MapDraw，在Excel中绘制遗传连锁图的宏

MAPMAKER是现今广泛使用的遗传连锁数据分析软件,然而其广泛使用的DOS版本却不具有连锁图绘制功能,给连锁作图工作带来了相当大的麻烦。为了解决这一问题,我们以大家广泛使用的数据处理软件Microsoft Excel为平台,编写了一个Excel宏——MapDraw来在轻松的操作中实现遗传连锁图的绘制。 Abstract:MAPMAKER is one of the most widely used computer software package for constructing genetic linkage maps.However,the PC version,MAPMAKER 3.0 for PC,could not draw the genetic linkage maps that its Macintosh version,MAPMAKER 3.0 for Macintosh,was able to do.Especially in recent years,Macintosh computer is much less popular than PC.Most of the geneticists use PC to analyze their genetic linkage data.So a new computer software to draw the same genetic linkage maps on PC as the MAPMAKER for Macintosh to do on Macintosh has been crying for.Microsoft Excel,one component of Microsoft Office package,is one of the most popular software in laboratory data processing.Microsoft Visual Basic for Applications (VBA) is one of the most powerful functions of Microsoft Excel.Using this program language,we can take creative control of Excel,including genetic linkage map construction,automatic data processing and more.In this paper,a Microsoft Excel macro called MapDraw is constructed to draw genetic linkage maps on PC computer based on given genetic linkage data.Use this software,you can freely construct beautiful genetic linkage map in Excel and freely edit and copy it to Word or other application.This software is just an Excel format file.You can freely copy it from ftp://211.69.140.177 or ftp://brassica.hzau.edu.cn and the source code can be found in Excel′s Visual Basic Editor.     

利用Excel的VBA语言自动分析大量共聚焦线扫描图像数据的方法

目的：Microsoft Excel的内置控制语言是VBA(visual basic for application)。它可以极大地增强Excel的数据处理能力。本文通过一个简单的例子说明如何利用VBA自动分析大量共聚焦线扫描图像数据并图示分析结果。方法与结果：文中首先描述了取自共聚焦线扫描图像的实验数据的结构及处理要求。然后具体说明宏程序(用VBA编写)的录制、修改和使用的详细方法。宏程序代码很接近自然语言,较好理解,而且在大多数情况下可通过“录制宏”功能自动生成,把编程的工作减至最少。结论：与手工使用Excel一步步进行数据处理相比,使用Excel中的VBA处理数据可少花时间、少犯错误、减少大量单调重复的劳动．．这些可极大地提高数据处理效率,使研究者可把更多的时间用于数据处理方案的设计和完善上。特别在处理量大而复杂的实验数据时更需要如此。这样,数据中蕴含的有用信息才能更好地被有效而准确地提取出来并加以显示。     

DNA array analysis in a Microsoft Windows environment.

Microsoft Windows-based computers have evolved to the point that they provide sufficient computational and visualization power for robust analysis of DNA array data. In fact, smaller laboratories might prefer to carry out some or all of their analyses and visualization in a Windows environment, rather than alternative platforms such as UNIX. We have developed a series of manually executed macros written in Visual Basic for Microsoft Excel spreadsheets, that allows for rapid and comprehensive gene expression data analysis. The first macro assigns gene names to spots on the DNA array and normalizes individual hybridizations by expressing the signal intensity for each gene as a percentage of the sum of all gene intensities. The second macro streamlines statistical consideration of the confidence in individual gene measurements for sets of experimental replicates by calculating probability values with the Student's t test. The third macro introduces a threshold value, calculates expression ratios between experimental conditions, and calculates the standard deviation of the mean of the log ratio values. Selected columns of data are copied by a fourth macro to create a processed data set suitable for entry into a Microsoft Access database. An Access database structure is described that allows simple queries across multiple experiments and export of data into third-party data visualization software packages. These analysis tools can be used in their present form by others working with commercial E. coli membrane arrays, or they may be adapted for use with other systems. The Excel spreadsheets with embedded Visual Basic macros and detailed instructions for their use are available at http://www.ou.edu/microarray.     

Automated High-throughput Behavioral Analyses in Zebrafish Larvae

We have created a novel high-throughput imaging system for the analysis of behavior in 7-day-old zebrafish larvae in multi-lane plates. This system measures spontaneous behaviors and the response to an aversive stimulus, which is shown to the larvae via a PowerPoint presentation. The recorded images are analyzed with an ImageJ macro, which automatically splits the color channels, subtracts the background, and applies a threshold to identify individual larvae placement in the lanes. We can then import the coordinates into an Excel sheet to quantify swim speed, preference for edge or side of the lane, resting behavior, thigmotaxis, distance between larvae, and avoidance behavior. Subtle changes in behavior are easily detected using our system, making it useful for behavioral analyses after exposure to environmental toxicants or pharmaceuticals.     

用EXCEL中的VBA编写“多项式的三角函数拟合单峰曲线”程序

Excel是常用的电子表格处理软件,笔者采用基于Excel的VBA编程方法,编写了“多项式的三角函数拟合单峰曲线”程序,经教学科研工作中使用,获得了理想的效果。文中发表了该程序的源代码及使用方法,供广大科教人员下载使用。     

MAD: a suite of tools for microarray data management and processing

SUMMARY: Microarray data management and processing (MAD) is a set of Windows integrated software for microarray analysis. It consists of a relational database for data storage with many user-interfaces for data manipulation, several text file parsers and Microsoft Excel macros for automation of data processing, and a generator to produce text files that are ready for cluster analysis. AVAILABILITY: Executable is available free of charge on http://pompous.swmed.edu. The source code is also available upon request.     

Electrophoretic data classification for phylogenetics and biostatistics

SUMMARY: This paper presents ClassMaker, a macro of MS Excel able to classify continuous data of molecular weight data as binary (1/0) values. The output is represented by a binary matrix, which can be introduced in every software application for phylogenetics or multivariate statistics. This application is designed in order to be a link between image analysis programs and statistical or phylogenetic applications, in order to produce a complete series of free programs able to carry out the complete analysis from the gel to the dendrogram. AVAILABILITY: ClassMaker is freely available from http://www.agr.unipg.it/cardinali/index.html, where a list of the URLs from which programs of image analysis, statistics and phylogenetics can be freely downloaded.     

Automated quantification of nuclear immunohistochemical markers with different complexity

Manual quantification of immunohistochemically stained nuclear markers is still laborious and subjective and the use of computerized systems for digital image analysis have not yet resolved the problems of nuclear clustering. In this study, we designed a new automatic procedure for quantifying various immunohistochemical nuclear markers with variable clustering complexity. This procedure consisted of two combined macros. The first, developed with a commercial software, enabled the analysis of the digital images using color and morphological segmentation including a masking process. All information extracted with this first macro was automatically exported to an Excel datasheet, where a second macro composed of four different algorithms analyzed all the information and calculated the definitive number of positive nuclei for each image. One hundred and eighteen images with different levels of clustering complexity was analyzed and compared with the manual quantification obtained by a trained observer. Statistical analysis indicated a great reliability (intra-class correlation coefficient > 0.950) and no significant differences between the two methods. Bland–Altman plot and Kaplan–Meier curves indicated that the results of both methods were concordant around 90% of analyzed images. In conclusion, this new automated procedure is an objective, faster and reproducible method that has an excellent level of accuracy, even with digital images with a high complexity.     

Excel在药学数据分析工作中的应用

目的：采用常用的电子表格处理系统Microsoft Excel解决药学实验过程中遇到的数据分析问题。方法：应用工作表函数中内置的统计函数,以线性回归为例说明源数据的输入与结果返回的具体操作过程;对数据分析工具中的＂描述统计＂工具、t检验与方差分析,结合具体实例对药学实践中遇到的药学统计实际问题进行综合探讨。结果：用Excel表中内置的统计函数工具进行线性回归分析,方法简单、结果可靠;Excel表中的数据分析工具适用于日常药学实验数据分析过程中遇到的描述统计分析、t检验与方差分析。Excel与其它数据处理软件相比具有操作快捷、使用方便、计算精确、易于学习与掌握等优点。结论：Excel友好的界面,清晰的统计分析结果,使医药工作者在使用Excel的数据分析软件时会感到非常的方便快捷,灵活实用,值得在药学实践中应用推广。     

Microarray data analysis made easy

DNA microarrays are valuable tools for analyzing global gene expression. Because of the increasing popularity and the large volume of data produced, tools for facile microarray data analysis are essential. FiRe, a recently introduced computer program, has now solved the seemingly insuperable discrepancy between simplicity and evaluation of DNA microarray data. The program is available as a macro for the popular Microsoft Office Excel software and is user-friendly, interactive, versatile and platform-independent, paving the way for a further push in the evaluation of DNA microarrays.     

A software tool for standardised non-destructive biomass estimation in short rotation forestry

Following an evaluation of the various methods available for non-destructive biomass estimation in short rotation forestry, a standardised procedure was defined and incorporated into a computer programme (BioEst). Special efforts were made to ensure that the system can be used by people who are unfamiliar with computers and mathematics. BioEst provides an interface between a calliper and a spreadsheet programme which was written in Microsoft Excel macro language. Therefore, it is simple to modify the programme and create personal protocols. BioEst can be run on a portable PC with Microsoft Excel for Windows. The computer continuously recalculates an estimate of the amount of biomass per hectare, as well as some summary statistics, when fed data on shoot diameter obtained by making row-section-wise measurements with a standard digital calliper. BioEst is available without cost from the author.     

ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data

ChIPOTle (Chromatin ImmunoPrecipitation On Tiled arrays) takes advantage of two unique properties of ChIP-chip data: the single-tailed nature of the data, caused by specific enrichment but not specific depletion of genomic fragments; and the predictable enrichment of DNA fragments adjacent to sites of direct protein-DNA interaction. Implemented as a Microsoft Excel macro written in Visual Basic, ChIPOTle uses a sliding window approach that yields improvements in the identification of bona fide sites of protein-DNA interaction.     

FiRe and microarrays: a fast answer to burning questions

FiRe is a user-friendly Excel macro designed to survey microarray data rapidly. This software interactively assembles data from different experiments and produces lists of candidate genes according to patterns of gene expression. Furthermore, macros bundled with FiRe can compare lists of genes, merge information from different spreadsheets, link candidates to information available from web-based databases, and produce heat-maps for easy visualization of microarray data. FiRe is freely available at http://www.unifr.ch/plantbio/FiRe/main.html .     

Software for analysis of bacterial genomes

GenomeExplorer is a program for comparative analysis of regulation in prokaryotic genomes. The program has options for signal search, comparison of gene samples, search for paralogs and orthologs, iterative construction of signal profiles. The program has a convenient graphic interface, allowing for navigation in the annotation window, in the genome map, and in the table of gene similarities. The use of the system clipboard allows one to export the results of analysis into Word and Excel, and to call external programs via the Internet.     

Simulations of the cardiac action potential based on the Hodgkin-Huxley kinetics with the use of Microsoft Excel spreadsheets

The purpose of this study was to develop a method to simulate the cardiac action potential using a Microsoft Excel spreadsheet. The mathematical model contained voltage-gated ionic currents that were modeled using either Beeler-Reuter (B-R) or Luo-Rudy (L-R) phase 1 kinetics. The simulation protocol involves the use of in-cell formulas directly typed into a spreadsheet. The capability of spreadsheet iteration was used in these simulations. It does not require any prior knowledge of computer programming, although the use of the macro language can speed up the calculation. The normal configuration of the cardiac ventricular action potential can be well simulated in the B-R model that is defined by four individual ionic currents, each representing the diffusion of ions through channels in the membrane. The contribution of Na+ inward current to the rate of depolarization is reproduced in this model. After removal of Na+ current from the model, a constant current stimulus elicits an oscillatory change in membrane potential. In the L-R phase 1 model where six types of ionic currents were defined, the effect of extracellular K+ concentration on changes both in the time course of repolarization and in the time-independent K+ current can be demonstrated, when the solutions are implemented in Excel. Using the simulation protocols described here, the users can readily study and graphically display the underlying properties of ionic currents to see how changes in these properties determine the behavior of the heart cell. The method employed in these simulation protocols may also be extended or modified to other biological simulation programs.     

Community structure or function: effects of environmental stress on benthic macroinvertebrates at different spatial scales

1. This study investigated the relation of benthic macroinvertebrates to environmental gradients in Central European lowland rivers. Taxonomic structure (taxa) and functional composition (metrics) were related to gradients at four different spatial scales (ecoregion, catchment, reach and site). The environmental variables at the catchment‐, reach‐ and site scales reflected the intensity of human impact: catchment and floodplain land use, riparian and floodplain degradation, flow regulation and river bank and bed modification. 2. Field surveys and GIS yielded 130 parameters characterising the hydromorphology and land use of 75 river sections in Sweden, the Netherlands, Germany and Poland. Two hundred and forty‐four macroinvertebrate taxa and 84 derived community metrics and biotic indices such as functional guilds, diversity and composition measures were included in the analysis. 3. Canonical Correspondence Analysis (CCA) and Redundancy Analysis (RDA) showed that hydromorphological and land use variables explained 11.4%, 22.1% and 15.8% of the taxa variance at the catchment (‘macro’), reach (‘meso’) and site (‘micro’) scales, respectively, compared with 14.9%, 33.2% and 21.5% of the variance associated with the derived metrics. Ecoregion and season accounted for 10.9% and 20.5% of the variance of the taxonomic structure and functional composition, respectively. 4. Partial CCA (pCCA) and RDA (pRDA) showed that the unique variance explained was slightly higher for taxa than for metrics. By contrast, the joint variance explained for metrics was much higher at all spatial scales and largest at the reach scale. Environmental variables explained 46.8% of metric variance and 32.4% of taxonomic structure. 5. Canonical Correspondence Analysis and RDA identified clear environmental gradients along the two main ordination axes, namely, land use and hydromorphological degradation. The impact of catchment land use on benthic macroinvertebrates was mainly revealed by the proportion of urban areas. At the reach scale, riparian and floodplain attributes (bank fixation, riparian wooded vegetation, shading) and the proportion of large woody debris were strong predictors of the taxonomic structure and functional composition of benthic macroinvertebrates. At the site scale, artificial substrata indicated human impact, particularly the proportion of macro‐ and mesolithal used for bank enforcement (rip–rap). 6. Our study revealed the importance of benthic macroinvertebrate functional measures (functional guilds, composition and abundance measures, sensitivity and tolerance measures, diversity measures) for detecting the impact of hydromorphological stress at different spatial scales.     

中国生物多样性在线数据处理平台的构建

高质量的生物多样性数据能够为生物多样性的研究与保护提供数据支撑。目前研究人员开发了大量的生物多样性数据处理软件或工具, 包括工作流系统、R语言包、Python语言包和Excel工具等, 但是使用这些软件或工具需要用户安装相应的软件客户端, 并掌握一定的编程语言、软件开发和复杂的Excel公式等知识和技能。为降低用户的学习成本和使用门槛, 本文采用了Browser/Server模式设计技术、Web技术、可视化技术、响应式开发技术、网络爬虫技术、数据处理技术和Solr智能检索技术等, 针对不同维度的生物多样性数据设计和开发了相应的数据处理模块, 构建了中国生物多样性在线数据处理平台(http://dp.iflora.cn/)。该平台能够有效地帮助科研人员对物种名称、地理位置、时间日期和经纬度等数据进行处理, 并提供数据格式转换、数据质量评测和资源统计分析等辅助功能, 帮助科研人员实现零代码和低门槛地处理生物多样性数据, 提供便捷、高效和简单的数据清洗、校正、转换和整合等数据处理渠道, 为生物多样性研究和保护提供信息化技术支持与服务。     

Kgtests: a simple Excel Macro program to detect signatures of population expansion using microsatellites

A simple Microsoft Excel Macro application (kgtests) that performs the k and g tests for detecting population expansion is described. The application, being an Excel Macro, facilitates the ease of preparation of the input file and makes it possible to use the application in any machine that can run Excel.     

A modern tool for classical plant growth analysis

We present an all-inclusive software tool for dealing with the essential core of mathematical and statistical calculations in plant growth analysis. The tool calculates up to six of the most fundamental growth parameters according to a purely 'classical' approach across one harvest-interval. All of the estimates carry standard errors and 95 % confidence limits. The tool is written in Microsoft Excel 2000 and is available free of charge for use in teaching and research from www.aob.oupjournals.org article supplementary data.     

Microsoft Word macro for analysis of cytosine methylation by the bisulfite deamination reaction

Cytosine methylation at CpG dinucleotides is an important control mechanism in development, differentiation, and neoplasia. Bisulfite genomic sequencing and its modifications have been developed to examine methylation at these CpG dinucleotides. To use these methods, one has to (i) manually convert the sequence to that produced by bisulfite conversion and PCR amplification, taking into account that cytosine residues at CpG dinucleotides may or may not be converted depending on their methylation status, (ii) identify relevant restriction sites that may be used for methylation analysis, and (iii) conduct similar steps with the other DNA strand since the two strands of DNA are no longer complementary after bisulfite conversion. To automate these steps, we have developed a macro that can be used with Microsoft Word. This macro (i) converts genomic sequence to modified sequence that would result after bisulfite treatment facilitating primer design for bisulfite genomic sequencing and methylation-sensitive PCR assay and (ii) identifies restriction sites that are preserved in bisulfite-converted and PCR-amplified product only if cytosine residues at relevant CpG dinucleotides are methylated (and thereby not converted to uracil) in the genomic DNA.