【bioinfo】生物信息学——代码遇见生物学的地方 (5)

【bioinfo】生物信息学——代码遇见生物学的地方

 图2:生物信息学 vs 数据科学

按照上图的理解,生物信息学就是一种特别的数据科学。Dr. Maria Nattestad认为生物信息学非常有趣的原因之一是:该学科聚集了不同领域的人,这些人带着不同的背景和倾向,使用不同的方式来思考生物学问题。她将生物信息学分成了以下三个部分:

Data analysis is the most natural starting point for biologists and involves the most domain expertise because it specifically involves interpreting the data. The ability to detect oddities or interesting patterns in the data can heavily depend on your knowledge of the biological system the data comes from.

Bioinformatics software development is an approach to bioinformatics that I see computer scientists naturally take on. They may also do data analysis, but will have a hard time resisting building real software products. The software they develop can take many forms, from command-line tools to web applications.

Modeling is very fashionable with physicists and mathematicians. You can tell their work apart by the fact that it’s full of equations and written in LateX.

 

2018年

【定义11】2018年是瑞士生物信息学研究所(Swiss Institute of Bioinformatics, SIB)建立20周年。在其官网上对生物信息学的定义如下:

 The application of computer technology to the understanding and effective use of biological and clinical data. It is the discipline that stores, analyses and interprets the ‘big data’ generated by life science experiments, or clinical data, using computer science.

 相对于其他定义,这里强调对数据的高效利用,以及对生命科学大数据的处理。

下面是SIB定义的生物信息学的研究内容:

Databases and knowledgebases for storing, retrieving and organizing biological information to maximize the value of biological data;

Software tools for modelling, visualizing, analysing, interpreting and comparing biological data;

Computing and storage infrastructure to process large amounts of data;

Analysis of complex biological datasets or systems in the context of particular research projects;

Research in a wide variety of biological fields using computer- and data science and leading to applications in diverse areas, from agriculture to precision medicine.

Bioinformatics is thus a multidisciplinary field bringing together biologists, computer scientists and mathematicians, as well as statisticians and physicists.

 

【定义12】下面是宾夕法尼亚州立大学的生物信息学教授István Albert,在他的书《The Biostar Handbook: A Beginner's Guide to Bioinformatics》中对生物信息学的定义:

Bioinformatics is a data science that investigates how information is stored within and processed by living organisms.

上面的定义非常简洁,将生物信息学看做是数据科学,研究生物体中的信息如何保存和处理。

该书的介绍部分,讲了生物信息学的变化过程:

In its early days––perhaps until the beginning of the 2000s––bioinformatics was synonymous with sequence analysis. Scientists typically obtained just a few DNA sequences, then analyzed them for various properties. Today, sequence analysis is still central to the work of bioinformaticians, but it has also grown well beyond it.

In the mid-2000s, the so-called next-generation, high-throughput sequencing instruments (such as the Illumina HiSeq) made it possible to measure the full genomic content of a cell in a single experimental run. With that, the quantity of data shot up immensely as scientists were able to capture a snapshot of everything that is DNA-related.

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