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有读书笔记有附件Bioinformatics software for biologists in the genomics era

热4 quwubin 添加于 2010-6-10 09:33 | 2429 次阅读 | 0 个评论

  •  作 者

    Kumar S, Dudley J

  •  摘 要

    Motivation: The genome sequencing revolution is approaching a landmark figure of 1000 completely sequenced genomes. Coupled with fast-declining, per-base sequencing costs, this influx of DNA sequence data has encouraged laboratory scientists to engage large datasets in comparative sequence analyses for making evolutionary, functional and translational inferences. However, the majority of the scientists at the forefront of experimental research are not bioinformaticians, so a gap exists between the user-friendly software needed and the scripting/programming infrastructure often employed for the analysis of large numbers of genes, long genomic segments and groups of sequences. We see an urgent need for the expansion of the fundamental paradigms under which biologist-friendly software tools are designed and developed to fulfill the needs of biologists to analyze large datasets by using sophisticated computational methods. We argue that the design principles need to be sensitive to the reality that comparatively small teams of biologists have historically developed some of the most popular biological software packages in molecular evolutionary analysis. Furthermore, biological intuitiveness and investigator empowerment need to take precedence over the current supposition that biologists should re-tool and become programmers when analyzing genome scale datasets.

  •  详细资料

    • 文献种类:期刊
    • 期刊名称: Bioinformatics
    • 期刊缩写: Bioinformatics
    • 期卷页: 2007年  第23卷 第14期 1713-1717页
    • ISBN: 1367-4803

  • 相关链接 DOI URL 

  •  附 件

    PDF附件Bioinformatics software for biologists in the genomics era 

  •  quwubin 的文献笔记  订阅

    生物信息学软件开发趋势
    看到这篇文章，深有感触。文中提到了生物信息学软件设计与终端用户之家的关系，一方面是软件设计与开发者，另一方面是没有多少计算机背景的生物学家，如何让生物学家喜欢你开发的软件，那么就必须遵守下面的几条规则：
    1. GUI user-friendly: 友好的图形界面，其实这里面很复杂，不但是界面友好，还有操作简单，默认参数适用范围广等
    2. Multiple-platform supported：多系统支持，Web-server不存在这个问题，但是standalone版本的程序就需要注意了，有的人就喜欢使用装在自己电脑上的程序；
    3. Sufficient descriptions：注释充分且详细，要让用户对程序了如指掌。
    其实，有这三点也不够，理想的目标或者模板是苹果的产品以及理念。另外一点，整合性的，能综合性的完成复杂信息学分析的软件或者系统已经成为一种趋势。

     

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