Input File Format Research Articles

LS-VISM: A software package for analysis of biomolecular solvation.

We introduce a software package for the analysis of biomolecular solvation. The package collects computer codes that implement numerical methods for a variational implicit-solvent model (VISM). The input of the package includes the atomic data of biomolecules under consideration and the macroscopic parameters such as solute-solvent surface tension, bulk solvent density and ionic concentrations, and the dielectric coefficients. The output includes estimated solvation free energies and optimal macroscopic solute-solvent interfaces that are obtained by minimizing the VISM solvation free-energy functional among all possible solute-solvent interfaces enclosing the solute atoms. We review the VISM with various descriptions of electrostatics. We also review our numerical methods that consist mainly of the level-set method for relaxing the VISM free-energy functional and a compact coupling interface method for the dielectric Poisson-Boltzmann equation. Such numerical methods and algorithms constitute the central modules of the software package. We detail the structure of the package, format of input and output files, workflow of the codes, and the postprocessing of output data. Our demo application to a host-guest system illustrates how to use the package to perform solvation analysis for biomolecules, including ligand-receptor binding systems. The package is simple and flexible with respect to minimum adjustable parameters and a wide range of applications. Future extensions of the package use can include the efficient identification of ligand binding pockets on protein surfaces.

Алгоритм идентификации помещений в FDS-проектах для моделирования пожара интегральным методом

In solving problems of fire safety, it is often necessary to perform a series of calculations with different initial conditions: space-planning decisions, the parameters of operation of fire protection systems, and others. In such cases using FDS becomes difficult because each calculation requires significant time and computing resources. To solve this problem we have developed a program - FIM (Fire Integral (one-zone) Model). FIM implements calculation of the dynamics of fire hazards by using a one-zone integral model, using the input file format of FDS. If the building topology corresponds to the definition of the integral model, the FIM significantly speeds estimation, before launching into a lengthy calculation FDS. There is no need to create a new model of the building in any other format: the program reads the source FDS file, calculates the dynamics of the fire hazards and generates output files similar to FDS, which can be analyzed in programs like Smokeview, FireRisk and others. Limitations of FIM 1.0: • sealed room (no openings) are ignored in the calculation; • the material of walls is the concrete; • in ventilation ignored the task of certain types of gas (MASSFRACTION - mass fraction of the incoming gases); • ignored job control facilities (open/closed, on/off); • ignored the ventilation systems HVAC; • ignored complex parameters of combustion (the ignition of surfaces from high temperature, the effect of fire extinguishing systems, etc.). Output data are only the sensors and slices, measuring the following parameters: temperature, visibility, concentration of oxygen, carbon dioxide, carbon monoxide, hydrogen chloride. Other output data set in the file FDS is ignored.

4P: fast computing of population genetics statistics from large DNA polymorphism panels.

Massive DNA sequencing has significantly increased the amount of data available for population genetics and molecular ecology studies. However, the parallel computation of simple statistics within and between populations from large panels of polymorphic sites is not yet available, making the exploratory analyses of a set or subset of data a very laborious task. Here, we present 4P (parallel processing of polymorphism panels), a stand-alone software program for the rapid computation of genetic variation statistics (including the joint frequency spectrum) from millions of DNA variants in multiple individuals and multiple populations. It handles a standard input file format commonly used to store DNA variation from empirical or simulation experiments. The computational performance of 4P was evaluated using large SNP (single nucleotide polymorphism) datasets from human genomes or obtained by simulations. 4P was faster or much faster than other comparable programs, and the impact of parallel computing using multicore computers or servers was evident. 4P is a useful tool for biologists who need a simple and rapid computer program to run exploratory population genetics analyses in large panels of genomic data. It is also particularly suitable to analyze multiple data sets produced in simulation studies. Unix, Windows, and MacOs versions are provided, as well as the source code for easier pipeline implementations.

3D printing of crystallographic models and open access databases

Although introduced 30 years ago, cost and performance improvements have only recently made 3D printing affordable. The industry wide input file format for 3D printers incorporates explicit mesh - `STL' data. Molecules and crystal structures, when including symmetry, crystal morphologies, or crystal defects are encoded in the parametrical `CIF' syntax. Free software for converting directly CIF data to STL files has just been developed, available online [1]. First examples of printed 3D models from STL-files created with these programs include molecules of sucrose, herapathite [2a], caffeine, humulone [2b], an alpha-quartz crystal and its Japanese {112} twin or a brilliant cut diamond. Far more CIF encoded models are available, even open access. The Crystallography Open Database (COD) features over 245,000 entries and has recently developed into the world's premier open-access source for structures of small to medium unit cell-sized inorganic and molecular crystals [3a], complementing the well-established open-access Worldwide Protein Data Bank [3b]. The Cambridge Crystallographic Data Centre in the United Kingdom provides crystal structure data of small (organic) molecules free for bona fide research [3c]. Structural data on inorganic crystals, metals and alloys can be obtained free of charge from the Inorganic Material Database (AtomWork) [3d]. Related to the COD, the crystallographic open-access databases [3e] ("COD offspring") provide CIF data for interdisciplinary college education. With this basic infrastructure in place, any interested college educator may print out her or his favorite crystallographic structure model in 3D and use it in hands on class room demonstrations [3f].

Editorial: Nucleic Acids Research annual Web Server Issue in 2014

Editorial: Nucleic Acids Research annual Web Server Issue in 2014

Ycasd - a tool for capturing and scaling data from graphical representations.

BackgroundMathematical modelling of biological processes often requires a large variety of different data sets for parameter estimation and validation. It is common practice that clinical data are not available in raw formats but are provided as graphical representations. Hence, in order to include these data into environments used for model simulations and statistical analyses, it is necessary to extract them from their presentations in the literature. For this purpose, we developed the freely available open source tool ycasd. After establishing a coordinate system by simple axes definitions, it supports convenient retrieval of data points from arbitrary figures.ResultsAfter describing the general functionality and providing an overview of the programme interface, we demonstrate on an example how to use ycasd. A major advantage of ycasd is that it does not require a certain input file format to open and process figures. All options of ycasd are accessible through a single window which eases handling and speeds up data extraction. For subsequent processing of extracted data points, results can be formatted as a Matlab or an R matrix. We extensively compare the functionality and other features of ycasd with other publically available tools. Finally, we provide a short summary of our experiences with ycasd in the context of modelling.ConclusionsWe conclude that our tool is suitable for convenient and accurate data retrievals from graphical representations such as papers. Comparison of tools reveals that ycasd is a good compromise between easy and quick capturing of scientific data from publications and complexity. Our tool is routinely applied in the context of biological modelling, where numerous time series data are required to develop models. The software can also be useful for other kinds of analyses for which published data are required but are not available in raw formats such as systematic reviews and meta-analyses.

RAREMETAL: fast and powerful meta-analysis for rare variants.

Summary: RAREMETAL is a computationally efficient tool for meta-analysis of rare variants genotyped using sequencing or arrays. RAREMETAL facilitates analyses of individual studies, accommodates a variety of input file formats, handles related and unrelated individuals, executes both single variant and burden tests and performs conditional association analyses.Availability and implementation: http://genome.sph.umich.edu/wiki/RAREMETAL for executables, source code, documentation and tutorial.Contact: sfengsph@umich.edu or goncalo@umich.edu

Yell: a computer program for diffuse scattering analysisviathree-dimensional delta pair distribution function refinement

Yell, a program for routine refinement of disorder models against single-crystal diffuse scattering data, is presented. The analysis is based on the three-dimensional delta pair distribution function (3D-ΔPDF) method, which provides direct access to interatomic correlations in real crystal structures. Substitutional, displacive and size-effect disorder models are covered. The input file format supports flexible usage of arithmetic expressions for constraining dependent parameter values. The program is designed to be run on desktop computers. By using an efficient fast-Fourier-transform-based diffuse scattering calculation algorithm, full least-square refinements of medium complexity disorder models may be performed within minutes or hours, even if the experimental diffuse scattering is represented by large and fine-sampled reciprocal space volumes. The program is written in C++ and the source code is distributed under the GPL licence. Binary distributions are currently available for Mac and Windows operating systems.

Peach 퍼징을 위한 파일 분석 데이터 자동 생성 모델

소프트웨어가 산업 및 사회전반으로 저변을 확대함에 따라 소프트웨어의 취약점으로 인한 위험이 증가하고 있으며, 소프트웨어의 취약점을 악용하는 사례도 빈번하게 나타나고 있다. 스마트 퍼징은 이러한 소프트웨어 취약점을 발견하기 위한 자동화된 방법이다. 그러나 스마트 퍼징을 위해서는 우선 퍼징을 수행하고자 하는 대상 소프트웨어에 대한 데이터 모델을 생성해야하며, 데이터 파일 및 소프트웨어 자체에 대한 분석이 필요하기 때문에 많은 자원이 소모된다. 따라서 효율적인 스마트 퍼징을 위해서 데이터 모델을 자동으로 생성하기 위한 방법이 필요하다. 본 논문에서는 데이터 입력 파일에 대한 분석을 통해서 스마트 퍼징을 위한 데이터 모델을 자동으로 생성하기 위한 프레임워크를 제안하고 이를 구현함으로서 소프트웨어 취약점 발견에 도움을 줄 것으로 기대한다. The rapid expansion of the software industry has brought a serious security threat and vulnerability. Many softwares are constantly attacked by exploit codes using security vulnerabilities. Smart fuzzing is automated method to find software vulnerabilities. However, Many resources are consumed in fuzzing, because the fuzzing needs to create data model for target software and to analyze a data file and software binary. Therefore, The automated method for efficient smart fuzzing is needed to develop the automated data model. In this paper, through analysing the input file format and optimizing the data structure, we propose an efficient data modeling framework for smart fuzzing and implement the framework for detect software vulnerabilities.

Census 2: isobaric labeling data analysis

We introduce Census 2, an update of a mass spectrometry data analysis tool for peptide/protein quantification. New features for analysis of isobaric labeling, such as Tandem Mass Tag (TMT) or Isobaric Tags for Relative and Absolute Quantification (iTRAQ), have been added in this version, including a reporter ion impurity correction, a reporter ion intensity threshold filter and an option for weighted normalization to correct mixing errors. TMT/iTRAQ analysis can be performed on experiments using HCD (High Energy Collision Dissociation) only, CID (Collision Induced Dissociation)/HCD (High Energy Collision Dissociation) dual scans or HCD triple-stage mass spectrometry data. To improve measurement accuracy, we implemented weighted normalization, multiple tandem spectral approach, impurity correction and dynamic intensity threshold features. Census 2 supports multiple input file formats including MS1/MS2, DTASelect, mzXML and pepXML. It requires JAVA version 6 or later to run. Free download of Census 2 for academic users is available at http://fields.scripps.edu/census/index.php. jyates@scripps.edu Supplementary data are available at Bioinformatics online.

High-performance computing for climate change impact studies with the Pasture Simulation model

High-performance computing technology permits to efficiently achieve high-performance throughputs for intensive CPU load applications. We describe the development of an integrated tool for climate change impact studies on grassland ecosystems running with pixel-wise data. The pixel-based Pasture Simulation model (PaSim) is suited to work with a NetCDF format of input and output files. It includes the parallel job launcher, which dispatches individual jobs to execute simulations. In a case study covering metropolitan France, we demonstrate how this approach is configured and used to evaluate the impact of climate change on grassland productivity. Over ∼10,000pixels of 8×8km resolution, we report ∼25h to complete the simulation on a cluster machine (TITANE) with 200 processors, which is a speedup of 200.

Comparison of Computational Tools for Protein-Protein Interaction (PPI) Mapping and Analysis

Several visualization tools for the mapping of protein-protein interactions have been developed in recent years. However, a systematic comparison of the virtues and limitations of different PPI visualization tools has not been carried out so far. In this study, we compare seven commonly used visualization tools, based on input and output file format, layout algorithm, database integration, Gene Ontology annotation and accessibility of each tool. The assessment was carried out based on brain disease datasets. Our suggested tools, NAViGaTOR, Cytoscape and Gephi perform competitively as PPI network visualization tools, can be a reference for future researches on PPI mapping and analysis.

Statistical Assessment of Crosstalk Enrichment between Gene Groups in Biological Networks

MotivationAnalyzing groups of functionally coupled genes or proteins in the context of global interaction networks has become an important aspect of bioinformatic investigations. Assessing the statistical significance of crosstalk enrichment between or within groups of genes can be a valuable tool for functional annotation of experimental gene sets.ResultsHere we present CrossTalkZ, a statistical method and software to assess the significance of crosstalk enrichment between pairs of gene or protein groups in large biological networks. We demonstrate that the standard z-score is generally an appropriate and unbiased statistic. We further evaluate the ability of four different methods to reliably recover crosstalk within known biological pathways. We conclude that the methods preserving the second-order topological network properties perform best. Finally, we show how CrossTalkZ can be used to annotate experimental gene sets using known pathway annotations and that its performance at this task is superior to gene enrichment analysis (GEA).Availability and ImplementationCrossTalkZ (available at http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/) is implemented in C++, easy to use, fast, accepts various input file formats, and produces a number of statistics. These include z-score, p-value, false discovery rate, and a test of normality for the null distributions.

SNVerGUI: a desktop tool for variant analysis of next-generation sequencing data

BackgroundAdvances in next generation sequencing (NGS) technology have made it possible to interrogate comprehensively genome-wide genetic variations. However, most existing tools for variation detection are based on command-line interface, which...

Superclusteroid: a Web tool dedicated to data processing of protein-protein interaction networks

The study of proteins and the interactions between them, known as Protein-Protein Interactions (PPI), is extremely important in interpreting all biological cellular functions. In this article, a new web tool called Superclusteroid is presented which can analyse PPI data, in order to detect protein complexes or characterise the functionality of unknown proteins. The tool is essentially an intuitive PPI data processing pipeline. It supports various input file formats and provides services such as clustering, PPI network visualisation and protein cluster function prediction. Each Superclusteroid service can be used in a sequential manner or on an individual basis. In order to assess the reliability of our tool to infer PPIs, the results of the tool were compared to already known MIPS database complexes and a case scenario is presented where a known protein complex is predicted and the functionality of some of its proteins is revealed. Availability: Superclusteroid is freely available online at http://superclusteroid.uio.no/ .

Las Palmeras Molecular Dynamics: A flexible and modular molecular dynamics code

Las Palmeras Molecular Dynamics (LPMD) is a highly modular and extensible molecular dynamics (MD) code using interatomic potential functions. LPMD is able to perform equilibrium MD simulations of bulk crystalline solids, amorphous solids and liquids, as well as non-equilibrium MD (NEMD) simulations such as shock wave propagation, projectile impacts, cluster collisions, shearing, deformation under load, heat conduction, heterogeneous melting, among others, which involve unusual MD features like non-moving atoms and walls, unstoppable atoms with constant-velocity, and external forces like electric fields. LPMD is written in C++ as a compromise between efficiency and clarity of design, and its architecture is based on separate components or plug-ins, implemented as modules which are loaded on demand at runtime. The advantage of this architecture is the ability to completely link together the desired components involved in the simulation in different ways at runtime, using a user-friendly control file language which describes the simulation work-flow. As an added bonus, the plug-in API (Application Programming Interface) makes it possible to use the LPMD components to analyze data coming from other simulation packages, convert between input file formats, apply different transformations to saved MD atomic trajectories, and visualize dynamical processes either in real-time or as a post-processing step. Individual components, such as a new potential function, a new integrator, a new file format, new properties to calculate, new real-time visualizers, and even a new algorithm for handling neighbor lists can be easily coded, compiled and tested within LPMD by virtue of its object-oriented API, without the need to modify the rest of the code. LPMD includes already several pair potential functions such as Lennard-Jones, Morse, Buckingham, MCY and the harmonic potential, as well as embedded-atom model (EAM) functions such as the Sutton–Chen and Gupta potentials. Integrators to choose include Euler (if only for demonstration purposes), Verlet and Velocity Verlet, Leapfrog and Beeman, among others. Electrostatic forces are treated as another potential function, by default using the plug-in implementing the Ewald summation method. Program summary Program title: LPMD Catalogue identifier: AEHG_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEHG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 509 490 No. of bytes in distributed program, including test data, etc.: 6 814 754 Distribution format: tar.gz Programming language: C++ Computer: 32-bit and 64-bit workstation Operating system: UNIX RAM: Minimum 1024 bytes Classification: 7.7 External routines: zlib, OpenGL Nature of problem: Study of Statistical Mechanics and Thermodynamics of condensed matter systems, as well as kinetics of non-equilibrium processes in the same systems. Solution method: Equilibrium and non-equilibrium molecular dynamics method, Monte Carlo methods. Restrictions: Rigid molecules are not supported. Polarizable atoms and chemical bonds (proteins) either. Unusual features: The program is able to change the temperature of the simulation cell, the pressure, cut regions of the cell, color the atoms by properties, even during the simulation. It is also possible to fix the positions and/or velocity of groups of atoms. Visualization of atoms and some physical properties during the simulation. Additional comments: The program does not only perform molecular dynamics and Monte Carlo simulations, it is also able to filter and manipulate atomic configurations, read and write different file formats, convert between them, evaluate different structural and dynamical properties. Running time: 50 seconds on a 1000-step simulation of 4000 argon atoms, running on a single 2.67 GHz Intel processor.

METAL: fast and efficient meta-analysis of genomewide association scans

Summary: METAL provides a computationally efficient tool for meta-analysis of genome-wide association scans, which is a commonly used approach for improving power complex traits gene mapping studies. METAL provides a rich scripting interface and implements efficient memory management to allow analyses of very large data sets and to support a variety of input file formats.Availability and implementation: METAL, including source code, documentation, examples, and executables, is available at http://www.sph.umich.edu/csg/abecasis/metal/Contact: goncalo@umich.edu

ZOOM Lite: next-generation sequencing data mapping and visualization software

High-throughput next-generation sequencing technologies pose increasing demands on the efficiency, accuracy and usability of data analysis software. In this article, we present ZOOM Lite, a software for efficient reads mapping and result visualization. With a kernel capable of mapping tens of millions of Illumina or AB SOLiD sequencing reads efficiently and accurately, and an intuitive graphical user interface, ZOOM Lite integrates reads mapping and result visualization into a easy to use pipeline on desktop PC. The software handles both single-end and paired-end reads, and can output both the unique mapping result or the top N mapping results for each read. Additionally, the software takes a variety of input file formats and outputs to several commonly used result formats. The software is freely available at http://bioinfor.com/zoom/lite/.

Array2KEGG: Web-based tool of KEGG pathway analysis for gene expression profile

Over the past decade, microarray experiments have become popular with a common method of high-throughput omics technologies for understanding of gene expression patterns at the genome level. The objective of microarray experiments is to identify differentially expressed genes (DEGs) or similarly patterned genes groups from microarray experiments. For these reasons, several preprocessing methods for correction of experimental or systemic bias of microarray experiments have been proposed, and a number of statistical algorithms for selection of specially expressed genes within all genes on a microarray have been developed in order to support more reliable and significant results. With the results produced by these useful tools, researchers have examined common biological features, such as functional interactions in shared biological processes, direct-indirect regulation at the molecular level, or disease relation in a biological pathway or network. Of these biological identification analyses, pathway analysis has been mainly used for functional detection of biological features between these co-expressed genes. An advantage of pathway analysis is a visualization that has an important role in understanding of the intricate phenomena of pathways containing biochemical reactions or functional relations among a gene’s products, enzymes, substrates, activators, inhibitors, or other biological molecular elements. For these reasons, several bioinformatics tools for pathway analysis based on external pathway data sources, such as KEGG or BIOCARTA, have been developed. These tools have offered user-friendly and powerful interfaces, visual and graphical functions of pathway diagrams, and biological annotations. However, the problems encountered by users remain unresolved in certain respects that are a complicated input file format derived from gene expression profiles, a time-consuming work for collection of information on pathways that contain several genes identified as interesting genes, or a restriction in picturing a pathway image map that included more than two interesting genes. In an attempt to overcome these problems, we have developed Array2KEGG as a web-based tool for finding pathway diagrams from the KEGG PATHWAY database. Array2KEGG has focused on simplicity in user interface, integration in heterogeneous biological databases, and visualization in depiction of a pathway diagram that includes more than two interesting genes. Array2KEGG is freely available for use at http://www.koreagene.co.kr/cgi-bin/service/service1.pl.

Finite element method study of incremental sheet forming for complex shape and its improvement

In order to improve the incremental sheet forming process for the product of complex shape (e.g. human face), a combination of both computer-aided manufacturing (CAM) and finite-element modelling (FEM) simulation, is implemented and evaluated from the histories of stress and strain value by means of finite-element analysis. Here, the results, using ABAQUS/Explicit finite-element code, are compared with forming limit curve at fracture in order to predict and improve the forming conditions by changing process variables of tool radius, tool down-step, and friction coefficient according to the orthogonal array of Taguchi's method. First, the CAM simulation is used to create cutter location data. This data are then calculated, modified, and exported to the input file format required by ABAQUS through using MATLAB programming. The FEM results are implemented for negative incremental sheet forming and then investigated by experiment.