COMPUTER PROGRAM FOR THREE-DIMENSIONAL RECONSTRUCTIONS AND NUMERICAL ANALYSES OF PLANT ORGANS FROM SERIAL SECTIONS

A computer program (SECTION) is presented which allows for the three-dimensional reconstruction of serial cross sections through biological materials. The program provides a numerical analysis of perimeter length and transverse area of each anatomical feature designated in a cross section, as well as surface area and volume computations for features that pass from one section to another. In addition to rotating and tilting the 3-D reconstruction in any desired orientation, the program has editing capabilities which allow different combinations of anatomical features to be shown in neutral gray outline or interconnected by colored lines.     

WinCD: Windows Software for Complex Demodulation

We describe WinCD, a program for extracting quantitative information about periodicity in time-series data using the method of complex demodulation (CD). The method is particularly well suited for the analysis of the effects of variables that may produce changes in biological rhythms, such as sleep deprivation, adaptation to changes in work schedules, time zone displacements, and various sorts of pathology. WinCD enables exploratory analysis of time series data by providing graphical displays of raw and processed time series, as well as numerous options for viewing and saving quantitative data. We describe WinCD operations and examples of the use of the program.     

WinCD: Windows Software for Complex Demodulation

We describe WinCD, a program for extracting quantitative information about periodicity in time-series data using the method of complex demodulation (CD). The method is particularly well suited for the analysis of the effects of variables that may produce changes in biological rhythms, such as sleep deprivation, adaptation to changes in work schedules, time zone displacements, and various sorts of pathology. WinCD enables exploratory analysis of time series data by providing graphical displays of raw and processed time series, as well as numerous options for viewing and saving quantitative data. We describe WinCD operations and examples of the use of the program.     

Use of the Computer Automated Structure Evaluation program in determining quantitative structure-activity relationships within hallucinogenic phenylalkylamines

The Computer Automated Structure Evaluation (CASE) program has been successfully used to generate automatically and identify molecular fragments relevant to the hallucinogenic activity expressed by some phenylalkylamines. Utilizing these major fragments, Quantitative Structure-Activity Relationship (QSAR) calculations were carried out to obtain an equation which was used for predictions of potencies. Correlations of these major activating/inactivating fragments with the biological activity of the compounds, as well as predictive capabilities of the CASE program, are discussed.     

BicAT: a biclustering analysis toolbox

SUMMARY: Besides classical clustering methods such as hierarchical clustering, in recent years biclustering has become a popular approach to analyze biological data sets, e.g. gene expression data. The Biclustering Analysis Toolbox (BicAT) is a software platform for clustering-based data analysis that integrates various biclustering and clustering techniques in terms of a common graphical user interface. Furthermore, BicAT provides different facilities for data preparation, inspection and postprocessing such as discretization, filtering of biclusters according to specific criteria or gene pair analysis for constructing gene interconnection graphs. The possibility to use different biclustering algorithms inside a single graphical tool allows the user to compare clustering results and choose the algorithm that best fits a specific biological scenario. The toolbox is described in the context of gene expression analysis, but is also applicable to other types of data, e.g. data from proteomics or synthetic lethal experiments. AVAILABILITY: The BicAT toolbox is freely available at http://www.tik.ee.ethz.ch/sop/bicat and runs on all operating systems. The Java source code of the program and a developer's guide is provided on the website as well. Therefore, users may modify the program and add further algorithms or extensions.     

Principles and Perspectives for Educational Biology

Computer-aided learning (CAL) techniques are now used at many levels of biological education. Many of these CAL programs are written by teachers because suitable material is unavailable. However, the amount of time required for the design and coding of a reliable CAL program can deter many teachers. Any CAL program can be split into two components: the ‘non-educational’ part, for example, program control structures, input–output routines; and the educational material. The ‘non-educational’ component can be organized into a program shell which can then be used with a wide range of biological topics. A program shell, for use on the BBC microcomputer, is described with an example of an application. The example is ‘LINKAGE’, a genetics teaching program.     

An "enactive" approach to integrative and comparative biology: thoughts on the table

We discuss the concept of Enaction as originally proposed by Varela. We attempt to exemplify through two specific topics, sensory ecology and behavior, as well as physiological and behavioral ecology, on which the enactive approach is based. We argue that sensory physiology allows us to explore the biological and cognitive meaning of animal 'private' sensory channels, beyond the scope of our own sensory capacity. Furthermore, after analyzing the interplay between factors that may impose limits upon an animal's use of time and energy, we call for a program of research in integrative and comparative biology that simultaneously considers evolutionary ecology (including physiological and behavioral ecology) and neurobiology (including cognitive mechanisms as well structural design). We believe that this approach represents a shift in scientific attitude among biologists concerning the place of biological and ecological topics in studies of integrative and comparative biology and biological diversity and vice versa.     

Synthetic biology in various cellular and molecular fields: applications,limitations, and perspective

Molecular Biology Reports - Synthetic biology breakthroughs have facilitated genetic circuit engineering to program cells through novel biological functions, dynamic gene expressions, as well as...     

3-D clustering: a tool for high throughput docking

This report describes a computer program for clustering docking poses based on their 3-dimensional (3D) coordinates as well as on their chemical structures. This is chiefly intended for reducing a set of hits coming from high throughput docking, since the capacity to prepare and biologically test such molecules is generally far more limited than the capacity to generate such hits. The advantage of clustering molecules based on 3D, rather than 2D, criteria is that small variations on a scaffold may bring about different binding modes for molecules that would not be predicted by 2D similarity alone. The program does a pose-by-pose/atom-by-atom comparison of a set of docking hits (poses), scoring both spatial and chemical similarity. Using these pair-wise similarities, the whole set is clustered based on a user-supplied similarity threshold. An output coordinate file is created that mirrors the input coordinate file, but contains two new properties: a cluster number and similarity to the cluster center. Poses in this output file can easily be sorted by cluster and displayed together for visual inspection with any standard molecular viewing program, and decisions made about which molecule should be selected for biological testing as the best representative of this group of similar molecules with similar binding modes.     

Issues Concerning the Eradication or Establishment and Biological Control of the Mediterranean Fruit Fly,Ceratitis capitata(Wiedemann) (Diptera: Tephritidae), in California

Classical biological control is suggested as a tool worth developing now for possible future use in the integrated pest management of the Mediterranean fruit fly (Medfly),Ceratitis capitata(Wiedemann), in California. Three factors that impact broadly on developing and implementing such a biological control program are: (1) the question of Medfly establishment, (2) quarantine considerations, and (3) agricultural and urban concerns. Each of these factors and their combined effects must be considered when discussing biological control of Medfly in California as shaped by historical perspectives on Medfly invasions, methods of Medfly eradication, and past biological control efforts against Medfly. We believe that biological control research should play a foundational role in any future Medfly management programs in California. Development of biological control should involve life history studies of Medfly and its natural enemies in their area of endemicity in sub-Saharan, southeast Africa. Medfly has been studied and should continue to be studied in areas it has invaded, because information derived from such studies provides insights into the potential distribution, abundance, and impact of Medfly populations in California. A plan for a biological research program on Medfly and its relatives and a biological control strategy are presented.     

Computer-assisted mathematical analysis of sigmoid biological events

A program in BASIC is described which allows accurate quantificationof some numerical parameters that can be objectively correlatedto biological indexes in sigmoid biological events. Attentionwas focused on the polymerization process of actin (a muscleprotein with a mol. wt of 42 000 daltons) studied as the variationin the OD₃₆₀ index with time. The experimental points, if plotted,can be well approximated by a rational function of the typeOD₃₆₀ = f(t), which passes through the origin and can be representedgraphically by a sigmoid curve. The program was very helpfulin comparing the experimental curves and in analysing significantparameters, such as maximum velocity and asymptote, that characterizethese curves and whose interpretation would otherwise be purelysubjective. Received on July 11, 1985; accepted on January 13, 1986     

MorphoJ: an integrated software package for geometric morphometrics

Increasingly, data on shape are analysed in combination with molecular genetic or ecological information, so that tools for geometric morphometric analysis are required. Morphometric studies most often use the arrangements of morphological landmarks as the data source and extract shape information from them by Procrustes superimposition. The MorphoJ software combines this approach with a wide range of methods for shape analysis in different biological contexts. The program offers an integrated and user-friendly environment for standard multivariate analyses such as principal components, discriminant analysis and multivariate regression as well as specialized applications including phylogenetics, quantitative genetics and analyses of modularity in shape data. MorphoJ is written in Java and versions for the Windows, Macintosh and Unix/Linux platforms are freely available from http://www.flywings.org.uk/MorphoJ_page.htm.     

EvoluZion: a computer simulator for teaching genetic and evolutionary concepts

EvoluZion is a forward-in-time genetic simulator developed in Java and designed to perform real time simulations on the evolutionary history of virtual organisms. These model organisms harbour a set of 13 genes that codify an equal number of phenotypic features. These genes change randomly during replication, and mutant genes can have null, positive or negative effects on the organisms’ fitness, allowing to model effects of both selection pressures and drift on gene evolution. There are two versions of this program: version 1.6.x_haploid; focused on macroevolutionary events and depicting prokaryote-like organisms, and version 2.3.x_diploid that simulate diploid, sexually reproducing organisms, and it is more adequate to teach micro-evolution as well as key genetic concepts such as Mendel’s laws, epistasis, genetic linkage, genetic mapping among others. Different data sets can be collected periodically during running in order to perform further analyses. In addition, the complete genealogy of extant as well as extinct organisms can be recorded. EvoluZion is well suited for teaching evolutionary biology concepts to students of all levels in a pedagogic way. This is mainly due to three main program features: (i) its intuitive and simple graphical interface (ii) a visualisation similar to videogames (iii) flexible integration of a wide range of biological phenomena into a single simulation.     

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.     

Prediction of Protein Function Improving Sequence Remote Alignment Search by a Fuzzy Logic Algorithm

The functional annotation of the new protein sequences represents a major drawback for genomic science. The best way to suggest the function of a protein from its sequence is by finding a related one for which biological information is available. Current alignment algorithms display a list of protein sequence stretches presenting significant similarity to different protein targets, ordered by their respective mathematical scores. However, statistical and biological significance do not always coincide, therefore, the rearrangement of the program output according to more biological characteristics than the mathematical scoring would help functional annotation. A new method that predicts the putative function for the protein integrating the results from the PSI-BLAST program and a fuzzy logic algorithm is described. Several protein sequence characteristics have been checked in their ability to rearrange a PSI-BLAST profile according more to their biological functions. Four of them: amino acid content, matched segment length and hydropathic and flexibility profiles positively contributed, upon being integrated by a fuzzy logic algorithm into a program, BYPASS, to the accurate prediction of the function of a protein from its sequence. Antonio Gómez and Juan Cedano contributed equally to this work.     

Dynamic exploration and editing of KEGG pathway diagrams

MOTIVATION: The Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway database is a very valuable information resource for researchers in the fields of life sciences. It contains metabolic and regulatory processes in the form of wiring diagrams, which can be used for browsing and information retrieval as well as a base for modeling and simulation. Thus it helps in understanding biological processes and higher-order functions of biological systems. Currently the KEGG website uses semi-static visualizations for the presentation and navigation of its pathway information. While this visualization style offers a good pathway presentation and navigation, it does not provide some of the possibilities related to dynamic visualizations, most importantly, the creation and visualization of user-specific pathways. RESULTS: This paper presents methods for the dynamic visualization, interactive navigation and editing of KEGG pathway diagrams. These diagrams, given as KEGG Markup Language (KGML) files, can be visually explored using novel approaches combining semi-static and dynamic visualization, but also edited or even newly created and then exported into KGML files. AVAILABILITY: KGML-ED, a program implementing the presented methods, is available free of charge to the scientific community at http://kgml-ed.ipk-gatersleben.de.     

LOGIT: a program for dose-response analysis.

We describe a FORTRAN computer program for fitting the logistic distribution function: (formula: see text) Where x represents dose or time, to dose-response data. The program determines both weighted least squares and maximum likelihood estimates for the parameters alpha and beta. It also calculates the standard errors of alpha and beta under both estimation methods, as well as the median lethal dose (LD50) and its standard error. Dose--response curves found by both fitting methods can be plotted as well as the 95% confidence bands for these lines.