This proposed UFS ACM is the best preventive control around the world for heterogeneous applications on multiple hardware and software. The subject and object can be able to map, integrate, ...synchronize, and communicate through reading, writing, and executing over a UFS on the complex web infrastructure. We have to investigate the basic concepts behind access control design and enforcement and point out different security requirements that may need to be taken into consideration as per business, resources, and technology available to us. This paper has to formulate and implement several access control mechanisms, methods, and models on normalizing them step by step, which has been highlighted in the proposed model for present and future requirements. This research paper contributes to the development of an optimization model that aims to determine the optimal cost, time, and maximize the quality of services to be invested into security model and mechanisms deciding on the measure components of UFS.
With more microbiome studies being conducted by African-based research groups, there is an increasing demand for knowledge and skills in the design and analysis of microbiome studies and data. ...However, high-quality bioinformatics courses are often impeded by differences in computational environments, complicated software stacks, numerous dependencies, and versions of bioinformatics tools along with a lack of local computational infrastructure and expertise. To address this, H3ABioNet developed a 16S rRNA Microbiome Intermediate Bioinformatics Training course, extending its remote classroom model. The course was developed alongside experienced microbiome researchers, bioinformaticians, and systems administrators, who identified key topics to address. Development of containerised workflows has previously been undertaken by H3ABioNet, and Singularity containers were used here to enable the deployment of a standard replicable software stack across different hosting sites. The pilot ran successfully in 2019 across 23 sites registered in 11 African countries, with more than 200 participants formally enrolled and 106 volunteer staff for onsite support. The pulling, running, and testing of the containers, software, and analyses on various clusters were performed prior to the start of the course by hosting classrooms. The containers allowed the replication of analyses and results across all participating classrooms running a cluster and remained available posttraining ensuring analyses could be repeated on real data. Participants thus received the opportunity to analyse their own data, while local staff were trained and supported by experienced experts, increasing local capacity for ongoing research support. This provides a model for delivering topic-specific bioinformatics courses across Africa and other remote/low-resourced regions which overcomes barriers such as inadequate infrastructures, geographical distance, and access to expertise and educational materials.
Next-generation sequencing (NGS) is widely used in all areas of genetic research, such as genetic disease diagnosis and breeding, and it can produce massive amounts of data. The identification of ...sequence variants is an important step when processing large NGS datasets; however, currently, the process is complicated, repetitive, and requires concentration, which can be taxing on the researcher. Therefore, to support researchers who are not familiar enough with bioinformatics to identify sequence variations regularly from large datasets, we have developed a fully automated desktop software, NGSpop. NGSpop includes functionalities for all the variant calling and visualization procedures used when processing NGS data, such as quality control, mapping, filtering details, and variant calling. In the variant calling step, the user can select the GATK or DeepVariant algorithm for variant calling. These algorithms can be executed using pre-set pipelines and options or customized with the user-specified options. NGSpop is implemented using JavaFX (version 1.8) and can thus be run on Unix-like operating systems such as Ubuntu Linux (version 16.04, 18.0.4). Although several pipelines and visualization tools are available for NGS data analysis, most integrated environments do not support batch processes; thus, variant detection cannot be automated for population-level studies. The NGSpop software developed in this study has an easy-to-use interface and helps in rapid analysis of multiple NGS data from population studies. According to a benchmark test, it effectively reduced the carbon footprint in bioinformatics analysis by expending the least central processing unit heat and power. Additionally, this software makes it possible to use the GATK and DeepVariant algorithms more flexibly and efficiently than other programs by allowing users to choose between the algorithms. As a limitation, NGSpop currently supports only the sequencing reads in fastq format produced by the Illumina platform. NGSpop is freely available at
https://sourceforge.net/projects/ngspop/
.
We describe recent extensions of the program SPhenoincluding flavour aspects, CP-phases, R-parity violation and low energy observables. In case of flavour mixing all masses of supersymmetric ...particles are calculated including the complete flavour structure and all possible CP-phases at the 1-loop level. We give details on implemented seesaw models, low energy observables and the corresponding extension of the SUSY Les Houches Accord. Moreover, we comment on the possibilities to include MSSM extensions in SPheno.
Program title: SPheno
Catalogue identifier: ADRV_v2_0
Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADRV_v2_0.html
Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland
Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html
No. of lines in distributed program, including test data, etc.: 154062
No. of bytes in distributed program, including test data, etc.: 1336037
Distribution format: tar.gz
Programming language: Fortran95.
Computer: PC running under Linux, should run in every Unix environment.
Operating system: Linux, Unix.
Classification: 11.6.
Catalogue identifier of previous version: ADRV_v1_0
Journal reference of previous version: Comput. Phys. Comm. 153(2003)275
Does the new version supersede the previous version?: Yes
Nature of problem:
The first issue is the determination of the masses and couplings of supersymmetric particles in various supersymmetric models, the R-parity conserved MSSM with generation mixing and including CP-violating phases, various seesaw extensions of the MSSM and the MSSM with bilinear R-parity breaking. Low energy data on Standard Model fermion masses, gauge couplings and electroweak gauge boson masses serve as constraints. Radiative corrections from supersymmetric particles to these inputs must be calculated. Theoretical constraints on the soft SUSY breaking parameters from a high scale theory are imposed and the parameters at the electroweak scale are obtained from the high scale parameters by evaluating the corresponding renormalisation group equations. These parameters must be consistent with the requirement of correct electroweak symmetry breaking. The second issue is to use the obtained masses and couplings for calculating decay widths and branching ratios of supersymmetric particles as well as the cross sections for these particles in electron–positron annihilation. The third issue is to calculate low energy constraints in the B-meson sector such as BR(b s), MB s, rare lepton decays, such as BR(e), the SUSY contributions to anomalous magnetic moments and electric dipole moments of leptons, the SUSY contributions to the ρ parameter as well as lepton flavour violating Z decays.
Solution method:
The renormalisation connecting a high scale and the electroweak scale is calculated by the Runge-Kutta method. Iteration provides a solution consistent with the multi-boundary conditions. In case of three-body decays and for the calculation of initial state radiation Gaussian quadrature is used for the numerical solution of the integrals.
Reasons for new version: Inclusion of new models as well as additional observables. Moreover, a new standard for data transfer had been established, which is now supported.
Summary of revisions: The already existing models have been extended to include also CP-violation and flavour mixing. The data transfer is done using the so-called SLHA2 standard. In addition new models have been included: all three types of seesaw models as well as bilinear R-parity violation. Moreover, additional observables are calculated: branching ratios for flavour violating lepton decays, EDMs of leptons and of the neutron, CP-violating mass difference in the B-meson sector and branching ratios for flavour violating b-quark decays.
Restrictions: In case of R-parity violation the cross sections are not calculated.
Running time: 0.2 seconds on an Intel(R) Core(TM)2 Duo CPU T9900 with 3.06 GHz
Based on the OPP technique and the HELAC framework, HELAC-1LOOP is a program that is capable of numerically evaluating QCD virtual corrections to scattering amplitudes. A detailed presentation of the ...algorithm is given, along with instructions to run the code and benchmark results. The program is part of the HELAC-NLO framework that allows for a complete evaluation of QCD NLO corrections.
Program title:HELAC-1LOOP
Catalogue identifier: AEOC_v1_0
Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOC_v1_0.html
Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland
Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html
No. of lines in distributed program, including test data, etc.: 290945
No. of bytes in distributed program, including test data, etc.: 3013326
Distribution format: tar.gz
Programming language: Fortran (gfortran(http://gcc.gnu.org/fortran/), lahey95 (http://www.lahey.com), ifort3(http://software.intel.com)).
Computer: Any.
Operating system: Linux, Unix, Mac OS.
Classification: 11.1.
Nature of problem:
The evaluation of virtual one-loop amplitudes for multi-particle scattering is a long-standing problem 1. In recent years the OPP reduction technique 2 opened the road for a fully numerical approach based on the evaluation of the one-loop amplitude for well-defined values of the loop momentum.
Solution method:
By using HELAC 3–5 and CutTools 6, HELAC-1LOOP is capable of evaluating QCD virtual corrections 7. The one-loop n-particle amplitudes are constructed as part of the n+2 tree-order ones, by using the basic recursive algorithm used in HELAC. A Les Houches Event (LHE) file is produced, combining the complete information from tree-order and virtual one-loop contributions. In conjunction with real corrections, obtained with the use of HELAC-DIPOLES 8, the full NLO corrections can be computed. The program has been successfully used in many applications.
Running time:
Depending on the number of particles and generated events from seconds to days.
References:
1R.K. Ellis, Z. Kunszt, K. Melnikov and G. Zanderighi, arXiv:1105.4319hepph.2G. Ossola, C. G. Papadopoulos and R. Pittau, Nucl. Phys. B 763 (2007) 147 arXiv:hep-ph/0609007.3A. Kanaki and C. G. Papadopoulos, Comput. Phys. Commun. 132 (2000) 306 arXiv:hep-ph/0002082.4C. G. Papadopoulos, Comput. Phys. Commun. 137 (2001) 247 arXiv:hepph/ 0007335.5A. Cafarella, C. G. Papadopoulos and M. Worek, Comput. Phys. Commun. 180 (2009) 1941 arXiv:0710.2427 hep-ph.6G. Ossola, C. G. Papadopoulos and R. Pittau, JHEP 0803 (2008) 042 arXiv:0711.3596 hep-ph.7A. van Hameren, C. G. Papadopoulos and R. Pittau, JHEP 0909, 106 (2009) arXiv:0903.4665 hep-ph.8M. Czakon, C. G. Papadopoulos and M. Worek, JHEP 0908, 085 (2009) arXiv:0905.0883 hep-ph.
SweepFinder is a widely used program that implements a powerful likelihood-based method for detecting recent positive selection, or selective sweeps. Here, we present SweepFinder2, an extension of ...SweepFinder with increased sensitivity and robustness to the confounding effects of mutation rate variation and background selection. Moreover, SweepFinder2 has increased flexibility that enables the user to specify test sites, set the distance between test sites and utilize a recombination map.
SweepFinder2 is a freely-available (www.personal.psu.edu/mxd60/sf2.html) software package that is written in C and can be run from a Unix command line.
mxd60@psu.edu.
In the second article of the series, we present the Gibbs2 code, a Fortran90 reimplementation of the original Gibbs program Comput. Phys. Commun. 158 (2004) 57 for the calculation of ...pressure–temperature dependent thermodynamic properties of solids under the quasiharmonic approximation. We have taken advantage of the detailed analysis carried out in the first paper to implement robust fitting techniques. In addition, new models to introduce temperature effects have been incorporated, from the simple Debye model contained in the original article to a full quasiharmonic model that requires the phonon density of states at each calculated volume. Other interesting novel features include the empirical energy corrections, that rectify systematic errors in the calculation of equilibrium volumes caused by the choice of the exchange-correlation functional, the electronic contributions to the free energy and the automatic computation of phase diagrams. Full documentation in the form of a userʼs guide and a complete set of tests and sample data are provided along with the source code.
Program title:Gibbs2
Catalogue identifier: AEJI_v1_0
Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJI_v1_0.html
Program obtainable from: CPC Program Library, Queenʼs University, Belfast, N. Ireland
Licensing provisions: GNU General Public License, v3
No. of lines in distributed program, including test data, etc.: 936 087
No. of bytes in distributed program, including test data, etc.: 8 596 671
Distribution format: tar.gz
Programming language: Fortran90
Computer: Any running Unix/Linux
Operating system: Unix, GNU/Linux
Classification: 7.8
External routines: Part of the minpack, pppack and slatec libraries (downloaded from www.netlib.org) are distributed along with the program.
Nature of problem: Given the static E(V) curve, and possibly vibrational information such as the phonon density of states, calculate the equilibrium volume and thermodynamic properties of a solid at arbitrary temperatures and pressures in the framework of the quasiharmonic approximation.
Additional comments: A detailed analysis concerning the fitting of equations of state has been carried out in the first part of this article, and implemented in the code presented here.
Running time: The tests provided only take a few seconds to run.
► Calculation of thermodynamic properties from first principles data. ► Robust fitting of energy versus volume curves using averages of strain polynomials. ► Models for introducing ab initio temperature effects under the quasiharmonic approximation. ► A Fortran90 program implementing the techniques: Gibbs2.
The classification of transposable elements (TEs) is key step towards deciphering their potential impact on the genome. However, this process is often based on manual sequence inspection by TE ...experts. With the wealth of genomic sequences now available, this task requires automation, making it accessible to most scientists. We propose a new tool, PASTEC, which classifies TEs by searching for structural features and similarities. This tool outperforms currently available software for TE classification. The main innovation of PASTEC is the search for HMM profiles, which is useful for inferring the classification of unknown TE on the basis of conserved functional domains of the proteins. In addition, PASTEC is the only tool providing an exhaustive spectrum of possible classifications to the order level of the Wicker hierarchical TE classification system. It can also automatically classify other repeated elements, such as SSR (Simple Sequence Repeats), rDNA or potential repeated host genes. Finally, the output of this new tool is designed to facilitate manual curation by providing to biologists with all the evidence accumulated for each TE consensus.
PASTEC is available as a REPET module or standalone software (http://urgi.versailles.inra.fr/download/repet/REPET_linux-x64-2.2.tar.gz). It requires a Unix-like system. There are two standalone versions: one of which is parallelized (requiring Sun grid Engine or Torque), and the other of which is not.
A priori prediction of phase stability of materials is a challenging practice, requiring knowledge of all energetically competing structures at formation conditions. Large materials ...repositorieshousing properties of both experimental and hypothetical compoundsoffer a path to prediction through the construction of informatics-based, ab initio phase diagrams. However, limited access to relevant data and software infrastructure has rendered thermodynamic characterizations largely peripheral, despite their continued success in dictating synthesizability. Herein, a new module is presented for autonomous thermodynamic stability analysis, implemented within the open-source, ab initio framework AFLOW. Powered by the AFLUX Search-API, AFLOW-CHULL leverages data of more than 1.8 million compounds characterized in the AFLOW.org repository, and can be employed locally from any UNIX-like computer. The module integrates a range of functionality: the identification of stable phases and equivalent structures, phase coexistence, measures for robust stability, and determination of decomposition reactions. As a proof of concept, thermodynamic characterizations have been performed for more than 1300 binary and ternary systems, enabling the identification of several candidate phases for synthesis based on their relative stability criterionincluding 17 promising C15 b -type structures and 2 half-Heuslers. In addition to a full report included herein, an interactive, online web application has been developed showcasing the results of the analysis and is located at aflow.org/aflow-chull.
The Dalton quantum chemistry program system Aidas, Kestutis; Angeli, Celestino; Bak, Keld L. ...
Wiley interdisciplinary reviews. Computational molecular science,
May/June 2014, Letnik:
4, Številka:
3
Journal Article
Recenzirano
Odprti dostop
Dalton is a powerful general‐purpose program system for the study of molecular electronic structure at the Hartree–Fock, Kohn–Sham, multiconfigurational self‐consistent‐field, Møller–Plesset, ...configuration‐interaction, and coupled‐cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic‐structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge‐origin‐invariant manner. Frequency‐dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one‐, two‐, and three‐photon processes. Environmental effects may be included using various dielectric‐medium and quantum‐mechanics/molecular‐mechanics models. Large molecules may be studied using linear‐scaling and massively parallel algorithms. Dalton is distributed at no cost from http://www.daltonprogram.org for a number of UNIX platforms.
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Software > Quantum Chemistry
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