scholarly journals A Fast and Memory-Efficient Implementation of the Transfer Bootstrap

2019 ◽  
Author(s):  
Sarah Lutteropp ◽  
Alexey M. Kozlov ◽  
Alexandros Stamatakis
Keyword(s):  
General Public ◽  
Efficient Implementation ◽  
Random Tree ◽  
Bootstrap Support ◽  
Original Algorithm ◽  
Link Type ◽  
Branch Support ◽  
General Public License ◽  
Memory Efficient

AbstractRecently, Lemoine et al. suggested the Transfer Bootstrap Expectation (TBE) branch support metric as an alternative to classical phylogenetic bootstrap support metric on taxon-rich datasets. However, the original TBE implementation in the booster tool is compute- and memory-intensive. Therefore, we developed a fast and memory-efficient TBE implementation. We improved upon the original algorithm described by Lemoine et al. by introducing multiple algorithmic and technical optimizations. On empirical as well as on random tree sets with varying taxon counts, our implementation is up to 480 times faster than booster. Furthermore, it only requires memory that is linear in the number of taxa, which leads to 10× - 40× memory savings compared to booster. Our implementation has been partially integrated into pll-modules and RAxML-NG and is available under the GNU Affero General Public License v3.0 at https://github.com/ddarriba/pll-modules and https://github.com/amkozlov/raxml-ng. The parallelized version that also computes additional TBE-related statistics is available in pll-modules and RAxML-NG forks at: https://github.com/lutteropp/pll-modules/tree/tbe and https://github.com/lutteropp/raxml-ng/tree/tbe.

scholarly journals A fast and memory-efficient implementation of the transfer bootstrap

2019 ◽  
Vol 36 (7) ◽  
pp. 2280-2281 ◽  
Author(s):  
Sarah Lutteropp ◽  
Alexey M Kozlov ◽  
Alexandros Stamatakis
Keyword(s):  
General Public ◽  
Efficient Implementation ◽  
Supplementary Information ◽  
Bootstrap Support ◽  
Supplementary Data ◽  
Original Algorithm ◽  
Parallel Version ◽  
Branch Support ◽  
General Public License ◽  
Memory Efficient

Abstract Motivation Recently, Lemoine et al. suggested the transfer bootstrap expectation (TBE) branch support metric as an alternative to classical phylogenetic bootstrap support for taxon-rich datasets. However, the original TBE implementation in the booster tool is compute- and memory-intensive. Results We developed a fast and memory-efficient TBE implementation. We improve upon the original algorithm by Lemoine et al. via several algorithmic and technical optimizations. On empirical as well as on random tree sets with varying taxon counts, our implementation is up to 480 times faster than booster. Furthermore, it only requires memory that is linear in the number of taxa, which leads to 10× to 40× memory savings compared with booster. Availability and implementation Our implementation has been partially integrated into pll-modules and RAxML-NG and is available under the GNU Affero General Public License v3.0 at https://github.com/ddarriba/pll-modules and https://github.com/amkozlov/raxml-ng. The parallel version that also computes additional TBE-related statistics is available at: https://github.com/lutteropp/raxml-ng/tree/tbe. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals dsSwissKnife: An R package for federated data analysis

2020 ◽  
Author(s):  
Iulian Dragan ◽  
Thomas Sparsø ◽  
Dmitry Kuznetsov ◽  
Roderick Slieker ◽  
Mark Ibberson
Keyword(s):  
Type 2 Diabetes ◽  
Data Analysis ◽  
General Public ◽  
Biomarker Discovery ◽  
R Package ◽  
Link Type ◽  
General Public License

ABSTRACTSummarydsSwissKnife is an R package that enables several powerful analyses to be performed on federated datasets. The package works alongside DataSHIELD and extends its functionality. We have developed and implemented dsSwissKnife in a large IMI project on type 2 diabetes, RHAPSODY, where data from 10 observational cohorts have been harmonised and federated in CDISC SDTM format and made available for biomarker discovery.Availability and implementationdsSwissKnife is freely available online at https://github.com/sib-swiss/dsSwissKnife. The package is distributed under the GNU General Public License version [email protected]

scholarly journals Bashing irreproducibility with shournal

2020 ◽  
Author(s):  
Tycho Kirchner ◽  
Konstantin Riege ◽  
Steve Hoffmann
Keyword(s):  
Software Development ◽  
Computer Science ◽  
General Public ◽  
Development Projects ◽  
Entire Process ◽  
Link Type ◽  
Processing Steps ◽  
General Public License

AbstractArguably, one of the most important tools for computer science is the Linux shell. Processing steps carried out there are critical for many analyses and software development projects. However, manual documentation of the work is time-consuming and error-prone. To remedy this problem, shournal tightly integrates with the shell and automatically records all shell commands along with associated file events. For any file, shournal allows the reconstruction of the command history and is able to create detailed reports for whole project directories. shournal is based on the fanotify API and mount namespaces and allows the efficient monitoring of entire process trees.AvailabilityThe code for shournal is freely available at https://github.com/tycho-kirchner/shournal under the GNU General Public License v3.0 or [email protected]

7.2: A Memory-Efficient Implementation of Video Window Detection for a Digital Display Controller

2002 ◽  
Vol 33 (1) ◽  
pp. 64 ◽  
Author(s):  
Hemant Mallapur ◽  
N. Sakuntala ◽  
Hari Nair ◽  
Muthukrishnan Chinnasamy ◽  
Arun Johary
Keyword(s):  
Efficient Implementation ◽  
Digital Display ◽  
Memory Efficient

scholarly journals Does GPLv2 Include an ‘Installation Information’ Obligation? A Textual & Historical Analysis

2021 ◽  
Vol 12 (1) ◽  
pp. 21-33
Author(s):  
McCoy Smith
Keyword(s):  
General Public ◽  
Textual Analysis ◽  
Historical Analysis ◽  
Historical Record ◽  
Identical Result ◽  
Information Requirement ◽  
General Public License

One of the features included in version 3 of the GNU General Public License (GPLv3) was a requirement, in certain circumstances, to provide ‘Installation Information.’ This was a new addition to the licence to address a ‘loophole’ that existed in version 2 of the licence (GPLv2); a loophole that was perceived as being exploited, at the time, by certain device vendors. Recently, it has been asserted that this requirement was inherent, or explicitly called for, in GPLv2. This paper examines the historical record around the time that the ‘Installation Information’ requirement was proposed, and eventually ratified, in GPLv3, to show that this requirement was understood to be both new, and not a part of GPLv2. A textual analysis of GPLv2 yields an identical result.

scholarly journals Does GPLv2 Include an ‘Installation Information’ Obligation? A Textual & Historical Analysis

2021 ◽  
Vol 12 (1) ◽  
pp. 21-33
Author(s):  
McCoy Smith
Keyword(s):  
General Public ◽  
Textual Analysis ◽  
Historical Analysis ◽  
Historical Record ◽  
Identical Result ◽  
Information Requirement ◽  
General Public License

One of the features included in version 3 of the GNU General Public License (GPLv3) was a requirement, in certain circumstances, to provide ‘Installation Information.’ This was a new addition to the licence to address a ‘loophole’ that existed in version 2 of the licence (GPLv2); a loophole that was perceived as being exploited, at the time, by certain device vendors. Recently, it has been asserted that this requirement was inherent, or explicitly called for, in GPLv2. This paper examines the historical record around the time that the ‘Installation Information’ requirement was proposed, and eventually ratified, in GPLv3, to show that this requirement was understood to be both new, and not a part of GPLv2. A textual analysis of GPLv2 yields an identical result.

scholarly journals What is MySQL, History and Functions

2018 ◽  
Author(s):  
Charzon
Keyword(s):  
General Public ◽  
Management System ◽  
Database Management ◽  
Database Management System ◽  
Free Software ◽  
Audio Files ◽  
General Public License

What is MySQL - MySQL is a database management system (English: database management system) or a multi-purpose, multi-user DBMS, with around 6 million installations worldwide. MySQL AB makes MySQL available as free software under the GNU General Public License (GPL), but they also sell under commercial licenses for cases where its use does not match the use of GPL.You can think of a MySQL database as a container that stores strings (text based) data. Images, media, files, audio files, and things that are truly natural do not have to be stored in the database. The trick is to put the file file on the server in the folder and only reference the name and path in the database

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.

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