PedVizApi: a Java API for the interactive, visual analysis of extended pedigrees

PedVizApi is a Java API (application program interface) for the visual analysis of large and complex pedigrees. It provides all the necessary functionality for the interactive exploration of extended genealogies. While available packages are mostly focused on a static representation or cannot be added to an existing application, PedVizApi is a highly flexible open source library for the efficient construction of visual-based applications for the analysis of family data. An extensive demo application and a R interface is provided. AVAILABILITY: http://www.pedvizapi.org     

KISS for STRAP: user extensions for a protein alignment editor

SUMMARY: The Structural Alignment Program STRAP is a comfortable comprehensive editor and analyzing tool for protein alignments. A wide range of functions related to protein sequences and protein structures are accessible with an intuitive graphical interface. Recent features include mapping of mutations and polymorphisms onto structures and production of high quality figures for publication. Here we address the general problem of multi-purpose program packages to keep up with the rapid development of bioinformatical methods and the demand for specific program functions. STRAP was remade implementing a novel design which aims at Keeping Interfaces in STRAP Simple (KISS). KISS renders STRAP extendable to bio-scientists as well as to bio-informaticians. Scientists with basic computer skills are capable of implementing statistical methods or embedding existing bioinformatical tools in STRAP themselves. For bio-informaticians STRAP may serve as an environment for rapid prototyping and testing of complex algorithms such as automatic alignment algorithms or phylogenetic methods. Further, STRAP can be applied as an interactive web applet to present data related to a particular protein family and as a teaching tool. REQUIREMENTS: JAVA-1.4 or higher. AVAILABILITY: http://www.charite.de/bioinf/strap/     

SURFNET: A program for visualizing molecular surfaces,cavities, and intermolecular interactions

The SURFNET program generates molecular surfaces and gaps between surfaces from 3D coordinates supplied in a PDB-format file. The gap regions can correspond to the voids between two or more molecules, or to the internal cavities and surface grooves within a single molecule. The program is particularly useful in clearly delineating the regions of the active site of a protein. It can also generate 3D contour surfaces of the density distributions of any set of 3D data points. All output surfaces can be viewed interactively, along with the molecules or data points in question, using some of the best-known molecular modeling packages. In addition, PostScript output is available, and the generated surfaces can be rendered using various other graphics packages.     

Nexplorer: phylogeny-based exploration of sequence family data

SUMMARY: Nexplorer is a web-based program for interactive browsing and manipulation of character data in NEXUS format, well suited for use with alignments and trees representing families of homologous genes or proteins. Users may upload a sequence family dataset, or choose from one of several thousand already available. Nexplorer provides a flexible means to develop customized views that combine a tree and a data matrix or alignment, to create subsets of data, and to output data files or publication-quality graphics. AVAILABILITY: Web access is from http://www.molevol.org/nexplorer     

Application of a small microcomputer to cell image analysis

Solutions to three problems in using small microcomputers for interactive cell image analysis are discussed. (1) To allow interactive processing of up to 62 X 88 pixels on inexpensive screens, data can be displayed in gray levels with an approximate logarithmic grading. Each pixel is composed of 32 screen coordinates, applying the dither matrix method to avoid artificial structures. (2) To mark special regions of interest in the image, a graphic cursor, handled from the keyboard, was implemented. (3) To evaluate parts of the image, as outlined by the cursor, the program must distinguish whether a particular pixel is outside, inside or on the border of the region. The developed algorithms permit practical interactive evaluation of cell images on a small microcomputer, with no image analysis implementation. However, it is necessary that the assembly language of the microprocessor be available for some sophisticated programming and that the operating system support graphic facilities with an appropriate resolution.     

Novel Television-Based Cognitive Training Improves Working Memory and Executive Function

The main study objective was to investigate the effect of interactive television-based cognitive training on cognitive performance of 119 healthy older adults, aged 60–87 years. Participants were randomly allocated to a cognitive training group or to an active control group in a single-blind controlled two-group design. Before and after training interactive television cognitive performance was assessed on well validated tests of fluid, higher-order ability, and system usability was evaluated. The participants in the cognitive training group completed a television-based cognitive training programme, while the participants in the active control group completed a TV-based programme of personally benefiting activities. Significant improvements were observed in well validated working memory and executive function tasks in the cognitive training but not in the control group. None of the groups showed statistically significant improvement in life satisfaction score. Participants'' reports of “adequate” to “high” system usability testify to the successful development and implementation of the interactive television-based system and compliant cognitive training contents. The study demonstrates that cognitive training delivered by means of an interactive television system can generate genuine cognitive benefits in users and these are measurable using well-validated cognitive tests. Thus, older adults who cannot use or afford a computer can easily use digital interactive television to benefit from advanced software applications designed to train cognition.     

A shell program for the design of PCR primers using genetics computer group (GCG) software (7.1) on VAX/VMS systems.

A number of software analysis packages for the design of PCR primers are available for PCs; however, software for users that depend on VAX/VMS operating systems is not available. By treating oligonucleotides as RNA molecules, I have designed an alternative means toward studying oligonucleotide interactions using software that is currently available from The Genetics Computer Group (GCG, Madison, WI). The oligonucleotide interactions with self and non-self are analyzed by the GCG FOLD program, a program which finds a secondary structure of minimum free energy for an RNA molecule. This approach allows the identification of self-priming primer pairs, and the interaction energies provide a guideline for the prediction of optimal PCR primers.     

Reviewing the curriculum

The potential use of IT in secondary biology teaching is enormous, although it is a huge undertaking and fairly daunting to newcomers. Computer learning packages and the web can offer a variety of opportunities for learning, ranging from non-interactive content provision to highly interactive student-centred learning experiences. The learning materials in use in New South Wales (NSW) schools include information web sites, computer learning packages as tutorial or revision material, computer learning packages made by the students, virtual field trips, simulations, and virtual laboratories. In addition, students and teachers are using the web for communicating amongst themselves via email, newsgroups and discussion lists, videoconferencing for both local and global communications, and telecollaborative projects. This article will focus on materials used in student learning, and on the forms of electronic communication in use within the school system. A list of resources is provided.     

SOMAP: a novel interactive approach to multiple protein sequences alignment

A novel interactive method for generating multiple protein sequencealignments is described. The program has no internal limit tothe number or length of sequences it can handle and is designedfor use with DEC VAX processors running the VMS operating system.The approach used is essentially one of manual sequence manipulation,aided by built-in symbolic displays of identities and similarities,and strict and ‘fuzzy’ (ambiguous) pattern-matchingfacilities. Additional flexibility is provided by means of aninterface to a publicly available automatic alignment systemand to a comprehensive sequence analysis package. Received on August 28, 1990; accepted on November 20, 1990     

A simulation program examining the use of ratios as raw variables in analyses of variance

An interactive, BASIC-PLUS, simulation program is described for performing a large number of multivariate analyses in accord with, or in violation of, known underlying models. Using a PDP 11/40 computer, random numbers are generated and converted into bivariate normal observations X and Y. These data are then analyzed according to three models. The three analyses are: (1) a standard analysis of variance ignoring the concomitant variable; (2) an analysis of covariance; (3) an analysis of variance on the ratio Y/X. The program can be used to examine the effect of performing multivariate analyses on data transformed into ratios. The utility of the program is the simplicity with which one can alter the underlying models and/or the mathematical relationships between X and Y. Output provides comparisons between models by accumulating rejections and other statistics on critical F-values for each model.     

SeqSQC: A Bioconductor Package for Evaluating the Sample Quality of Next-generation Sequencing Data

As next-generation sequencing (NGS) technology has become widely used to identify genetic causal variants for various diseases and traits,a number of packages for checking NGS data quality have sprung up in public domains. In addition to the quality of sequencing data,sample quality issues,such as gender mismatch,abnormal inbreeding coefficient,cryptic relatedness,and population outliers,can also have fundamental impact on downstream analysis. However,there is a lack of tools specialized in identifying problematic samples from NGS data,often due to the limitation of sample size and variant counts. We developed SeqSQC,a Bioconductor package,to automate and accelerate sample cleaning in NGS data of any scale. SeqSQC is designed for efficient data storage and access,and equipped with interactive plots for intuitive data visualization to expedite the identification of problematic samples. SeqSQC is available at http://bioconductor. org/packages/SeqSQC.     

STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes

Background  

The integration of many aspects of protein/DNA structure analysis is an important requirement for software products in general area of structural bioinformatics. In fact, there are too few software packages on the internet which can be described as successful in this respect. We might say that what is still missing is publicly available, web based software for interactive analysis of the sequence/structure/function of proteins and their complexes with DNA and ligands. Some of existing software packages do have certain level of integration and do offer analysis of several structure related parameters, however not to the extent generally demanded by a user.     

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.     

An interactive modeling program for DNA

An interactive program for modeling A-, B- and Z-DNA in a schematic and nonatomic representation has been developed for the Evans and Sutherland PS300. The program lets users display several molecules for which parameters determining the three-dimensional structure can be calculated either on the basis of theoretical models or inferred from experimental data. The calculation of the curvature and torsion of the helical axis, by a method based on Frenet's equations, makes it possible to quantify the effects of the parameters on the helical axis.     

JDotter: a Java interface to multiple dotplots generated by dotter

Java-Dotter (JDotter) is a platform-independent Java interactive interface for the Linux version of Dotter, a widely used program for generating dotplots of large DNA or protein sequences. JDotter runs as a client-server application and can send new sequences to the Dotter program for alignment as well as rapidly access a repository of preprocessed dotplots. JDotter also interfaces with a sequence database or file system to display supplementary feature data. Thus, JDotter greatly simplifies access to dotplot data in laboratories that deal with large numbers of genomes and have a multi-platform organization. AVAILABILITY: Currently, JDotter is used via Java Web Start by the Poxvirus Bioinformatics Resource for examining dotplots of complete poxvirus genomes; http://athena.bioc.uvic.ca/pbr/jdotter/. The software is available for download from the same location. SUPPLEMENTARY INFORMATION: Installation instructions, the User's Manual, screenshots and examples are available at the JDotter home page http://athena.bioc.uvic.ca/pbr/jdotter/. The software and source code is free for non-commercial applications.