A short description of DL_POLY

DL_POLY is a general purpose molecular dynamics simulation package with in-built parallel algorithms. It may be run on a wide selection of distributed memory parallel computers, from national supercomputers with thousands of processors, to single processor workstations and can simulate small systems with order 100 atoms, to systems with millions of atoms. This introduction provides an outline of the features of the package and the underlying methodology.     

Acquiring Fluorescence Time-lapse Movies of Budding Yeast and Analyzing Single-cell Dynamics using GRAFTS

Fluorescence time-lapse microscopy has become a powerful tool in the study of many biological processes at the single-cell level. In particular, movies depicting the temporal dependence of gene expression provide insight into the dynamics of its regulation; however, there are many technical challenges to obtaining and analyzing fluorescence movies of single cells. We describe here a simple protocol using a commercially available microfluidic culture device to generate such data, and a MATLAB-based, graphical user interface (GUI) -based software package to quantify the fluorescence images. The software segments and tracks cells, enables the user to visually curate errors in the data, and automatically assigns lineage and division times. The GUI further analyzes the time series to produce whole cell traces as well as their first and second time derivatives. While the software was designed for S. cerevisiae, its modularity and versatility should allow it to serve as a platform for studying other cell types with few modifications.     

Sliding Box Docking: a new stand-alone tool for managing docking-based virtual screening along the DNA helix axis

Sliding Box Docking is a program that manages simulations of ligand docking at different defined positions of a three-dimensional DNA structure. The procedure is similar to inverse docking, which is a method that performs docking simulations of a single ligand in the active sites of different targets. Sliding Box Docking manages docking simulations of one ligand into a box that slides along the DNA helix axis in regular steps. For each box position a score is calculated using the separate Autodock Vina software, and the results are automatically plotted. The evaluation of ligand interaction at different DNA locations can highlight the specificity of ligands for different DNA- sequences. When assessing the affinity between ligans AT base pairs, results for docking simulations with a test set that included berenil, distamycin, hoechst 33258, and netropsin were as expected, agreeing well with affinities previously described in the literature.

Availability

Binaries are freely available at https://sourceforge.net/projects/slidingboxdocki     

Implementation of the perfect plasticity approximation with biogeochemical compartments in R

Modeling forest ecosystems is a landmark challenge in science, due to the complexity of the processes involved and their importance in predicting future planetary conditions. While there are a number of open-source forest biogeochemistry models, few papers exist detailing the software development approach used to develop these models. This has left many forest biogeochemistry models large, opaque and/or difficult to use, typically implemented in compiled languages for speed. Here, we present a forest biogeochemistry model from the SORTIE-PPA class of models, PPA-SiBGC. Our model is based on the perfect plasticity approximation with simple biogeochemistry compartments and uses empirical vegetation dynamics rather than detailed prognostic processes to drive the estimation of carbon and nitrogen fluxes. This allows our model to be used with traditional forest inventory data, making it widely applicable and simple to parameterize. We detail the conceptual design of the model as well as the software implementation in the R language for statistical computing. Our aim is to provide a useful tool for the biogeochemistry modeling community that demonstrates the importance of vegetation dynamics in biogeochemical models.     

蛋白质组学中色谱保留时间对齐算法的研究进展北大核心CSCD

色谱是目前蛋白质组学流程中的一个基本环节,而色谱的保留时间对齐是有效提高鉴定和定量准确性的重要步骤之一。经过多年的发展,目前已经产生了一系列保留时间对齐算法。文中主要从可用性角度对蛋白质组学分析中色谱保留时间对齐算法及工具进行了系统总结,并对其发展趋势及应用方向进行了展望。     

数据处理和分析方法在MALDI-TOF MS鉴定微生物中的应用

基质辅助激光解吸电离飞行时间质谱（MALDI-TOF MS）因其具有快速、准确、高通量等特点在食品微生物检测和临床微生物鉴定领域有广泛的应用。对MALDI-TOF MS数据的预处理和分析是微生物鉴定的关键步骤,通过对数据的处理可以从大量的数据中提取微生物的特征肽或者蛋白信息,并通过有监督和无监督学习方法对这些特征信息进行分类和聚类,从而实现对微生物的鉴定、分型和同源性分析。本文就MALDI-TOF MS鉴定微生物中所应用的数理统计分析方法和数据分析软件进行综述。     

中国高寒草甸研究进展——基于文献计量分析

高寒草甸作为我国草原的重要组成部分,发挥着极其重要的气候调节和水源涵养等生态功能,是我国重要的战略资源储备要地和生态安全屏障。为了解高寒草甸的研究态势,本文从文献计量学的角度,基于36年间国内外发表的8505篇论文,分析了有关高寒草甸的论文发表数量、发文来源、被引频次、主要作者、研究机构和研究热点等。结果表明：（1）1999年后关于高寒草甸的论文数量增长较快,年均发表355.09篇,且英文论文的增幅最大,但发文的质量还有待进一步提高;（2）李英年,周华坤,杜国祯、赵新全等人是高寒草甸研究的主要贡献人,中国科学院西北高原生物研究所、兰州大学、甘肃农业大学等单位在研究机构合作方面发挥了重要作用,但相关学者和研究机构间的合作较少,以同一单位或同一课题组的研究团队为主,与国内外不同单位、不同团队间的交流合作较少;（3）研究的热点主要聚焦于高寒草甸植被群落特征及其构建机制、高寒草甸植被退化机理与管理利用、高寒草甸植被-土壤-微生物对气候变化的响应等聚类方面。今后应重视原创性、突破性的论文,提升和扩大高寒草甸方面研究成果的国际影响力,同时,应加强不同研究机构、不同学科交叉、理论创新-实际应用等方面的多元合作,从而为高寒草甸的研究注入新生力量。期望本文能为拓展高寒草甸研究的广度与深度提供借鉴。     

应用CiteSpace对生态学科meta分析的文献计量学和可视化分析

Meta分析是针对一系列独立研究结果进行定量综合分析的方法。从20世纪90年代初开始被应用于生态学的研究中,已经对这一学科的数据汇总方式产生重大影响。为了探究meta分析方法在生态学领域的研究现状及热点,以Web of Science论文核心合集为检索数据库,通过输入关键词检索了1992至2018年之间的论文,并利用Web of Science自带的文献分析工具和Histcite对检索的文献信息进行统计分析,分析了不同年份、国家、期刊、学科基础知识论文的发表和被引情况,用CiteSpace软件对其进行热点分析并绘制了知识图谱。研究发现,我国生态学研究在meta分析方法的改进和利用方面与美国、英国等国家相比尚有差距;使用meta分析方法开展研究越来越多,但研究方向上出现了一些转变,越来越多的研究关注全球变化背景下植物光合作用、物种入侵的机理以及模拟氮循环过程对物候和植被生产力的影响及价值评估的研究,并成为本领域的研究前沿。     

蛋白质双向电泳图像分析

随着人类基因组计划的接近完成,蛋白质组（proteome）研究成为新的热点.其中高分辨率的双向电泳（two-dimensional gel electrophoresis, 2-DE）技术使对组织或细胞的整个蛋白质组的综合分析成为可能.近年来这一技术有了很大的改进和提高,特别是图像分析系统,算法更为先进,功能日益强大,操作也更简便,为大规模研究提供了良好的工具.使用新一代的2D图像分析系统,对离体培养的雪旺氏细胞的蛋白质样品双向电泳结果进行了初步分析,探讨了在图像扫描、点检测、背景消除、匹配、结果报告和数据分析各步中的技术问题,并报告了进行2D图像分析的体会.     

Applying climwin to dendrochronology: A breakthrough in the analyses of tree responses to environmental variability

Observational, correlative approaches are one of the backbones of dendrochronology. For instance, climate-growth relationships are usually quantified by calculating Pearson correlations. However, the ability to detect these relationships and the probability of declaring significant correlations by chance pose multiple challenges to such correlative framework. The R climwin package, developed a few years ago within the discipline of animal ecology, overcomes these limitations. In this paper we apply climwin to study relationships between climate and tree-ring widths and anatomy to show the advantages of using this package in the field of dendrochronology. This package allows calculating several models considering multiple windows relating a response variable to the climatic factors at different time resolutions. Then, the most parsimonious model is selected through an information-theoretic approach and randomization tests are computed to establish the significance of the selected model. We compare analyses based on Pearson correlations with climwin results using several environmental drivers (climate variables, drought indices, river flow), response variables (tree-ring width, tracheid lumen area and cell-wall thickness), and tree species from ecologically contrasting sites (cold- and water-limited conifers, Mediterranean riparian ash forests). Analyses of climate-growth/anatomy relationships based on the use of climwin showed several advantages over simple Pearson correlations: (i) they did not depend on the use of arbitrary time intervals of fixed duration, (ii) they allowed reducing probabilities associated with type I and II errors, (iii) they resulted in more consistent findings, (iv) they increased the capacity to detect differences between sites or periods in a time series, and (v) they provided more explanatory power.