CRYStallize: A crystallographic symmetry display and handling subpackage in TOM/FRODO

We have implemented in TOM/FRODO a protein crystallographic symmetry display and handling package, called CRYStallize. This package is designed as an aid in solving protein structures by molecular replacement methods. It allows the rotation/translation solutions provided by molecular replacement programs to be checked in a fast and easy way. Using CRYStallize, approximate solutions can also be improved by manual modifications. Symmetry-related objects, represented as surfaces, can be generated and handled in the same way as the reference molecules, thus permitting an efficient analysis of crystal packing and site accessibility. This program is available in the TOM/FRODO software release, which runs on the Silicon-Graphics workstations.     

PEAS V1.0: a package for elementary analysis of SNP data

We have developed a software package named PEAS to facilitate analyses of large data sets of single nucleotide polymorphisms (SNPs) for population genetics and molecular phylogenetics studies. PEAS reads SNP data in various formats as input and is versatile in data formatting; using PEAS, it is easy to create input files for many popular packages, such as STRUCTURE, frappe, Arlequin, Haploview, LDhat, PLINK, EIGENSOFT, PHASE, fastPHASE, MEGA and PHYLIP. In addition, PEAS fills up several analysis gaps in currently available computer programs in population genetics and molecular phylogenetics. Notably, (i) It calculates genetic distance matrices with bootstrapping for both individuals and populations from genome-wide high-density SNP data, and the output can be streamlined to MEGA and PHYLIP programs for further processing; (ii) It calculates genetic distances from STRUCTURE output and generates MEGA file to reconstruct component trees; (iii) It provides tools to conduct haplotype sharing analysis for phylogenetic studies based on high-density SNP data. To our knowledge, these analyses are not available in any other computer program. PEAS for Windows is freely available for academic users from http://www.picb.ac.cn/~xushua/index.files/Download_PEAS.htm.     

Software for analysis and manipulation of genetic linkage data.

We present eight computer programs written in the C programming language that are designed to analyze genotypic data and to support existing software used to construct genetic linkage maps. Although each program has a unique purpose, they all share the common goals of affording a greater understanding of genetic linkage data and of automating tasks to make computers more effective tools for map building. The PIC/HET and FAMINFO programs automate calculation of relevant quantities such as heterozygosity, PIC, allele frequencies, and informativeness of markers and pedigrees. PREINPUT simplifies data submissions to the Centre d'Etude du Polymorphisme Humain (CEPH) data base by creating a file with genotype assignments that CEPH's INPUT program would otherwise require to be input manually. INHERIT is a program written specifically for mapping the X chromosome: by assigning a dummy allele to males, in the nonpseudoautosomal region, it eliminates falsely perceived noninheritances in the data set. The remaining four programs complement the previously published genetic linkage mapping software CRI-MAP and LINKAGE. TWOTABLE produces a more readable format for the output of CRI-MAP two-point calculations; UNMERGE is the converse to CRI-MAP's merge option; and GENLINK and LINKGEN automatically convert between the genotypic data file formats required by these packages. All eight applications read input from the same types of data files that are used by CRI-MAP and LINKAGE. Their use has simplified the management of data, has increased knowledge of the content of information in pedigrees, and has reduced the amount of time needed to construct genetic linkage maps of chromosomes.     

AmberFFC, a flexible program to convert AMBER and GLYCAM force fields for use with commercial molecular modeling packages

A program for converting the different existing AMBER and GLYCAM force fields for use with commercial molecular modeling packages is presented, using the Molecular Simulations Inc. (MSI or Accelrys) software package as a case model. Called AmberFFC, the program creates AMBER and GLYCAM force field files suitable for use with the Accelrys molecular mechanics modules by transforming the amino acid, nucleotide, and monosaccharide topology databases and force field parameter files to the Accelrys file format. It is intended for any modeler who is interested in using the current AMBER and GLYCAM force fields with the Accelrys FDiscover and CDiscover programs. AmberFFC has been written entirely with the Perl programming language, making it highly flexible and portable. In order to compare the implementation of the force fields converted by AmberFFC in the Accelrys package with their corresponding execution in the AMBER software, and also to verify the efficiency of the AmberFFC program, results from single point energy calculations for 13 model molecules were obtained with the two programs. It is demonstrated that results obtained with the CDiscover and FDiscover modules compare well to those found using Sander_classic, thus showing that AmberFFC is a highly efficient program. Some energy differences between the AMBER and Accelrys software have been observed, and their origin has been characterized and discussed.     

Life cycle assessment through on-line database linked with various enterprise database systems

Goal, Scope and Background  Performing a life cycle assessment (LCA) has been a rather resource and time-consuming business. The method of data collection may be problematic, and the quality of the final results can be influenced by the reliability of the data. Therefore, it is helpful to utilize an on-line data gathering system to save time and to improve the reliability of the collected raw data. Main Features  We have developed an LCA software package for a steel company. The software consists of two major parts: an LCA tool kit and an interface program. The LCA tool kit is a user interface for handling an LCA database server. It has powerful functions to execute systematic analysis, not only for the amount of energy and raw materials, but also for the volume of pollutants generated by each component. The latter is an interface program between a data handling system and an on-line data gathering system. This interface program is linked with three enterprise database systems, such as enterprise resource planning (ERP), an environmental management system (EMS) and an energy server system (ESS). In this study, we compared three different ways of performing LCA. Two of them are on-line methods, and another is manual. Results and Discussion  Among the three methods, the best method was on-line LCA linked with ERP, EMS and ESS. Case studies in steel works have shown that the current method is superior to manual data gathering in terms of time and cost (man-month) savings, data reliability and other applications. Results of life cycle inventory and life cycle impact assessment for steel products have shown monthly fluctuations due to fuel usage ratio, which have not been detected before using manual data gathering. Conclusions  An LCA can be performed quickly, if one is to employ the on-line data gathering system we have developed. The system consists of an LCA software package including the interface program and LCA tool kit, and the enterprise database systems. Case studies for LCA with the on-line system have shown superior performance to that carried out using the manual data entry method. Recommendations and Perspective  This system enables an enterprise to take Type III and conduct benchmarking to other companies or societies within a short time. Also, combining this tool with an environmental performance evaluation or accounting system can allow one to achieve a more progressive environmental management.     

The CCPN data model for NMR spectroscopy: development of a software pipeline

To address data management and data exchange problems in the nuclear magnetic resonance (NMR) community, the Collaborative Computing Project for the NMR community (CCPN) created a "Data Model" that describes all the different types of information needed in an NMR structural study, from molecular structure and NMR parameters to coordinates. This paper describes the development of a set of software applications that use the Data Model and its associated libraries, thus validating the approach. These applications are freely available and provide a pipeline for high-throughput analysis of NMR data. Three programs work directly with the Data Model: CcpNmr Analysis, an entirely new analysis and interactive display program, the CcpNmr FormatConverter, which allows transfer of data from programs commonly used in NMR to and from the Data Model, and the CLOUDS software for automated structure calculation and assignment (Carnegie Mellon University), which was rewritten to interact directly with the Data Model. The ARIA 2.0 software for structure calculation (Institut Pasteur) and the QUEEN program for validation of restraints (University of Nijmegen) were extended to provide conversion of their data to the Data Model. During these developments the Data Model has been thoroughly tested and used, demonstrating that applications can successfully exchange data via the Data Model. The software architecture developed by CCPN is now ready for new developments, such as integration with additional software applications and extensions of the Data Model into other areas of research.     

Set of novel tools for PCR primer design.

We have developed a new package of computer programs and algorithms for different PCR applications, including allele-specific PCR, multiplex PCR, and long PCR. The package is included in the upcoming VectorNTI suite software and attempts to incorporate most of the current knowledge about PCR primer design. A wide range of primer characteristics is available for user manipulation to provide improved efficiency and increased flexibility of primer design. To accelerate the primer calculations, we have optimized algorithms using recent advances in computer science such as dynamic trees and lazy evaluation. Proper structural organization of input parameters provides further program acceleration. New Vector NTI primer design software allows calculations of primer pairs for long PCR amplification of 120-kb genomic DNA in 5 min under most stringent input parameters and clustering 435 primer pairs for multiplex PCR within 30 min on a standard Pentium III PC. Our program allows the user to take advantage of molecule annotation by applying different kinds of filtering features during PCR primer design.     

TURBOVEG,a comprehensive data base management system for vegetation data

Abstract. The computer software package TURBOVEG (for Microsoft® Windows®) was developed in The Netherlands for the processing of phytosociological data. This package comprises an easy‐to‐use data base management system. The data bank to be managed can be divided into several data bases which may consist of up to 100 000 relevés each. The program provides methods for input, import, selection, and export of relevés. In 1994, TURBOVEG was accepted as the standard computer package for the European Vegetation Survey. Currently it has been installed in more than 25 countries throughout Europe and overseas.     

Generalized ordering parameter S2 for N-H peptide bonding as measure of the conformational flexibility of proteins: comparison of algorithms of S2 calculation from molecular dynamics simulation data

NMR spectroscopy in combination with molecular dynamics (MD) simulation technique is a powerful tool for investigation of biomolecule conformations. In the present study we compare the two algorithms of calculation of the generalized order parameter S2 for the peptide N-H bond from MD simulation data. The program based on this algorithm has been written and the effect of an adjustible parameter on results of calculation was studied. HIV-1 protease MD simulation was performed during 7.36 ns using GROMACS 3.1.4. software package. The calculated order parameter values are in good agreement with those obtained by other authors using NMR.     

A computerized system for rapid interpretation of acid/base disorders

Rapid and correct interpretation of arterial blood gas results is necessary in the operating room or intensive care unit. However, manual calculation and interpretation is tedious and prone to error. A computer system consisting of two programs written in BASIC has been created to address these problems. The program uses a series of decisions to arrive at a conclusion. Data generated by the Interpreter may be used by a subsequent program, the Manager, in determining ventilation parameters.     

metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella

The metabolic SearcH And Reconstruction Kit (metaSHARK) is a new fully automated software package for the detection of enzyme-encoding genes within unannotated genome data and their visualization in the context of the surrounding metabolic network. The gene detection package (SHARKhunt) runs on a Linux system and requires only a set of raw DNA sequences (genomic, expressed sequence tag and/or genome survey sequence) as input. Its output may be uploaded to our web-based visualization tool (SHARKview) for exploring and comparing data from different organisms. We first demonstrate the utility of the software by comparing its results for the raw Plasmodium falciparum genome with the manual annotations available at the PlasmoDB and PlasmoCyc websites. We then apply SHARKhunt to the unannotated genome sequences of the coccidian parasite Eimeria tenella and observe that, at an E-value cut-off of 10⁻²⁰, our software makes 142 additional assertions of enzymatic function compared with a recent annotation package working with translated open reading frame sequences. The ability of the software to cope with low levels of sequence coverage is investigated by analyzing assemblies of the E.tenella genome at estimated coverages from 0.5× to 7.5×. Lastly, as an example of how metaSHARK can be used to evaluate the genomic evidence for specific metabolic pathways, we present a study of coenzyme A biosynthesis in P.falciparum and E.tenella.     

Interactive program for visualization and modelling of proteins,nucleic acids and small molecules

The graphics package Insight for the DEC VAX and Evans and Sutherland PS300, created as part of a joint university-industry research project, provides a broad set of capabilities which allow the user to display molecular models in stick figure and surface representation. The Insight program allows the user to model and manipulate proteins, nucleic acids and small molecules. The software accepts coordinate input from several possible sources and provides both a command and menu interface for manipulation of the graphics objects. The command language and program structure make it easy for the biochemist or molecular biologist to use.     

EZ-FIT: a practical curve-fitting microcomputer program for the analysis of enzyme kinetic data on IBM-PC compatible computers

EZ-FIT, an interactive microcomputer software package, has been developed for the analysis of enzyme kinetic and equilibrium binding data. EZ-FIT was designed as a user-friendly menu-driven package that has the facility for data entry, editing, and filing. Data input permits the conversion of cpm, dpm, or optical density to molar per minute per milligram protein. Data can be fit to any of 14 model equations including Michaelis-Menten, Hill, isoenzyme, inhibition, dual substrate, agonist, antagonist, and modified integrated Michaelis-Menten. The program uses the Nelder-Mead simplex and Marquardt nonlinear regression algorithms sequentially. A report of the results includes the parameter estimates with standard errors, a Student t test to determine the accuracy of the parameter values, a Runs statistic test of the residuals, identification of outlying data, an Akaike information criterion test for goodness-of-fit, and, when the experimental variance is included, a chi 2 statistic test for goodness-of-fit. Several different graphs can be displayed: an X-Y, a Scatchard, an Eadie-Hofstee, a Lineweaver-Burk, a semilogarithmic, and a residual plot. A data analysis report and graphs are designed to evaluate the goodness-of-fit of the data to a particular model.     

A visual data flow environment for macromolecular crystallographic computing

This article describes the integration of programs from the widely used CCP4 macromolecular crystallography package into a modern data flow visualization environment (application visualization system [AVS]), which provides a simple graphical user interface, a visual programming paradigm, and a variety of 1-, 2-, and 3-D data visualization tools for the display of graphical information and the results of crystallographic calculations, such as electron density and Patterson maps. The CCP4 suite comprises a number of separate Fortran 77 programs, which communicate via common file formats. Each program is encapsulated into an AVS macro module, and may be linked to others in a data flow network, reflecting the nature of many crystallo-graphic calculations. Named pipes are used to pass input parameters from a graphical user interface to the program module, and also to intercept line printer output, which can be filtered to extract graphical information and significant numerical parameters. These may be passed to downstream modules, permitting calculations to be automated if no user interaction is required, or giving the user the opportunity to make selections in an interactive manner.     

A computer program for linear nonparametric and parametric identification of biological data

A computer program package for parametric and nonparametric linear system identification of both static and dynamic biological data, written for an LSI-11 minicomputer with 28 K of memory, is described. The program has 11 possible commands including an instructional help command. A user can perform nonparametric spectral analysis and estimation of autocorrelation and partial autocorrelation functions of univariate data and estimate nonparametrically the transfer function and possibly an associated noise series of bivariate data. In addition, the commands provide the user the means to derive a parametric autoregressive moving average model for univariate data, to derive a parametric transfer function and noise model for bivariate data, and to perform several model evaluation tests such as pole-zero cancellation, examination of residual whiteness and uncorrelatedness with the input. The program, consisting of a main program and driver subroutine as well as six overlay segments, may be run interactively or automatically.     

The reconstruction of structure from electron micrographs of randomly oriented particles

A new method for enhancing and reconstructing the three dimensional structure of randomly oriented particles from their electron micrographs is developed. The method requires as an input many pictures of randomly oriented identical particles. The analysis is based on the calculation and accumulation of the spatial correlation of the densities on the electron micrographs, from which the spherical harmonic coefficients of the structure can be found. The process of enhancement of the spatial correlation and the averaging out of background noise enables reconstructions by use of pictures with low signal-to-noise ratio. The theory is presented and implemented in a computer program package. Simulated electron micrographs of ellipses, rods and a model of hexameric glutamate dehydrogenase are analyzed to demonstrate reconstructions using the computer programs.     

NEUREC - a program package for 3D-reconstruction from serial sections using a microcomputer

A software package is described to reconstruct three-dimensional pictures in true perspective from a series of parallel sections using a low-cost computer system (Apple II plus). Data sampling via a graphic tablet and graphical output on the monitor screen or a digital plotter are assigned to different programs under control of a menu program. The number of data representing the object under study is unlimited. Originally written in BASIC, the programs were translated to machine language. As an application of the package, reconstructions of an identified large interneuron of the locust brain are presented.     

SCoP: An interactive simulation control program for micro- and minicomputers

A nes software system is described for building simulation programs on micro- and minicomputers. Model equations are written as C subroutines, compiled and linked to the SCoP package to produce a menu-driven, interactive program. The system maintains a database of names, values, and units for all model parameters and variables. Run-time options include several methods for interactive parameter modification and both graphic and tabular outputs, with output values presented as they are calculated. Simulation output values can be compared with experimental data graphically and a companion program SCoPFit is provided for formal optimization of parameter values.