scholarly journals Next Generation HGVS Nomenclature Checker

Author(s):  
Mihai Lefter ◽  
Jonathan K Vis ◽  
Martijn Vermaat ◽  
Johan T den Dunnen ◽  
Peter E M Taschner ◽  
...  

ABSTRACT Motivation Unambiguous variant descriptions are of utmost importance in clinical genetic diagnostics, scientific literature, and genetic databases. The Human Genome Variation Society (HGVS) publishes a comprehensive set of guidelines on how variants should be correctly and unambiguously described. We present the implementation of the Mutalyzer 2 tool suite, designed to automatically apply the HGVS guidelines so users do not have to deal with the HGVS intricacies explicitly to check and correct their variant descriptions. Results Mutalyzer is profusely used by the community, having processed over 133 million descriptions since its launch. Over a five year period, Mutalyzer reported a correct input in approximately 50% of cases. In 41% of the cases either a syntactic or semantic error was identified and for approximately 7% of cases, Mutalyzer was able to automatically correct the description. Availability Mutalyzer is an Open Source project under the GNU Affero General Public License. The source code is available on GitHub (https://github.com/mutalyzer/mutalyzer) and a running instance is available at: https://mutalyzer.nl.

2020 ◽  
Author(s):  
Mihai Lefter ◽  
Jonathan K. Vis ◽  
Martijn Vermaat ◽  
Johan T. den Dunnen ◽  
Peter E.M. Taschner ◽  
...  

AbstractUnambiguous variant descriptions are of utmost importance in clinical genetic diagnostics, scientific literature, and genetic databases. The Human Genome Variation Society (HGVS) publishes a comprehensive set of guidelines on how variants should be correctly and unambiguously described. We present the implementation of the Mutalyzer 2 tool suite, designed to automatically apply the HGVS guidelines so users do not have to deal with the HGVS intricacies explicitly to check and correct their variant descriptions. Mutalyzer is profusely used by the community, having processed over 133 million descriptions since its launch. Over a five year period, Mutalyzer reported a correct input in approximately 50% of cases. In 41% of the cases either a syntactic or semantic error was identified and for approximately 7% of cases, Mutalyzer was able to automatically correct the description.


Author(s):  
Shuai Zhang ◽  
Yi Tay ◽  
Lina Yao ◽  
Bin Wu ◽  
Aixin Sun

Deep learning based recommender systems have been extensively explored in recent years. However, the large number of models proposed each year poses a big challenge for both researchers and practitioners in reproducing the results for further comparisons. Although a portion of papers provides source code, they adopted different programming languages or different deep learning packages, which also raises the bar in grasping the ideas. To alleviate this problem, we released the open source project: \textbf{DeepRec}. In this toolkit, we have implemented a number of deep learning based recommendation algorithms using Python and the widely used deep learning package - Tensorflow. Three major recommendation scenarios: rating prediction, top-N recommendation (item ranking) and sequential recommendation, were considered. Meanwhile, DeepRec maintains good modularity and extensibility to easily incorporate new models into the framework. It is distributed under the terms of the GNU General Public License. The source code is available at github: https://github.com/cheungdaven/DeepRec


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.


Author(s):  
D. Berry

Open source software (OSS) is computer software that has its underlying source code made available under a licence. This can allow developers and users to adapt and improve it (Raymond, 2001). Computer software can be broadly split into two development models: • Proprietary, or closed software, owned by a company or individual. Copies of the binary are made public; the source code is not usually made public. • Open-source software (OSS), where the source code is released with the binary. Users and developers can be licenced to use and modify the code, and to distribute any improvements they make. Both OSS and proprietary approaches allow companies to make a profit. Companies developing proprietary software make money by developing software and then selling licences to use the software. For example, Microsoft receives a payment for every copy of Windows sold with a personal computer. OSS companies make their money by providing services, such as advising clients on the GPL licence. The licencee can either charge a fee for this service or work free of charge. In practice, software companies often develop both types of software. OSS is developed by an ongoing, iterative process where people share the ideas expressed in the source code. The aim is that a large community of developers and users can contribute to the development of the code, check it for errors and bugs, and make the improved version available to others. Project management software is used to allow developers to keep track of the various versions. There are two main types of open-source licences (although there are many variants and subtypes developed by other companies): • Berkeley Software Distribution (BSD) Licence: This permits a licencee to “close” a version (by withholding the most recent modifications to the source code) and sell it as a proprietary product; • GNU General Public Licence (GNU, GPL, or GPL): Under this licence, licencees may not “close” versions. The licencee may modify, copy, and redistribute any derivative version, under the same GPL licence. The licencee can either charge a fee for this service or work free of charge. Free software first evolved during the 1970s but in the 1990s forked into two movements, namely free software and open source (Berry, 2004). Richard Stallman, an American software developer who believes that sharing source code and ideas is fundamental to freedom of speech, developed a free version of the widely used Unix operating system. The resulting GNU program was released under a specially created General Public Licence (GNU, GPL). This was designed to ensure that the source code would remain openly available to all. It was not intended to prevent commercial usage or distribution (Stallman, 2002). This approach was christened free software. In this context, free meant that anyone could modify the software. However, the term “free” was often misunderstood to mean no cost. Hence, during the 1990s, Eric Raymond and others proposed that open-source software was coined as a less contentious and more business-friendly term. This has become widely accepted within the software and business communities; however there are still arguments about the most appropriate term to use (Moody, 2002). The OSMs are usually organised into a network of individuals who work collaboratively on the Internet, developing major software projects that sometimes rival commercial software but are always committed to the production of quality alternatives to those produced by commercial companies (Raymond, 2001; Williams, 2002). Groups and individuals develop software to meet their own and others’ needs in a highly decentralised way, likened to a Bazaar (Raymond, 2001). These groups often make substantive value claims to support their projects and foster an ethic of community, collaboration, deliberation, and intellectual freedom. In addition, it is argued by Lessig (1999) that the FLOSS community can offer an inspiration in their commitment to transparency in their products and their ability to open up governmental regulation and control through free/libre and open source code.


Author(s):  
Robert Cunningham

This chapter examines the development of open source computer software with specific reference to the political economy of copyleft and the legalities associated with the General Public License (GPL). It will be seen that within the context of computer software development the notion of copyleft provides an important contrast to more traditional uses of copyright. This contrast symbolizes political, economic, and social struggles which are contextualized within this chapter. As the GPL is an important legal embodiment of copyleft, its legalities are preliminarily explored so as to determine its future potential. While there is some scope to further refine the legal strength of the GPL, it will be seen that it remains a strong and subversive legal instrument which will continue to underlie open source initiatives in the years to come.


2018 ◽  
Author(s):  
Zoltan Siki ◽  
Bence Takács ◽  
Csaba Égető

Ulyxes is an open source project to drive robotic total stations as well as other sensors, collect their measurements in database and finally publish the results for authorized users on the web. On special requests the results are also presented with web based maps in the background. This project is like an instant coffee: three in one (coffee, sugar and milk). The coffee and the strongest part is the research and coding. The sugar is the application of the program in industrial environment and the milk on the top is the educational usage. The software development started in 2008 connected to a monitoring task in the Hungarian Nuclear Power Plant. Since then the development has been extended from total stations to different positioning capable sensors. In 2012 the development of a new Python based object oriented framework started. The code is based on the results of some other open source projects, Python, PySerial, GNUGama, SQLite, OpenCV, etc. After connecting to the international Geo4All network in 2014, Ulyxes became a project of our Geo4All Lab. The project has its own home page (http://www.agt.bme.hu/ulyxes) and the source code is available on the GitHub portal (https://github.com/zsiki/ulyxes). The code is maintained by the colleagues at the Department of Geodesy and Surveying at the Budapest University of Technology, volunteers from all over the World are welcome. BSc and MSc students are also involved in the development and testing. More theses were connected to this project in the recent five years. In the curriculum of an MSc subject called Surveying Automation, Ulyxes is used to demonstrate automatized tasks in engineering surveying. The system has been applied for several projects during the last 10+ years. Typical applications are the load tests of bridges and other engineering structures and on the other hand Ulyxes can be used to monitor the movements of buildings in the nearby of constructional works, like metro stations, underground garage and other buildings as well. Raspberry Pi small, single board computers are used with Raspbian operating system during on-site works. The source code is divided into three parts. The first one is the Ulyxes API which is the core of the system. The second one, Ulyxes Apps is a collection of applications based upon the API. Some of them were developed by our students. The third part is the server side scripts to publish observation results through the Internet. Moreover it is also planned to implement SOS standard using IstSOS. Our Geo4All Lab maintains another open source software, called GeoEasy to process observation data in engineering and land surveying. A closer cooperation is also planned between our two open source projects. In this paper the most important features of Ulyxes will be presented with examples, an actual monitoring project in Budapest and test loads of bridges and overpasses.


2003 ◽  
Vol 2 (1) ◽  
Author(s):  
Dudi Anandya

Linux is an operating system that it's presence offer many "new concepts" to the market. It’s an open source software developed under GNU project using General Public License (GPL), that gives everyone freedom to run, copy, distribute, study, change, and improve the software. The GNU Project was launched in 1984 to develop a complete Unix-like operating system which is free software: the GNU system. GNU is a recursive acronym for "GNU's Not Unix”; it is pronounced “guh-NEW", In Other way we can say that Linux developed, manufactured, and distributed by it's own costumers. They joined together in the Linux communities and create a network among them. It has a unique lateral pattern of relationship. The Author named all of this as the “Linux Phenomenon". This articles will begin by explaining theories about network, and then discuss the and then discuss the Linux phenomenon. Later, the author will explore the Linux's "breakthrough" in networking, and the implication of "how to do business".


Author(s):  
Pierre-Alain Chaumeil ◽  
Aaron J Mussig ◽  
Philip Hugenholtz ◽  
Donovan H Parks

Abstract Summary The GTDB Toolkit (GTDB-Tk) provides objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB). GTDB-Tk is computationally efficient and able to classify thousands of draft genomes in parallel. Here we demonstrate the accuracy of the GTDB-Tk taxonomic assignments by evaluating its performance on a phylogenetically diverse set of 10,156 bacterial and archaeal metagenome-assembled genomes. Availability GTDB-Tk is implemented in Python and licensed under the GNU General Public License v3.0. Source code and documentation are available at: https://github.com/ecogenomics/gtdbtk Supplementary information Supplementary data are available at Bioinformatics online.


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