A public domain image-analysis program for the single-cell gel-electrophoresis (comet) assay

The single-cell gel electrophoresis (or comet) assay has gained widespread acceptance as a cheap and simple genotoxicity test, but it requires a computer-assisted image-analysis system. As commercial programs are expensive and inflexible, we decided to develop an image-analysis system based on public domain programs and make it publicly available for the scientific community. Our system is based on the scientific image-processing program NIH Image, and was written in its Pascal-like macro language. User interaction was kept as simple as possible, to enable the measurement of a large number of cells with a few keystrokes. Therefore, the time for image analysis is very low, even on slow computers. The comet macro can be obtained from http://mailbox.univie.ac.at/christoph.helma++ +/comet/, NIH Image is available at http://rsb.info.nih.gov/nih-image/. Both programs are free of charge.     

Computer quantification of intracellular gold particles

We describe the use of image software programs available for both PC and Macintosh computers to quantify the accumulation and distribution of gold-labeled constructs within two-dimensional cell sections. The compartmentalization of a biotinylated-peptide was visualized in radiation-induced fibrosarcoma cells by transmission electron microscopy, using a gold particle-streptavidin conjugate. This study illustrates the ease of tabulating gold particles observed in scanned electron micrographs, using Adobe Photoshop in conjunction with the public domain NIH Image program (Version 1.61). Quantitative information regarding the localization of molecules inside cells is crucial in defining their sites of action and in developing more effective therapeutic agents.     

A computer program that simulates cloning of DNA

Easy Cloner is a computer program that manipulates DNA sequences as in cloning experiments and produces maps of the resulting plasmids. The program runs in the graphics mode of an IBM PC or compatible computer and is operated by using a mouse to point to the required actions. The program is available in the public domain.     

Inclusion counter: a public domain image analysis system for measurement of Chlamydiaceae growth in vitro

The traditional method of measuring chlamydial growth in vitro, counting Chlamydiaceae inclusions by eye, is time-consuming and error prone. This paper describes a novel automated image analysis system suitable for high-throughput screening of novel anti-Chlamydiaceae compounds. The software, Inclusion Counter v3.0, is freely available in the public domain (http://www.image-analysis.co.uk).     

shinyChromosome:An R/Shiny Application for Interactive Creation of Non-circular Plots of Whole Genomes

Non-circular plots of whole genomes are natural representations of genomic data aligned along all chromosomes.Currently,there is no specialized graphical user interface(GUI) designed to produce non-circular whole genome diagrams,and the use of existing tools requires considerable coding effort from users.Moreover,such tools also require improvement,including the addition of new functionalities.To address these issues,we developed a new R/Shiny application,named shiny Chromosome,as a GUI for the interactive creation of non-circular whole genome diagrams.shiny Chromosome can be easily installed on personal computers for own use as well as on local or public servers for community use.Publication-quality images can be readily generated and annotated from user input using diverse widgets.shiny Chromosome is deployed at http://150.109.59.144:3838/shiny Chromosome/,http://shiny Chromosome.ncpgr.cn,and https://yimingyu.shinyapps.io/shiny Chromosome for online use.The source code and manual of shiny Chromosome are freely available at https://github.com/venyao/shiny Chromosome.     

Predict7, a program for protein structure prediction

We describe a program for protein sequence analysis which runs in IBM PC computers. Protein sequences are loaded from files in Mount-Conrad and Lipman-Pearson format. Seven features are analyzed: hydrophilicity, hydropathy, surface probability, side chain flexibility, antigenicity, secondary structure and N-glycosylation sites. Numeric results can be shown, printed or stored in files exportable to other programs. Graphics of up to four predictions can be displayed on the screen, printed out or plotted, with several definable options. This program has been designed to be fast, user-friendly and to be shared with the scientific community.     

Datamonkey: rapid detection of selective pressure on individual sites of codon alignments

Datamonkey is a web interface to a suite of cutting edge maximum likelihood-based tools for identification of sites subject to positive or negative selection. The methods range from very fast data exploration to the some of the most complex models available in public domain software, and are implemented to run in parallel on a cluster of computers. AVAILABILITY: http://www.datamonkey.org. In the future, we plan to expand the collection of available analytic tools, and provide a package for installation on other systems.     

Algamica: revisions to a key-based computerized counting program for free-living,attached, and benthic algae

A computerized counting program for algae and other microscopic bodies, named Algamica, is presented here. This program is a revised version of the original computer counting program of Hamilton published in 1990. This DOS-based software can enumerate all types of microscopic algae (i.e. phytoplankton, periphyton, diatoms), for which adequate expression of results are provided. Automated calculations of densities, biovolumes, surface areas and carbon biomass are available at the termination of each sample count. A simple counter for other micro-organisms is also available. A comprehensive guide manual file has been added to allow for a friendly first contact with the program and its options. This software conforms to current enumeration methodology. This version is available for PC computers, from website Algamica.ibelgique.com. Minimum required memory is 200 KB.     

Computer program for the IBM personal computer which searches for approximate matches to short oligonucleotide sequences in long target DNA sequences.

We describe a program which may be used to find approximate matches to a short predefined DNA sequence in a larger target DNA sequence. The program predicts the usefulness of specific DNA probes and sequencing primers and finds nearly identical sequences that might represent the same regulatory signal. The program is written in the C programming language and will run on virtually any computer system with a C compiler, such as the IBM/PC and other computers running under the MS/DOS and UNIX operating systems. The program has been integrated into an existing software package for the IBM personal computer (see article by Mount and Conrad, this volume). Some examples of its use are given.     

Threat displays are not handicaps

Within a general framework of handicap signalling it was proposed that threat displays are handicaps, they can work only if they put the signaller at a disadvantage, which is only acceptable to honest signallers. The aim of the present article is to investigate this proposal with the help of a simple game-theoretical model. It was found: (1) that the use of cost-free signals is an ESS against the invasion of handicapped signals even if cheating is played as part of a mixed strategy in the population; (2) that the use of handicaps may be an ESS against cost-free signals but only if we assume that the invading cost-free signal is not accepted by weak individuals as a signal of strength; (3) that the establishment of a handicapped signal in the first place is an unresolved problem, because both cost free signals and negative-handicaps are evolutionarily stable against the invasion of handicaps; (4) that in contrast to handicaps the use of negative-handicaps can invade a population using cost-free signals (a negative-handicap is a signal which may serve other functions as well); (5) that negative-handicaps are ESS against cost-free signals as well as against handicaps; and (6) thus, the most likely evolutionary end point is that the biggest negative-handicap would be used as a threat display. This is a posture, which prepares the animal most efficiently to fight; hence, most probably it is the initial position of the fighting technique of the given species. (7) Finally, the investigation of the threat displays of well-studied taxa (great tit, cats, dogs, and hoofed mammals) confirms that threat displays are indeed negative-handicaps. They do not put the user into a disadvantaged position, instead the initial position of the species specific fighting technique is used as a threat display as predicted by the present model.     

Models@Home: distributed computing in bioinformatics using a screensaver based approach

MOTIVATION: Due to the steadily growing computational demands in bioinformatics and related scientific disciplines, one is forced to make optimal use of the available resources. A straightforward solution is to build a network of idle computers and let each of them work on a small piece of a scientific challenge, as done by Seti@Home (http://setiathome.berkeley.edu), the world's largest distributed computing project. RESULTS: We developed a generally applicable distributed computing solution that uses a screensaver system similar to Seti@Home. The software exploits the coarse-grained nature of typical bioinformatics projects. Three major considerations for the design were: (1) often, many different programs are needed, while the time is lacking to parallelize them. Models@Home can run any program in parallel without modifications to the source code; (2) in contrast to the Seti project, bioinformatics applications are normally more sensitive to lost jobs. Models@Home therefore includes stringent control over job scheduling; (3) to allow use in heterogeneous environments, Linux and Windows based workstations can be combined with dedicated PCs to build a homogeneous cluster. We present three practical applications of Models@Home, running the modeling programs WHAT IF and YASARA on 30 PCs: force field parameterization, molecular dynamics docking, and database maintenance.     

Relational database model for DNA mutations and a software program for implementation of the model

A relational database model for describing DNA mutations is presented. The model was developed in conjunction with the human hprt database and was succesful in representing over 1800 hprt mutations. Mutants showing aberrant mRNA splicing can be adequately described using the model, as well as mutants showing more than one mutation. The basic aspects of the relational model should be applicable to mutations in a variety of genes. A data entry program developed using Microsoft Access 2.0 is also described that implements the relational model The data entry program ensures that relational integrity is maintained between the tables and automatically generates key fields as needed. The program also has the ability to convert between the various numbering schemes that are used to decribed base pair location in the hprt gene. The program and source code are placed in the public domain so that other experimenters can adapt the program for use with other genes.     

Iterative cluster analysis of protein interaction data

MOTIVATION: Generation of fast tools of hierarchical clustering to be applied when distances among elements of a set are constrained, causing frequent distance ties, as happens in protein interaction data. RESULTS: We present in this work the program UVCLUSTER, that iteratively explores distance datasets using hierarchical clustering. Once the user selects a group of proteins, UVCLUSTER converts the set of primary distances among them (i.e. the minimum number of steps, or interactions, required to connect two proteins) into secondary distances that measure the strength of the connection between each pair of proteins when the interactions for all the proteins in the group are considered. We show that this novel strategy has advantages over conventional clustering methods to explore protein-protein interaction data. UVCLUSTER easily incorporates the information of the largest available interaction datasets to generate comprehensive primary distance tables. The versatility, simplicity of use and high speed of UVCLUSTER on standard personal computers suggest that it can be a benchmark analytical tool for interactome data analysis. AVAILABILITY: The program is available upon request from the authors, free for academic users. Additional information available at http://www.uv.es/genomica/UVCLUSTER.     

BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics

Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software.     

Blind docking of pharmaceutically relevant compounds using RosettaLigand

It is difficult to properly validate algorithms that dock a small molecule ligand into its protein receptor using data from the public domain: the predictions are not blind because the correct binding mode is already known, and public test cases may not be representative of compounds of interest such as drug leads. Here, we use private data from a real drug discovery program to carry out a blind evaluation of the RosettaLigand docking methodology and find that its performance is on average comparable with that of the best commercially available current small molecule docking programs. The strength of RosettaLigand is the use of the Rosetta sampling methodology to simultaneously optimize protein sidechain, protein backbone and ligand degrees of freedom; the extensive benchmark test described here identifies shortcomings in other aspects of the protocol and suggests clear routes to improving the method.     

AGScan: a pluggable microarray image quantification software based on the ImageJ library

Many different programs are available to analyze microarray images. Most programs are commercial packages, some are free. In the latter group only few propose automatic grid alignment and batch mode. More often than not a program implements only one quantification algorithm. AGScan is an open source program that works on all major platforms. It is based on the ImageJ library [Rasband (1997-2006)] and offers a plug-in extension system to add new functions to manipulate images, align grid and quantify spots. It is appropriate for daily laboratory use and also as a framework for new algorithms. AVAILABILITY: The program is freely distributed under X11 Licence. The install instructions can be found in the user manual. The software can be downloaded from http://mulcyber.toulouse.inra.fr/projects/agscan/. The questions and plug-ins can be sent to the contact listed below.     

Hand-held computer program for field-capture and analysis of herbage yield and composition data using a modified dry-weight-rank and yield estimate method

A BASIC program is described which is used to collect, checkand analyse rank estimates of plant yield in the field. Theprogram operates in a portable, battery-powered Sharp PCI500Ahand-held computer than can be used in a field environment.Data are collected using a modified dry-weight-rank method andcomparative yield estimates. Much of the software is designedto trap incorrect data entry. Raw data or summary data may beprinted, displayed, and stored on cassette tape or transferredto another computer through a communications interface. Theprogram can be easily modified to run on other models of theSharp PC series or other portable computers that use a similarBASIC interpreter. Received on July 2, 1987; accepted on August 6, 1987     

MultiPLX: automatic grouping and evaluation of PCR primers

SUMMARY: MultiPLX is a new program for automatic grouping of PCR primers. It can use many different parameters to estimate the compatibility of primers, such as primer-primer interactions, primer-product interactions, difference in melting temperatures, difference in product length and the risk of generating alternative products from the template. A unique feature of the MultiPLX is the ability to perform automatic grouping of large number (thousands) of primer pairs. AVAILABILITY: Binaries for Windows, Linux and Solaris are available from http://bioinfo.ebc.ee/download/. A graphical version with limited capabilities can be used through a web interface at http://bioinfo.ebc.ee/multiplx/. The source code of the program is available on request for academic users. CONTACT: maido.remm@ut.ee.     

Databases and software for the analysis of mutations in the human p53 gene, the human hprt gene and both the lacI and lacZ gene in transgenic rodents.

We have created databases and software applications for the analysis of DNA mutations at the humanp53gene, the humanhprtgene and both the rodent transgeniclacIandlacZlocus. The databases themselves are stand-alone dBASE files and the software for analysis of the databases runs on IBM-compatible computers. Each database has a separate software analysis program. The software created for these databases permit the filtering, ordering, report generation and display of information in the database. In addition, a significant number of routines have been developed for the analysis of single base substitutions. One method of obtaining the databases and software is via the World Wide Web (WWW). Open the following home page with a Web Browser: http://sunsite.unc.edu/dnam/mainpage.ht ml . Alternatively, the databases and programs are available via public FTP from: anonymous@sunsite.unc.edu . There is no password required to enter the system. The databases and software are found beneath the subdirectory: pub/academic/biology/dna-mutations. Two other programs are available at the site-a program for comparison of mutational spectra and a program for entry of mutational data into a relational database.