Input File Format Research Articles

JClust: a clustering and visualization toolbox

jClust is a user-friendly application which provides access to a set of widely used clustering and clique finding algorithms. The toolbox allows a range of filtering procedures to be applied and is combined with an advanced implementation of the Medusa interactive visualization module. These implemented algorithms are k-Means, Affinity propagation, Bron–Kerbosch, MULIC, Restricted neighborhood search cluster algorithm, Markov clustering and Spectral clustering, while the supported filtering procedures are haircut, outside–inside, best neighbors and density control operations. The combination of a simple input file format, a set of clustering and filtering algorithms linked together with the visualization tool provides a powerful tool for data analysis and information extraction.Availability: http://jclust.embl.de/Contact: pavlopou@embl.de; rschneid@embl.de; skossida@bioacademy.grSupplementary information: Supplementary data are available at Bioinformatics online.

SuperIso v2.3: A program for calculating flavor physics observables in supersymmetry

We describe SuperIso v2.3 which is a public program for evaluation of flavor physics observables in the minimal supersymmetric extension of the Standard Model (MSSM). SuperIso v2.3, in addition to the isospin asymmetry of B → K ∗ γ , which was the main purpose of the first version, incorporates new flavor observables such as the branching ratio of B s → μ + μ − , the branching ratio of B → τ ν τ , the branching ratio of B → D τ ν τ and the branching ratio of K → μ ν μ . The calculation of the branching ratio of B → X s γ is also improved in this version, as it now includes NNLO Standard Model contributions in addition to partial NLO supersymmetric contributions. The program also computes the muon anomalous magnetic moment ( g − 2 ) . Four sample models are included in the package, namely mSUGRA, NUHM, AMSB and GMSB. SuperIso uses a SUSY Les Houches Accord file (SLHA1 or SLHA2) as input, which can be either generated automatically by the program via a call to external spectrum calculators, or provided by the user. The calculation of the observables is detailed in the Appendices, where a suggestion for the allowed intervals for each observable is also provided. Program summary Program title: SuperIso Catalogue identifier: AEAN_v2_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEAN_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public Licence No. of lines in distributed program, including test data, etc.: 5977 No. of bytes in distributed program, including test data, etc.: 39 375 Distribution format: tar.gz Programming language: C (C99 Standard compliant) Computer: 32- or 64-bit PC, Mac Operating system: Linux, MacOS RAM: less than 1 Mb Classification: 11.6 Catalogue identifier of previous version: AEAN_v1_0 Journal reference of previous version: Comput. Phys. Comm. 178 (2008) 745 External routines: ISASUGRA/ISAJET and/or SOFTSUSY Does the new version supersede the previous version?: yes Nature of problem: Calculation of flavor physics observables as well as the muon anomalous magnetic moment in the Minimal Supersymmetric Standard Model with minimal flavor violation, in order to derive constraints on the supersymmetric parameter space. Solution method: SuperIso uses a SUSY Les Houches Accord file, which can be either generated automatically via a call to SOFTSUSY or ISAJET, or provided by the user. This file contains the masses and couplings of the supersymmetric particles. SuperIso then computes the most constraining flavor physics observables and the muon ( g − 2 ). SuperIso is able to perform the calculations in different supersymmetry breaking scenarios, such as mSUGRA, NUHM, AMSB and GMSB. Reasons for new version: This new version incorporates the calculation of several additional observables, and the inclusive branching ratio of b → s γ is now computed at NNLO accuracy for the Standard Model. The implemented routines are therefore extensively modified. Summary of revisions: • Compatibility with the SLHA2 input file format • Implementation of the calculation of the muon anomalous magnetic moment • Implementation of observables related to leptonic and semi-leptonic B meson decays • Implementation of observables related to K meson decays • Improvement of the calculations of the branching ratio of b → s γ (now at NNLO accuracy) and the isospin asymmetry of B → K ∗ γ • Update of parameters to their latest values Unusual features: The code is very modular, and new routines for calculating new observables can be easily added. Running time: less than 1 sec

A quantitative analysis software tool for mass spectrometry–based proteomics

We describe Census, a quantitative software tool compatible with many labeling strategies as well as with label-free analyses, single-stage mass spectrometry (MS1) and tandem mass spectrometry (MS/MS) scans, and high- and low-resolution mass spectrometry data. Census uses robust algorithms to address poor-quality measurements and improve quantitative efficiency, and it can support several input file formats. We tested Census with stable-isotope labeling analyses as well as label-free analyses.

Numerical system utilising a Monte Carlo calculation method for accurate dose assessment in radiation accidents

A system utilising radiation transport codes has been developed to derive accurate dose distributions in a human body for radiological accidents. A suitable model is quite essential for a numerical analysis. Therefore, two tools were developed to setup a 'problem-dependent' input file, defining a radiation source and an exposed person to simulate the radiation transport in an accident with the Monte Carlo calculation codes-MCNP and MCNPX. Necessary resources are defined by a dialogue method with a generally used personal computer for both the tools. The tools prepare human body and source models described in the input file format of the employed Monte Carlo codes. The tools were validated for dose assessment in comparison with a past criticality accident and a hypothesized exposure.

Numerical simulation of particle dynamics in a storage ring by using BETACOOL program

The BETACOOL program, developed by electron cooling group of the Joint Institute for Nuclear Research (JINR), is a set of algorithms based on common format of input and output files. The program is oriented toward simulation of the ion beam dynamics in a storage ring in the presence of cooling and heating effects. The version presented in this report includes three basic algorithms: simulation of root-mean-square (rms) parameters of the particle distribution function evolving in time, simulation of the distribution function evolution using the Monte Carlo method, and a tracking algorithm based on a molecular dynamics technique. The general processes investigated with the program are intrabeam scattering in the ion beam, electron cooling, and interaction with residual gas and an internal target.

MODi : a powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectra

MODi () is a powerful and convenient web service that facilitates the interpretation of tandem mass spectra for identifying post-translational modifications (PTMs) in a peptide. It is powerful in that it can interpret a tandem mass spectrum even when hundreds of modification types are considered and the number of potential PTMs in a peptide is large, in contrast to most of the methods currently available for spectra interpretation that limit the number of PTM sites and types being used for PTM analysis. For example, using MODi, one can consider for analysis both the entire PTM list published on the unimod webpage () and user-defined PTMs simultaneously, and one can also identify multiple PTM sites in a spectrum. MODi is convenient in that it can take various input file formats such as .mzXML, .dta, .pkl and .mgf files, and it is equipped with a graphical tool called MassPective developed to display MODi's output in a user-friendly manner and helps users understand MODi's output quickly. In addition, one can perform manual de novo sequencing using MassPective.

Inverting for Slip on Three-Dimensional Fault Surfaces Using Angular Dislocations

The increasing quality of geodetic data (synthetic aperture radar interferometry [insar] dense Global Positioning System [gps] arrays) now available to geophysicists and geologists are not fully exploited in slip-inversion procedures. Most common methods of inversion use rectangular dislocation segments to model fault ruptures and therefore oversimplify fault geometries. These geometric simplifications can lead to inconsistencies when inverting for slip on earthquake faults, and they preclude a more complete understanding of the role of fault geometry in the earthquake process. We have developed a new three-dimensional slip-inversion method based on the analytical solution for an angular dislocation in a linear-elastic, homogeneous, isotropic, half-space. The approach uses the boundary element code Poly3D that employs a set of planar triangular elements of constant displacement discontinuity to model fault surfaces. The use of triangulated surfaces as discontinuities permits one to construct fault models that better approximate curved three-dimensional surfaces bounded by curved tiplines: shapes that commonly are imaged by three-dimensional reflection seismic data and inferred from relocated aftershock data. We demonstrate the method’s ability to model three-dimensional rupture geometries by inverting for slip associated with the 1999 Hector Mine earthquake. The resulting model avoids displacement anomalies associated with the overlapping rectangular dislocations used in previous models, improving the fit to the geodetic data by 32%, and honors the observed surface ruptures, thereby allowing more direct comparisons between geologic and geodetic data on slip distributions. Online Material : Hector Mine input files and file format description.

AUTOGSCAN: Powerful Tools for Automated Genome-Wide Linkage and Linkage Disequilibrium Analysis

AbstractGenome-wide linkage analysis using multiple traits and statistical software packages is a tedious process which requires a significant amount of manual file manipulation. Different linkage analysis programs require different input file formats, making the task of analyzing data with multiple methods even more time-consuming. We have developed a software tool, AUTOGSCAN, that automates file formatting, the running of statistical analyses, and the summarizing of resulting statistics for whole genome scans with a push of a button, using several independent, and often idiosyncratic, statistical software packages such as MERLIN, SOLAR and GENEHUNTER. We also describe a program, ANALYZE, designed to run qualitative linkage analysis with several different statistical strategies and programs to efficiently screen for linkage and linkage disequilibrium for a given discrete trait. The ANALYZE program can also be used by AUTOGSCAN in a genome-wide sense.

AUTOGSCAN: Powerful Tools for Automated Genome-Wide Linkage and Linkage Disequilibrium Analysis

Genome-wide linkage analysis using multiple traits and statistical software packages is a tedious process which requires a significant amount of manual file manipulation. Different linkage analysis programs require different input file formats, making the task of analyzing data with multiple methods even more time-consuming. We have developed a software tool, AUTOGSCAN, that automates file formatting, the running of statistical analyses, and the summarizing of resulting statistics for whole genome scans with a push of a button, using several independent, and often idiosyncratic, statistical software packages such as MERLIN, SOLAR and GENEHUNTER. We also describe a program, ANALYZE, designed to run qualitative linkage analysis with several different statistical strategies and programs to efficiently screen for linkage and linkage disequilibrium for a given discrete trait. The ANALYZE program can also be used by AUTOGSCAN in a genome-wide sense.

Fast transport simulation with an adaptive grid refinement.

One of the main difficulties in transport modeling and calibration is the extraordinarily long computing times necessary for simulation runs. Improved execution time is a prerequisite for calibration in transport modeling. In this paper we investigate the problem of code acceleration using an adaptive grid refinement, neglecting subdomains, and devising a method by which the Courant condition can be ignored while maintaining accurate solutions. Grid refinement is based on dividing selected cells into regular subcells and including the balance equations of subcells in the equation system. The connection of coarse and refined cells satisfies the mass balance with an interpolation scheme that is implicitly included in the equation system. The refined subdomain can move with the average transport velocity of the subdomain. Very small time steps are required on a fine or a refined grid, because of the combined effect of the Courant and Peclet conditions. Therefore, we have developed a special upwind technique in small grid cells with high velocities (velocity suppression). We have neglected grid subdomains with very small concentration gradients (zero suppression). The resulting software, MODCALIF, is a three-dimensional, modularly constructed FORTRAN code. For convenience, the package names used by the well-known MODFLOW and MT3D computer programs are adopted, and the same input file structure and format is used, but the program presented here is separate and independent. Also, MODCALIF includes algorithms for variable density modeling and model calibration. The method is tested by comparison with an analytical solution, and illustrated by means of a two-dimensional theoretical example and three-dimensional simulations of the variable-density Cape Cod and SALTPOOL experiments. Crossing from fine to coarse grid produces numerical dispersion when the whole subdomain of interest is refined; however, we show that accurate solutions can be obtained using a fraction of the execution time required by uniformly fine-grid solutions.

Large Scale Simulation of Protein Mechanics and Function

The chapter illustrates the state of art in large-scale biomolecular modeling. Such modeling has become feasible only through parallel computing utilizing hundreds and soon thousands of processors. Fortunately, the necessary computers are available to many researchers and the needed new generation of molecular dynamics and molecular visualization programs has been developed and these resources are widely shared. Harnessing them effectively requires great effort, to which purpose the authors' group has developed the molecular dynamics program Not (just) Another Molecular Dynamics program (NAMD). For the graphical analysis of the ensuing gigabytes and terabytes of data the group has developed the program Visual Molecular Dynamics (VMD). These programs are widely used today since the increasing availability of protein structures has led to most biomedical researchers using structural information for the design and analysis of their experiments. The chapter describes NAMD and VMD and illustrates three exemplary simulations of large-scale systems that are presently the subject of intense research. The functions of all three proteins investigated are mainly mechanical. NAMD is primarily designed to work with Chemistry at HARvard Molecular Mechanics (CHARMM) force field parameters. Input files for NAMD can be generated using CHARMM, X-PLOR, or VMD. NAMD has also been extended to read Assisted Model Building with Energy Refinement (AMBER) and GROningen MAchine for Chemical Simulations (GROMACS) input file formats. NAMD running on 768 processors has enabled a record-breaking two million atom 5 ns simulation of the ribosome using an AMBER force field. To relate the observed mechanics to the architecture of proteins is the domain of so-called steered molecular dynamics simulations, contributing to the founding of the new field of mechanobiology, which studies the role of forces in cellular processes.

Automatic extraction of machining primitives with respect to preformed stock for process planning

There is a need for the integration of computer-aided design (CAD) information with manufacturing models, such as machining process simulation models, upstream with concurrent engineering activities. Because it is often difficult to interface various CAD formats with such applications, there is a need to standardize input file formats, which then can be used by any module that has the appropriate interface. The STEP standard is a very useful standard for the neutral file format specification. The present work describes in detail the building of a STEP parser for the Application Protocol for Configuration Controlled Design of 3-D mechanical parts (AP203). Such a STEP parser is complemented with a visualization front end in the form of a Java applet, which is used to display the STEP entities in 3-D within a web browser over the Internet. The current work outlines a generic framework for a STEP parser module. Its use in the design and development of CAD-based process engineering applications is illustrated by example of a CAD interface to a machining process simulation program, which requires the workpiece CAD information, namely the surface geometry, to be machined to determine chip loads and hence cutting forces. The applicability of the STEP parser in the building of a CAD database cataloging system is also discussed.

STRAP: editor for STRuctural Alignments of Proteins.

STRAP is a comfortable and extensible tool for the generation and refinement of multiple alignments of protein sequences. Various sequence ordered input file formats are supported. These are the SwissProt-,GenBank-, EMBL-, DSSP- PDB-, MSF-, and plain ASCII text format. The special feature of STRAP is the simple visualization of spatial distances C(alpha)-atoms within the alignment. Thus structural information can easily be incorporated into the sequence alignment and can guide the alignment process in cases of low sequence similarities. Further STRAP is able to manage huge alignments comprising a lot of sequences. The protein viewers and modeling programs INSIGHT, RASMOL and WEBMOL are embedded into STRAP. STRAP is written in JAVA: The well-documented source code can be adapted easily to special requirements. STRAP may become the basis for complex alignment tools in the future.

PrimeArray: genome-scale primer design for DNA-microarray construction.

PrimeArray is a Windows program that computes oligonuceotide primer pairs for genome-scale gene amplification by the Polymerase Chain Reaction (PCR). The program supports the automated extraction of coding sequences (CDS) from various input-file formats and allows highly automated primer pair-optimization.

CAD data visualization for machining simulation using the STEP standard

There is a need for the integration of computer-aided design (CAD) information with manufacturing models, such as machining process simulation models, upstream with concurrent engineering activities. Because it is often difficult to interface various CAD formats with such applications, there is a need to standardize input file formats, which then can be used by any module that has the appropriate interface. The STEP standard is a very useful standard for the neutral file format specification. The present work describes in detail the building of a STEP parser for the Application Protocol for Configuration Controlled Design of 3-D mechanical parts (AP203). Such a STEP parser is complemented with a visualization front end in the form of a Java applet, which is used to display the STEP entities in 3-D within a web browser over the Internet. The current work outlines a generic framework for a STEP parser module. Its use in the design and development of CAD-based process engineering applications is illustrated by example of a CAD interface to a machining process simulation program, which requires the workpiece CAD information, namely the surface geometry, to be machined to determine chip loads and hence cutting forces. The applicability of the STEP parser in the building of a CAD database cataloging system is also discussed.

Routing airlift aircraft by the double-sweep algorithm

In this paper, we describe the problem of modeling the routing of aircraft across a network of enroute bases. This is done to provide routes for scenarios that are being studied by the analysis tools at the Airlift Mobility Command. We are primarily concerned with the development of routes that can be easily implemented with the airlift operations analysis tools in use at AMC. We will describe the specific implementation issues that have been addressed. One such issue is the use of available data in a specific input file format. Another crucial issue is adapting the base-to-base route set provided by the double-sweep algorithm into a region-to-region route set which can be used by the airlift analysis models. The methods used to adapt the route sets appropriately are described, and test results are provided for two different scenarios. Finally, recommendations that were given to the analysts at AMC for use of the k-shortest path routine are given.

Two Programs to Estimate Significance of χ2 Values Using Pseudo-Probability Tests

where o, and e, are observed and expected (under the null hypothesis) numbers of the fth category (see any textbook on biometry or population genetics, e.g., Ayala and Kiger 1984; Sokal and Rohlf 1981). An unfortunate requirement of the test is that the expected numbers (e,) should not be small. Different authors give different recommendations; common opinion is that e, should not be less than 4 (see cited books). Introduction into population genetics of molecular techniques revealed a great wealth of genetic variation—allozymic, DNA restriction fragment length polymorphisms, etc.—in both plants and animals. Hence, samples of practical size (say, hundreds of individuals) will very often contain rare phenotypic or allelic categories. To obtain reliable x estimates one should then pool these rare categories, otherwise the calculated x will be inflated. Unfortunately, this causes loss of information, which is undesirable. An alternative is to use Fisher's exact probability test, but in the case of many categories and considerable total sample size, this is impractical. Roff and Bentzen (1989) suggested another practical alternative (without any pooling of data) for testing heterogeneity in R x C contingency tables containing rare categories. They used a Monte Carlo procedure, which was termed by Hernandez and Weir (1989) a pseudo-probability test, to test Hardy-Weinberg equilibrium. The procedure consists of (1) generating a sample of all possible data sets having the same marginal totals as the original data set and (2) computing x for each derived data set and counting all the sets for which x is larger than that of the original sample. The ratio of the obtained number to the overall number of generated data sets is the estimate of probability of the null hypothesis. We present here two programs, CHIRXC and CHIHW, which estimate the significance of x statistics using pseudo-probability tests. Thus, our programs permit analysis of sparse table data without pooling rare categories. This saves time and prevents loss of information. The CHIRXC analyzes R x C contingency tables. For the 2 x 2 case, it can perform Fisher's exact probability test as well. The CHIHW estimates conformity of genotypic proportions in a sample to Hardy-Weinberg expectations. It also computes an index of heterozygote deficiency or excess [D = (Ho He)/He] (Koehn et al. 1973) and estimates its significance through the pseudoprobability test. The programs are written in C (Turbo C, ver. 2, Copyright Borland International 1988). They will run on an IBM PC and compatibles. Sample sizes and dimensionality of R x C tables under analysis are limited only by the available computer memory. The approach of Roff and Bentzen (1989) was used in the MONTE program in REAP (McElroy et al. 1991). Our algorithm of randomization is different from theirs and much faster (Pudovkin Al and Zaykin DV, unpublished). The programs are available from the authors. To receive a copy, send a nonformatted 5.25-in diskette, and we will supply the disk with the programs (executables and listings), README files with user instructions, and input file formats.

The MCHF atomic-structure package

The multi-configuration Hartree-Fock code (MCHF) determines radial functions that define the orbitals of configuration state in the expansion of a non-relativistic wave function of a many-electron system. This code has been combined with others that perform angular and/or radial integrations to form an atomic-structure package for the prediction of atomic properties, called the MCHF atomic-structure package. This article describes the scope of the package, its design philosophy, organization, data input, and common file formats. Through examples it also outlines the series of steps that typically are required in the prediction of an atomic property. The present package is restricted to energy levels and transition probabilities, either in the non-relativistic LS framework or the Breit-Pauli, relativistic LSJ framework.

XREF: A Subject Thesaurus Generated with WordPerfect 5.0

Presents the XREF macro which demonstrates the use of programming variables with advanced WordPerfect macros to generate a cross‐referencing subject thesaurus. Considers the XREF macro procedure, structure, input file format and output file, including an example to show how re‐running the macro generates an updated subject thesaurus.