PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order

PermutMatrix is a work space designed to graphically explore gene expression data. It relies on the graphical approach introduced by Eisen and also offers several methods for the optimal reorganization of rows and columns of a numerical dataset. For example, several methods are proposed for optimal reorganization of the leaves of a hierarchical clustering tree, along with several seriation or unidimensional scaling methods that do not require any preliminary hierarchical clustering. This program, developed for MS Windows, with MS-Visual C++, has a clear and efficient graphical interface. Large datasets can be thoroughly and quickly analyzed.     

Graphical Methods for Analysing Combination Effects in Dose-Response Experiments

An organbath experiment with bovine tracheal muscle strips with cumulative increases in concentrations of a substance A in the absence and presence of a fixed concentration of a second substance B is considered as an example for demonstrating graphical methods to analyse drug combination effects. The response of each strip is individually described and estimated by a nonlinear dose response curve. From the curves of the combined action theoretical curves of substance A are derived, which were expected if the combination effect was simple similar or independent, respectively. The first graphical method consists in comparing the derived curves for substance A with the curves for substance A directly fitted. It is cheeked by eye if the group of derived curves can clearly be distinguished from the group of directly fitted curves. The second graphical method differs from the first method in so far, as not the curves are visualized but the parameter vectors corresponding to them. In contrast to widely used analytical methods the proposed graphical methods allow to treat individual instead of averaged dose response relationships. The methods can help to decide if the combination effect may be considered as independent, simple similar or none of both.     

The limiting information capacity of a neuronal link

The maximum rate at which a synaptic link could theoretically transmit information depends on the type of coding used. In a binary modulation system it depends chiefly on the relaxation time, and the limiting capacity equals the maximum attainable impulse rate. In a system using pulse-interval modulation, temporal precision may be a more important limiting factor. It is shown that in a number of typical cases a system of the second type could transmit several times more information per second through a synaptic link than a binary system, and the relation between relative efficiency, relaxation-time, and temporal resolving power is generalized in graphical form. It is concluded, not that interval modulation rather than binary modulation “ought” to be the mode of action of the central nervous system, but that the contrary assumption is unsupported by considerations of efficiency.     

A quantitative analysis of secondary RNA structure using domination based parameters on trees

Background  

It has become increasingly apparent that a comprehensive database of RNA motifs is essential in order to achieve new goals in genomic and proteomic research. Secondary RNA structures have frequently been represented by various modeling methods as graph-theoretic trees. Using graph theory as a modeling tool allows the vast resources of graphical invariants to be utilized to numerically identify secondary RNA motifs. The domination number of a graph is a graphical invariant that is sensitive to even a slight change in the structure of a tree. The invariants selected in this study are variations of the domination number of a graph. These graphical invariants are partitioned into two classes, and we define two parameters based on each of these classes. These parameters are calculated for all small order trees and a statistical analysis of the resulting data is conducted to determine if the values of these parameters can be utilized to identify which trees of orders seven and eight are RNA-like in structure.     

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.     

Cryptography with DNA binary strands

Biotechnological methods can be used for cryptography. Here two different cryptographic approaches based on DNA binary strands are shown. The first approach shows how DNA binary strands can be used for steganography, a technique of encryption by information hiding, to provide rapid encryption and decryption. It is shown that DNA steganography based on DNA binary strands is secure under the assumption that an interceptor has the same technological capabilities as sender and receiver of encrypted messages. The second approach shown here is based on steganography and a method of graphical subtraction of binary gel-images. It can be used to constitute a molecular checksum and can be combined with the first approach to support encryption. DNA cryptography might become of practical relevance in the context of labelling organic and inorganic materials with DNA 'barcodes'.     

AnthropMMD: An R package with a graphical user interface for the mean measure of divergence

The mean measure of divergence is a dissimilarity measure between groups of individuals described by dichotomous variables. It is well suited to datasets with many missing values, and it is generally used to compute distance matrices and represent phenograms. Although often used in biological anthropology and archaeozoology, this method suffers from a lack of implementation in common statistical software. A package for the R statistical software, AnthropMMD, is presented here. Offering a dynamic graphical user interface, it is the first one dedicated to Smith's mean measure of divergence. The package also provides facilities for graphical representations and the crucial step of trait selection, so that the entire analysis can be performed through the graphical user interface. Its use is demonstrated using an artificial dataset, and the impact of trait selection is discussed. Finally, AnthropMMD is compared to three other free tools available for calculating the mean measure of divergence, and is proven to be consistent with them.     

A simulation support system for solving large physiological models on microcomputers

Although physiological modeling and computer simulation have become useful research tools to test new scientific theories and to design and analyze laboratory experiments, developing a new model can be a tedious process because the investigator must often write very complex and specific routines for data input and output. To facilitate the design of new models (as well as the use of existing models), we have developed MODSIM, a FORTRAN-based simulation support system for the IBM PC computer than can accommodate very large dynamic models having up to several thousand equations. It provides the investigator with utilities for continuous on-line graphical and/or tubular output, as well as facilities for dynamic interaction with the model. The user must only supply a model as a list of mathematical equations written in FORTRAN, along with the initial values of the model variables and parameters. The model is precompiled, compiled, and then linked to the MODSIM utilities. Without further programming, the user can then solve the model, select variables for graphical output, and stop the model at any time to analyze the data or to change a parameter before resuming the simulation. This simulation system makes it very easy to develop new models that actively interact with the experimental research of the investigator.     

OMSSAGUI: An open-source user interface component to configure and run the OMSSA search engine

We here present a user-friendly and extremely lightweight tool that can serve as a stand-alone front-end for the Open MS Search Algorithm (OMSSA) search engine, or that can directly be used as part of an informatics processing pipeline for MS driven proteomics. The OMSSA graphical user interface (OMSSAGUI) tool is written in Java, and is supported on Windows, Linux, and OSX platforms. It is an open source under the Apache 2 license and can be downloaded from http://code.google.com/p/mass-spec-gui/.     

New method of determining kinetic constants for immobilized enzymes in a packet-bed reactor system.

A new graphical method of determining the kinetic constants for immobilized-enzyme systems is proposed and illustrated with some examples. The advantages of using this method are that these kinetic constants can be determined accurately and conveniently from the conversion data of a packed-column enzyme-reactor system.     

Phase4: automatic evaluation of database search methods

It has become standard to evaluate newly devised database search methods in terms of sensitivity and selectivity and to compare them with existing methods. This involves the construction of a suitable evaluation scenario, the execution of the methods, the assessment of their performances, and the presentation of the results. Each of these four phases and their smooth connection usually imposes formidable work. To relieve the evaluator of this burden, a system has been designed with which evaluations can be effected rapidly. It is implemented in the programming language Python whose object-oriented features are used to offer a great flexibility in changing the evaluation design. A graphical user interface is provided which offers the usual amenities such as radio- and checkbuttons or file browsing facilities.     

SNPCEQer II: the integrated detection and analysis of SNPs in DNA sequences

SNPCEQer II is a graphical user interface (GUI)-based application that integrates single nucleotide polymorphism (SNP) detection, SNP analysis and SNP editing in the Microsoft Windows (R) environment. SNPCEQer II detects SNPs in DNA sequences generated by the Beckman CEQ TM 2000 XL DNA analysis system. It provides tools to analyse SNPs by inspecting and comparing trace data (chromatograms) around putative SNPs with that of other related DNA sequences, and it can search for those SNPs in the National Center for Biotechnology Information (NCBI) databases. SNPCEQer II can determine the mutation type of a coding SNP and generate data for submission to the dbSNP database. The SNP report can be edited and printed, as can the chromatograms. SNPCEQer II is implemented in Visual C++.     

Graphical approach to model reduction for nonlinear biochemical networks

Model reduction is a central challenge to the development and analysis of multiscale physiology models. Advances in model reduction are needed not only for computational feasibility but also for obtaining conceptual insights from complex systems. Here, we introduce an intuitive graphical approach to model reduction based on phase plane analysis. Timescale separation is identified by the degree of hysteresis observed in phase-loops, which guides a "concentration-clamp" procedure for estimating explicit algebraic relationships between species equilibrating on fast timescales. The primary advantages of this approach over Jacobian-based timescale decomposition are that: 1) it incorporates nonlinear system dynamics, and 2) it can be easily visualized, even directly from experimental data. We tested this graphical model reduction approach using a 25-variable model of cardiac β(1)-adrenergic signaling, obtaining 6- and 4-variable reduced models that retain good predictive capabilities even in response to new perturbations. These 6 signaling species appear to be optimal "kinetic biomarkers" of the overall β(1)-adrenergic pathway. The 6-variable reduced model is well suited for integration into multiscale models of heart function, and more generally, this graphical model reduction approach is readily applicable to a variety of other complex biological systems.     

Restriction fragment length polymorphism maps and the concept of graphical genotypes

Summary With the advent of high density restriction fragment length polymorphism (RFLP) maps, it has become possible to determine the genotype of an individual at many genetic loci simultaneously. Often, such RFLP data are expressed as long strings of numbers or letters indicating the genotype for each locus analyzed. In this form, RFLP data can be difficult to interpret or utilize without complex statistical analysis. By contrast, numerical genotype data can also be expressed in a more useful, graphical form, known as a graphical genotype, which is described in detail in this paper. Ideally, a graphical genotype portrays the parental origin and allelic composition throughout the entire genome, yet is simple to comprehend and utilize. In order to demonstrate the usefulness of this concept, graphical genotypes for individuals from backcross and F2 populations in tomato are described. The concept can also be utilized in more complex mating schemes involving two or more parents. A model that predicts the accuracy of graphical genotypes is presented for hypothetical RFLP maps of varying marker spacing. This model indicates that graphical genotypes can be more than 99% correct in describing a genome of total size, 1000 cM, with RFLP markers located every 10 cM. In order to facilitate the application of graphical genotypes to genetics and breeding, we have developed computer software that generates and manipulates graphical genotypes. The concept of graphical genotypes should be useful in whole genome selection for polygenic traits in plant and animal breeding programs and in the diagnosis of heterogenously based genetic diseases in humans.     

Description of the ratios between metabolite concentrations in a polyenzyme system

It was demonstrated that the relations between substrate and product concentrations for a reaction catalyzed by michaelian enzyme incorporated in a multienzyme system can be graphically represented by a diverging set of straight lines intersecting in one point, the flux velocity being treated as a parameter. A competitive inhibitor shifts the intersection point along the line of equilibrium state. The relations between the concentrations of more than two reagents are represented by a set of equivelocity surfaces. The relations between substrate and product concentrations for a kinetically cooperative reaction conforming to the graphical representation by the second--order curves were analyzed. The stability criterion was obtained for a multienzyme system with the first enzyme allosterically regulated by products of subsequent reactions.     

Content-based image retrieval system using neural networks

An effective image retrieval system is developed based on the use of neural networks (NNs). It takes advantages of association ability of multilayer NNs as matching engines which calculate similarities between a user's drawn sketch and the stored images. The NNs memorize pixel information of every size-reduced image (thumbnail) in the learning phase. In the retrieval phase, pixel information of a user's drawn rough sketch is inputted to the learned NNs and they estimate the candidates. Thus the system can retrieve candidates quickly and correctly by utilizing the parallelism and association ability of NNs. In addition, the system has learning capability: it can automatically extract features of a user's drawn sketch during the retrieval phase and can store them as additional information to improve the performance. The software for querying, including efficient graphical user interfaces, has been implemented and tested. The effectiveness of the proposed system has been investigated through various experimental tests.     

JADE: An approach for interconnecting bioinformatics databases

To achieve the integration of biological data available on the World Wide Web and maintained in diverse sources such as GDB, Genbank or Acedb, we have developed a software called Jade. Jade allows programmers to create analytic tools and graphical user interfaces for one or more existing bioinformatics data sources. These tools can then be interchanged, compared and reused without making modifications in the data sources themselves. The system is implemented in the Java programming language and will run equally well on Macintosh, Windows or Unix workstations. Jade is free and can be used immediately by all interested parties.