生物数学方法

将数学知识应用于生物科学产生了生物数学的边缘科学。按研究对象和任务的不同,生物数学可分为数学生物学和生物数学两个分支。数学生物学主要是指生物各个学科应用数学方法所形成的一些新的生物学分支,例如数值分类学、数量进化论、数学生态学,数量遗传学、数量生理学、数量仿生学等等;生物数学主要是指用于生物科学研究的一些数学理论和方法,诸如生物统计学、生物概率论、生物数学模型、电子计算机     

基于分子数据的系统发生树构建

系统发生学是研究生物类群间进化关系的学科。随着测序技术、分析方法和计算能力的改进,分子数据被广泛应用,促进了系统发生学的快速发展。系统发生树已成为生态学和比较生物学等研究领域的有力工具。然而,许多研究在进行系统发生树构建时更侧重各种软件的使用,一些基本原则或注意事项有时会被弱化甚至忽视。该文详细介绍了基于分子数据进行系统发生树构建的工作流程和基本方法,包括类群取样、分子标记选择、序列比对、分区及模型选择、序列联合分析以及拓扑结构检验等关键步骤。此外,该文还为系统发生树构建常用的3种方法(最大简约法、最大似然法和贝叶斯法)提供了相应的软件操作流程和运行命令,以期为相关研究提供参考。     

科研技术的飞速发展

目前,华大拥有近千名具有不同专业背景的生物信息领域专业人才和强大的数据处理、分析存储能力。开发出了一系列具有国际影响力的软件、数据库和服务平台,培养了大量的生物信息以及相关实验技术专业人才。在基因组研究的各个层面都具有强大的科研能力和丰富的科研经验,建立了一整套针对第二     

GPGPU加速生物序列比对研究进展

序列比对是生物信息学中最常用和最经典的研究手段。生物序列比对需要有强大计算能力的硬件支撑,而近年快速发展起来的GPGPU正好可堪此任。本文首先介绍GPGPU的发展过程,进而讲述GPGPU硬件设备与其编程环境,然后对GPGPU做科学计算时需要的数学库函数做一介绍,最后综述近年来国内外基于GPGPU的生物序列比对软件和相关研究工作,并总结和展望其辉煌前景。     

系统分析与害虫的综合管理

<正> 系统理论发源于电工学的数学理论,如电路网络理论、无线电通讯理论、控制论、信息论等,已有30多年的历史,但真正成为一门学科则是在七十年代初期。在欧美等国大学里,开设系统科学系也是从七十年代初期开始的。系统分析和计算机在生态学中大量的应用,也始于这个时期。系统科学进入生态学是科学发展的必然趋势。从系统科学方面来说,由于大型计算机的出现,以及各种计算机越来越普及,使这门学科日趋成熟,并需要寻找应用的市场。从生态学方面来说,对复杂的生态系统的研究,诸如资源管理、害虫管理、环境污染等问题的研究,     

简讯

由陈兰荪主编的《生物数学引论》将于1988年1月由科学出版社出版,该书介绍生物数学中几个主要分支的研究对象、内容、方法以及它们的实际应用。该书将使生物学工作者了解在生物学中,研究生物量数量关系的有关数学方法;也将使数学工作者了解,在近代生物学研究中所涉及的一些有意义的数学问题。书中包括了有关生态学、生物分类学、     

我国植被数量分析方法的研究概况和发展趋势

植被数量分析是现代植被研究的重要手段,数量分类和排序是现代植被生态学研究最重要的,也是应用最广泛的生态学技术。数量分析方法在20世纪50年代引入植被生态学研究领域,我国学者在70年代后期开始研究植被的数量分类和排序。本文主要从相关资料、应用研究、新方法研究三个方面论述了我国植被数量分析方法的发展,重点阐述了从20世纪70年代后期以来出现的并且被广泛应用的新方法及其应用研究概况,并在此基础上分析了植被数量分析方法未来的发展趋势。     

用于生物大分子晶体结构修正的差值Fourier综合程序系统

在国产大型通用电子计算机013上建立了用于生物大分子晶体结构晶体学修正的差值Fourier综合程序系统。该程序包括坐标和温度因子增量的自动分析和计算,配合适当的人工干预可使繁杂而艰苦的修正过程连续进行,实现了差值Fourier修正的半自动化。应用本程序系统对1.8埃分辨率的胰岛素晶体结构进行了十一轮差值Fourier修正。偏离因子R值从38.8%降到21.0%。修正后的Fourier图提供了包括蛋白质和水在内的更精细的结构信息。     

用于生物大分子晶体结构修正的差值Fourier综合程序系统

在国产大型通用电子计算机013上建立了用于生物大分子晶体结构晶体学修正的差值Fourier综合程序系统。该程序包括坐标和温度因子增量的自动分析和计算,配合适当的人工干预可使繁杂而艰苦的修正过程连续进行,实现了差值Fourier修正的半自动化。应用本程序系统对1.8埃分辨率的胰岛素晶体结构进行了十一轮差值Fourier修正。偏离因子R值从38.8%降到21.0%。修正后的Fourier图提供了包括蛋白质和水在内的更精细的结构信息。     

数学思想在高中生物教学中的应用

新课标课程体系改革背景下对于高中学生的生物课程学习和课堂教学提出了新的更高的要求。在学科综合的指导思想下,运用数学科目的逻辑推理和分析能力以及计算能力可以有效提高生物课堂的效率及高中生在高考生物试卷答题中的解题能力。本文就针对数学思想在高中生物教学中的应用进行分析探究。     

microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets

In molecular ecology the analysis of large microsatellite data sets is becoming increasingly popular. Here we introduce a new software tool, which is specifically designed to facilitate the analysis of large microsatellite data sets. All common microsatellite summary statistics and distances can be calculated. Furthermore, the microsatellite analyser (msa ) software offers an improved method to deal with inbred samples (such as Drosophila isofemale lines). Executables are available for Windows and Macintosh computers.     

基于"斑块-廊道-基质"和"源-流-汇"范式景观格局分析的景观生态学工具箱原理与应用

景观格局的定量分析是评价其对生态过程影响的先决条件,也是生态系统规划和管理的重要依据。当前的景观格局分析软件都仅提供基于"斑块-廊道-基质"景观分析范式的格局指数计算,不包含基于"源-流-汇"的范式的指数计算。这不仅无法适应景观生态学理论的发展,也无法满足大数据时代对计算场景和速率的需求。针对该问题,在研发基于"源-流-汇"的范式的指数算法的基础上,开发了景观生态学工具箱(Landscape Ecology Toolbox,LET)。不仅同时提供基于两种分析范式下的景观格局指数计算,也提供了图形用户界面和命令行两种运行方式。在对LET主要功能进行介绍的基础上,将LET同现有景观分析软件在操作逻辑、景观指数计算范围、特色功能等方面进行了详细的对比,最后对软件未来的发展方向进行了讨论。     

旅游生态学研究进展

作为生态学和旅游学相交叉的一门新兴分支学科,旅游生态学关注旅游发展中的生态环境问题,以生态学原理指导旅游生态系统管理,是促进旅游业可持续发展的重要理论支撑。论文采用引文可视化分析软件CiteSpace5.3和文献阅读相结合的方法分析旅游生态学研究的国际进展。分析发现,文献数量在进入21世纪后快速增长,文献来源地集中在北美和欧洲国家,研究方法呈现多学科综合性和最新科学技术成果应用及时等特点,研究内容主要集中在旅游活动的生态环境影响、旅游生态系统管理和旅游可持续发展的测度及实现途径3个方面。基于国际进展的分析,论文最后提出我国旅游生态学研究应在学科的基础理论、旅游影响的系统性和持续性、旅游生态修复、旅游开发活动的生态环境影响、生态环境变化对旅游业发展的影响和本土性旅游生态系统管理方法等方面加强。     

2009年第五届“现代生态学讲座”国际会议综述

"现代生态学讲座"系列会议是由国内外华人生态学家联合发起、为加强现代生态学的新理论、新观点、新方法和热点问题的交流与合作的国际会议.总结了2009年6月27～29日在兰州大学举行的第五届现代生态学讲座国际会议的全部二十五场报告,围绕"宏观生态学和可持续发展科学"的会议主题,分别从森林生态学、草地生态学、全球变化生态学、根际和土壤生态学、分子和行为生态学以及农业生态学等角度进行了分类总结.全部报告可归纳为"生态系统服务功能的物质基础"和"生态系统服务的生态学机制"两个大的基础理论问题,而解决问题的途径必须在人类-自然耦合生态系统的大框架下进行探索.对该会议的进一步改善提出了一些建议.     

Towards quantitative cytotaxonomy of primates: Idiogram construction of great ape chromosomes by «fourier-warping»

To faciliate quatitative comparative cytogenetics of primate chromosomes we present a new type of idiogram from human and great ape chromosomes. These idiograms were obtained by computer densitometry and «Fourier-Warping» (FW) as described elsewhere (Maurier & Wienberg, 1991). In contrast to published idiograms, the «FW-idiograms» represent the mean position, width and density of each band and the mean resolution of the chromosome sample under investigation. In species that deverged about 6–12 my we were able to extract the representative banding features and to demonstrate conservation and change in the karyotype of human and great apes.     

oSCR: a spatial capture–recapture R package for inference about spatial ecological processes

Spatial capture–recapture (SCR) methods have become widely applied in ecology. The immediate adoption of SCR is due to the fact that it resolves some major criticisms of traditional capture–recapture methods related to heterogeneity in detectabililty, and the emergence of new technologies (e.g. camera traps, non‐invasive genetics) that have vastly improved our ability to collection spatially explicit observation data on individuals. However, the utility of SCR methods reaches far beyond simply convenience and data availability. SCR presents a formal statistical framework that can be used to test explicit hypotheses about core elements of population and landscape ecology, and has profound implications for how we study animal populations. In this software note, we describe the technical basis and analytical workflow of oSCR, an R package for analyzing spatial encounter history data using a multi‐session sex‐structured likelihood. The impetus for developing oSCR was to create an accessible and transparent analysis tool that allows users to conveniently and intuitively formulate statistical models that map directly to fundamental processes of interest in spatial population ecology (e.g. space use, resource selection, density and connectivity). We have placed an emphasis on creating a transparent and accessible code base that is coupled with a logical workflow that we hope stimulates active participation in further technical developments.     

Free and open source geographic information tools for landscape ecology

Geographic Information tools (GI tools) have become an essential component of research in landscape ecology. In this article we review the use of GIS (Geographic Information Systems) and GI tools in landscape ecology, with an emphasis on free and open source software (FOSS) projects. Specifically, we introduce the background and terms related to the free and open source software movement, then compare eight FOSS desktop GIS with proprietary GIS to analyse their utility for landscape ecology research. We also provide a summary of related landscape analysis FOSS applications, and extensions. Our results indicate that (i) all eight GIS provide the basic GIS functionality needed in landscape ecology, (ii) they all facilitate customisation, and (iii) they all provide good support via forums and email lists. Drawbacks that have been identified are related to the fact that most projects are relatively young. This currently affects the size of their user and developer communities, and their ability to include advanced spatial analysis functions and up-to-date documentation. However, we expect these drawbacks to be addressed over time, as systems mature. In general, we see great potential for the use of free and open source desktop GIS in landscape ecology research and advocate concentrated efforts by the landscape ecology community towards a common, customisable and free research platform.     

Metaxa2 Diversity Tools: Easing microbial community analysis with Metaxa2

DNA sequencing has become an integrated part of microbial ecology, and taxonomic marker genes such as the SSU and LSU rRNA are frequently used to assess community structure. One solution for taxonomic community analysis based on shotgun metagenomic data is the Metaxa2 software, which can extract and classify sequence fragments belonging to the rRNA genes. This paper describes the Metaxa2 Diversity Tools, a set of new open-source software programs that extends the capabilities of the Metaxa2 software. These tools allow for better handling of data from multiple samples, improved species classifications, rarefaction analysis accounting for unclassified entries, and determination of significant differences in community composition of different samples. We demonstrate the performance of the software tools on rRNA data extracted from different shotgun metagenomes, and find the tools to streamline and improve the assessments of community diversity, particularly for samples from environments for which few reference genomes are available. Finally, we establish that our resampling algorithm for determining community dissimilarity is robust to differences in coverage depth, suggesting that it forms a complement to multidimensional visualization approaches for finding differences between communities. The Metaxa2 Diversity Tools are included in recent versions (2.1 and later) of Metaxa2 (http://microbiology.se/software/metaxa2/) and facilitate implementation of Metaxa2 within software pipelines for taxonomic analysis of environmental communities.     

Automatic recognition and measurement of butterfly eyespot patterns

A favorite wing pattern element in butterflies that has been the focus of intense study in evolutionary and developmental biology, as well as in behavioral ecology, is the eyespot. Because the pace of research on these bull's eye patterns is accelerating we sought to develop a tool to automatically detect and measure butterfly eyespot patterns in digital images of the wings. We used a machine learning algorithm with features based on circularity and symmetry to detect eyespots on the images. The algorithm is first trained with examples from a database of images with two different labels (eyespot and non-eyespot), and subsequently is able to provide classification for a new image. After an eyespot is detected the radius measurements of its color rings are performed by a 1D Hough Transform which corresponds to histogramming. We trained software to recognize eyespot patterns of the nymphalid butterfly Bicyclus anynana but eyespots of other butterfly species were also successfully detected by the software.     

daime, a novel image analysis program for microbial ecology and biofilm research

Combinations of microscopy and molecular techniques to detect, identify and characterize microorganisms in environmental and medical samples are widely used in microbial ecology and biofilm research. The scope of these methods, which include fluorescence in situ hybridization (FISH) with rRNA-targeted probes, is extended by digital image analysis routines that extract from micrographs important quantitative data. Here we introduce daime (digital image analysis in microbial ecology), a new computer program integrating 2-D and 3-D image analysis and visualization functionality, which has previously not been available in a single open-source software package. For example, daime automatically finds 2-D and 3-D objects in images and confocal image stacks, and offers special functions for quantifying microbial populations and evaluating new FISH probes. A novel feature is the quantification of spatial localization patterns of microorganisms in complex samples like biofilms. In combination with '3D-FISH', which preserves the 3-D structure of samples, this stereological technique was applied in a proof of principle experiment on activated sludge and provided quantitative evidence that functionally linked ammonia and nitrite oxidizers cluster together in their habitat. This image analysis method complements recent molecular techniques for analysing structure-function relationships in microbial communities and will help to characterize symbiotic interactions among microorganisms.