化学信息学与开源软件

化学信息学研究需要性能强大而又能随时修订的、开放性的软件工具。通过回顾自由软件到开源软件的发展历史,展示开源式程序开发的丰富成就,包括操作系统如Linux、社区如SourceForge和我国的共创软件联盟等,澄清与copyright针锋相对的copyleft式版权概念,介绍并比较多种软件许可证,对开源软件的发展机制进行简要分析,认为开源软件是满足化学信息学要求的最佳选择。     

Organizational adoption of open source software

Organizations and individuals can use open source software (OSS) for free, they can study its internal workings, and they can even fix it or modify it to make it suit their particular needs. These attributes make OSS an enticing technological choice for a company. Unfortunately, because most enterprises view technology as a proprietary differentiating element of their operation, little is known about the extent of OSS adoption in industry and the key drivers behind adoption decisions. In this article we examine factors and behaviors associated with the adoption of OSS and provide empirical findings through data gathered from the US Fortune-1000 companies. The data come from each company's web browsing and serving activities, gathered by sifting through more than 278 million web server log records and analyzing the results of thousands of network probes. We show that the adoption of OSS in large US companies is significant and is increasing over time through a low-churn transition, advancing from applications to platforms. Its adoption is a pragmatic decision influenced by network effects. It is likelier in larger organizations and those with many less productive employees, and is associated with IT and knowledge-intensive work and operating efficiencies.     

Code quality analysis in open source software development

Abstract Proponents of open source style software development claim that better software is produced using this model compared with the traditional closed model. However, there is little empirical evidence in support of these claims. In this paper, we present the results of a pilot case study aiming: (a) to understand the implications of structural quality; and (b) to figure out the benefits of structural quality analysis of the code delivered by open source style development. To this end, we have measured quality characteristics of 100 applications written for Linux, using a software measurement tool, and compared the results with the industrial standard that is proposed by the tool. Another target of this case study was to investigate the issue of modularity in open source as this characteristic is being considered crucial by the proponents of open source for this type of software development. We have empirically assessed the relationship between the size of the application components and the delivered quality measured through user satisfaction. We have determined that, up to a certain extent, the average component size of an application is negatively related to the user satisfaction for this application.     

开源平台下软件管理技术的研究

基于开源软件平台基本特点的分析,对目前具有代表性的apt/dpkg、yum/RPM、BSD ports和portage等软件管理技术进行分析,对比和总结了现有技术特征和一般结构,探索了开源平台下软件管理技术可能的发展方向.     

User acceptance model of open source software

The development and implementation of open source software (OSS) is one of the most current topics within the academic, business and political environments. Traditionally, research in OSS has focused on identifying individual personal motives for participating in the development of an OSS project, analyzing specific OSS solutions, or the OSS movement, itself. Nevertheless, user acceptance towards this type of technology has received very little attention. For this reason, the main purpose of the current study is to identify the variables and factors that have a direct effect on individual attitude towards OSS adoption. Therefore, we have developed a technological acceptance model on behalf of the users towards a solution based on OSS. For this development, we have considered the technology acceptance model. Findings show that OSS is a viable solution for information management for organizations.     

On the security of open source software

Abstract With the rising popularity of so‐called ‘open source’ software there has been increasing interest in both its various benefits and disadvantages. In particular, despite its prominent use in providing many aspects of the Internet's basic infrastructure, many still question the suitability of such software for the commerce‐oriented Internet of the future. This paper evaluates the suitability of open source software with respect to one of the key attributes that tomorrow's Internet will require, namely security. It seeks to present a variety of arguments that have been made, both for and against open source security and analyses in relation to empirical evidence of system security from a previous study. The results represent preliminary quantitative evidence concerning the security issues surrounding the use and development of open source software, in particular relative to traditional proprietary software.     

开放源代码软件开发的基本问题

尽管开放源代码软件运动发展得相当成功,但是普通大众总感到它不易使用。本文讨论当前开放源代码软件开发趋势中的5个基本问题,并提出可能有助于克服这些问题的解决方案。1.　用户界面设计出于某种原因,开放源代码项目在用户界面设计上有许多问题。我猜想用户界面的低质量并非是一种原因造成的。在开放源代码圈内存在一种认识,认为要在完成了真正的工作之后再去设计友好的用户界面,而不把用户界面设计当成真正的工作。然而,如果开放源代码希望真正繁荣起来,使普通大众使用其工具,他们必须承认,大多数用户可能从来不知道开放源代码人员曾为复…     

Virtual organizational learning in open source software development projects

We studied virtual organizational learning in open source software (OSS) development projects. Specifically, our research focused on learning effects of OSS projects and the factors that affect the learning process. The number and percentage of resolved bugs and bug resolution time of 118 SourceForge.net OSS projects were used to measure the learning effects. Projects were characterized by project type, number and experience of developers, number of bugs, and bug resolution time. Our results provided evidence of virtual organizational learning in OSS development projects and support for several factors as determinants of performance. Team size was a significant predictor, with mid-sized project teams functioning best. Teams of three to seven developers exhibited the highest efficiency over time and teams of eight to 15 produced the lowest mean time for bug resolution. Increasing the percentage of bugs assigned to specific developers or boosting developer participation in other OSS projects also improved performance. Furthermore, project type introduced variability in project team performance.     

开放源代码软件的应用研究

目前,开放源代码的软件开发模式已经越来越多的被采用,其基本思想是通过公开软件的源代码使得不同的开发人员可以互相交流、发现错误从而提升软件质量.在某些环境下运行的软件由于对可靠性的高度要求,采用开放源代码的模式进行软件开发将能最大化的做到这一点,本文试从商业模型、法律规范、实现技术这三个角度论述了开放源代码软件的应用.     

JSMAA: open source software for SMAA computations

Most software for multi-criteria decision analysis (MCDA) implement a small set of compatible methods as a closed monolithic program. With such software tools, the decision models have to be input by hand. In some applications, however, the model can be generated using external information sources, and thus it would be beneficial if the MCDA software could integrate in the comprehensive information infrastructure. This article motivates for the need of model generation in the methodological context of stochastic multicriteria acceptability analysis (SMAA), and describes the JSMAA software that implements SMAA-2, SMAA-O and SMAA-TRI methods. JSMAA is an open source and divided in separate graphical user interface and library components, enabling its use in systems with a model generation subsystem.     

化学信息学开源软件的集成与复用

软件集成与复用是提高开发效率和质量的重要途径,而开发标准是实现集成与复用的重要因素。通过分析InChI、Jmol和BALL等实例,提出了化学信息学开源软件开发的数据通信标准、界面标准和模块标准问题。在此基础上,以作者进行的分子相似性与差异性研究为例,展示了对开源科学计算软件SciLab的主成分分析(PCA)模块进行改进、集成和复用的情况,说明对开源软件应采取扬弃态度,保障集成、复用的成效。     

利用开源软件构建OLAP系统

在开源软件的基础上，实现应用系统的开发，已被证明是一种可靠和有效的方式。提出了一个基于开放源码软件构建联机分析处理系统的技术框架。在实际开发过程中，在遵循相关的许可证制度的前提下，通过对多个相关开源软件的源代码进行详细剖析，结合实际需求进行修改，最终成为一个完整的产品化系统，并成功地投入实际应用。     

开源软件FreeBSD内核进化研究

摘要：归纳开源软件项目的数据源及数据收集方法,给出FreeBSD内核的软件进化分析方法和相关分析结果。重点分析了FreeBSD系统和主要子系统的复杂性进化趋势及推动进化的主要原因,提出了快速测算大型开源软件复杂性的方法。     

开源软件自动化评估证据框架

互联网上已形成了规模巨大、种类丰富的开源软件资源。如何准确、快速地判断一个开源项目的各种可信属性是否满足需求是当前软件工程领域研究的热点。深入分析已有开源软件评估模型,总结互联网上软件质量相关的各种信息,提出了面向开源软件的可信评估证据框架,并基于该框架构建了一种开源软件可信证据查询平台。利用该平台能够极大地提高评估效率,用户可以准确、快速、全面地了解相关软件项目的各种信息。最后,以一个知名开源软件证实了该证据框架及证据查询平台的可行性。     

大型自由和开源软件进化研究

大型自由和开源软件的各种版本源代码和相关开发信息是软件工程研究者研究开源软件项目的重要数据源.归纳开源软件项目的数据源及数据收集方法,给出Linux、FreeBSD操作系统内核的软件进化的分析方法和相关分析结果.重点分析了系统和主要子系统的复杂性进化趋势及推动进化主要原因,提出了快速测算大型开源软件复杂性的方法.得出系统目前以超线性方式进化,而进化的主要推动力是适应系统硬件资源的进化.     

Managing license compliance in free and open source software development

License compliance in Free and Open Source Software development is a significant issue today and organizations using free and open source software are predominately focusing on this issue. The non-compliance to licenses in free and open source software development leads to the loss of reputation and the high costs of litigation for organizations. Towards an automated compliance management, we use the Open Digital Rights Language to implement the clauses of open source software licenses in a machine interpretable way and propose a novel algorithm that analyzes compatibility between free and open source software licenses. Also, we describe a framework that inductively manages compliance of license clauses in a free and open source software development. We simulate and evaluate the formalized license compliance management by analyzing a real-time open source software project GRASS.     

Using open source software in product development: a primer

There are important legal aspects involved in using open source software in commercial products. Here are answers to common questions on how to handle these issues to mitigate risk. The use of open source software in industrial products is growing rapidly because its many advantages are well known. However although we in industry understand liability and intellectual-property-right risks fairly well, the implication of OSS-related legal and managerial issues are new to many of us. Legal aspects can vary greatly from one piece of OSS to another depending on the license scheme used. We discuss the major legal aspects and risks in using OSS and how to mitigate them in product development. We've ordered the information in a top-down approach, starting with a definition of OSS, its benefits, and then some risks and experiences with managing it in software engineering practice.     

Data mining source code for locating software bugs: A case study in telecommunication industry

In a large software system knowing which files are most likely to be fault-prone is valuable information for project managers. They can use such information in prioritizing software testing and allocating resources accordingly. However, our experience shows that it is difficult to collect and analyze fine-grained test defects in a large and complex software system. On the other hand, previous research has shown that companies can safely use cross-company data with nearest neighbor sampling to predict their defects in case they are unable to collect local data. In this study we analyzed 25 projects of a large telecommunication system. To predict defect proneness of modules we trained models on publicly available Nasa MDP data. In our experiments we used static call graph based ranking (CGBR) as well as nearest neighbor sampling for constructing method level defect predictors. Our results suggest that, for the analyzed projects, at least 70% of the defects can be detected by inspecting only (i) 6% of the code using a Naïve Bayes model, (ii) 3% of the code using CGBR framework.