论文：Empowering Beginners in Bioinformatics with ChatGPT. 2023
对于生信初学者而言，最大的困难是身边没有经验丰富的人给予指导。而ChatGTP的出现可能改变这一现状，学生可以自己作为导师，指导ChatGPT完成数据分析工作。
众所周知，与ChatGPT互动，给予的指令越精确，那么它给出的答案越精准。这篇论文提出一个与ChatGPT互动的模型：OPTICAL。其基本思想是通过迭代不断优化给予ChatGPT的指令。
该模型的流程图如下：
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给予初始提示。
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机器人产生分析代码。
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运行代码。
如果出现错误，转向优化提示词。
如果代码正确，继续下一步。
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评估结果。
如果结果不符合预期，转向优化提示词。
如果结果符合预期，继续下一步。
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审查代码，得到最终提示词并归档方法。
这个模型本身平平无奇，符合平常人们使用ChatGPT的习惯：即不断优化提示词，直至得到正确答案。下面两个案例很好地体现了这一过程。
案例一：下一代测序的短读段比对和视觉检查
定义聊天机器人的行为：
Act as an experienced bioinformatician proficient in ChIP-Seq data analysis, you will assist me by writing code with number of lines as minimal as possible. Rest the thread if asked to. Reply "YES" if understand.
迭代0
I have two fastq files in current folder from single-end sequencing of a ChIP-Seq library: ENCFF000AVS_1m.fastq.gz, and ENCFF000AVS_10m.fastq.gz. For each fastq file, align reads to the human reference genome, save to bam file, and then covert it to bigwig file. Tools to use: bowtie2, samtools, and deepTools. The index for bowtie2 is in the folder "../data/indx/bowtie2_whole_genome/" with "hg38" as the prefix. Use 24 CPU for the alignment. Please draft the code in bash.
迭代1
E::idx_find_and_load\] Could not retrieve index file for 'ENCFF000AVS_1m.bam' **迭代2** Wait, I saw that you have "samtools index" before "bamcoverage". Does bamcoverage as bam to be sorted before using as input? **审查代码** I need to insert line-by-line comments to the below code which works well to address the needs for the data analysis task. Wait for my code. **最终提示词（粗体字是经过迭代加入的提示细节）：** Act as an experienced bioinformatician proficient in ChIP-Seq data analysis, you will assist me by writing code with number of lines as minimal as possible. Rest the thread if asked to. Reply "YES" if understand. I have two fastq files in current folder from single-end sequencing of a ChIP-Seq library: ENCFF000AVS_1m.fastq.gz, and ENCFF000AVS_10m.fastq.gz. For each fastq file, align reads to the human reference genome, save to bam file, **index it** , and then covert it to bigwig file with **CPM normalization**. Tools to use: bowtie2, samtools, and deepTools. The index for bowtie2 is in the folder "../data/indx/bowtie2_whole_genome/" with "hg38" as the prefix. Use 24 CPU for the alignment. Please draft the code in bash. **安全二：推断DNA序列的分子进化系统发育树** **定义聊天机器人的行为：** Act as an experienced bioinformatician proficient in R, you will write code with number of lines as minimal as possible. Rest the thread if asked to. Reply "YES" if understand. **迭代0** You have a multiple alignment file named as tp53.clustal in ClustalW format. Please write R code that can load the file, calculate evolutionary distance, build a NJ tree, and visualize the phylogeny. **迭代1** I got an error message complaining "could not find function "read.alignment". Please fix it. **迭代2** I got a warning message " In dist.dna(aln) : NAs introduced by coercion". Please fix it. **迭代3** I wrote an R program to read a multiple alignment file named as tp53.clustal in ClustalW format, calculate evolutionary distance, build a NJ tree, and visualize the phylogeny. But I want to root the tree with the Zebrafish sequence as the outgroup. Can you help me revise the R code? Below is my R code. ```php # Load the required packages library(seqinr) library(ape) # Read in the alignment file aln <- read.alignment("tp53.clustal", format="clustal") # Calculate the evolutionary distance dist <- dist.dna(as.DNAbin(aln)) # Build the NJ tree tree <- nj(dist) # Plot the phylogeny plot(tree) ``` **迭代4** I got an error message complaining " Error in nj(dist, outgroup = zebrafish_idx) unused argument (outgroup = zebrafish_idx)". Please fix it. **迭代5** I got an error message complaining "Error in if (newroot == ROOT) { : argument is of length zero". Please fix it. **审查代码** I created the following R code. Please add inline comments. **最终提示词** 无。 ### 关于简说基因 * #### 生信平台 Galaxy中国（UseGalaxy.cn）致力于打造中国人的云上生物信息基础设施。大量在线工具免费使用。无需安装，用完即走。活跃的用户社区，随时交流使用心得。 * #### 生信培训 #### 简说基因的生信培训班，荣获学员的一致好评。如果你也对生物信息学感兴趣，欢迎来跟[**简说基因，学真生信**]()。 * #### 生信分析 #### 我们能够承接所有 NGS 组学数据分析业务，包括但不限于 WGS / WES / RNA-seq 等。基因组组装、注释，以及各种重测序业务都可以与简说基因合作。