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

2015 ◽  
Author(s):  
Robert P Milius ◽  
Michael Heuer ◽  
Mike George ◽  
Jane Pollack ◽  
Jill A Hollenbach ◽  
...  
Keyword(s):  
Web Service ◽  
Open Source Software ◽  
Source Code ◽  
Service Users ◽  
Unique Identifier ◽  
Lesser General Public License ◽  
Hla Genotypes ◽  
Restful Web Service ◽  
Kir Genotypes ◽  
General Public License

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.

scholarly journals cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats

2020 ◽  
Vol 36 (8) ◽  
pp. 2620-2622 ◽  
Author(s):  
Irina Balaur ◽  
Ludovic Roy ◽  
Alexander Mazein ◽  
S Gökberk Karaca ◽  
Ugur Dogrusoz ◽  
...  
Keyword(s):  
Systems Biology ◽  
Web Service ◽  
Large Scale ◽  
Supplementary Information ◽  
Markup Language ◽  
File Format ◽  
Signalling Network ◽  
Lesser General Public License ◽  
Systems Biology Markup Language ◽  
General Public License

Abstract 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.

scholarly journals PaxtoolsR: Pathway Analysis in R Using Pathway Commons

2015 ◽  
Author(s):  
Augustin Luna ◽  
Özgün Babur ◽  
Bülent Arman Aksoy ◽  
Emek Demir ◽  
Chris Sander
Keyword(s):  
Source Code ◽  
Enrichment Analysis ◽  
R Package ◽  
Gene Set Enrichment Analysis ◽  
Gene Set Enrichment ◽  
R Language ◽  
Pathway Data ◽  
Lesser General Public License ◽  
Free Open Source ◽  
General Public License

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.

scholarly journals Open Plot Project: an open-source toolkit for 3-D structural data analysis

Solid Earth ◽  
2011 ◽  
Vol 2 (1) ◽  
pp. 53-63 ◽  
Author(s):  
S. Tavani ◽  
P. Arbues ◽  
M. Snidero ◽  
N. Carrera ◽  
J. A. Muñoz
Keyword(s):  
Spatial Distribution ◽  
Data Analysis ◽  
Open Source ◽  
Open Source Software ◽  
Source Code ◽  
Structural Data ◽  
Geological Modelling ◽  
Analysis Tools ◽  
Transect Analysis ◽  
Selection Of

Abstract. In this work we present the Open Plot Project, an open-source software for structural data analysis, including a 3-D environment. The software includes many classical functionalities of structural data analysis tools, like stereoplot, contouring, tensorial regression, scatterplots, histograms and transect analysis. In addition, efficient filtering tools are present allowing the selection of data according to their attributes, including spatial distribution and orientation. This first alpha release represents a stand-alone toolkit for structural data analysis. The presence of a 3-D environment with digitalising tools allows the integration of structural data with information extracted from georeferenced images to produce structurally validated dip domains. This, coupled with many import/export facilities, allows easy incorporation of structural analyses in workflows for 3-D geological modelling. Accordingly, Open Plot Project also candidates as a structural add-on for 3-D geological modelling software. The software (for both Windows and Linux O.S.), the User Manual, a set of example movies (complementary to the User Manual), and the source code are provided as Supplement. We intend the publication of the source code to set the foundation for free, public software that, hopefully, the structural geologists' community will use, modify, and implement. The creation of additional public controls/tools is strongly encouraged.

scholarly journals JSON Web Token (JWT) untuk Authentication pada Interoperabilitas Arsitektur berbasis RESTful Web Service

2019 ◽  
Vol 5 (1) ◽  
pp. 74
Author(s):  
Rohmat Gunawan ◽  
Alam Rahmatulloh
Keyword(s):  
Web Service ◽  
Blood Donors ◽  
Restful Web Service

Permasalahan donor darah merupakan masalah disetiap negara, termasuk di Indonesia. Walaupun sudah ada sistem di Palang Merah Indonesia (PMI) namun belum bisa mengatasi permasalahan pencarian maupun distribusi donor darah. Sesuai trend sekarang di jaman gadget yaitu maraknya penggunaan Android, maka untuk mengatasi masalah ini diperlukan aplikasi berbasis Android. Sementara untuk integrasi dengan sistem yang sudah ada diperlukan web service sebagai backend system sehingga layanan donor darah dapat diakses oleh berbagai platform. Arsitektur yang digunakan pada web service menggunakan REST, namun masih ada beberapa masalah pada REST yaitu mengenai keamanan pada proses otentikasi. Pada arsitektur REST diperlukan metode otentikasi yang tidak bernegara (stateless), salah satunya dapat menggunakan JSON Web Token. Hasil penelitian ini menunjukan bahwa penggunaan JSON Web Token Authentication pada Web Service and Backend System Blood Donors dapat membentuk sistem yang sangat skalabel, aman, mampu berinteraksi multi-platform serta dapat diandalkan.

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

2020 ◽  
Vol 13 (3) ◽  
pp. 203
Author(s):  
Andrii Neugodnikov ◽  
Tetiana Barsukova ◽  
Roman Kharytonov
Keyword(s):  
Law Enforcement ◽  
Intellectual Property ◽  
Property Rights ◽  
European Integration ◽  
Intellectual Property Rights ◽  
General Public ◽  
Legal Regulation ◽  
Foreign Countries ◽  
Lesser General Public License ◽  
General Public License

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.

scholarly journals A Prologue of Git and SVN

2019 ◽  
Vol 9 (1) ◽  
pp. 988-990
Keyword(s):  
Control System ◽  
Open Source ◽  
Control Systems ◽  
Source Code ◽  
Version Control ◽  
Control Software ◽  
The World ◽  
Revision Control ◽  
Version Control System ◽  
General Public License

Version Control Software or Revision Control Software are the most important things in the world of software development. In this paper, we have described two version control tools: Git and Apache Subversion. Git comes as free and open source code management and version control system which is disseminated with the GNU general public license. Apache Subversion abbreviated as SVN is one amongst a software versioning and revision control systems given as open source under Apache License. Git design, its functionality, and usage of Git and SVN are discussed in this paper. The goal of this research paper is to accentuate on GIT and SVN tools, evaluate and compare five version control tools to ascertain their usage and efficacy.

Review of Open Source Software (OSS)

2012 ◽  
pp. 26-40
Author(s):  
Bhasker Mukerji ◽  
Ramaraj Palanisamy
Keyword(s):  
Developing Countries ◽  
Public Sector ◽  
Open Source ◽  
Open Source Software ◽  
Low Cost ◽  
Source Code ◽  
Developed Countries ◽  
Economic Resources ◽  
Large Pool ◽  
Public Sector Organizations

The popularity of Open Source Software (OSS) in developing countries is quiet evident from its widespread adoption across government departments and public sector organizations. The use of OSS saves economic resources of cash starved countries, provides an opportunity to promote e-government, and to utilize their resources in other sectors. Many developing countries have a large pool of skilled developers who can modify the source code of the OSS at a very low cost. Many governments in developing and developed countries have switched to OSS which probably encourages others to follow the trend. It was not possible to follow the adoption trend in all the developing countries but the usage of OSS in countries like India, Brazil, and Venezuela provides us an insight. The successful adoption of OSS requires thorough analysis of its advantages as well as the issues associated with it. This chapter will provide an overview of OSS, characteristics of OSS developers, and their motivation to volunteer by contributing in OSS projects, followed by the advantages and issues associated with OSS.

Key Concepts and Definitions of Open Source Communities

2010 ◽  
pp. 753-760
Author(s):  
Ruben van Wendel de Joode ◽  
Sebastian Spaeth
Keyword(s):  
Software Development ◽  
Open Source ◽  
Open Source Software ◽  
Online Communities ◽  
Source Code ◽  
Professional Organizations ◽  
Large Numbers ◽  
Key Concepts ◽  
Open Source Communities ◽  
Do So

Most open source software is developed in online communities. These communities are typically referred to as “open source software communities” or “OSS communities.” In OSS communities, the source code, which is the human-readable part of software, is treated as something that is open and that should be downloadable and modifiable to anyone who wishes to do so. The availability of the source code has enabled a practice of decentralized software development in which large numbers of people contribute time and effort. Communities like Linux and Apache, for instance, have been able to connect thousands of individual programmers and professional organizations (although most project communities remain relatively small). These people and organizations are not confined to certain geographical places; on the contrary, they come from literally all continents and they interact and collaborate virtually.

Migrating Web Services in Mobile and Wireless Environments

2011 ◽  
pp. 706-723
Author(s):  
Myung-Woo Park ◽  
Yeon-Seok Kim ◽  
Kyong-Ho Lee
Keyword(s):  
Web Services ◽  
Web Service ◽  
Mobile Devices ◽  
Wireless Network ◽  
Efficient Method ◽  
Source Code ◽  
Context Information ◽  
Wireless Environments ◽  
Migration Method ◽  
The Web

Mobile devices enabled with Web services are being considered as equal participants of the Web services environment. The frequent mobility of devices and the intermittent disconnection of wireless network require migrating or replicating Web services onto adjacent devices appropriately. This article proposes an efficient method for migrating and replicating Web services among mobile devices through code splitting. Specifically, the proposed method splits the source code of a Web service into subcodes based on users’ preferences for its constituent operations. The subcode with a higher preference is migrated earlier than others. The proposed method also replicates a Web service to other devices to enhance its performance by considering context information such as network traffic or the parameter size of its operations. To evaluate the performance of the proposed method, the effect of the code splitting on migration was analyzed. Furthermore, to show the feasibility of the proposed migration method, three application scenarios were devised and implemented.

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