使用数字绘图方法绘制透翅毛瓣寄蝇彩图

【目的】传统彩色昆虫绘图技法技术难度大,且受限于颜料、纸张等绘画媒介。新近出现的数字绘图技法难度较低,便于修改,在绘制科学图方面有着显著的优势。本文详细叙述了使用数字绘图技术绘制透翅毛瓣寄蝇(双翅目:寄蝇科)彩图的步骤及操作方法,向昆虫学工作者介绍这一高清绘图新技术,便于提高昆虫物种形态描述或重新描述的效果。【方法】新的彩色数字绘图技术利用数位板和SAI绘图软件,借助于该软件中的铅笔工具、喷枪和作者开发的"厚涂笔"、"炭笔"、"粉被"等笔刷工具和绘图素材,对透翅毛瓣寄蝇不同形态部位的线稿图层进行细化、底色、阴影、高光、翻转等绘制处理,创造了一套图层命名管理方法及绘图技巧组合方法。【结果】利用本文介绍的彩色数字绘图技术可以很好地表现透翅毛瓣寄蝇的色泽和质感,完成7 000×5 000像素(35 M)的超高清整体背面观形态图的绘制。【结论】利用这种数字彩色绘图技术绘制的昆虫图像具有色泽丰富、容易修改、节约时间、节省储藏空间、细节逼真、保存和携带方便、永不褪色。这种数字彩色绘图技术具有很强的实用性。     

MapGene2Chrom基于Perl和SVG语言绘制基因物理图谱

遗传图谱表现形式简洁明了,为分析遗传规律、克隆基因提供了便利。Gbrowse、MapViewer等工具虽然能够协助研究人员绘制相似形式的物理图谱,但有很大的局限性:(1)数据需提前布置好;(2)输出结果无法灵活修改。鉴于此,文章基于Perl和SVG语言,开发了一款生物辅助作图软件MapGene2Chrom的本地版与网页版,该软件能够依据输入数据快速绘制相应的物理图谱。该软件输入数据格式简单,输出结果易于修改,图片格式为SVG矢量图,具有很好的移植性,以期为研究人员绘制物理图谱提供便利。     

地层古生物研究辅助绘图软件StratDraw 1.0

为了减少绘制化石延限图的误差和工作量,设计了StratDraw1.0,自动对化石延限资料进行汇总,并借助于专业矢量绘图软件CorelDraw,自动生成初始延限图。在此基础上,可利用CorelDraw做各种编辑和修饰,获得可直接出版的化石延限图。该软件也可根据用户的选择对化石种级、属级或更高分类单元的地质延限进行自动绘制,借助于这一功能,用户可以直观地进行生物宏演化方面的数据统计。     

一种利用ViewGIS软件绘制生物墨线图的方法

本文介绍一种利用ViewGIS地信之窗软件绘制生物墨线图的方法,该方法较好地克服了传统手工绘图中存在的问题,具有操作简单、结构特征准确、耗时短、比例准确等特点.     

生物墨线绘图的方法与技巧

介绍生物墨线绘图基本方法与技巧,包括缩放的方法与技巧、绘图工具的选择和应用以及在草图的绘制和上墨过程中的方法技巧。     

生物多样性评价软件BiodiversityMapping的设计与实现

针对目前国内生物多样性相关软件缺乏的情况,利用可视化开发方法和地理信息系统组件包shape Viewer Objects开发了一个综合性的生物多样性评价软件BiodiversityMapping。该软件运行于Windows98／NT操作系统下,是一个32位Windows应用软件;可以计算8类37种d、D生物多样性测度并能利用地理信息系统技术将结果空间化表达。利用该软件计算了北京东灵山地区3个研究区域(小龙门、梨园岭和东灵山主峰)内11个生境中大步甲属(Carabus)昆虫的Shannon-Wiener多样性指数并制图,然后对这3个地区进行了右尾和排序。结果表明,BiodjversityMapping软件能够准确方便地计算多种生物多样性测度,是生物多样性评价的一个有力工具。     

简单快速的序列定位搜索软件GeneGo的开发

运用Java语言编写了基因定位搜索软件GeneGo，该软件用户界面简洁清晰，操作简单易行，即使初学者也无需耗费大量时间学习软件使用。该软件可用于在基因组序列中快速定位搜索目标序列，进而找到感兴趣的基因，为研究基因功能提供了非常实用的工具。     

一款方便实用的分子生物学软件E-Kit for Plasmid

以目前国内分子生物实验室中使用最多的质粒分子生物学常规操作为对象,利用Visual BASIC语言和Access数据库,开发了一款在PC下运行的简单实用的生物学软件——E-Kit for Plasmid。该软件能够轻松完成质粒操作中常见的序列分析、序列作图,虚拟酶切和克隆等功能。     

基因表达时间延迟调控关系识别软件ITdGR

基因表达调控网络的深入研究有利于分子药物靶标的发现以及推新药的研发,是未来生物医学研究的重要内容。针对基因表达调控的时间延迟问题,我们初步设计开发了一套基于基因表达谱数据识别基因表达时间延迟调控关系的软件ITdGR(Identification of Time-delayed Gene Regulations)。并已经成功地将该软件应用于酿酒酵母细胞周期的基因表达谱数据中,识别出的调控关系与已有的知识相符。该软件为基因调控网络重构以及基因表达动态研究提供了一个方便和快捷的工具。     

“AutoCAD”在植物分类学绘图中的应用

本文概述用制图软件AutoCAD绘制植物分类学插图的基本方法,介绍“图层”的概念及其应用管理、绘图时表现分类学特征的要点和绘制步骤,以及各种编辑工具的运用。认为运用AutoCAD绘制植物插图可达到手工绘制效果,明显提高绘图效率。     

Spreadsheet-based program for alignment of overlapping DNA sequences.

Molecular biology laboratories frequently face the challenge of aligning small overlapping DNA sequences derived from a long DNA segment. Here, we present a short program that can be used to adapt Excel spreadsheets as a tool for aligning DNA sequences, regardless of their orientation. The program runs on any Windows or Macintosh operating system computer with Excel 97 or Excel 98. The program is available for use as an Excel file, which can be downloaded from the BioTechniques Web site. Upon execution, the program opens a specially designed customized workbook and is capable of identifying overlapping regions between two sequence fragments and displaying the sequence alignment. It also performs a number of specialized functions such as recognition of restriction enzyme cutting sites and CpG island mapping without costly specialized software.     

AMIDE: a free software tool for multimodality medical image analysis

Amide's a Medical Image Data Examiner (AMIDE) has been developed as a user-friendly, open-source software tool for displaying and analyzing multimodality volumetric medical images. Central to the package's abilities to simultaneously display multiple data sets (e.g., PET, CT, MRI) and regions of interest is the on-demand data reslicing implemented within the program. Data sets can be freely shifted, rotated, viewed, and analyzed with the program automatically handling interpolation as needed from the original data. Validation has been performed by comparing the output of AMIDE with that of several existing software packages. AMIDE runs on UNIX, Macintosh OS X, and Microsoft Windows platforms, and it is freely available with source code under the terms of the GNU General Public License.     

Beyond standardization: dynamic software infrastructures for systems biology

Progress in systems biology is seriously hindered by slow production of suitable software infrastructures. Biologists need infrastructure that easily connects to work that is done in other laboratories, for which standardization is helpful. However, the infrastructure must also accommodate the specifics of their biological system, but appropriate mechanisms to support variation are currently lacking. We argue that a minimal computer language, and a software tool called a generator, can be used to quickly produce customized software infrastructures that 'systems biologists really want to have'.     

Drug Guru: a computer software program for drug design using medicinal chemistry rules

Drug Guru (drug generation using rules) is a new web-based computer software program for medicinal chemists that applies a set of transformations, that is, rules, to an input structure. The transformations correspond to medicinal chemistry design rules-of-thumb taken from the historical lore of drug discovery programs. The output of the program is a list of target analogs that can be evaluated for possible future synthesis. A discussion of the features of the program is followed by an example of the software applied to sildenafil (Viagra) in generating ideas for target analogs for phosphodiesterase inhibition. Comparison with other computer-assisted drug design software is given.     

Conversion of capillary electrophoresis microchip genotyping data for analysis with Genetic Profiler software

The collection and conversion of 4-color fluorescent genotyping data from capillary array electrophoresis microchip devices and its conversion to a format easily and rapidly analyzed by Genetic Profiler genotyping software is presented. Microchip fluorescence intensity data are acquired and stored as 4-color tab-delimited text. These files are converted to electrophoretic signal data (ESD) files using a utility program (TEXT-to-ESD) written in C. TEXT-to-ESD generates an ESD file by converting text data to binary data and then appending a 632-byte ESD-file trailer. Up to 96 ESD files are then assembled into a run folder and imported into Genetic Profiler, where data are reduced to 4-color electropherograms and analyzed. In this manner, DNA fragment sizing data acquired with our high-speed electrophoretic microchip devices can be rapidly analyzed using robust commercial software. Additionally, the conversion program allows sizing of data with Genetic Profiler that have been preprocessed using other third-party software, such as BaseFinder.     

A microcomputer program for hydropathic analysis of proteins with I/O through word processing and graphics software

A BASIC program has been devised for the hydropathic analysisof protein sequences according to the method of Kyte and Doolittle(1982). The program uses sequence data from input files thatare created with a word processor and produces two types ofoutput file: one contains a bar graph of the hydropathic profilein a format that can be easily edited; the other is a tabulationof hydropathic indices along a protein's sequence that can beused as input by the program for the production of a bar graphor as input into other graphics and analysis software. An MS-DOSmicrocomputer, operating under IBM BASICA or GWBASIC and a dotmatrix printer with block graphics capabilities are the onlyhardware requirements for graphic display of hydropathy profiles.The program is capable of unattended analysis from a list ofup to 15 input files. ; accepted on March 10, 1986     

BCETM: a tool for software integration

The integration of software into special-purpose systems (e.g.for gene sequence analysis) can be a difficult task. We describea general-purpose software integration tool, the BCETM program,that facilitates assembly of VAX-based software into applicationsystems and provides an easy-to-use, intuitive user interface.We describe the use of BCE to integrate a heterogeneous collectionof sequence analysis tools. Many BCE design features are generallyapplicable and can be implemented in other language or hardwareenvironments. Received on May 13, 1987; accepted on October 2, 1987     

Electrophoretic gel image analysis software for the molecular biology laboratory

We present GelReader 1.0, a microcomputer program designed to make precision, digital analysis of one-dimensional electrophoretic gels accessible to the molecular biology laboratory of modest means. Images of electrophoretic gels are digitized via a desktop flatbed scanner from instant photographs, autoradiograms or chromogenically stained blotting media. GelReader is then invoked to locate lanes and bands and generate a report of molecular weights of unknowns, based on specified sets of standards. Frequently used standards can be stored in the program. Lanes and bands can be added or removed, based upon users' subjective preferences. A unique lane histogram feature facilitates precise manual addition of bands missed by the software. Image enhancement features include palette manipulation, histogram equalization, shadowing and magnification. The user interface strikes a balance between program autonomy and user intervention, in recognition of the variability in electrophoretic gel quality and users' analytical needs.     

The primer generator: a program that facilitates the selection of oligonucleotides for site-directed mutagenesis.

Site-directed mutagenesis is a powerful tool that has enabled molecular biologists to perform functional analysis of altered nucleic acids and proteins. Newer PCR-based mutagenesis techniques have reduced the process of mutagenesis to as little as one day. While each technique has its advantages, both require a strategy to isolate the desired clone from a population that contains mutagenized and wild-type genes. In this report, we describe a World Wide Web-based computer program that facilitates the design of mutagenic primers such that successfully mutagenized clones can be identified by the presence or absence of a unique restriction site.