public License (LGPL), Berkeley Software Distribution (BSD), and Creative Commons are explored with the integration of these OSS solutions into organizations. Lastly, the chapter covers the software assurance and cyber security controls to associate with OSS to deploy a hardened product that meets the needs of today's dynamically evolving global business enterprise.