blocks|key|2103744|text|你可能会对BioStar上的这个帖子感兴趣：|type|unstyled|depth|inlineStyleRanges|entityRanges|data|2103745|2103746|Which+are+the+best+programming+languages+to+study+for+a+bioinformatician?|unordered-list-item|offset|length|2103747|2103748|对于我们大多数生物信息学家来说，这包括Python、R、Perl和bash命令行实用程序(如sed、awk、cut、sort等)。还有一些人用Java、Ruby、C%2B%2B和Matlab编写代码。|2103749|那么底线是什么呢？无论哪种语言让你最容易完成工作，那就是最适合你的语言。回答这个问题应该包括仔细调查您可以从中提取的库和其他代码，以及关于您自己的偏好和经验的信息。如果你正在做微阵列分析，很难击败R/bioconductor库，但对于那些争论大多数类型的大型测序数据集的人来说，这绝对不是一种错误的语言。|2103750|entityMap|0|LINK|mutability|MUTABLE|url|http://biostar.stackexchange.com/questions/34/which-are-the-best-programming-languages-to-study-for-a-bioinformatician^0|0|0|0|21|0|0|0|0|0^^$0|@$1|2|3|4|5|6|7|U|8|@]|9|@]|A|$]]|$1|B|3|-4|5|6|7|V|8|@]|9|@]|A|$]]|$1|C|3|D|5|E|7|W|8|@]|9|@$F|X|G|Y|1|Z]]|A|$]]|$1|H|3|-4|5|6|7|10|8|@]|9|@]|A|$]]|$1|I|3|J|5|6|7|11|8|@]|9|@]|A|$]]|$1|K|3|L|5|6|7|12|8|@]|9|@]|A|$]]|$1|M|3|-4|5|6|7|13|8|@]|9|@]|A|$]]]|N|$O|$5|P|Q|R|A|$S|T]]]]

You'll likely be interested in this thread over at BioStar: 

<ul>
<li><a href="http://biostar.stackexchange.com/questions/34/which-are-the-best-programming-languages-to-study-for-a-bioinformatician" rel="noreferrer">Which are the best programming languages to study for a bioinformatician?</a></li>
</ul>

For most of us bioinformaticians, this includes Python, R, Perl, and bash command line utilities (like sed, awk, cut, sort, etc). There are also people who code in Java, Ruby, C++, and Matlab. 

So the bottom line? Whichever language lets you get the work done most easily is the right one for you. Answering this question should include a careful survey of the libraries and other code that you can pull from, as well as information on your own preferences and experience. If you're doing microarray analysis, it's hard to beat the R/bioconductor libraries, but that's absolutely the wrong language for someone wrangling most types of large sequencing data sets.

blocks|key|569417|text|对于生物信息学来说，没有一种合适的语言。|type|unstyled|depth|inlineStyleRanges|offset|length|style|BOLD|entityRanges|data|569418|569419|重要的BLAST测序工具是用C%2B%2B编写的|unordered-list-item|569420|用于比对蛋白质结构的MATT工具是用C|569421|编写的，我在计算生物学领域的一些同事使用|569422|。|569423|569424|一般而言，我看到许多C和C%2B%2B用于性能关键型代码，而其他方面则大量使用脚本语言。|569425|entityMap|0|LINK|mutability|MUTABLE|url|http://blast.ncbi.nlm.nih.gov/Blast.cgi|1|http://groups.csail.mit.edu/cb/matt/^0|0|K|0|0|3|5|0|0|A|4|1|0|0|0|0|0^^$0|@$1|2|3|4|5|6|7|12|8|@$9|13|A|14|B|C]]|D|@]|E|$]]|$1|F|3|-4|5|6|7|15|8|@]|D|@]|E|$]]|$1|G|3|H|5|I|7|16|8|@]|D|@$9|17|A|18|1|19]]|E|$]]|$1|J|3|K|5|I|7|1A|8|@]|D|@$9|1B|A|1C|1|1D]]|E|$]]|$1|L|3|M|5|6|7|1E|8|@]|D|@]|E|$]]|$1|N|3|O|5|I|7|1F|8|@]|D|@]|E|$]]|$1|P|3|-4|5|6|7|1G|8|@]|D|@]|E|$]]|$1|Q|3|R|5|6|7|1H|8|@]|D|@]|E|$]]|$1|S|3|-4|5|6|7|1I|8|@]|D|@]|E|$]]]|T|$U|$5|V|W|X|E|$Y|Z]]|10|$5|V|W|X|E|$Y|11]]]]

There's no one right language for bioinformatics.

<ul>
<li>The important <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi" rel="noreferrer">BLAST</a> sequencing tool is written in C++</li>
<li>The <a href="http://groups.csail.mit.edu/cb/matt/" rel="noreferrer">MATT</a> tool for aligning protein structures is written in C</li>
<li>Some of my colleagues in computational biology use Ruby.</li>
</ul>

In general, I see a lot of C and C++ for performance-critical code and a lot of scripting languages otherwise.

blocks|key|2103687|text|Python+%2B+scipy是不错的(而且是免费的)。|type|unstyled|depth|inlineStyleRanges|entityRanges|data|2103688|http://www.vetta.org/2008/05/scipy-the-embarrassing-way-to-code/|offset|length|2103689|http://www.google.com/search?hl=en&source=hp&q=python%2Bbioinformatics&aq=0&aqi=g9g-m1&aql=&oq=python%2Bbio&gs_rfai=CeE1nPpMNTN2IJZ-yMZX6pcIKAAAAqgQFT9DLSgo|2103690|当你放弃Matlab时，你甚至不需要学习新的语法。|2103691|entityMap|0|LINK|mutability|MUTABLE|url|1|http://www.google.com/search?hl=en&source=hp&q=python%2Bbioinformatics&aq=0&aqi=g9g-m1&aql=&oq=python%2Bbio&gs_rfai=CeE1nPpMNTN2IJZ-yMZX6pcIKAAAAqgQFT9DLSgo^0|0|0|1S|0|0|0|48|1|0|0^^$0|@$1|2|3|4|5|6|7|S|8|@]|9|@]|A|$]]|$1|B|3|C|5|6|7|T|8|@]|9|@$D|U|E|V|1|W]]|A|$]]|$1|F|3|G|5|6|7|X|8|@]|9|@$D|Y|E|Z|1|10]]|A|$]]|$1|H|3|I|5|6|7|11|8|@]|9|@]|A|$]]|$1|J|3|-4|5|6|7|12|8|@]|9|@]|A|$]]]|K|$L|$5|M|N|O|A|$P|C]]|Q|$5|M|N|O|A|$P|R]]]]

Python + scipy are decent (and FREE). 

<a href="http://www.vetta.org/2008/05/scipy-the-embarrassing-way-to-code/" rel="nofollow noreferrer">http://www.vetta.org/2008/05/scipy-the-embarrassing-way-to-code/</a>

<a href="http://www.google.com/search?hl=en&amp;source=hp&amp;q=python+bioinformatics&amp;aq=0&amp;aqi=g9g-m1&amp;aql=&amp;oq=python+bio&amp;gs_rfai=CeE1nPpMNTN2IJZ-yMZX6pcIKAAAAqgQFT9DLSgo" rel="nofollow noreferrer">http://www.google.com/search?hl=en&amp;source=hp&amp;q=python+bioinformatics&amp;aq=0&amp;aqi=g9g-m1&amp;aql=&amp;oq=python+bio&amp;gs_rfai=CeE1nPpMNTN2IJZ-yMZX6pcIKAAAAqgQFT9DLSgo</a>

You do not even need to learn new syntax really when when dropping Matlab for SciPy.

blocks|key|1318103|text|无论是不是最好的，SAS都是生物制药中事实上的编程环境。如果你要为世界上生物信息学领域的辉瑞、默克和拜耳工作，你最好具备SAS技能。SAS程序员的需求量很大。|type|unstyled|depth|inlineStyleRanges|entityRanges|data|1318104|entityMap^0|0^^$0|@$1|2|3|4|5|6|7|D|8|@]|9|@]|A|$]]|$1|B|3|-4|5|6|7|E|8|@]|9|@]|A|$]]]|C|$]]

Best or not, SAS is the de facto programming enviroment in biopharmas. If you were to work for the Pfizers, Mercks and Bayers of the world in bioinformatics, you had better have SAS skills. SAS programmers are in great demand.

blocks|key|1314107|text|什么是“最好的”语言既是主观的，也可能因任务而异，但对于生物信息学工作，我个人使用R、Perl、Delphi和C(通常是这些语言的组合)。|type|unstyled|depth|inlineStyleRanges|entityRanges|data|1314108|entityMap^0|0^^$0|@$1|2|3|4|5|6|7|D|8|@]|9|@]|A|$]]|$1|B|3|-4|5|6|7|E|8|@]|9|@]|A|$]]]|C|$]]

What's the "best" language is both subjective and potentially different from task to task, but for bioinformatic work, I personally use R, Perl, Delphi and C (quite frequently a combination of several of these).

blocks|key|2103880|text|我主要处理HMM和蛋白质序列。我一开始是用C语言写的，但后来换成了Python，我对Python很满意。我发现更容易快速构建原型，并且更容易维护代码。|type|unstyled|depth|inlineStyleRanges|entityRanges|data|2103881|entityMap^0|0^^$0|@$1|2|3|4|5|6|7|D|8|@]|9|@]|A|$]]|$1|B|3|-4|5|6|7|E|8|@]|9|@]|A|$]]]|C|$]]

I work mainly with HMMs and protein sequences. I started out writing in C, but have since switched to Python, which I'm happy with. I find it's easier to prototype something quickly and results in easier to maintain code.

blocks|key|2103894|text|这是一篇免费提供的学术论文，该论文对不同的语言和不同的情况进行了评估：http://www.biomedcentral.com/1471-2105/9/82|type|unstyled|depth|inlineStyleRanges|entityRanges|offset|length|data|2103895|他们将6种常用语言分成3个不同的级别。|2103896|2+compiled+languages:+C,+C%2B%2B
2+semi-compiled+languages:+C#,+Java
2+interpreted+languages:+Perl,+Python|code-block|syntax|javascript|2103897|一些一般性的结论：|2103898|在全局对齐和相邻连接programs|2103899|Interpreted语言中，编译语言的性能优于解释语言。除了Python|unordered-list-item|2103900|
|2103901|Compiled语言需要更多的编写代码行来执行相同的BLAST计算之外，|2103902|编译语言通常使用更多的内存|ordered-list-item|2103903|所有语言在BLAST计算中表现大致相同。tasks|2103904|Compiled语言往往更适合于算法implementation|2103905|Interpreted语言往往更适合于文件parsing/manipulation|2103906|2103907|2103908|这里有另一篇很好的免费学术文章，讨论了构建生物信息学技能的方法：http://dx.plos.org/10.1371/journal.pcbi.1000589|2103909|entityMap|0|LINK|mutability|MUTABLE|url|http://www.biomedcentral.com/1471-2105/9/82|1|http://dx.plos.org/10.1371/journal.pcbi.1000589^0|Z|17|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|W|1B|1|0^^$0|@$1|2|3|4|5|6|7|1I|8|@]|9|@$A|1J|B|1K|1|1L]]|C|$]]|$1|D|3|E|5|6|7|1M|8|@]|9|@]|C|$]]|$1|F|3|G|5|H|7|1N|8|@]|9|@]|C|$I|J]]|$1|K|3|L|5|6|7|1O|8|@]|9|@]|C|$]]|$1|M|3|N|5|6|7|1P|8|@]|9|@]|C|$]]|$1|O|3|P|5|Q|7|1Q|8|@]|9|@]|C|$]]|$1|R|3|S|5|6|7|1R|8|@]|9|@]|C|$]]|$1|T|3|U|5|Q|7|1S|8|@]|9|@]|C|$]]|$1|V|3|W|5|X|7|1T|8|@]|9|@]|C|$]]|$1|Y|3|Z|5|X|7|1U|8|@]|9|@]|C|$]]|$1|10|3|11|5|X|7|1V|8|@]|9|@]|C|$]]|$1|12|3|13|5|X|7|1W|8|@]|9|@]|C|$]]|$1|14|3|-4|5|6|7|1X|8|@]|9|@]|C|$]]|$1|15|3|-4|5|6|7|1Y|8|@]|9|@]|C|$]]|$1|16|3|17|5|6|7|1Z|8|@]|9|@$A|20|B|21|1|22]]|C|$]]|$1|18|3|-4|5|6|7|23|8|@]|9|@]|C|$]]]|19|$1A|$5|1B|1C|1D|C|$1E|1F]]|1G|$5|1B|1C|1D|C|$1E|1H]]]]

Here's a freely available academic paper written on the subject that evaluates the different languages, and in different situations: <a href="http://www.biomedcentral.com/1471-2105/9/82" rel="nofollow">http://www.biomedcentral.com/1471-2105/9/82</a>

They grouped 6 commonly used languages into 3 different levels.

<pre><code>2 compiled languages: C, C++
2 semi-compiled languages: C#, Java
2 interpreted languages: Perl, Python
</code></pre>

Some general conclusions:

<ol>
<li>Compiled languages outperformed interpreted languages in global alignments and Neighbour-Joining programs</li>
<li>Interpreted languages generally used more memory</li>
<li>All languages performed roughly the same for BLAST computations, except for Python</li>
<li>Compiled languages require more written lines of code to perform the same tasks</li>
<li>Compiled languages tend to be better for algorithm implementation</li>
<li>Interpreted languages tend to be better for file parsing/manipulation</li>
</ol>

Here's another good free academic article discussing ways to build bioinformatics skills: <a href="http://dx.plos.org/10.1371/journal.pcbi.1000589" rel="nofollow">http://dx.plos.org/10.1371/journal.pcbi.1000589</a>

I have done a couple research jobs in Bio-informatics and I have used Matlab for them. Matlab had a lot of powerful tools and was easy to use. I did thinks with genome sequencing and predicting metabolic pathways. I am wondering what other people think is best? or there might not be one specific language but a few that lend themselves best to Bio-informatics work that is math heavy and deals with a large amount of data.

What do you think is the best language for Bioinformatics?

翻译质量差，导致语言生硬或混乱。

没有提供实际的解决方法或示例。

解答不清晰，无法理解或解决问题。

页面排版不美观，阅读体验差。

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我在生物信息学方面做了几项研究工作，并使用Matlab进行研究。Matlab有很多强大的工具，而且很容易使用。我确实考虑过基因组测序和预测代谢途径。我想知道其他人认为什么是最好的？或者，可能没有一种特定的语言，而是几种最适合生物信息学工作的语言，这些工作数学繁重，需要处理大量数据。

问你认为生物信息学最好的语言是什么？
EN

回答 7

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