We present the TRIQS library, a Toolbox for Research on Interacting Quantum Systems. It is an open-source, computational physics library providing a framework for the quick development of ...applications in the field of many-body quantum physics, and in particular, strongly-correlated electronic systems. It supplies components to develop codes in a modern, concise and efficient way: e.g. Green’s function containers, a generic Monte Carlo class, and simple interfaces to HDF5. TRIQS is a C++/Python library that can be used from either language. It is distributed under the GNU General Public License (GPLv3). State-of-the-art applications based on the library, such as modern quantum many-body solvers and interfaces between density-functional-theory codes and dynamical mean-field theory (DMFT) codes are distributed along with it.
Program title: TRIQS
Catalogue identifier: AEWR_v1_0
Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEWR_v1_0.html
Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland
Licensing provisions: GNU General Public License (GPLv3)
No. of lines in distributed program, including test data, etc.: 93228
No. of bytes in distributed program, including test data, etc.: 2979367
Distribution format: tar.gz
Programming language: C++/Python.
Computer: Any architecture with suitable compilers including PCs and clusters.
Operating system: Unix, Linux, OSX.
RAM: Highly problem-dependent
Classification: 7.3, 20.
External routines: cmake, mpi, boost, FFTW, GMP, BLAS, LAPACK, HDF5, NumPy, SciPy, h5py, mpi4py, mako.
Nature of problem:
Need for a modern programming framework to quickly write simple, efficient and higher-level code applicable to the studies of strongly-correlated electron systems.
Solution method:
We present a C++/Python open-source computational library that provides high-level abstractions for common objects and various tools in the field of quantum many-body physics, thus forming a framework for developing applications.
Running time:
Tests take less than a minute. Otherwise it is highly problem dependent (from minutes to several days).
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We present TRIQS/CTHYB, a state-of-the art open-source implementation of the continuous-time hybridisation expansion quantum impurity solver of the TRIQS package. This code is mainly designed to be ...used with the TRIQS library in order to solve the self-consistent quantum impurity problem in a multi-orbital dynamical mean field theory approach to strongly-correlated electrons, in particular in the context of realistic electronic structure calculations. It is implemented in C++ for efficiency and is provided with a high-level Python interface. The code ships with a new partitioning algorithm that divides the local Hilbert space without any user knowledge of the symmetries and quantum numbers of the Hamiltonian. Furthermore, we implement higher-order configuration moves and show that such moves are necessary to ensure ergodicity of the Monte Carlo in common Hamiltonians even without symmetry-breaking.
Program title: TRIQS/CTHYB
Catalogue identifier: AEYU_v1_0
Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEYU_v1_0.html
Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland.
Licensing provisions: GNU General Public Licence (GPLv3)
No. of lines in distributed program, including test data, etc.: 159,017
No. of bytes in distributed program, including test data, etc.: 10,215,893
Distribution format: tar.gz
Programming language: C++/Python.
Computer: Any architecture with suitable compilers including PCs and clusters.
Operating system: Unix, Linux, OSX.
RAM: Highly problem-dependent
Classification: 7.3, 4.4.
External routines: TRIQS, cmake.
Nature of problem: Accurate solvers for quantum impurity problems are needed in condensed matter theory.
Solution method: We present an efficient C++/Python open-source implementation of a continuous-time hybridisation expansion solver.
Running time: Tests take less than a minute. Otherwise it is highly problem dependent (from minutes to several days).
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Scratch is a visual programming environment that allows users (primarily ages 8 to 16) to learn computer programming while working on personally meaningful projects such as animated stories and ...games. A key design goal of Scratch is to support self-directed learning through tinkering and collaboration with peers. This article explores how the Scratch programming language and environment support this goal. (Contains 10 figures, 1 table, and 1 footnote.)
A review of spline function procedures in R Perperoglou, Aris; Sauerbrei, Willi; Abrahamowicz, Michal ...
BMC medical research methodology,
03/2019, Volume:
19, Issue:
1
Journal Article
Peer reviewed
Open access
With progress on both the theoretical and the computational fronts the use of spline modelling has become an established tool in statistical regression analysis. An important issue in spline ...modelling is the availability of user friendly, well documented software packages. Following the idea of the STRengthening Analytical Thinking for Observational Studies initiative to provide users with guidance documents on the application of statistical methods in observational research, the aim of this article is to provide an overview of the most widely used spline-based techniques and their implementation in R.
In this work, we focus on the R Language for Statistical Computing which has become a hugely popular statistics software. We identified a set of packages that include functions for spline modelling within a regression framework. Using simulated and real data we provide an introduction to spline modelling and an overview of the most popular spline functions.
We present a series of simple scenarios of univariate data, where different basis functions are used to identify the correct functional form of an independent variable. Even in simple data, using routines from different packages would lead to different results.
This work illustrate challenges that an analyst faces when working with data. Most differences can be attributed to the choice of hyper-parameters rather than the basis used. In fact an experienced user will know how to obtain a reasonable outcome, regardless of the type of spline used. However, many analysts do not have sufficient knowledge to use these powerful tools adequately and will need more guidance.
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Motivation: Robust large-scale sequence analysis is a major challenge in modern genomic science, where biologists are frequently trying to characterize many millions of sequences. Here, we describe a ...new Java-based architecture for the widely used protein function prediction software package InterProScan. Developments include improvements and additions to the outputs of the software and the complete reimplementation of the software framework, resulting in a flexible and stable system that is able to use both multiprocessor machines and/or conventional clusters to achieve scalable distributed data analysis. InterProScan is freely available for download from the EMBl-EBI FTP site and the open source code is hosted at Google Code.
Availability and implementation: InterProScan is distributed via FTP at ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/ and the source code is available from http://code.google.com/p/interproscan/.
Contact:
http://www.ebi.ac.uk/support or interhelp@ebi.ac.uk or mitchell@ebi.ac.uk
The aim of this study is to examine the effect of programming instruction with Scratch on student motivation and their programming achievements. The study group consisted of 52 sophomore students ...attending the Department of Computer Education and Instructional Technologies of Mehmet Akif Ersoy University's Faculty of Education, Turkey. Participants were randomly divided into two groups in order to have 26 students in both the test group and the control group. During the first seven weeks of the study, it is aimed that the students will understand programming logic and learn basic programming structures. For this purpose, participants in the test group were instructed using Scratch, whilst in the control group, flowcharting and problem-solving activities were conducted as per the curriculum. During the second seven weeks of the study, C# programming language instruction was conducted using the same method for both the test and control groups. Achievement Test and Motivated Strategies for Learning Questionnaire were utilized as data collection tools in the study, and a 3 × 2 (measurement time x groups) factorial design was employed. Study findings revealed that programming achievement scores for both the test and control groups increased at the end of the whole process; however, the increase was significantly different in favor of the test group at the end of the whole process. It was observed that motivation scores decreased in the control group, while the test group's scores increased.
•Flow chart activities decrease participants' motivation.•Scratch activities increase participants' motivation.•The rise of motivation continue during C# instruction process.•Scratch activities are more effective in improving the programming achievements then flowcharts activities.
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Ontologies are invaluable in the life sciences, but building and maintaining ontologies often requires a challenging number of distinct tasks such as running automated reasoners and quality control ...checks, extracting dependencies and application-specific subsets, generating standard reports, and generating release files in multiple formats. Similar to more general software development, automation is the key to executing and managing these tasks effectively and to releasing more robust products in standard forms. For ontologies using the Web Ontology Language (OWL), the OWL API Java library is the foundation for a range of software tools, including the Protégé ontology editor. In the Open Biological and Biomedical Ontologies (OBO) community, we recognized the need to package a wide range of low-level OWL API functionality into a library of common higher-level operations and to make those operations available as a command-line tool.
ROBOT (a recursive acronym for "ROBOT is an OBO Tool") is an open source library and command-line tool for automating ontology development tasks. The library can be called from any programming language that runs on the Java Virtual Machine (JVM). Most usage is through the command-line tool, which runs on macOS, Linux, and Windows. ROBOT provides ontology processing commands for a variety of tasks, including commands for converting formats, running a reasoner, creating import modules, running reports, and various other tasks. These commands can be combined into larger workflows using a separate task execution system such as GNU Make, and workflows can be automatically executed within continuous integration systems.
ROBOT supports automation of a wide range of ontology development tasks, focusing on OBO conventions. It packages common high-level ontology development functionality into a convenient library, and makes it easy to configure, combine, and execute individual tasks in comprehensive, automated workflows. This helps ontology developers to efficiently create, maintain, and release high-quality ontologies, so that they can spend more time focusing on development tasks. It also helps guarantee that released ontologies are free of certain types of logical errors and conform to standard quality control checks, increasing the overall robustness and efficiency of the ontology development lifecycle.
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Metagenomics Data Visualization Using R Coleman, Alex; Bose, Anupam; Mitra, Suparna
Methods in molecular biology (Clifton, N.J.),
2023, Volume:
2649
Journal Article
Communicating key finds is a crucial part of the research process. Data visualization is the field of graphically representing data to help communicate key findings. Building on previous chapters ...around data manipulating using the R programming language this, chapter will explore how to use R to plot data and generate high-quality graphics. It will cover plotting using the base R plotting functionality and introduce the famous ggplot2 package 2 that is widely used for data visualization in R. After this general introduction to data visualization tools, the chapter will explore more specific data visualization techniques for metagenomics data and their use cases using these basic packages.
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