Input File Format Research Articles

Grenedalf: population genetic statistics for the next generation of pool sequencing.

Pool sequencing is an efficient method for capturing genome-wide allele frequencies from multiple individuals, with broad applications such as studying adaptation in Evolve-and-Resequence experiments, monitoring of genetic diversity in wild populations, and genotype-to-phenotype mapping. Here, we present grenedalf, a command line tool written in C++ that implements common population genetic statistics such as θ, Tajima's D, and FST for Pool sequencing. It is orders of magnitude faster than current tools, and is focused on providing usability and scalability, while also offering a plethora of input file formats and convenience options. grenedalf is published under the GPL-3, and freely available at github.com/lczech/grenedalf.

FaultQuake: An open-source Python tool for estimating Seismic Activity Rates in faults

In regions experiencing ongoing aseismic deformation, fault’s Activity Rate (AR) calculations often lead to an overestimation of hazard potential. This study proposes a novel methodology that integrates the Seismic Coupling Coefficient (SCC) into the fault Seismic Activity Rate (SAR) calculation process to discriminate seismic moment rates. We introduce FaultQuake, an open-source Python tool equipped with a Graphical User Interface (GUI), designed to implement this methodology and accurately estimate SAR for faults. These activity rates can be included in Probabilistic Seismic Hazard Assessment (PSHA) frameworks and assist in differentiating the seismic and aseismic deformation. FaultQuake also presents an innovative embedded workflow, the Optimal Value Computation Workflow (OVCW), based on Conflation of Probabilities (CoP), for calculating the Maximum Magnitude (Mmax) from the empirical relationships and the observed magnitudes (Mobs) assigned to a single fault. This enhancement improves the estimation of seismic moment rates and the SAR calculation process. FaultQuake outputs are provided in the format of OpenQuake engine input files to facilitate the PSHA process. We present a sample case study focusing on the PSHA of a region in southern Iran characterized by a substantial aseismic deformation to illustrate the practical application of FaultQuake in seismic hazard analysis. Peak Ground Acceleration (PGA) maps for 10% and 2% Probabilities of Exceedance (PoE) are plotted to compare PGAs with and without applying the FaultQuake algorithm. The results provide an enhanced view of the area’s hazard with mitigation of the overestimation, resulting in more representative hazard maps. The source codes of FaultQuake are available at the FaultQuake GitHub repository, contributing to the computer and geoscience community.

MzDOCK: A free ready-to-use GUI-based pipeline for molecular docking simulations.

Molecular docking is by far the most preferred approach in structure-based drug design for its effectiveness to predict the scoring and posing of a given bioactive small molecule into the binding site of its pharmacological target. Herein, we present MzDOCK, a new GUI-based pipeline for Windows operating system, designed with the intent of making molecular docking easier to use and higher reproducible even for inexperienced people. By harmonic integration of python and batch scripts, which employs various open source packages such as Smina (docking engine), OpenBabel (file conversion) and PLIP (analysis), MzDOCK includes many practical options such as: binding site configuration based on co-crystallized ligands; generation of enantiomers from SMILES input; application of different force fields (MMFF94, MMFF94s, UFF, GAFF, Ghemical) for energy minimization; retention of selectable ions and cofactors; sidechain flexibility of selectable binding site residues; multiple input file format (SMILES, PDB, SDF, Mol2, Mol); generation of reports and of pictures for interactive visualization. Users can download for free MzDOCK at the following link: https://github.com/Muzatheking12/MzDOCK.

Male Pedigree Toolbox: A Versatile Software for Y-STR Data Analyses.

Y-chromosomal short tandem repeats (Y-STRs) are widely used in forensic, genealogical, and population genetics. With the recent increase in the number of rapidly mutating (RM) Y-STRs, an unprecedented level of male differentiation can be achieved, widening and improving the applications of Y-STRs in various fields, including forensics. The growing complexity of Y-STR data increases the need for automated data analyses, but dedicated software tools are scarce. To address this, we present the Male Pedigree Toolbox (MPT), a software tool for the automated analysis of Y-STR data in the context of patrilineal genealogical relationships. The MPT can estimate mutation rates and male relative differentiation rates from input Y-STR pedigree data. It can aid in determining ancestral haplotypes within a pedigree and visualize the genetic variation within pedigrees in all branches of family trees. Additionally, it can provide probabilistic classifications using machine learning, helping to establish or prove the structure of the pedigree and the level of relatedness between males, even for closely related individuals with highly similar haplotypes. The tool is flexible and easy to use and can be adjusted to any set of Y-STR markers by modifying the intuitive input file formats. We introduce the MPT software tool v1.0 and make it publicly available with the goal of encouraging and supporting forensic, genealogical, and other geneticists in utilizing the full potential of Y-STRs for both research purposes and practical applications, including criminal casework.

H-wave – A Python package for the Hartree-Fock approximation and the random phase approximation

H-wave is an open-source software package for performing the Hartree–Fock approximation (HFA) and random phase approximation (RPA) for a wide range of Hamiltonians of interacting fermionic systems. In HFA calculations, H-wave examines the stability of several symmetry-broken phases, such as anti-ferromagnetic and charge-ordered phases, in the given Hamiltonians at zero and finite temperatures. Furthermore, H-wave calculates the dynamical susceptibilities using RPA to examine the instability toward the symmetry-broken phases. By preparing a simple input file for specifying the Hamiltonians, users can perform HFA and RPA for standard Hamiltonians in condensed matter physics, such as the Hubbard model and its extensions. Additionally, users can use a Wannier90-like format to specify fermionic Hamiltonians. A Wannier90 format is implemented in RESPACK to derive ab initio Hamiltonians for solids. HFA and RPA for the ab initio Hamiltonians can be easily performed using H-wave. In this paper, we first explain the basis of HFA and RPA, and the basic usage of H-wave, including download and installation. Thereafter, the input file formats implemented in H-wave, including the Wannier90-like format for specifying the interacting fermionic Hamiltonians, are discussed. Finally, we present several examples of H-wave such as zero-temperature HFA calculations for the extended Hubbard model on a square lattice, finite-temperature HFA calculations for the Hubbard model on a cubic lattice, and RPA in the extended Hubbard model on a square lattice. Program summaryProgram Title:H-waveCPC Library link to program files:https://doi.org/10.17632/9gr6pxhfjm.1Developer's repository link:https://github.com/issp-center-dev/H-waveCode Ocean capsule:https://codeocean.com/capsule/6875177Licensing provisions: GNU General Public License version 3Programming language: Python3External routines/libraries: NumPy, SciPy, Tomli, Requests.Nature of problem: Physical properties of strongly correlated electrons are examined such as ground state phase structure and response functions at zero and finite temperatures.Solution method: Calculations based on the unrestricted Hartree-Fock approximation and the random phase approximation are performed for the quantum lattice models such as the Hubbard model and its extensions.

Bayesian hybrid index and genomic cline estimation with the R package gghybrid.

Admixture, the interbreeding of individuals from differentiated source populations, is now known to be a widespread phenomenon. Genomic studies of natural hybridisation can help to answer many questions on the impacts of admixture on adaptive evolution, reproductive isolation, and speciation. When a large variety of admixture proportions between two source populations exist, both geographic and genomic cline analysis are suitable methods for inferring biased, restricted or excessive gene flow at individual loci into the foreign genomic background, providing evidence for reproductive isolation, selection across an environmental transition, balancing selection, and adaptive introgression. Genomic cline analysis replaces geographic location with genome-wide hybrid index and is therefore useable in circumstances that violate geographic cline assumptions. Here, I introduce gghybrid, an R package for simple and flexible Bayesian estimation of Buerkle's hybrid index and Fitzpatrick's logit-logistic genomic clines using bi-allelic data, suitable for both small and large datasets. gghybrid allows any ploidy and uses Structure input file format. It has separate functions for hybrid index and cline estimation, treating each individual and locus respectively as an independent analysis, making it highly parallelisable. Admixture proportions from other software can alternatively be used in cline analysis, alongside parental allele frequencies. Parameters can be fixed and samples pooled for statistical model comparison with AIC or waic. Here, I describe the functions, pipeline, and statistical properties of gghybrid. Simulations reveal that model comparison with waic is preferred, and use of Bayesian posterior distributions and p values to select candidate non-null loci is problematic and should be avoided.

Phasor identifier: A cloud-based analysis of phasor-FLIM data on Python notebooks

This paper introduces an innovative approach utilizing Google Colaboratory for the versatile analysis of phasor fluorescence lifetime imaging microscopy (FLIM) data collected from various samples (e.g., cuvette, cells, tissues) and in various input file formats. In fact, phasor-FLIM widespread adoption has been hampered by complex instrumentation and data analysis requirements. We mean to make advanced FLIM analysis more accessible to researchers through a cloud-based solution that 1) harnesses robust computational resources, 2) eliminates hardware limitations, and 3) supports both CPU and GPU processing. We envision a paradigm shift in FLIM data accessibility and potential, aligning with the evolving field of artificial intelligence-driven FLIM analysis. This approach simplifies FLIM data handling and opens doors for diverse applications, from studying cellular metabolism to investigating drug encapsulation, benefiting researchers across multiple domains. The comparative analysis of freely distributed FLIM tools highlights the unique advantages of this approach in terms of adaptability, scalability, and open-source nature.

Darfix - data analysis for dark-field X-ray microscopy.

A Python package for the analysis of dark-field X-ray microscopy (DFXM) and rocking curve imaging (RCI) data is presented. DFXM is a non-destructive diffraction imaging technique that provides three-dimensional maps of lattice strain and orientation. The darfix package enables fast processing and visualization of these data, providing the user with the essential tools to extract information from the acquired images in a fast and intuitive manner. These data processing and visualization tools can be either imported as library components or accessed through a graphical user interface as an Orange add-on. In the latter case, the different analysis modules can be easily chained to define computational workflows. Operations on larger-than-memory image sets are supported through the implementation of online versions of the data processing algorithms, effectively trading performance for feasibility when the computing resources are limited. The software can automatically extract the relevant instrument angle settings from the input files' metadata. The currently available input file format is EDF and in future releases HDF5 will be incorporated.

VSFlow: an open-source ligand-based virtual screening tool

Ligand-based virtual screening is a widespread method in modern drug design. It allows for a rapid screening of large compound databases in order to identify similar structures. Here we report an open-source command line tool which includes a substructure-, fingerprint- and shape-based virtual screening. Most of the implemented features fully rely on the RDKit cheminformatics framework. VSFlow accepts a wide range of input file formats and is highly customizable. Additionally, a quick visualization of the screening results as pdf and/or pymol file is supported.Graphical

Performance Evaluation of Large-Scale Green Roofs Based on Qualitative and Quantitative Runoff Modeling Using MUSICX

Green roofs (GR) are known as one of the most effective water-sensitive urban design (WSUD) strategies to deal with numerous environmental and social issues that urbanized cities face today. The overall quality of research on GRs has significantly improved and an increasing trend is observed in the amount of research over the last decade. Among several approaches, the application of modeling tools is observed to be an effective method to simulate and evaluate the performance of GRs. Given that studies on GRs at a catchment scale are limited, this paper aims to provide a simple but effective framework for estimating the catchment-scale impacts of GR on runoff quantity and quality. MUSICX, an Australian-developed software that possesses the advantages of a conceptual model, is chosen as the modeling tool in this study. While MUSICX has built-in meteorological templates for Australian regions, this tool also supports several climate input file formats for application by modelers in other parts of the world. This paper presents two different modeling approaches using the Land Use node and Bioretention node in MUSICX. The steps used for model calibration are also provided in this paper. The modeling results present the annual reductions in runoff volume, total suspended solid (TSS), total phosphate (TP), and total nitrogen (TN) load. The largest reductions of roughly 30% per year were observed in runoff volume and TN load. The annual runoff reduction rate reported in this study is close to that of other published results. Similar research outcomes quantifying the benefits of GRs play a major role in facilitating the widespread implementation of GRs due to the awareness of both positive and negative impacts of GRs. Future studies are recommended to concentrate on modeling the impacts of implementing GRs at a large scale (i.e., scales exceeding the single-building scale) to fill the research gaps and enhance the modeling accuracy.

ExRec: a python pipeline for generating recombination-filtered multi-locus datasets

Abstract Summary ExRec (Exclusion of Recombined DNA) is a dependency-free Python pipeline that implements the four-gamete test to automatically filter out recombined DNA blocks from thousands of DNA sequence loci. This procedure helps all loci better meet the “no intralocus recombination” assumption common to many coalescent-based analyses in population genomic, phylogeographic, and shallow-scale phylogenomic studies. The user-friendly pipeline contains five standalone applications—four file conversion scripts and one main script that performs the recombination filtering procedures. The pipeline outputs recombination-filtered data in a variety of common formats and a tab-delimited table that displays descriptive statistics for all loci and the analysis results. A novel feature of this software is that the user can select whether to output the longest nonrecombined sequence blocks from recombined loci (current best practice) or randomly select nonrecombined blocks from loci (a newer approach). We tested ExRec with six published phylogenomic datasets that ranged in size from 27 to 2237 loci and came in a variety of input file formats. In all trials the data could be easily analyzed in only seconds for the smaller datasets and <30 min for the largest using a simple laptop computer. Availability and implementation ExRec was written in Python 3 under the MIT license. The program applications, user manual (including step-by-step tutorials), and sample data are freely available at https://github.com/Sammccarthypotter/ExRec.

Using PlaPPISite to Predict and Analyze Plant Protein-Protein Interaction Sites.

Proteome-wide characterization of protein-protein interactions (PPIs) is crucial to understand the functional roles of protein machinery within cells systematically. With the accumulation of PPI data in different plants, the interaction details of binary PPIs, such as the three-dimensional (3D) structural contexts of interaction sites/interfaces, are urgently demanded. To meet this requirement, we have developed a comprehensive and easy-to-use database called PlaPPISite ( http://zzdlab.com/plappisite/index.php ) to present interaction details for 13 plant interactomes. Here, we provide a clear guide on how to search and view protein interaction details through the PlaPPISite database. Firstly, the running environment of our database is introduced. Secondly, the input file format is briefly introduced. Moreover, we discussed which information related to interaction sites can be achieved through several examples. In addition, some notes about PlaPPISite are also provided. More importantly, we would like to emphasize the importance of interaction site information in plant systems biology through this user guide of PlaPPISite. In particular, the easily accessible 3D structures of PPIs in the coming post-AlphaFold2 era will definitely boost the application of plant interactome to decipher the molecular mechanisms of many fundamental biological issues.

Interchange, Extension and Validation of R-matrix fits for gamma production

The R-matrix method of Lane and Thomas is the standard procedure for modeling resonances at low energies, to determine widths and angular distributions needed for nuclear evaluations. Many different codes have been written with different input and output file formats, so a new code FERDINAND is available to interchange parameters. The standard procedure requires fixed boundary condition constants, so the ansatz of allowing energy-dependence for such ‘constants’ should be deprecated. The future need for larger R-matrix fits with more target excited states, to enable better prediction of gamma-rays from the decays of those states, will almost certainly be facilitated by the GPU parallel methods that are now appearing.

Predicting Protein Interaction Sites Using PITHIA.

Several proteins work independently, but the majority work together to maintain the functions of the cell. Thus, it is crucial to know the interaction sites that facilitate protein-protein interactions. The development of effective computational methods is essential because experimental methods are expensive and time-consuming. This chapter is a guide to predicting protein interaction sites using the program "PITHIA." First, some installation guides are presented, followed by descriptions of input file formats. Afterward, PITHIA's commands and options are outlined with examples. Moreover, some notes are provided on how to extend PITHIA's installation and usage.

Probabilistic computations of virial coefficients of polymeric structures described by rigid configurations of spherical particles: A fundamental extension of the ZENO program.

We describe an extension of the ZENO program for polymer and nanoparticle characterization that allows for precise calculation of the virial coefficients, with uncertainty estimates, of polymeric structures described by arbitrary rigid configurations of hard spheres. The probabilistic method of virial computation used for this extension employs a previously developed Mayer-sampling Monte Carlo method with overlap sampling that allows for a reduction of bias in the Monte Carlo averaging. This capability is an extension of ZENO in the sense that the existing program is also based on probabilistic sampling methods and involves the same input file formats describing polymer and nanoparticle structures. We illustrate the extension's capabilities, demonstrate its accuracy, and quantify the efficiency of this extension of ZENO by computing the second, third, and fourth virial coefficients and metrics quantifying the difficulty of their calculation, for model polymeric structures having several different shapes. We obtain good agreement with literature estimates available for some of the model structures considered.

GenRisk: a tool for comprehensive genetic risk modeling.

SummaryThe genetic architecture of complex traits can be influenced by both many common regulatory variants with small effect sizes and rare deleterious variants in coding regions with larger effect sizes. However, the two kinds of genetic contributions are typically analyzed independently. Here, we present GenRisk, a python package for the computation and the integration of gene scores based on the burden of rare deleterious variants and common-variants-based polygenic risk scores. The derived scores can be analyzed within GenRisk to perform association tests or to derive phenotype prediction models by testing multiple classification and regression approaches. GenRisk is compatible with VCF input file formats.Availability and implementationGenRisk is an open source publicly available python package that can be downloaded or installed from Github (https://github.com/AldisiRana/GenRisk).Supplementary information Supplementary data are available at Bioinformatics online.

DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets.

DNA metabarcoding is broadly used in biodiversity studies encompassing a wide range of organisms. Erroneous amplicons, generated during amplification and sequencing procedures, constitute one of the major sources of concern for the interpretation of metabarcoding results. Several denoising programs have been implemented to detect and eliminate these errors. However, almost all denoising software currently available has been designed to process non-coding ribosomal sequences, most notably prokaryotic 16S rDNA. The growing number of metabarcoding studies using coding markers such as COI or RuBisCO demands a re-assessment and calibration of denoising algorithms. Here we present DnoisE, the first denoising program designed to detect erroneous reads and merge them with the correct ones using information from the natural variability (entropy) associated to each codon position in coding barcodes. We have developed an open-source software using a modified version of the UNOISE algorithm. DnoisE implements different merging procedures as options, and can incorporate codon entropy information either retrieved from the data or supplied by the user. In addition, the algorithm of DnoisE is parallelizable, greatly reducing runtimes on computer clusters. Our program also allows different input file formats, so it can be readily incorporated into existing metabarcoding pipelines.

ScAnalyzeR: A Comprehensive Software Package With Graphical User Interface for Single-Cell RNA Sequencing Analysis and its Application on Liver Cancer.

Introduction: The application of single-cell RNA sequencing to delineate tissue heterogeneity and complexity has become increasingly popular. Given its tremendous resolution and high-dimensional capacity for in-depth investigation, single-cell RNA sequencing offers an unprecedented research power. Although some popular software packages are available for single-cell RNA sequencing data analysis and visualization, it is still a big challenge for their usage, as they provide only a command-line interface and require significant level of bioinformatics skills. Methods: We have developed scAnalyzeR, which is a single-cell RNA sequencing analysis pipeline with an interactive and user-friendly graphical interface for analyzing and visualizing single-cell RNA sequencing data. It accepts single-cell RNA sequencing data from various technology platforms and different model organisms (human and mouse) and allows flexibility in input file format. It provides functionalities for data preprocessing, quality control, basic summary statistics, dimension reduction, unsupervised clustering, differential gene expression, gene set enrichment analysis, correlation analysis, pseudotime cell trajectory inference, and various visualization plots. It also provides default parameters for easy usage and allows a wide range of flexibility and optimization by accepting user-defined options. It has been developed as a docker image that can be run in any docker-supported environment including Linux, Mac, and Windows, without installing any dependencies. Results: We compared the performance of scAnalyzeR with 2 other graphical tools that are popular for analyzing single-cell RNA sequencing data. The comparison was based on the comprehensiveness of functionalities, ease of usage and flexibility, and execution time. In general, scAnalyzeR outperformed the other tested counterparts in various aspects, demonstrating its superior overall performance. To illustrate the usefulness of scAnalyzeR in cancer research, we have analyzed the in-house liver cancer single-cell RNA sequencing dataset. Liver cancer tumor cells were revealed to have multiple subpopulations with distinctive gene expression signatures. Conclusion: scAnalyzeR has comprehensive functionalities and demonstrated usability. We anticipate more functionalities to be adopted in the future development.

Py-fmas: A python package for ultrashort optical pulse propagation in terms of forward models for the analytic signal

We present a flexible, open-source Python package for the accurate simulation of the z-propagation dynamics of ultrashort optical pulses in nonlinear waveguides, especially valid for few-cycle pulses and their interaction. The simulation approach is based on unidirectional propagation equations for the analytic signal. The provided software allows to account for dispersion, attenuation, four-wave mixing processes including, e.g., third-harmonic generation, and features various models for the Raman response. The propagation equations are solved on a periodic temporal domain. For z-propagation, a selection of pseudospectral methods is available. Propagation scenarios for a custom propagation constant and initial field pulses can either be specified in terms of a HDF5 based input file format or by direct implementation using a python script. We demonstrate the functionality for a test-case for which an exact solution is available, by reproducing exemplary results documented in the scientific literature, and a complex propagation scenario involving multiple pulses. Program summaryProgram Title: py-fmasCPC Library link to program files:https://doi.org/10.17632/7s2cv9kjfs.1Developer's repository link:https://github.com/omelchert/py-fmasCode Ocean capsule:https://codeocean.com/capsule/8221780Licensing provisions: MITProgramming language: Python3Supplementary material: Reference manual, extended user guide, and usage examples are hosted on gitHub pages under https://omelchert.github.io/py-fmas.Nature of problem: Solves for the z-propagation dynamics of spectrally broad ultrashort optical pulses in single mode nonlinear waveguides in terms of propagation models for the analytic signal of the optical field [1–3]. The implemented models include, e.g., third-harmonic generation and the Raman effect.Solution method: The initial real-valued optical field is defined on a periodic one-dimensional temporal grid and converted to the complex-valued analytic signal. z-stepping is performed via spectral methods. The software implements a selection of algorithms with fixed or adaptive stepsize, commonly used in nonlinear optics for solving nonlinear Schrödinger type equations.Additional comments including restrictions and unusual features: The range of applicability of the provided software is equivalent to that of the forward Maxwell equation [4]. For reasonably chosen initial conditions, it can be used beyond the unidirectional approximation as a bidirectional model for a complex field, allowing to describe forward and backward waves coupled through nonlinear interactions [1]. The software implements various models for the Raman response and allows to calculate spectrograms, detailing the time-frequency composition of the analytic signal. Additionally, a convenience class for analyzing propagation constants is provided.

Methrix: an R/Bioconductor package for systematic aggregation and analysis of bisulfite sequencing data.

Whole-genome bisulfite sequencing (WGBS) measures DNA methylation at base pair resolution resulting in large bedGraph like coverage files. Current options for processing such files are hindered by discrepancies in file format specification, speed, and memory requirements. We developed methrix, an R package, which provides a toolset for systematic analysis of large datasets. Core functionality of the package includes a comprehensive bedGraph or similar tab-separated text file reader-which summarizes methylation calls based on annotated reference indices, infers and collapses strands and handles uncovered reference CpG sites while facilitating a flexible input file format specification. Additional optimized functions for quality control filtering, subsetting and visualization allow user-friendly and effective processing of WGBS results. Easy integration with tools for differentially methylated region (DMR) calling and annotation further eases the analysis of genome-wide methylation data. Overall, methrix enriches established WGBS workflows by bringing together computational efficiency and versatile functionality. Methrix is implemented as an R package, made available under MIT license at https://github.com/CompEpigen/methrix and can be installed from the Bioconductor repository. Supplementary data are available at Bioinformatics online.