Developing manufacturing control software: A survey and critique

The complexity and diversity of manufacturing software and the need to adapt this software to the frequent changes in the production requirements necessitate the use of a systematic approach to developing this software. The software life-cycle model (Royce, 1970) that consists of specifying the requirements of a software system, designing, implementing, testing, and evolving this software can be followed when developing large portions of manufacturing software. However, the presence of hardware devices in these systems and the high costs of acquiring and operating hardware devices further complicate the manufacturing software development process and require that the functionality of this software be extended to incorporate simulation and prototyping. This paper reviews recent methods for planning, scheduling, simulating, and monitoring the operation of manufacturing systems. A synopsis of the approaches to designing and implementing the real-time control software of these systems is presented. It is concluded that current methodologies support, in a very restricted sense, these planning, scheduling, and monitoring activities, and that enhanced performance can be achieved via an integrated approach.     

质粒绘图软件PCircle的编制及Flash作为生物软件编制工具的可行性分析

以Flash作为软件编程工具 ,根据Flash在生物软件编制方面具有的优点 ,利用其优秀的图形图像处理能力与动作脚本语言 (ActionScript)相结合所具有的优势 ,编制了质粒绘图软件Pcircle。该软件克服了以往的质粒绘图软件在绘制图谱过程中不能随意修改操作的缺点 ,在绘制过程中 ,可在任意时候对生成的部件进行修改甚至删除。该软件已被生物软件网收录 ,供免费下载。同时详细分析了Flash作为生物软件编制工具所具有的优缺点 ,确定了作为生物软件编制工具的适用范围 ,可为Flash作为生物软件编制工具的使用起到指引作用。     

Current Practice in Software Development for Computational Neuroscience and How to Improve It

Almost all research work in computational neuroscience involves software. As researchers try to understand ever more complex systems, there is a continual need for software with new capabilities. Because of the wide range of questions being investigated, new software is often developed rapidly by individuals or small groups. In these cases, it can be hard to demonstrate that the software gives the right results. Software developers are often open about the code they produce and willing to share it, but there is little appreciation among potential users of the great diversity of software development practices and end results, and how this affects the suitability of software tools for use in research projects. To help clarify these issues, we have reviewed a range of software tools and asked how the culture and practice of software development affects their validity and trustworthiness.We identified four key questions that can be used to categorize software projects and correlate them with the type of product that results. The first question addresses what is being produced. The other three concern why, how, and by whom the work is done. The answers to these questions show strong correlations with the nature of the software being produced, and its suitability for particular purposes. Based on our findings, we suggest ways in which current software development practice in computational neuroscience can be improved and propose checklists to help developers, reviewers, and scientists to assess the quality of software and whether particular pieces of software are ready for use in research.     

数字化表达谱差异分析方法-DGE-P

目的：目前,关于数字化表达谱差异分析的方法及软件极少,且需懂得R语言等,操作繁琐,这给数字表达谱分析带来了不少困难,DGE-P软件针对数字化表达谱开发的差异分析软件。方法：DGE-P软件,利用倍数分析及数字化基因表达谱差异基因检测方法,对通过本软件标准化后的数据进行差异显著性分析。结果：DGE-P软件包含了丰度统计、数据标准化、求倍数分析和p-value值三个模块。可得出倍数分析与数字化基因表达谱差异基因检测方法（p-value）两个值。结论：DGE-P较以前的差异分析软件相比是一款针对数字化表达谱分析的软件,克服了其他软件在无重复实验数据时无法避免误差的缺陷。并且DGE-P较其他的软件相比使用方便,可在windows系统下运行,操作简单。     

Integration of software tools for integrative modeling of biomolecular systems

Integrative modeling computes a model based on varied types of input information, be it from experiments or prior models. Often, a type of input information will be best handled by a specific modeling software package. In such a case, we desire to integrate our integrative modeling software package, Integrative Modeling Platform (IMP), with software specialized to the computational demands of the modeling problem at hand. After several attempts, however, we have concluded that even in collaboration with the software’s developers, integration is either impractical or impossible. The reasons for the intractability of integration include software incompatibilities, differing modeling logic, the costs of collaboration, and academic incentives. In the integrative modeling software ecosystem, several large modeling packages exist with often redundant tools. We reason, therefore, that the other development groups have similarly concluded that the benefit of integration does not justify the cost. As a result, modelers are often restricted to the set of tools within a single software package. The inability to integrate tools from distinct software negatively impacts the quality of the models and the efficiency of the modeling. As the complexity of modeling problems grows, we seek to galvanize developers and modelers to consider the long-term benefit that software interoperability yields. In this article, we formulate a demonstrative set of software standards for implementing a model search using tools from independent software packages and discuss our efforts to integrate IMP and the crystallography suite Phenix within the Bayesian modeling framework.     

用于寡核苷酸探针设计的ARB软件

探针设计是制备高质量基因芯片的重中之重。ARB软件是用于设计系统发育芯片(Phylo Chip)探针的主要软件,然而由于安装困难、相关中文文章较少等原因,阻碍了其在国内的广泛使用。本文详细介绍了ARB软件的安装方法、探针设计及其他功能。这将有助于用户快速使用ARB软件进行探针设计,促进系统发育芯片的发展及其在各领域的应用。     

QuantWorm: A Comprehensive Software Package for Caenorhabditis elegans Phenotypic Assays

Phenotypic assays are crucial in genetics; however, traditional methods that rely on human observation are unsuitable for quantitative, large-scale experiments. Furthermore, there is an increasing need for comprehensive analyses of multiple phenotypes to provide multidimensional information. Here we developed an automated, high-throughput computer imaging system for quantifying multiple Caenorhabditis elegans phenotypes. Our imaging system is composed of a microscope equipped with a digital camera and a motorized stage connected to a computer running the QuantWorm software package. Currently, the software package contains one data acquisition module and four image analysis programs: WormLifespan, WormLocomotion, WormLength, and WormEgg. The data acquisition module collects images and videos. The WormLifespan software counts the number of moving worms by using two time-lapse images; the WormLocomotion software computes the velocity of moving worms; the WormLength software measures worm body size; and the WormEgg software counts the number of eggs. To evaluate the performance of our software, we compared the results of our software with manual measurements. We then demonstrated the application of the QuantWorm software in a drug assay and a genetic assay. Overall, the QuantWorm software provided accurate measurements at a high speed. Software source code, executable programs, and sample images are available at www.quantworm.org. Our software package has several advantages over current imaging systems for C. elegans. It is an all-in-one package for quantifying multiple phenotypes. The QuantWorm software is written in Java and its source code is freely available, so it does not require use of commercial software or libraries. It can be run on multiple platforms and easily customized to cope with new methods and requirements.     

人类疾病动物模型制备效果评价软件应用评测

目的建立人类疾病动物模型制备效果评价软件,并将其应用于科研模型制备效果评价工作,推动模型制备效果评价数量化、精确化和标准化。方法以研制模型制备效果评估软件为基本内容,采用面向对象程序设计方法 ,通过对GUI图形界面的操作完成模型制备效果评价工作。结果通过上海市内业界人员的实际应用,该软件显示了稳定性、快捷性和科学性。结论应用人类疾病动物模型制备效果评价软件可以提高模型制备效果评估的效率,推动了实验动物模型制备效果评价的精确量化和标准化进程。     

Bioinformatics software resources

This review looks at internet archives, repositories and lists for obtaining popular and useful biology and bioinformatics software. Resources include collections of free software, services for the collaborative development of new programs, software news media and catalogues of links to bioinformatics software and web tools. Problems with such resources arise from needs for continued curator effort to collect and update these, combined with less than optimal community support, funding and collaboration. Despite some problems, the available software repositories provide needed public access to many tools that are a foundation for analyses in bioscience research efforts.     

数量生态学软件研发及应用

数量生态学是生物数学的重要组成部分,其数学基础是统计分析．由于数量生态学问题本身的复杂性以及研究中需要大量的数据处理,因此,大部分数量运算都要依赖于计算机完成．国际通用数学软件Matlab是一个具有强大数值计算能力、图形处理能力的交互式计算机代数系统,其强大的函数库和独特的内建程序设计语言为科学计算及程序设计提供了友好平台．本研究选择国际通用计算机代数系统Matlab作为程序设计平台,应用Matlab下强大的图形用户界面GUI软件包研发了植被数量生态学分析软件Quatitatlve Ecology中英文版,内容包括生物多样性,种间关联等简单的计算方法以及排序、分类、格局分析,生物一环境关系分析等复杂的分析方法．当进入应用状态时,只需要在相应的框中输入基本数据或者调用文本数据文件或Excel文件,即会得到具体的计算公式,计算结果,图形以及相应的分析或结论．特别是强大的帮助系统涵盖了所有数量分析方法并辅以应用实例供使用者参考．这将为数量生态学的发展注入新的活力．     

泛函连接网络计算软件及其在生物多样性研究中的应用

针对农田生物多样性分析的需要,研制出泛函连接网络（FLANN）计算软件。该软件由7个Java类和1个HTML文件组成,是一种Internet在线计算工具,可运行于多种操作系统和Web浏览器上,并在各种类型的PC及工作站上使用,可读取多种类型的数据库文件。对水稻田昆虫生物多样性的两组取样调查数据Zmar18和Zapr15,用生物多样性工具软件LUMP和非监督分类－离差平方和聚类法进行统计归纳及分类,分别划分为21个和20个功能群,各包含60个样本。以FLANN计算软件对昆虫生物多样性进行了模式分类分析。结果表明,泛函连接网络的模式分类及预测与实际测查结果吻合良好。泛函连接网络Internet在线计算软件的应用可促进生物多样性数据采集和分析的规范化,有利于数据和信息共享,也为形成高度的生物多样性智能分析系统提供了一种工具。     

Combination system in advanced image processing for improving image contrast and a conventional row-ratio grid for an indirect flat-panel detector system: An experimental study

Conventional grids with high grid ratios are not ideal for use in bedside radiography because of the difficulty in maintaining the required alignment. To address this issue, the potential usefulness of a combination system that employs removal processing software for scattered radiation and a conventional grid with a low grid ratio (3:1) for an indirect-conversion-type flat-panel detector system was evaluated by measuring image quality and observer performance. The hypothetical grid ratios for the software were 2:1, 3:1, 6:1, 8:1, and 10:1. The scatter fraction of the combination system was lower than that of the software alone. Significant improvement was observed in the effect of scattered radiation removal up to a hypothetical software grid ratio of 6:1. However, the Wiener spectrum increased (radiographic noise degraded) with an increase in the hypothetical grid ratio. The contrast ratios of the combination system were improved compared to those of the software alone for anthropomorphic chest radiographs. An observer test was also conducted using the contrast-detail phantom. The combination system indicated higher low-contrast detectability compared to the software alone, although there were no statistical differences between the hypothetical grid ratios of 6:1, 8:1, and 10:1 in all combinations of the software alone and the combination system. We concluded that a combination system with software that uses a hypothetical grid ratio of 6:1 or more and a 3:1 conventional grid would be more useful for reducing the scattered radiation component compared to the software alone with a hypothetical higher grid ratio for thicker objects.     

Insulin and leptin relations in obesity: a multimedia approach

Obesity has been recognized as a worldwide public health problem. It significantly increases the chances of developing several diseases, including Type II diabetes. The roles of insulin and leptin in obesity involve reactions that can be better understood when they are presented step by step. The aim of this work was to design software with data from some of the most recent publications on obesity, especially those concerning the roles of insulin and leptin in this metabolic disturbance. The most notable characteristic of this software is the use of animations representing the cellular response together with the presentation of recently discovered mechanisms on the participation of insulin and leptin in processes leading to obesity. The software was field tested in the Biochemistry of Nutrition web-based course. After using the software and discussing its contents in chatrooms, students were asked to answer an evaluation survey about the whole activity and the usefulness of the software within the learning process. The teaching assistants (TA) evaluated the software as a tool to help in the teaching process. The students' and TAs' satisfaction was very evident and encouraged us to move forward with the software development and to improve the use of this kind of educational tool in biochemistry classes.     

A toolbox for developing bioinformatics software

Creating useful software is a major activity of many scientists, including bioinformaticians. Nevertheless, software development in an academic setting is often unsystematic, which can lead to problems associated with maintenance and long-term availibility. Unfortunately, well-documented software development methodology is difficult to adopt, and technical measures that directly improve bioinformatic programming have not been described comprehensively. We have examined 22 software projects and have identified a set of practices for software development in an academic environment. We found them useful to plan a project, support the involvement of experts (e.g. experimentalists), and to promote higher quality and maintainability of the resulting programs. This article describes 12 techniques that facilitate a quick start into software engineering. We describe 3 of the 22 projects in detail and give many examples to illustrate the usage of particular techniques. We expect this toolbox to be useful for many bioinformatics programming projects and to the training of scientific programmers.     

Quantitative Assessment of Lesion Characteristics and Disease Severity Using Digital Image Processing

This work describes a dedicated software which detects and characterizes disease lesions on leaves to provide data on the number and type of lesions and the percentage of leaf area diseased (severity). The software, written in C²⁺, can be used with a standard computer in combination with a colour CCD camera and a frame grabber for image acquisition. The usefulness and adaptability of the software was evaluated using two foliar diseases, Alternaria blight of sunflower and oat leaf rust (Puccinia coronata f.sp. avenae), which differ in symptoms. Using image segmentation and classification techniques, the software discriminated disease symptoms from the healthy leaf area. The number and size of lesions and severity, obtained using the image processing software, were compared with those calculated using a software planimeter or visual assessment. Significant linear relationships between planimeter and the imaging software were obtained for lesion number and severity in oat leaf rust and for severity in sunflower blight. Artefacts, mistakenly classified as blight lesions by the imaging software resulted in an over-estimation of the number of lesions. Future research is aimed at improving accuracy through better illumination during image capture. A dedicated, compact and portable hardware is currently being developed for field use as a self-contained device for disease assessment.     

ContinuousFlex: Software package for analyzing continuous conformational variability of macromolecules in cryo electron microscopy and tomography data

ContinuousFlex is a user-friendly open-source software package for analyzing continuous conformational variability of macromolecules in cryo electron microscopy (cryo-EM) and cryo electron tomography (cryo-ET) data. In 2019, ContinuousFlex became available as a plugin for Scipion, an image processing software package extensively used in the cryo-EM field. Currently, ContinuousFlex contains software for running (1) recently published methods HEMNMA-3D, TomoFlow, and NMMD; (2) earlier published methods HEMNMA and StructMap; and (3) methods for simulating cryo-EM and cryo-ET data with conformational variability and methods for data preprocessing. It also includes external software for molecular dynamics simulation (GENESIS) and normal mode analysis (ElNemo), used in some of the mentioned methods. The HEMNMA software has been presented in the past, but not the software of other methods. Besides, ContinuousFlex currently also offers a deep learning extension of HEMNMA, named DeepHEMNMA. In this article, we review these methods in the context of the ContinuousFlex package, developed to facilitate their use by the community.     

基于DNA分子标记数据构建系统进化树的新策略

结合DPS软件和MEGA软件优点,进行DNA分子标记数据处理和系统发育树构建的新策略：首先使用DPS软件进行0,1数据系统聚类方法获得遗传距离矩阵,然后将此矩阵输入MEGA3,利用NJ或者UPGMA进行系统进化树的构建和树的优化。该方法操作简单,得到的树形美观。     

On skin dose estimation software in interventional radiology

In recent years, a growing interest has been shown in the implementation of software dedicated to the skin dose calculation, since the Fluoroscopically Guided Interventions are expanding in various medical areas. In this regard, a review article recently published by Malchair et al. (2020) is of great importance as it provides the reader with useful references to the software currently available to estimate the patient's skin dose. Despite the usefulness of collecting and summarizing in one paper the different software solutions, a few critical issues have emerged related to some parameters and configurations used in the estimation; additional details concerning patient’s size and position can be added to the information cited by the authors, giving greater robustness to the software calculation. Furthermore, software results cited in the benchmarking without reference cause a lack of solid information. Our suggestion is to adopt the given criteria to evaluate every available software solutions thus helping the eventual user to analyse the tool before adopting it.     

arrayQCplot: software for checking the quality of microarray data

SUMMARY: arrayQCplot is a software for the exploratory analysis of microarray data. This software focuses on quality control and generates newly developed plots for quality and reproducibility checks. It is developed using R and provides a user-friendly graphical interface for graphics and statistical analysis. Therefore, novice users will find arrayQCplot as an easy-to-use software for checking the quality of their data by a simple mouse click. AVAILABILITY: arrayQCplot software is available from Bioconductor at http://www.bioconductor.org. A more detailed manual is available at http://bibs.snu.ac.kr/software/arrayQCplot CONTACT: tspark@stats.snu.ac.kr.