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1.
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.  相似文献   

2.
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.  相似文献   

3.
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.  相似文献   

4.
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).  相似文献   

5.
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.  相似文献   

6.
Predict7, a program for protein structure prediction   总被引:4,自引:0,他引:4  
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.  相似文献   

7.
8.
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.  相似文献   

9.
Gosselain  Véronique  Hamilton  Paul B. 《Hydrobiologia》2000,438(1-3):139-142
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.  相似文献   

10.
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.  相似文献   

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