Datac: A multipurpose biological data analysis program based on a mathematical interpreter

The use of a mathematical command interpreter combined with the structural facility of the C-language allowed us to design a data treatment program having considerable flexibility and being able to handle any types of data (electrophysiological, biochemical and theoretical data). Ensembles of data are treated by the interpreter as if they were simple variables so that an elaborate computation can be performed on the spot by simply writing the appropriate equation on the terminal. These facilities combined with the ability of editing macrocommands at run time provide the user with data treatment possibilities that extends far beyond the possibilities actually implemented in the program. The originality of this program is that the user can easily implement the commands he most often needs, writing them in a language that most scientists will know, algebra.     

A minicomputer program for automatic saccade detection and linear analysis of eye movement systems using sine wave stimulus

A FORTRAN IV program is described, which may be run interactively or in batch and which allows a user to obtain the frequency response amplitude ratio and phase resulting from the linear analysis of an eye movement system using sine wave stimuli. The response (eye position) signal may contain components contributed by the saccadic eye movements. The program can digitize analog signals and store data on a magnetic tape. With the aid of digital filters, the program can detect saccades without requiring any input parameters from the user. The program interpolates the saccade interval using a method of least square curve fitting with a sine wave. The interpolation is relatively noise immune and works well regardless of the stimulus frequencies and the width of a saccade interval. Moreover, the program can handle long duration of signals such as 90 min of data which covers about 5 cycles of a 0.001 Hz sine wave signal. Sample runs for the cases of 0.001 and 0.1 Hz are given. The resident driver and the overlayable segments of the program have been implemented on a DEC (Digital Equipment Corp.) LAB-11 minicomputer (PDP 11/20).     

Iris: Interactive all‐in‐one graphical validation of 3D protein model iterations

Iris validation is a Python package created to represent comprehensive per‐residue validation metrics for entire protein chains in a compact, readable and interactive view. These metrics can either be calculated by Iris, or by a third‐party program such as MolProbity. We show that those parts of a protein model requiring attention may generate ripples across the metrics on the diagram, immediately catching the modeler's attention. Iris can run as a standalone tool, or be plugged into existing structural biology software to display per‐chain model quality at a glance, with a particular emphasis on evaluating incremental changes resulting from the iterative nature of model building and refinement. Finally, the integration of Iris into the CCP4i2 graphical user interface is provided as a showcase of its pluggable design.     

A large database DNA sequence handling program with generalized searching specifications.

The program described allows for the creation and manipulation of files of DNA sequence data up to very great lengths. The program uses its own paging system to load segments of the sequence into a small internal buffer so that the program does not have excessive memory requirements. The program offers a menu of functions to the user, and has been written to be forgiving of user errors. A code for the generalised specification of bases as a series of groups (i.e. A or T, Purine, etc.) has been devised and can be used in search specifications or in sequence files. Versions of the program have been developed to run with special efficiency under DIGITAL's RT11 operating system or to run under systems with a suitable implementation of FORTRAN VI.     

MOL3D,a modular and interactive program for molecular modeling and conformational analysis: I — basic modules

MOL3D is a generalized machine-independent computer program that lets the user interactively build 3D structures with different display options, such as wire, ball-and-stick and CPK representations. The program, which uses its own graphics package and driver, is designed to be very user friendly through the use of commands and menus. It has powerful transformation capabilities, such as software rotations, superpositions and zooming, and it is equipped with a fragment database that allows the user to build complex structures. The algorithm presented here is designed to perform computations in all the conformational space and therefore can be used to predict experimentally available quantities, such as NMR coupling constants. The program is efficient in the sense that it handles only dihedral angles in the first steps; as a result, it allows a rapid sampling of a great number of points through the entire conformational space. The user can choose between grid and Monte-Carlo searches of energy minimization, using a reasonable amount of computer time.     

An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences.

This paper describes a computer program designed to look for similarities between pairs of nucleic or amino acid sequences. The program looks both for segments of perfect identity or for regions where, using a scoring matrix, a minimum value is exceeded. The results of comparisons are presented as a matrix which is displayed on a simple graphics terminal. Use of a graphics terminal allows the user to display the whole of the two sequences in one screenful or to home-in on regions of interest to examine them in more detail. The program is interactive and so the user can easily see the effect of changes to variables and can use inbuilt editing functions to make insertions to produce alignments of the two sequences. These aligned sequences can then be saved on disk files for further processing.     

Imagene: an integrated computer environment for sequence annotation and analysis

MOTIVATION: To be fully and efficiently exploited, data coming from sequencing projects together with specific sequence analysis tools need to be integrated within reliable data management systems. Systems designed to manage genome data and analysis tend to give a greater importance either to the data storage or to the methodological aspect, but lack a complete integration of both components. RESULTS: This paper presents a co-operative computer environment (called Imagenetrade mark) dedicated to genomic sequence analysis and annotation. Imagene has been developed by using an object-based model. Thanks to this representation, the user can directly manipulate familiar data objects through icons or lists. Imagene also incorporates a solving engine in order to manage analysis tasks. A global task is solved by successive divisions into smaller sub-tasks. During program execution, these sub- tasks are graphically displayed to the user and may be further re- started at any point after task completion. In this sense, Imagene is more transparent to the user than a traditional menu-driven package. Imagene also provides a user interface to display, on the same screen, the results produced by several tasks, together with the capability to annotate these results easily. In its current form, Imagene has been designed particularly for use in microbial sequencing projects. AVAILABILITY: Imagene best runs on SGI (Irix 6.3 or higher) workstations. It is distributed free of charge on a CD-ROM, but requires some Ilog licensed software to run. Some modules also require separate license agreements. Please contact the authors for specific academic conditions and other Unix platforms. CONTACT: imagene home page: http://wwwabi.snv.jussieu.fr/imagene      

DRAWNA: A program for drawing schematic views of nucleic acids

A program for drawing automatically exact and schematic views of nucleic acids is described. The program is written in C ANSI and uses the Silicon Graphics GL and Xirisw libraries within the X1 1/Motif environment. Through menus, the user can choose, specify, and manipulate in real time the three-dimensional views to be displayed. Drawing options include partitioning of structures into differently colored or shaped fragments, representation of backbones as flat or with conic-section ribbons, display of paired or free bases as rods, and display of surfaces as filled or outlined and stereo or depth-cued views.     

Java Web Simulation (JWS); a web based database of kinetic models

Software to make a database of kinetic models accessible via the internet has been developed and a core database has been set up at http://jjj.biochem.sun.ac.za/. This repository of models, available to everyone with internet access, opens a whole new way in which we can make our models public. Via the database, a user can change enzyme parameters and run time simulations or steady state analyses. The interface is user friendly and no additional software is necessary. The database currently contains 10 models, but since the generation of the program code to include new models has largely been automated the addition of new models is straightforward and people are invited to submit their models to be included in the database.     

A set of programs for analysis of kinetic and equilibrium data

A program package that can be used for analysis of a wide rangeof kinetic and equilibrium data is described. The four programswere written in Turbo Pascal and run on PC, XT, AT and compatibles.The first of the programs allows the user to fit data with 16predefined and one user-defined function, using two differentnon-linear least-squares procedures. Two additional programsare used to test both the evaluation of model functions andthe least-squares fits. One of these programs uses two simpleprocedures to generate a Gaussian-distributed random variablethat is used to simulate the experimental error of measurements.The last program simulates kinetics described by differentialequations that cannot be solved analytically, using numericalintegration. This program helps the user to judge the validityof steady-state assumptions or treatment of kinetic measurementsas relaxations. Received on September 19, 1989; accepted on March 16, 1990     

A vector-based method for drawing RNA secondary structure.

MOTIVATION: To produce a polygonal display of RNA secondary structure with minimal overlap and distortion of structural elements, with minimal search for positioning them, and with minimal user intervention. RESULTS: A new algorithm for automatically drawing RNA secondary structure has been developed. The algorithm represents the direction and space for a structural element using vector and vector space. Two heuristics are used. The first heuristic is concerned with ordering structural elements to be positioned and the second with positioning them in space. The algorithm and a graphical user interface have been implemented in a working program called VizQFolder on IBM PC compatibles. Experimental results demonstrate that VizQFolder is capable of automatically generating nearly overlap-free polygonal displays for long RNA molecules. The only distortion performed to avoid overlap is the rotation of helices, leading to efficient generation of a polygonal display without sacrificing its readability. VizQFolder is not coupled to a specific prediction program of RNA secondary structure, and thus can be used for visualizing secondary structure models obtained by any means. AVAILABILITY: The executable code of VizQFolder is available at http://automation.inha.ac.kr/khan. It can also be obtained from the authors upon request.     

NMπ—improved re‐implementation of NM+, a software for estimating gene dispersal and mating patterns

This study introduces the NMπ computer program designed for estimation of plant mating system and seed and pollen dispersal kernels. NMπ is a re‐implementation of the NM+ program and provides new features such as support for multicore processors, explicit treatment of dioecy, the possibility of incorporating uniparentally cytoplasmic markers, the possibility of assessing assortative mating due to phenotypic similarity and inference about offspring genealogies. The probability model of parentage (the neighbourhood model) accounts for missing data and genotyping errors, which can be estimated along with regular parameters of the mating system. The program has virtually no restrictions with respect to a number of individuals, markers or phenotypic characters. A console version of NMπ can be run under a wide variety of operating systems, including Windows, Linux or Mac OS. For Windows users, a graphical user interface is provided to facilitate operating the software. The program, user manual and example data are available on http://www.ukw.edu.pl/pracownicy/plik/igor_chybicki/3694/ .     

MD display: An interactive graphics program for visualization of molecular dynamics trajectories

MD Display was developed as a means of visualizing molecular dynamic trajectories generated by Amber.¹ The program runs on Silicon Graphics workstations, and features a simple user interface, and convenient display and analysis options. The program has now been extended to accept input from several other molecular dynamics programs.     

StatFingerprints: a friendly graphical interface program for processing and analysis of microbial fingerprint profiles

Molecular fingerprint methods are widely used to compare microbial communities in various habitats. The free program StatFingerprints can import, process, and display fingerprint profiles and perform numerous statistical analyses on them, and also estimate diversity indexes. StatFingerprints works with the free program R, providing an environment for statistical computing and graphics. No programming knowledge is required to use StatFingerprints, thanks to its friendly graphical user interface. StatFingerprints is useful for analysing the effect of a controlled factor on the microbial community and for establishing the relationships between the microbial community and the parameters of its environment. Multivariate analyses include ordination, clustering methods and hypothesis-driven tests like 50-50 multivariate analysis of variance, analysis of similarity or similarity percentage procedure and the program offers the possibility of plotting ordinations as a three-dimensional display.     

A computer program for the graphical and iterative fitting of probability density functions to biological data.

A tutorially-assisted, interactive program, written for a Digital Equipment Corporation LAB-11 minicomputer (PDP-11/20, is described which allows a user to fit (with or without automatic estimation of initial parameter values), by a method of nonlinear least squres, any one of seven different types of probability density functions (p.d.f.'s) to an empirical frequency distribution; the latter of which may be input to the program or formed by the program whenever it is furnished a series of times between events. The iteratively-obtained, "best fit" p.d.f. is displayed on a two color, point-plot display against the background of a point-plot histogram. By selecting any one of nine output modes, the user is allowed: (1) to view histograms successively on the point-plot display, (2) to generate selected p.d.f.'s (3) to "force" p.d.f.'s having known parameters through the histogram data, (4) to obtain Chi-square (x2) and Kolmogorov-Smionov estimates of the goodness of fit to the data, and (5) to apply a special test [Williams and Kloot, 1953] in order to determine whether the least squares estimates of two candidate models are statistically different. The resident driver program and the four overlayable program segments are written in standard FORTRAN IV; except for two plot routines, which are written in PDP-11 assembly language.     

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.     

Gifa V. 4: A complete package for NMR data set processing

Summary The Gifa program is designed for processing, displaying and analysing 1D, 2D and 3D NMR data sets. It has been constructed in a modular fashion, based on three independent modules: a set of commands that perform all the basic processing operations such as apodisation functions, a complete set of Fourier Transforms, phasing and baseline correction, peak-picking and line fitting, linear prediction and maximum entropy processing; a set of command language primitives that permit the execution of complex macro commands; and a set of graphic commands that permit to build a complete graphic user interface, allowing the user to interact easily with the program. We have tried to create a versatile program that can be easily extended according to the user's requirements and that is adapted to a novice as well as an experienced user. The program runs on any UNIX computer, with or without graphic display, in interactive or batch mode.