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PubMed2003

CalcDose: a software for drug dosage conversion using metabolically active mass of animals.

This Visual Basic computer program has been developed for drug dosage conversions using metabolically active mass (MAM) of the animals. The two body weights (one with known dosage and the other, for which the dosage has to be calculated) and the known dosage are entered in the respective input boxes and the appropriate units are selected using the option buttons. The program displays the report in the form of both the animals' body weights and the respective dosages in milligram per kilogram body weight as well as the total actual doses in milligrams. The object oriented layout, flexible data entry and comprehensive report format render the CalcDose software a convenient and handy tool for dosage conversions.

Animals↗
PubMed2006

Dose response explorer: an integrated open-source tool for exploring and modelling radiotherapy dose-volume outcome relationships.

Radiotherapy treatment outcome models are a complicated function of treatment, clinical and biological factors. Our objective is to provide clinicians and scientists with an accurate, flexible and user-friendly software tool to explore radiotherapy outcomes data and build statistical tumour control or normal tissue complications models. The software tool, called the dose response explorer system (DREES), is based on Matlab, and uses a named-field structure array data type. DREES/Matlab in combination with another open-source tool (CERR) provides an environment for analysing treatment outcomes. DREES provides many radiotherapy outcome modelling features, including (1) fitting of analytical normal tissue complication probability (NTCP) and tumour control probability (TCP) models, (2) combined modelling of multiple dose-volume variables (e.g., mean dose, max dose, etc) and clinical factors (age, gender, stage, etc) using multi-term regression modelling, (3) manual or automated selection of logistic or actuarial model variables using bootstrap statistical resampling, (4) estimation of uncertainty in model parameters, (5) performance assessment of univariate and multivariate analyses using Spearman's rank correlation and chi-square statistics, boxplots, nomograms, Kaplan-Meier survival plots, and receiver operating characteristics curves, and (6) graphical capabilities to visualize NTCP or TCP prediction versus selected variable models using various plots. DREES provides clinical researchers with a tool customized for radiotherapy outcome modelling. DREES is freely distributed. We expect to continue developing DREES based on user feedback.

Computer Simulation↗
PubMed2002

Using CAVE technology for functional genomics studies.

We have established the first Java 3D-enabled CAVE (CAVE automated virtual environment). The Java application programming interface allows the complete separation of the program development from the program execution, opening new application domains for the CAVE technology. Programs can be developed on any Java-enabled computer platform, including Windows, Macintosh, and Linux workstations, and executed in the CAVE without modification. The introduction of Java, one of the major programming environments for bioinformatics, into the CAVE environment allows the rapid development applications for genome research, especially for the analysis of the spatial and temporal data that are being produced by functional genomics experiments. The CAVE technology will play a major role in the modeling of biological systems that is necessary to understand how these systems are organized and how they function.

Automation↗
PubMed2001

Simultaneous modelling of metabolic, genetic and product-interaction networks.

The creation of cell models from annotated genome information, as well as additional data from other databases, requires both a format and medium for its distribution. Standards are described for the representation of the data in the form of Document Type Definitions (DTDs) for XML files. Separate DTDs are detailed for genetic, metabolic and gene product-interaction networks, which can be used to hold information on individual subsystems, or which may be combined to create a whole cell DTD. In the execution of this work, a fifth DTD was also created for a metabolite thesaurus, which allows incorporation of metabolite synonyms and generic nomenclature data into the models. A gene-regulation classification scheme was also created, to facilitate incorporation of gene regulatory information in an efficient manner. The work is described with particular reference to the metabolic network of Escherichia coli, which contains 808 individual enzymes. The assignment of confidence levels to these data, through the use of Gene Ontology evidence codes, is highlighted. In silico investigations may now be performed using the mathematical simulation workbench, DBsolve, which incorporates the facility to introduce data directly from XML.

Computational Biology↗
PubMed2002

Pise: software for building bioinformatics webs.

Pise is interface construction software for bioinformatics applications that run by command-line operations. It creates common, easy-to-use interfaces to these applications for the Web, or other uses. It is adaptable to new bioinformatics tools, and offers program chaining, Unix system batch and other controls, making it an attractive method for building and using your own bioinformatics web services.

Computational Biology↗
PubMed2005

Detecting horizontal gene transfer with T-REX and RHOM programs.

As the Human Genome Project and other genome projects experience remarkable success and a flood of biological data is produced by means of high-throughout sequencing techniques, detection of horizontal gene transfer (HGT) becomes a promising field in bioinformatics. This review describes two freeware programs: T-REX for MS Windows and RHOM for Linux. T-REX is a graphical user interface program that offers functions to reconstruct the HGT network among the donor and receptor hosts from the gene and species distance matrices. RHOM is a set of command-line driven programs used to detect HGT in genomes. While T-REX impresses with a user-friendly interface and drawing of the reticulation network, the strength of RHOM is an extensive statistical framework of genome and the graphical display of the estimated sequence position probabilities for the candidate horizontally transferred genes.

Algorithms↗
PubMed2006

Computational aspects of systematic biology.

We review the resources available to systematic biologists who wish to use computers to build classifications. Algorithm development is in an early stage, and only a few examples of integrated applications for systematic biology are available. The availability of data is crucial if systematic biology is to enter the computer age.

Algorithms↗
PubMed2006

Representing, storing and accessing molecular interaction data: a review of models and tools.

One important aim within systems biology is to integrate disparate pieces of information, leading to discovery of higher-level knowledge about important functionality within living organisms. This makes standards for representation of data and technology for exchange and integration of data important key points for development within the area. In this article, we focus on the recent developments within the field. We compare the recent updates to the three standard representations for exchange of data SBML, PSI MI and BioPAX. In addition, we give an overview of available tools for these three standards and a discussion on how these developments support possibilities for data exchange and integration.

Computational Biology↗
PubMed1985

An approach to the collection and manipulation of time-based data using the IBM PC and BASICA.

With the advent of increasingly integrated, powerful and inexpensive digital electronics, relatively powerful computers have become available to the general public. Along with this technological boom there has been a concomitant increase in the availability of over-the-counter software packages which can be used by research scientists for program development. In the past, the development of computer programs for the collection of large amounts of time-based data was expensive and time consuming; however, the introduction of the current generation of 16-bit microcomputers and associated hardware and software packages has enabled investigators with only a rudimentary knowledge of computers and interfacing to begin to design programs. The schemes and algorithms, developed using BASICA on an IBM-Personal Computer, which are described in this article can serve other investigators as models for the assembly of their own programs for the collection, manipulation and plotting of time-based data. The incorporation of inexpensive computer graphics hardware and software, which provided a simple solution to the problem of analysis and presentation of large amounts of data, will also be discussed.

Algorithms↗
PubMed1985

A microcomputer program for the identification of tRNA genes.

A microcomputer program which locates tRNA genes within long DNA sequences is described. The search is performed either by identifying tRNA-like secondary structures or by locating eukaryotic RNA polymerase III promoter consensus sequences. The program is also useful in finding inverted repeats allowing the formation of stem-loop secondary structures in tRNA. The program has been developed in BASIC and 6502 Assembler and runs on the Apple II plus and IIe microcomputers. The execution is quite fast; all the operations are carried out in 1-90 s, depending on the required task and on the sequence length.

Base Sequence↗
PubMed1985

MOLECULAR DESIGNER: an interactive program for the display of protein structure on the IBM-PC.

A BASIC interactive graphics program has been developed for the IBM-PC which utilizes the graphics capabilities of that computer to display and manipulate protein structure from coordinates. Structures may be generated from typed files, or from Brookhaven National Laboratories' Protein Data Bank data tapes. Once displayed, images may be rotated, translated and expanded to any desired size. Figures may be viewed as ball-and-stick or space-filling models. Calculated multiple-point perspective may also be added to the display. Docking manipulations are possible since more than a single figure may be displayed and manipulated simultaneously. Further, stereo images and red/blue three-dimensional images may be generated using the accompanying DESIPLOT program and an HP-7475A plotter. A version of the program is also currently available for the Apple Macintosh. Full implementation on the Macintosh requires 512 K and at least one disk drive. Otherwise this version is essentially identical to the IBM-PC version described herein.

Computer Graphics↗