14

转一个Python的安利文章咯!

来自于我们生信技能树论坛的超级版主bioinfo.dong的好文一篇,比较符合我博客的思想,就友情转发一下:

原文链接见:http://www.biotrainee.com/thread-379-1-1.html 

刚接触生信的同学大都有个困惑,知道生物信息可能需要编程,可是选择什么语言呢?有人会说perl啊,Python啊,R啊,java啊,等等等等。目的不一样,选择也不一样,你可以说语言都没有区别,达到目的就行,当然没问题。可是我们也要知道每种语言都有其独特优势,你可以用perl倒腾出矩阵运算,也可以画出想要的图,可是没有R专业;你也可以用R的正则表达式处理文本,可是perl或者Python做正则会更方便一些。这不是比较帖,只是从一个Python体验者的角度来说一下为什么选择Python。我目前的编程组合是Python+R+Shell Scripting。

这篇文章比较适合编程初学者,常年用perl的老司机们可以随便看一下,虽说perl和Python很像,有了一门的基础,学另一门就容易多了,可是真让一个用了几年perl的人彻底换Python还是比较困难的,主要还是习惯问题。最初做生信的人大都以perl作为常用脚本语言。我也是从perl开始的,当年为了申请出国读Bioinformatics,认真把小骆驼书看了一遍。来美国之后的第一个导师刚好是教perl的,我又跟着学了一次,看完导师推荐的《Unix and Perl to the Rescue》,算是巩固加第二次入门。之后一年基本都是用perl来处理数据。一个偶然的机会,同学说一起学学Python吧,听说很好用,于是就在网上找了个教程把题目刷了一遍。虽说入了门,可是每次项目赶时间的时候第一个想到的还是用perl来解决,所以入门很久也没啥长进,我亲爱的同学因为perl用的太好,虽然知道Python很好用,可始终没法狠心转过来,而我因为本身perl学得也只是半斤八两,纠结了一段时间也就彻底放弃perl了。

先说用了很长时间perl再用Python觉得不习惯的点。

(1)首先是动物园的书,《learning perl》真是入门的典范。再看《Learning Python》,几千页,那么厚,我到现在也没法认真看下去。
(2)另外perl语句比较简洁,几个符号就可以讲清楚的,Python可能需要几行,比如按行读取,perl只要while(<>)就可以,而最初学Python的时候,光这个问题就困扰了很久。再比如perl正则匹配的$1, Python是match.group(1)。perl的简洁伴随的缺点是可读性较差,自己的代码写完了都不想再看,更不要说别人写的。
(3)perl的正则表达式是真的非常厉害,我已经不记得是怎么厉害的了,就只记得Python的re module刚开始接触不太好用,不过现在已经感觉不出区别了。
(4)通常一个Python脚本需要很多modules,不熟悉之前会觉得很痛苦,perl就比较少用到,我总共也没用几次,一方面说明我的perl确实学得不好,另一方面可能也真是不太好用,看到就觉得麻烦。但Python的modules一旦熟悉了会大大提高工作效率。

重点说一下Python的优点。Python作为编程语言真正的优势比如面向对象编程(OOP),可移植/扩展/嵌入,强大的爬虫功能,APP开发,web开发等都不在讨论范围之内,只从最实用的角度做一下说明:
(1)简单,适合作为入门语言。很多时候觉得读Python的代码像是在读简单的英文,或者觉得pseudocode稍微一改就可以在Python里run了。Python还规范了很好的写作格式,该缩进的必须缩进,这样更增强了可读性。同时提高了代码重复利用的可能(很多时候perl代码写完就不想读了,三个月不用再回来已经看不太懂了,Python的就可以留着慢慢用。。。)
(2)Python社区活跃。有问题可以很容易搜索到解决方案。我perl的老师现在也转教Python了,问他为什么,他说perl的community不活跃,用Python是一种趋势
(3)作为开源语言,Python有很多非常好用的包,可以最大程度让我们避免把时间浪费在重复造轮子上。刚接触Python的时候我就觉得这简直是perl和R的整合,之前提过Python的scipy,numpy,pandas,matlibplot等等packages使其同样拥有了很强大的统计画图功能,我曾一度弃用R,用Python做所有的数据处理,数据分析和画图。不过现在又将这些工作交回了R,实验室本身是做统计的,用R显得入流一点:-)
(4)Python的jupyter notebook!!!这个是要强力推荐的!!!以前叫ipython notebook。用过R的都知道R Studio。jupyter notebook就是Python的Studio。以前写perl或者Python是不是这样的流程:写好了,存成.pl或.py格式,在shell里python xxx.py或者perl xxx.pl。运行完发现不好,有bug,打开文件找找bug在哪,再运行,还不行,唉,反反复复,好累。有了jupyter notebook你就可以边写边跑边改程序。有任何不确定的地方,都可以在notebook里直接测试,有任何bug都可以在notebook里直接改。简直方便到爆。现在用Anaconda安装jupyter还附赠很多包,方便又实惠。
(5)学好Python可以转行!!!跳出生物坑,奔向美好的互联网坑。前面提到的爬虫,APP开发,web编程都是很实用的技能。许多互联网公司也会专门招Python程序员,比如Google,比如Youtube,比如Dropbox。。。

我本专业是Bioinformatics,需要上一些计算机和统计的研究生课程,还记得算法课上老师第一节课就问,java和C++都会吧,如果不会的话Python总会吧,都不会的话这门课的作业写不了。就因为觉得自己还算会一点Python,把一次学习java的好机会浪费掉了

暂时就想到这么多。说的未必对。都是自己的体会吧。希望对初学者有用~

05

生物学基础知识~CARM和SWI/SNF复合物

因为最近在研究CHIP-seq测序数据处理,发现有些文章重点并不是数据处理本身,而是对生物学基础知识的掌控以及实验设计,这篇文章我重点推荐一下,我略微翻译了一些,笔记如下:

SWI/SNF(BAF) chromatin remodeling complex  染色质重构复合物,以及被广泛发现在各种癌症患者体内均有突变,这个复合物利用ATP水解释放的能量来驱动核小体运动以及调控染色质的结构。
发现历史: 最新是在yeast里面发现它的突变会影响 mating type SWItching 和 导致sucrose nonfermenting 的表型,所以才简称为SWI/SNF,在哺乳动物体内也被广泛研究现在,它被发现参与了细胞分化、增殖、还有各种DNA修复功能的实现。
组成结构:本质是一个蛋白质复合物,约15个亚基,每个亚基都由一个独立的基因转录翻译而来,每个基因都有专门的文章研究过。
SWI-SNF-geneFamily-SMARCC1-BAF155
生物功能:早在1998年就被发现与癌症相关,在GO数据库里面还可以查到相关资料,所以很容易在各种通路分析结果里面看到它的身影
GO-0016514-SWI-SNF-complex
随着癌症基因组测序的进展,至少有8种染色质重构复合物的亚基有recurrent mutation情况,然后有一句话说得特别好:
This has resulted in interest in indentifying mechanisms by which activity of the SWI/SNF complex is regulated, with the hope that such mechanistic understanding may reveal novel opportunities for therapeutic intervention .
CARM1基因是PRMT系列的一种:protein arginine Methyltransferases一直与基因的转录与翻译相关,主要功能就是使得蛋白质的arginine甲基化,这个基因家族目前有9个基因,只有CARM1命名比较奇葩。
PRMT-gene-family-CARM1
其中RM都是 Arginine Methyltransferase的简称,很容易理解,
CARM1这个酶的底物不仅仅包括参与染色质重构,还有基因转录调控,剪切因子,组蛋白乙酰化还有RNA结合蛋白
chromatin remodeling (  SWI/SNF(BAF) chromatin remodeling complex  )
gene transcription   (histone H3(at R17))
histone acetyltransferases  ( p300/CBP )
splicing factors  ( CA150,SAP49,SmB,U1C  )
RNA-binding proteins   ( PABP1, HuR, HuD)
也有实验证明非常多的癌症种类病人都发现了CARM1表达异常升高,而且刺激乳腺癌的恶化,而且是很多癌症相关恶化蛋白的共刺激因子,比如p53,E2F1,NF-kB,b-catenin,steroid hormone receptors. 
但是CARM1到底是如何在乳腺癌体内发生作用的,其中机制并不完全清楚。
25

自学miRNA-seq分析第三讲~公共测序数据下载

前面已经讲到了该文章的数据已经上传到NCBI的SRA数据中心,所以直接根据索引号下载,然后用SRAtoolkit转出我们想要的fastq测序数据即可。下载的数据一般要进行质量控制,可视化展现一下质量如何,然后根据大题测序质量进行简单过滤。所以需要提前安装一些软件来完成这些任务,包括: sratoolkit /fastx_toolkit /fastqc/bowtie2/hg19/miRBase/SHRiMP

下面是我用新服务器下载安装软件的一些代码记录,因为fastx_toolkit /fastqc我已经安装过,就不列代码了,还有miRBase的下载,我在前面第二讲里面提到过,传送门:自学miRNA-seq分析第二讲~学习资料的搜集 Continue reading

05

用snpEFF对vcf格式的突变数据进行注释

这个软件比较重要,尤其是对做遗传变异相关研究的,很多人做完了snp-calling后喜欢用ANNOVAR来进行注释,但是那个注释还是相对比较简单,只能得到该突变位点在基因的哪个区域,那个基因这样的信息,如果想了解更具体一点,就需要更加功能化的软件了,snpEFF就是其中的佼佼者,而且是java平台软件,非常容易使用!而且它的手册写的非常详细:http://snpeff.sourceforge.net/SnpEff_manual.html

官网是:http://snpeff.sourceforge.net/

1       889455  .       G       A       .       .        ## 假设我们的vcf文件里面记录的突变是这个,那么我们可以用snpEFF进行注释,注释得到的信息非常完全!

信息用|符号分割,所有很容易用脚本提取需要的信息

ANN=A|stop_gained|HIGH|NOC2L|ENSG00000188976|transcript|ENST00000327044|protein_coding|7/19|c.706C>T|p.Gln236*|756/2790|706/2250|236/749||,A|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|transcript|ENST00000487214|processed_transcript||n.*865C>T|||||351|,A|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|transcript|ENST00000469563|retained_intron||n.*878C>T|||||4171|,A|non_coding_exon_variant|MODIFIER|NOC2L|ENSG00000188976|transcript|ENST00000477976|retained_intron|5/17|n.2153C>T||||||;LOF=(NOC2L|ENSG00000188976|6|0.17);NMD=(NOC2L|ENSG00000188976|6|0.17)

包括突变类型是:non_coding_exon_variant

突变在各种转录本上面,在每个转录本的第几个碱基呀,哪个氨基酸的改变呀,氨基酸第几位呀!

标准突变表示形式是:

突变发生在NOC2L这个基因上面,它的ensembl 数据库ID是ENSG00000188976

 

其余的看头文件自己慢慢理解:

"Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'

 

软件安装:

选择最新版软件下载:https://sourceforge.net/projects/snpeff/files/

wget https://sourceforge.net/projects/snpeff/files/snpEff_latest_core.zip

因为是java软件,unzip 解压之后就可以直接使用,当然前提是你有java平台。

1

输入数据:

首先下载用来做注释的数据库:java -jar snpEff.jar download GRCh37.75(自己选择需要的版本)

1

软件下载很快,但是数据库下载就需要一定时间啦,去喝杯咖啡吧。

然后软件本身会提供example文件,里面就是一堆各种各样的vcf数据,而且还提供了运行命令,非常简单(examples.sh) ,这些就是我们的输入数据啦!

运行命令:

运行也很简单:java -Xmx4G -jar snpEff.jar -i vcf -o vcf GRCh37.75 example.vcf > example_snpeff.vcf

指定输入输出格式都是vcf,然后指定刚才下载的必备数据库,然后输入输出文件即可!

也可以调用全路径,如果你写在脚本里面的话!

java -Xmx4G -jar path/to/snpEff/snpEff.jar \

-c path/to/snpEff/snpEff.config \

GRCh37.69 \

path/to/example.vcf > example_snpeff.vcf

 

结果解读:

这个非常复杂,对结果理解了多少,就是我们对软件理解了多少。

具体大家看readme吧,注释信息太多了,按需索取:

  1. chromosome_number_variation
  2. exon_loss_variant
  3. frameshift_variant
  4. stop_gained
  5. stop_lost
  6. start_lost
  7. splice_acceptor_variant
  8. splice_donor_variant
  9. rare_amino_acid_variant
  10. missense_variant
  11. inframe_insertion
  12. disruptive_inframe_insertion
  13. inframe_deletion
  14. disruptive_inframe_deletion
  15. 5_prime_UTR_truncation+exon_loss_variant
  16. 3_prime_UTR_truncation+exon_loss
  17. splice_branch_variant
  18. splice_region_variant
  19. splice_branch_variant
  20. stop_retained_variant
  21. initiator_codon_variant
  22. synonymous_variant
  23. initiator_codon_variant+non_canonical_start_codon
  24. stop_retained_variant
  25. coding_sequence_variant
  26. 5_prime_UTR_variant
  27. 3_prime_UTR_variant
  28. 5_prime_UTR_premature_start_codon_gain_variant
  29. upstream_gene_variant
  30. downstream_gene_variant
  31. TF_binding_site_variant
  32. regulatory_region_variant
  33. miRNA
  34. custom
  35. sequence_feature
  36. conserved_intron_variant
  37. intron_variant
  38. intragenic_variant
  39. conserved_intergenic_variant
  40. intergenic_region
  41. coding_sequence_variant
  42. non_coding_exon_variant
  43. nc_transcript_variant
  44. gene_variant
  45. chromosome

http://snpeff.sourceforge.net/VCFannotationformat_v1.0.pdf

 

12

R包精讲第二篇:如何安装旧版本的包?

既然你点进来看,肯定是有需求咯!
一般来说,R语言自带的install.packages函数来安装一个包时,都是默认安装最新版的。
但是有些R包的开发者他会引用其它的一些R包,但是它用的是人家旧版本的功能,但他自己来不及更新或者疏忽了。
而我们又不得不用他的包,这时候就不得不卸载最新版包,转而安装旧版本包。

Continue reading

15

基因组各种版本对应关系

我是受到了SOAPfuse的启发才想到整理各种基因组版本的对应关系,完整版!!!
以后再也不用担心各种基因组版本混乱了,我还特意把所有的下载链接都找到了,可以下载任意版本基因组的基因fasta文件,gtf注释文件等等!!!
首先是NCBI对应UCSC,对应ENSEMBL数据库:
GRCh36 (hg18): ENSEMBL release_52.
GRCh37 (hg19): ENSEMBL release_59/61/64/68/69/75.
GRCh38 (hg38): ENSEMBL  release_76/77/78/80/81/82.
可以看到ENSEMBL的版本特别复杂!!!很容易搞混!
但是UCSC的版本就简单了,就hg18,19,38, 常用的是hg19,但是我推荐大家都转为hg38
看起来NCBI也是很简单,就GRCh36,37,38,但是里面水也很深!
Feb 13 2014 00:00    Directory April_14_2003
Apr 06 2006 00:00    Directory BUILD.33
Apr 06 2006 00:00    Directory BUILD.34.1
Apr 06 2006 00:00    Directory BUILD.34.2
Apr 06 2006 00:00    Directory BUILD.34.3
Apr 06 2006 00:00    Directory BUILD.35.1
Aug 03 2009 00:00    Directory BUILD.36.1
Aug 03 2009 00:00    Directory BUILD.36.2
Sep 04 2012 00:00    Directory BUILD.36.3
Jun 30 2011 00:00    Directory BUILD.37.1
Sep 07 2011 00:00    Directory BUILD.37.2
Dec 12 2012 00:00    Directory BUILD.37.3
可以看到,有37.1,   37.2,  37.3 等等,不过这种版本一般指的是注释在更新,基因组序列一般不会更新!!!
反正你记住hg19基因组大小是3G,压缩后八九百兆即可!!!
如果要下载GTF注释文件,基因组版本尤为重要!!!
对于ensembl:
变幻中间的release就可以拿到所有版本信息:ftp://ftp.ensembl.org/pub/
对于UCSC,那就有点麻烦了:
需要选择一系列参数:
2. Select the following options:
clade: Mammal
genome: Human
assembly: Feb. 2009 (GRCh37/hg19)
group: Genes and Gene Predictions
track: UCSC Genes
table: knownGene
region: Select "genome" for the entire genome.
output format: GTF - gene transfer format
output file: enter a file name to save your results to a file, or leave blank to display results in the browser
3. Click 'get output'.
 现在重点来了,搞清楚版本关系了,就要下载呀!
UCSC里面下载非常方便,只需要根据基因组简称来拼接url即可:
或者用shell脚本指定下载的染色体号:
for i in $(seq 1 22) X Y M;
do echo $i;
wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr${i}.fa.gz;
## 这里也可以用NCBI的:ftp://ftp.ncbi.nih.gov/genomes/M_musculus/ARCHIVE/MGSCv3_Release3/Assembled_Chromosomes/chr前缀
done
gunzip *.gz
for i in $(seq 1 22) X Y M;
do cat chr${i}.fa >> hg19.fasta;
done
rm -fr chr*.fasta
12

bioconductor中文社区招募站长

我已经构建好bioconductor中文社区的雏形,大家可以进去看看!

写在前面

突然发现我的bioconductor.cn这个域名都快要过期了!

哈哈,才想起一年前的计划到现在还没开始实施,实在不像我的风格,可能是水平到了一定程度吧,很多初级工作不像以前那样事无巨细的把关了。正好,借这个机会找几个朋友帮我一起完成这个bioconductor中文社区计划!

 

Continue reading

18

生物信息学分析过程中常见文件格式

刚开始接触生物信息学的时候我也很纠结什么fastq,fastq,sam,bam,vcf,maf,gtf,bed,psl等等,甚至还有过时了的NCBI,ENSEMBL格式,如果是我刚开始 学的时候,我倒是很愿意把他们全部搞透彻,写详细的说明书,但是现在成长了,这些东西感觉很low了,正好我看到了一篇帖子讲数据格式的收集大全,分享给大家,希望初学者能多花点时间好好钻研!

https://www.biostars.org/p/55351/

每种文件格式的定义,都是有它的道理的,大部分是因为一个比较流行的软件,少量的数据格式是因为国际组织广泛认可而流行的
27

gene的symbol与entrez ID并不是绝对的一一对应的

很多时候,我们都无法确定到底是基于symbol来进行分析,还是基于entrez ID,当我们要进行ID转换的时候也想当然的以为它们的一一对应的, 但是最近我写了一个脚本来分析CCLE的数据的时候,发现其实有一些特例:

suppressMessages(library(org.Hs.eg.db))

all_symbol=mappedkeys(org.Hs.egSYMBOL2EG)

all_EGID =mappedkeys(org.Hs.egSYMBOL)
tmp=as.list(org.Hs.egSYMBOL2EG[all_symbol])
#tmp=as.list(org.Hs.egSYMBOL[all_EGID ])
tmp=unlist(lapply(tmp,length))
tmp=tmp[tmp>1]
as.list(org.Hs.egSYMBOL2EG[names(tmp)])
有多个entrez ID对应一个symbol的现象出现,但是没有一个symbol对应多个entrez ID的现象。而且entrez ID也会过期!
$CSNK1E
[1] "1454"      "102800317"
$HBD
[1] "3045"      "100187828"
$RNR1
[1] "4549" "6052"
$RNR2
[1] "4550" "6053"
$SFPQ
[1] "6421"   "654780"
$TEC
[1] "7006"      "100124696"
$MEMO1
[1] "7795"  "51072"
$KIR3DL3
[1] "115653"    "100133046"
$MMD2
[1] "221938"    "100505381"
$`LSAMP-AS1`
[1] "100506708" "101926903"
通过下面的链接可以看到具体情况
14

用broad出品的软件来处理bam文件几次遇到文件头错误

报错如下:ERROR MESSAGE: SAM/BAM file input.marked.bam is malformed: SAM file doesn't have any read groups defined in the header.  The GATK no longer supports SAM files without read groups !

有些人遇到的是bam的染色体顺序不一样,还有可能是染色体的名字不一样,比如>1和>chr1的区别,虽然很傻,但是遇到这样问题的还不少!
还有一些人是遇到基因组没有dict文件,也是用picard处理一下就好。

大部分人是在GATK遇到的,我是在RNA-SeQC遇到的,不过原理都是一样的。
都是因为做alignment的时候并未添加头信息,比如:
bwa samse ref.fa my.sai my.fastq > my.sam
samtools view -bS my.sam > my.bam
samtools sort my.bam my_sorted
java -jar ReordereSam.jar I=/path/my_sorted.bam O=/path/my_reordered.bam R=/path/ref.fa
通过这个代码可以得到排序好的bam,但是接下来用GATK就会报错
java -jar GenomeAnalysisTK.jar -T DepthOfCoverage -R /paht/ref.fa -I /path/aln_reordered.bam
就是因为没有头信息,group相关信息,解决方法有两种:
bwa samse -r @RG\tID:IDa\tSM:SM\tPL:Illumina ref.fa my.sai my.fastq > my.sam
java -jar AddOrReplaceReadGroups I=my.bam O=myGr.bam LB=whatever PL=illumina PU=whatever SM=whatever
一种是比对的时候就加入头信息,这个需要比对工具的支持。
第二种是用picard工具来修改bam,推荐用这个!虽然我其实并不懂这些头文件信息是干嘛的, 但是broad开发的软件就是需要!希望将来去读PHD能系统性的学习一些基础知识!

 

11

关于芯片平台GPL15308和GPL570

它们虽然被GEO数据标记了不同的ID号,但是其实都是一种芯片,都是昂飞公司的U133++2芯片,分析过芯片数据的人肯定不会陌生了

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL15308

事实上,这个平台应该是GPL570,但是被CCLE数据库给稍微变通了一下,就给了一个GPL15308的标签,平台主页也写的很清楚,它的探针ID是伪ID,其实就是entrez gene ID

1

本来这个芯片设计的是五万多个探针,最后只剩下了18926个基因
This array is identical to GPL570 but the data were analyzed with a custom CDF Brainarray Version 15, hgu133plus2hsentrezg.
十二 30

用GSEA来做基因集富集分析

how to use GSEA?
这个有点类似于pathway(GO,KEGG等)的富集分析,区别在于gene set(矫正好的基于文献的数据库)的概念更广泛一点,包括了

how to download GSEA ?

what's the input for the GSEA?

说明书上写的输入数据是:GSEA supported data files are simply tab delimited ASCII text files, which have special file extensions that identify them. For example, expression data usually has the extension *.gct, phenotypes *.cls, gene sets *.gmt, and chip annotations *.chip. Click the More on file formats help button to view detailed descriptions of all the data file formats.
实际上没那么复杂,一个表达矩阵即可!然后做一个分组说明的cls文件即可。
主要是自己看说明书,做出要求的数据格式:http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats
表达矩阵我这里下载GSE1009数据集做测试吧!
cls的样本说明文件,就随便搞一搞吧,下面这个是例子:
6 2 1
# good bad
good good good bad bad bad
文件如下,六个样本,根据探针来的表达数据,分组前后各三个一组。
clipboard
现在开始运行GSEA!

start to run the GSEA !

首先载入数据
clipboard
确定无误,就开始运行,运行需要设置一定的参数!
clipboard

what's the output ?

输出的数据非常多,对你选择的gene set数据集里面的每个set都会分析看看是否符合富集的标准,富集就出来一个报告。
点击success就能进入报告主页,里面的链接可以进入任意一个分报告。
最大的特色是提供了大量的数据集:You can browse the MSigDB from the Molecular Signatures Database page of the GSEA web site or the Browse MSigDB page of the GSEA application. To browse the MSigDB from the GSEA application:
 
有些文献是基于GSEA的:

 

十二 22

根据chrY独有区域的覆盖度及测序深度来判断性别

这个也是基于bam文件来的,判断chrY独有区域的覆盖度及测序深度
首先下载chrY独有区域的记录文件,https://www.familytreedna.com/documents/bigy_targets.txt
然后用samtools depth来统计测序深度,samtools  depth $i |grep 'chr[XY]'
depth统计结果文件如下:
mzeng@ubuntu:/home/jmzeng/gender_determination$ head Sample3.depth
chrX    60085    1
chrX    60086    1
chrX    60087    1
chrX    60088    1
chrX    60089    1
chrX    60090    1
chrX    60091    1
chrX    60092    1
chrX    60093    1
chrX    60094    1
然后我随便写了一个脚本来对测序深度文件进行再统计,统计覆盖度及测序深度

[perl]
open FH,"bigy_targets.txt";
while(<FH>){
 chomp;
 @F=split;
 $all+=$F[2]-$F[1]+1;
 foreach ($F[1]..$F[2]){
  $h{$_}=1;
 }
}
close FH;
open FH,$ARGV[0];
while(<FH>){
 chomp;
 @F=split;
 next unless $F[0] eq 'chrY';
 if (exists $h{$F[1]}){
  $pos++;
  $depth+=$F[2];
 }
}
close FH;
$average=$depth/$pos;
$coverage=$pos/$all;
print "$pos\t$average\t$coverage\n" ;

[/perl]

 

 
这样对那三个样本结果如下:
clipboard
可以看到只有sample4,是覆盖率极低的,而且记录到的pos位点也特别少,所以她是女性!
这里测序深度没有意义。
十一 05

点突变详解

DNA分子中某一个碱基为另一种碱基置换,导致DNA碱基序列异常,是基因突变的一种类型。可分为转换和颠换两类。转换(transitions)是同类碱基的置换(AT→GCGC→AT,颠换(transversions) 是不同类碱基的置换(AT→TACG,GC→CGTA

DNA substitution mutations are of two types. Transitions are interchanges of two-ring purines (A  G) or of one-ring pyrimidines (C  T): they therefore involve bases of similar shape. Transversions are interchanges of purine for pyrimidine bases, which therefore involve exchange of one-ring and two-ring structures.

我们在分析driver mutation的时候会区分各种点突变:

  • 1. CpG transitions
  • 2. CpG transversions
  • 3. C:G transitions
  • 4. C:G transversions
  • 5. A:T transitions
  • 6. A:T transversions

那么,我们有64种密码子,每种密码子都会有9种突变可能,我们如何得到一个所有的突变可能的分类并且打分表格呢?

类似于下面这样的表格:共576行!!!

head category.acgt
AAA>AAT 2 A T 6
AAA>AAC 2 A C 6
AAA>AAG 2 A G 5
AAA>ATA 1 A T 6
AAA>ACA 1 A C 6
AAA>AGA 1 A G 5
AAA>TAA 0 A T 6
AAA>CAA 0 A C 6
AAA>GAA 0 A G 5
AAT>AAA 2 T A 6

tail category.acgt
GGC>GGG 2 C G 2
GGG>AGG 0 G A 3
GGG>TGG 0 G T 4
GGG>CGG 0 G C 4
GGG>GAG 1 G A 3
GGG>GTG 1 G T 4
GGG>GCG 1 G C 4
GGG>GGA 2 G A 3
GGG>GGT 2 G T 4
GGG>GGC 2 G C 4

我本来以为这是一件很简单的事情,写起来,才发现好麻烦

1Capture

 

里面用到的一个函数如下:就是判断突变属于上述六种的哪一种!

2

参考:https://www.mun.ca/biology/scarr/Transitions_vs_Transversions.html

https://en.wikipedia.org/wiki/Transversion

http://www.uvm.edu/~cgep/Education/Mutations.html

突变,也称作单碱基替换(single base substitution),指由单个碱基改变发生的突变

可以分为转换(transitions)和颠换(transversions)两类。

转换:嘌呤和嘌呤之间的替换,或嘧啶和嘧啶之间的替换。

颠换:嘌呤和嘧啶之间的替换。

方便理解下面再附上一张示意图,如下:

 

Transitions_vs_Transversions

 

十一 01

WES(七)看de novo变异情况

de novo变异寻找这个也属于snp-calling的一部分,但是有点不同的就是该软件考虑了一家三口的测序文件,找de novo突变

软件有介绍这个功能:http://varscan.sourceforge.net/trio-calling-de-novo-mutations.html

而且还专门有一篇文章讲ASD和autism与de novo变异的关系,但是文章不清不楚的,没什么意思

Trio Calling for de novo Mutations

image001

Min coverage:   10

Min reads2:     4

Min var freq:   0.2

Min avg qual:   15

P-value thresh: 0.05

Adj. min reads2:        2

Adj. var freq:  0.05

Adj. p-value:   0.15

Reading input from trio.filter.mpileup

1371416525 bases in pileup file (137M的序列)

83123183 met the coverage requirement of 10 (其中有83M的测序深度大于10X)

145104 variant positions (132268 SNP, 12836 indel) (共发现15.5万的变异位点)

4403 were failed by the strand-filter

139153 variant positions reported (126762 SNP, 12391 indel)

502 de novo mutations reported (376 SNP, 126 indel) (真正属于 de novo mutations只有502个)

1734 initially DeNovo were re-called Germline

12 initially DeNovo were re-called MIE

3 initially DeNovo were re-called MultAlleles

522 initially MIE were re-called Germline

1 initially MIE were re-called MultAlleles

3851 initially Untransmitted were re-called Germline

然后我看了看输出的文件trio.mpileup.output.snp.vcf

软件是这样解释的:The output of the trio subcommand is a single VCF in which all variants are classified as germline (transmitted or untransmitted), de novo, or MIE.

  • FILTER - mendelError if MIE, otherwise PASS
  • STATUS - 1=untransmitted, 2=transmitted, 3=denovo, 4=MIE
  • DENOVO - if present, indicates a high-confidence de novo mutation call

里面的信息量好还是不清楚

我首先对我们拿到的trio.de_novo.mutaion.snp.vcf文件进行简化,只看基因型!
head status.txt   (顺序是dad,mom,child)
STATUS=2 0/0 0/1 0/1
STATUS=2 1/1 1/1 1/1
STATUS=2 0/1 0/0 0/1
STATUS=2 1/1 1/1 1/1
STATUS=1 0/1 0/0 0/0
STATUS=1 0/1 0/0 0/0
STATUS=2 1/1 1/1 1/1
STATUS=2 1/1 1/1 1/1
STATUS=2 1/1 1/1 1/1
STATUS=2 0/1 0/1 0/1
那么总结如下:
  26564 STATUS=1 无所以无 (0/0 0/1 0/0或者 0/1 0/0 0/0等等)
  97764 STATUS=2 有所以有 (1/1 1/1 1/1 或者0/1 0/1 1/1等等)
    385 STATUS=3 无中生有 (0/0 0/0 0/1 或者0/0 0/0 1/1)
   1485 STATUS=4 有中生无 (1/1 0/1 0/0 等等)

我用annovar注释了一下

/home/jmzeng/bio-soft/annovar/convert2annovar.pl -format vcf4  trio.mpileup.output.snp.vcf > trio.snp.annovar

/home/jmzeng/bio-soft/annovar/annotate_variation.pl -buildver hg19  --geneanno --outfile  trio.snp.anno trio.snp.annovar /home/jmzeng/bio-soft/annovar/humandb

结果是:

A total of 132268 locus in VCF file passed QC threshold, representing 132809 SNPs (86633 transitions and 46176 transversions) and 3 indels/substitutions

可以看到最后被注释到外显子上面的突变有两万多个

23794  284345 3123333 trio.snp.anno.exonic_variant_function

这个应该是非常有意义的,但是我还没学会后面的分析。只能先做到这里了

 

28

模拟Y染色体测序判断,并比对到X染色体上面,看同源性

首先下载两条染色体序列

wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chrX.fa.gz;

wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chrY.fa.gz;

152M Mar 21  2009 chrX.fa

58M Mar 21  2009 chrY.fa

然后把X染色体构建bwa的索引

bwa index chrX.fa

[bwa_index] Pack FASTA... 1.97 sec

[bwa_index] Construct BWT for the packed sequence...

[BWTIncCreate] textLength=310541120, availableWord=33850812

[BWTIncConstructFromPacked] 10 iterations done. 55838672 characters processed.

[BWTIncConstructFromPacked] 20 iterations done. 103157920 characters processed.

[BWTIncConstructFromPacked] 30 iterations done. 145211344 characters processed.

[BWTIncConstructFromPacked] 40 iterations done. 182584528 characters processed.

[BWTIncConstructFromPacked] 50 iterations done. 215797872 characters processed.

[BWTIncConstructFromPacked] 60 iterations done. 245313968 characters processed.

[BWTIncConstructFromPacked] 70 iterations done. 271543920 characters processed.

[BWTIncConstructFromPacked] 80 iterations done. 294853104 characters processed.

[bwt_gen] Finished constructing BWT in 88 iterations.

[bwa_index] 98.58 seconds elapse.

[bwa_index] Update BWT... 0.96 sec

[bwa_index] Pack forward-only FASTA... 0.91 sec

[bwa_index] Construct SA from BWT and Occ... 33.18 sec

[main] Version: 0.7.8-r455

[main] CMD: /lrlhps/apps/bioinfo/bwa/bwa-0.7.8/bwa index chrX.fa

[main] Real time: 141.623 sec; CPU: 135.605 sec

由于X染色体也就152M,所以很快,两分钟解决战斗!

然后模拟Y染色体的测序判断(PE100insert400

209M Oct 28 10:19 read1.fa

209M Oct 28 10:19 read2.fa

模拟的程序很简单

tmp

然后用bwa mem 来比对

bwa mem -t 12 -M chrX.fa read*.fa >read.sam

用了12个线层,所以也非常快

[main] Version: 0.7.8-r455

[main] CMD: /apps/bioinfo/bwa/bwa-0.7.8/bwa mem -t 12 -M chrX.fa read1.fa read2.fa

[main] Real time: 136.641 sec; CPU: 1525.360 sec

643M Oct 28 10:24 read.sam

然后统计比对结果

samtools view -bS read.sam >read.bam

158M Oct 28 10:26 read.bam

samtools flagstat read.bam

3801483 + 0 in total (QC-passed reads + QC-failed reads)

0 + 0 duplicates

2153410 + 0 mapped (56.65%:-nan%)

3801483 + 0 paired in sequencing

1900666 + 0 read1

1900817 + 0 read2

645876 + 0 properly paired (16.99%:-nan%)

1780930 + 0 with itself and mate mapped

372480 + 0 singletons (9.80%:-nan%)

0 + 0 with mate mapped to a different chr

0 + 0 with mate mapped to a different chr (mapQ>=5)

我自己看sam文件也发现真的同源性好高呀,总共就模拟了380万reads,就有120万是百分百比对上了。

所以对女性个体来说,测序判断比对到Y染色体是再正常不过的了。如果要判断性别,必须要找那些X,Y差异性区段

21

一个MIT的博士要离开学术圈,结果引发了上千人的热烈讨论(下)

Dr Petra EichelsdoerferFebruary 17, 2014 at 11:17 AM

My university lacked the funds to support me while applying for my first grant after my post-doc. So I was unable to re-write it after its first rejection. Although it was heartbreaking to walk away, I had a family to support. This was nearly four years ago. How many others have had to make the same decision I have? What will be the long-term consequences?

我们大学也是资金紧张,所以我直到博士后出站才拿到资金的第一笔科研基金。大约四年前把,当我第一次被基金会拒绝后,我实在难以鼓起勇气再次申请基金。尽管我必须去申请,因为我还得养家糊口。会有多少人曾与我经历过同样的处境呢,又有多少人与我一样做了同样的选择呢?

Lenny TeytelmanFebruary 17, 2014 at 5:30 PM

(By a professor at a research university, in response to my post.)

I wish I had more positive news on the funding front. I am now up to 18 grants. All rejections still very positive. But, I'm waiting to hear back from 2 of them in the beginning of March, keep your fingers crossed for me. Luckily, the University has given me some money to allow me to keep my postdoc and keep my lab running. Right now I'm okay for the next 9 months. the university has done a lot of things to make it obvious that they want to keep me, so I feel lucky about that...I'm just not sure how many more things they can do beyond this.

One thing that is positive is that I've become better at separating the inability to getting funding from me being a failure. Things in the lab are finally starting to come together with some exciting stories that are getting close to publication. And, I can finally appreciate that our work is good and we deserve funding. In the past, I thought of the rejections as saying that we just weren't good enough to deserve funding. I know it sounds weird, but this was an important transition for me.

I try to avoid giving advice to postdocs thinking about continuing in academia because I still really don't know if it is worth all of the sacrifice, but I haven't figured it out yet. I used to think that academia would be the only thing that would make me happy, but now I know that isn't true. I think there are a lot of things that we (highly trained scientists) can all do using our skills that we would be good at and would be fulfilling. I hope that you find (or have found) that thing.

我来给这次基金战役带来一些正能量吧,到目前为止我已经斩获了18个基金项目。那些被拒绝的项目也并非毫无希望,我还在等待他们中间的两个项目的消息,到三月初应该就可以看到结果了吧。幸运的是,我们学校也给予了我更多的钱来支持我博士后的工作,保证我的实验小组正常运行。至少在接下来的九个月之内,我的财务状况还是蛮好的。学校也尽他所能的做了能做的事情来挽留我,我也觉得非常幸运,我只是不能确定,他们这样又能持续多久呢?

另外一件正能量的事情是,在资金申请方面,我已经可以做得很好了,不再是一个失败者了。同时,实验室也出现很多好消息,我们有一些文章即将要发表了。而且,我对我们实验室的工作非常满意,我也坚信我们应该获得项目资金。在过去,如果我的基金申请被拒绝,我一般都会认为是我的工作做得还不够好。我知道这听起来有点奇怪,但那的确是我当初的心理状态。

我一向避免给那些正在做博士后的科学家对关于是否留在学术圈这样的问题给什么建议,因为我不确定所有的牺牲对他自己来说,是否值得,而我本身也没有完全看透这一点。我一直认为学术圈的活动是唯一能使我开心的事情,但是我现在不这么认为了。我认为这世上还好很多更美好,更有意义的事情值得像你我这样的受过高级技能训练的科学家可以做的,我们可以完全应用我们所擅长的,也可以做得更得心应手。我也希望你能找到同样的事情。

 

DorukArtFebruary 18, 2014 at 10:26 PM

Hi Lenny. Another one for your collection. I was, until recently, a postdoc at Stanford. The lab I worked in closed down, at least partially because the professor didn't want to deal with grants anymore. Unfortunately, I have been well-received in a number of other labs I applied for, yet none of them had funding to pay a new postdoc. Consequently, I may be leaving academia soon for good as well.

你好,Lenny,我也共享一下我的故事吧。我曾经是斯坦福大学的一名博士后,就在不久前还是。我所在的实验室几乎快倒闭了,至少看起来像是,因为实验室的教授不再想去搞那些资金项目的事情了。不幸的是,即使我被其它几个我所申请的实验室录取了,但是他们没有一个能负担得起一个新的博士后。因此,我可能马上也要离开学术圈了吧。

Jason MastaitisFebruary 19, 2014 at 5:05 PM

Nice piece, Lenny - very well said. About three years ago I was a postdoc at Yale who greatly enjoyed my position and research, but could see the writing on the wall as far as grant funding goes. Then I fortunately received a call from a biopharma company who was looking for a scientist in my field. Got an interview, then a job offer, jumped ship and never looked back. Best career decision I ever made. Still doing essentially the same research, but just in an industry setting and now I make a living wage to boot. Can't imagine what I'd be doing now if I hadn't received that call. Thank my lucky stars every day, as does my wife.

干得好,Lenny,写得非常棒。三年前,我也是耶鲁大学的一名博士后,那时我非常享受我的研究学习工作,但是也看到了资金危机来临的不祥之兆。然后,我幸运的接到了一个生物制药公司的咨询电话,他们正在寻找我所从事的这个领域的科学家。经过简单的面试,我拿到了他们的offer,从此跳出了学术圈,而且永不回头啦。这是我职业生涯所做的最棒的决定。我现在仍然做的是类似的研究,只不过工作环境换成了工业界,我的报酬也足够我谋生计了。我实在无法想象要是当初我没有接那个电话,我现在的生活将会何去何从呢。感谢我可爱的小女儿,同时也感谢我的妻子~

doctorpmsFebruary 27, 2014 at 5:25 PM

Thank you for posting this. There is so much resemblance to what I'm currently thinking! I'm still in the point of realizing how hard is the science funding situation and if I really want get myself into it. Reading your post adds food to my thoughts and brings a different perspective. Good luck in your new life!

谢谢你分享这些!你所提到的这些事情与我现在的经历实在是太像了。对于科学研究基金的的糟糕状况,我还在迷茫中,我也在纠结是否应该跳入这个火坑。读了你的文章,我有了一些新的想法,同时让我有机会从另一些视角来看待这个问题。祝愿你有一个精彩的新生活。

HenryFebruary 28, 2014 at 3:43 AM

Ahh, academia. A place where they think they know it all, but are so busy doing politics and fighting each other for funding like it's House of Cards that they have lost sight of the goal. I believe this very old article sums up how funding is meted out better than any other - entrenched power wins every single time, whether correct or not. And much science is filled with fraudulent activities: http://www.bmartin.cc/pubs/92prom.html ("Scientific fraud and the power structure of science").

Who am I? PhD Chicao, post-doc Chicago MIT. Tenured faculty. Left it all to go to law school and become a lawyer at a firm and then at a company and have never looked back. Starting this career so late means early retirement will be a bit stretched but better than it would have been if I had stayed in academia where my ideas were not "safe" and did not follow on "next step" science that is all that gets funded.

Leave academia, get a life, the water is fine.

哈哈,学术界!那个地方都是一堆白痴,以为自己什么都懂,却浪费大把时间在勾心斗角及对研究基金的你争我抢上面。就像纸牌屋里面那些迷失了人生目标的那群人一样。(我没看过纸牌屋,不知道这句话该怎么样翻译)我确信,收集自研究基金方面的文章,妄想改革基金分配制度已经是老生常谈的故事了。赢家通吃这个理论不管正确与否,它就是现实。

我是芝加哥大学的博士,曾经在芝加哥和MIT联合实验室做博士后。也拿到了终身教职。但是我放弃了在法学院的一切荣耀,成为了法庭上的一个普普通通的律师,然后又去了一个律师事务所,我从来没有后悔过。我的社会事业开启的太晚了,意味着我早点退休的想法将变得不切实际,但总比我还赖在学术界,惶惶不可终日,所有的科学进展都依赖于下一步能得到什么样的资金资助而活着要好很多。

Diane BouisFebruary 28, 2014 at 3:14 PM

Dear Lenny,
Congratulations! More power to you! And thank you for sparking the conversation!
What's missing is a clear exit strategy for PostDocs... deciding that academia is not for you, is still a silent, lonely process because most scientists hardly know anyone outside academia and the stereotype of "the smart and hard-working ones get tenure" lives.... But in this funding climate even the smart and hard working ones have to close their labs, so we need to get beyond the stigma.
You chose to be an entrepreneur and I wish you great success! But not all scientists were cut out to be entrepreneurs, so how do we empower PostDocs to leave towards equally (or more) fulfilling careers? Can (national and university) PostDoc associations to help with that transition? Can University Career Centers learn to not just cater to undergrads and fresh PhDs? Am I missing organizations?
In my free time, I give talks and privately mentor academics ready to exit and am thrilled anytime one of them gets a job, but that's by far not enough... I'd love to hear from you and others how we can prevent a "lost generation of scientists" and allow them the most successful exit possible, by providing a more structured -and thereby socially obvious and acceptable- exit.

恭喜你呀!你会变得更强大的,同时也谢谢你的分享。

我们刚才没有讨论的是博士后这个策略本身的问题,博士后本意是为了让你有充足的时间来思考学术生活是否适合你,但这是一个毫无生气,而且孤独的过程,因为大多数科学家对学术圈外面的世界了解甚少,而且他们固执的认为,只有最聪明最勤奋的那批人才能拿到终身教职。但是在现今的资金资助环境下,即使是最勤奋最聪明的那批人的实验室也不得不面临关门大吉的窘境,所以,我们应该勇于改变。

既然你选择了成为一个企业家,那我当然要祝你成功啦。但并不是所有的博士后都有这么好的机会能走入工业界,我们应该如何帮助他们走入一个差不多或者更精彩的人生呢?你觉得博士后委员会是不是应该做点什么帮助他们做一个好的转变呢?

我业余时间我喜欢做一些演讲,有点类似于学术界的精神导师那样,每次我听说有人找到了工作我都非常激动,但这样始终不够。我想听听你或者其他人对关于我们如何阻止这一代科学家的迷失的建议,如何帮助他们走入更成功更精彩的人生。

Nicole NeumanFebruary 28, 2014 at 3:55 PM

I can definitely relate. Throughout my scientific career I watched my fantasy of becoming the tenured academic who balances a family, an exciting research career, and fulfilling teaching duties get chipped away piece by piece. Nowhere to be found was the academic philosopher of olden days, who could afford to sit around and discuss scientific ideas and principles for hours on end with their colleagues. They had too much work to do writing grants to engage in leisurely discourse. At a certain point I looked around and realized the actuality of current academic life was not something I wanted. So I asked myself: in an ideal world, how would I like to spend my day? And looked for jobs that allowed me to do as much of the stuff I liked as possible, and a little as possible of the stuff I didn't like.

After some digging and testing out a few things, I landed on scientific editing and I couldn't be happier. I'm so incredibly thankful that I got my PhD, because I could not have gotten this job without it, but I do not regret leaving the beaten path. These days becoming an academic is not the norm. Of course it is a shame that we are losing so many great minds because of the structural problems supporting their academic careers, but I think that it is time to openly acknowledge in our training programs that a trainee is not a failure if they leave academia. A PhD isn't just a means to create professors; it teaches people a crucial skill that is useful in many different careers and ventures--how to think scientifically. That is a valuable thing, even outside of the domain knowledge you will learn.

Anyway, I will get off my soapbox now :-). Best of luck, Lenny, you've created something really interesting with ZappyLab and I look forward to seeing where it goes.

我就是楼主所描述的典型例子。纵观我的科学生涯,也曾幻想过拿到终身教职,既能从事那令人激动的研究工作,也能完成教学义务,还能养家糊口。但现在我所幻想的那些人已经是过去时了,他们以前的确可以坐起来一起聊聊科学思想,与同事一起参与合作研究,他们有着非常多非常重要的事情要做,写基金申请书只是闲暇时光的随意之举。不知道什么时候开始,我发现我发现现在的学术圈生活早就已经不是我以前想象中的那样了。所以我经常问自己,我这一生该如何度过呢?应该是去找一个工作,让我可以做更多感兴趣的事情,尽可能少的去参与那些我所讨厌的事情吧。

我实在是非常感谢我拿到了PHD学位,如果不是这样,我压根就无法得到我现在的工作机会,但是我不后悔我的人生走的这么曲折。现如今,想在学术圈混并不是一件容易的事情。当然,我们应该为学术圈感到羞耻,为我们失去了如此多的人才,就因为体制的原因,无法支持科学家的学术梦想。但同时,我们也应该开放我们的思想了,并不是说我们培训好的PHD最后离开了学术圈就是我们教育的失败。博士并非意味着一定要成为教授。博士教育也同时提供了非常多的其它技能能辅助他们在其它领域工作能如鱼得水,帮助他们如何科学的思考。这也是很有价值的事情,即使他们不再从事他们的研究领域。

 

Jochen WeberFebruary 28, 2014 at 4:19 PM

Hey Lenny,

While I am neither holding or pursuing a degree, I can very much relate to the pain you describe. My own career path led me, luckily, on a parallel and related, but also different track: after dropping out of an educations masters program in Germany, I received a professional certificate in CS/IT from a German chamber of commerce, and have worked as a programmer since--now at Columbia University in NYC.

I cannot even begin to offer a solution to the problem you describe *within the system*. For quite a while now, I have come to think of the current model of economic activity as a (very long-term) transition phase. Initially, people traded more or less directly goods and services, which has been essentially replaced by goods-and-services for currency--a virtual "good" that is being controlled in most markets by a small group of people with a specific set of goals. I am not a proponent of some conspiracy theory of any kind! I don't think that this is a grand master plan of sorts, but I do think that we have come to think of this paradigm as so "inevitable" that we are blinded by all the negative consequences it has. Equally as it probably took a lot of people a long time to consider a solar-centric planetary system--and that had very little consequence on the practical aspects of life--I believe it will take us a long time before we even *consider* alternatives for a centrally organized currency as means of exchanging (goods and) services.

As long as we think of human labor as a "marketable" good, work that carries greater intrinsic value (being enjoyable for what it's worth) will, if enough people can "afford" it both mentally and financially, always be less valuable from a market point of view. In simpler terms: I believe that it would be a much "smarter" allocation of resources if all unemployed people added their brain power to solve some real problems instead of just being unemployed. But the market does not lend itself to such a solution, because solving general problems is not something that anyone would pay money for--regardless of whether it is good for the "common good".

For those individuals who love science but also need to make ends meet, it is a tough choice to find a position that combines those aspects. I am glad I found mine (for now, although--as my "niche" is equally depending on funding--I may at some point have to move on to greener pastures as well). In principle, I am certainly *FOR* an even faster pace of science as well as any effort that will decouple science from the economic view on "problem solving", as it will, in the long term, only accelerate the necessary insight that scarce resources should be traded by a market, but when the scarce resource becomes abundant (in a generally desirable kind of way, such as more scientists, a.k.a. the people who solve problems), maybe it is time to think about ways to allocate resources in a "non-market" way?

Cheers!

 

Desiree H. FloydMarch 1, 2014 at 7:27 PM

Thanks Lenny. I've been postdocing for 8 years now. I'm happy doing the research I'm doing. One of the above posts could have been written by my PI/mentor--9 months of funding left, great projects close to publication, don't couple your success meter in life to the funding situation. He's brilliant. I'm brilliant. We're all brilliant, and we're so close to making some diseases go away, or understanding some basic things at completely new levels, and in the case of cancer research for invariably fatal brain tumors (my field) we are on the cusp of getting 5-year survivors. I thought about leaving academia to run for Congress against Eric Cantor (my rep) but decided not to because I want to see this out. If the lab closes, it closes. If it stays open, I'm here. I don't really care about the money. I love my job. I'm fortunate in other ways--I didn't pony up to move more than once, because I stopped believing in that particular side of "what you have to do to succeed." We moved where we wanted to, we live near family and on a farm. If the lab doesn't work out, I'll write, I'll get involved in politics and journalism and programming or web design, and I'll continue to "do science" by breeding livestock and growing crops. I'll figure out a way to teach or start a small company. I guess you could say that I didn't know what I was signing up for at the beginning of all this. I just wanted to play with all the toys. At this point I still get to do that. We'll see . . . all I can say is, good luck to you, best wishes, and I hope the protocol thing works out.

谢谢你,Lenny。我已经做了8年的博士后了,我本身是非常乐于从事我现在的研究工作的。我的导师跟你的遭遇非常像,他的资金也只能撑九个月了,他也有一个很伟大的文章要发表了。但这些成功都不能离开资金资助。他很聪明,我也很聪明,我们都很聪明,我们就快把一些疾病从此从人类身边赶走了,或者至少能从一些新的角度来诠释那些疾病机理,比如说癌症研究领域,我们关注的是致命性很高的脑肿瘤,我们已经提高了该癌症的五年存活率。我也曾想过离开学术界,去从政,但是最终还是没能下定决心,因为我放不下我的研究成果。如果实验室关闭了,研究就终止了,如果实验室还能继续运转,我就不会走。我并不怎么在乎那些报酬,我热爱我的工作。我也很幸运,不是像小马过河一样,因为我不再相信,你的人生追求只是成功这样的观点。我可以去任何我想去的地方,我一直与家人生活在一起,就在农场里面。如果实验室被关闭了,我就会去写文章报导这样的事情,我会从政,或者当记者,或者编程,网页设计。而且我会继续做科学研究,通过在农场里面摆弄庄家。我希望可以找到开一个小公司的途径,我想你可能会觉得我太理想化了,把一切都想得那么简单。

Blanca Carbajal-GonzalezMarch 1, 2014 at 7:43 PM

Thank you for sharing your experience. I can't say I got that far. I entered a PhD program in Molecular and Cell Biology very excited to be doing something I loved. However, after nearly 4 years of listening to the post-docs talk about how horrible their career prospects were ( as well as having a horrible mentor/PI), I decided to leave. Since I had only had experience in academia (although I already had publications), I could not get a job outside of academia. I returned to academia as a lab manager. While my boss is a huge improvement over the last and I love research, I worry I will not be able to pay off my school loans with the terrible salary I have. You would think that a MS in science would be worth something more....guess not. It doesn't seem like our dedication is valued much.

Also, the pressure to be a PI and only a PI is horrible. Academics can be so cruel if you have other career aspirations. Try telling your PI that you want to do some volunteer work or take extra classes to prepare yourself for another job. The PhD needs to be diversified. There aren't enough faculty positions for all those graduating with PhDs....

谢谢你分享你的经历。我不能说我的经历跟你完全类似。我在分子细胞生物学领域拿到了博士学位,而且我也很兴奋我可以从事我所喜欢的工作。然而,经过了四年的各种博士后分享他们的职业生涯是多么恐怖之后,我决定离开了。因为我只有在学术圈的经验,包括发表了一些文章,我很难在学术圈外面找到一份工作。我又回到了实验室做一名实验管理员,近年来我的老板进步也很大,我也很喜欢我的研究工作,但是我担心我微博的薪水很难负担得起我的学业贷款。你可能觉得一个科学性的硕士应该拿到更多的报酬,也许拿不到,但是对我们的定价这视乎不是由我们本身能决定的。

而且,成为一个PI的压力也是非常可怕的,学术圈是如此的残酷。试着去告诉拿到导师,你可以做一些义务工作或者参加一些额外的课程,做一些能帮助你走出学术圈拿到社会上的工作的事情吧。博士也必须多元化,毕竟,现实社会中没有那么多的教职能满足现在所有的在读博士。

labratMarch 1, 2014 at 10:58 PM

I was you... completely. I started doing science when I was 14 and working in a university lab by the time I was 17 and a Goldwater Fellow at 19. I loved science until I went to graduate school and saw it for what it was becoming. You don't even talk about in your article the things that I found truly demoralizing- the lying, cheating, stealing projects, fabricating data etc to get publications and funding. The amount of retractions that seem to be going up every year because of the need to publish. I don't trust the people in my graduate lab and I don't trust my adviser- he considers stealing and using untested reagents (because testing requires time) to be "ambitious". It is really sad and was heartbreaking for someone that loved science in its pure form so much. I met Jasper once and really was charmed by him. I think he is completely right- the people that are left in our generation of sciencists (I graduated in 2002) are the people that learned how to claw their way to the top by any means necessary and generally are more enamored with the idea of being a professor than of doing good science.

我跟你所经历的简直一模一样!我从14岁开始就从事科学研究了,到17岁的时候进入了一所大学的实验室,19岁的时候就拿到了教职。我热爱科学,直到我进入研究生学习阶段后,看到了一些现实。对于学术圈的肮脏,你还有很多东西没有提到,包括那些欺骗,谎言,偷窃学术成果,伪造经历来骗取研究基金资助。迫于发论文的压力,如此的事件发生的越来越频繁了。我不敢相信我研究生实验室里面的任何同事,甚至我的导师,他一直想使用那些未经批准的试剂(因为试剂要想得到批准必须要经过很多耗费时间的测试)。这些现实的问题对一个一直纯洁的热爱科学研究的人造成了很大的伤害。我以前见过你的导师Jasper一次,非常的仰慕他。我觉得他说的非常对,我们这一代人还留在科学界的都是学会了那些必须的申请基金的技巧,他们更擅长去做一个教授,而不是做科学研究工作。

MargitMarch 2, 2014 at 7:15 AM

Thanks for posting - there are many similar voices. As a tenured prof at a good University that still respects tenure, my position is not so fragile, but I am likely going to do a similar move but later - I am going to retire early to do something different. Also, my daughter, who has taught all through high school and college and was sure to go to academia, now that she is a grad student at MIT, had to switch mentor because hers didn't get tenure, has decided to likely do something else. It is sad that the best young people like you are quitting! But as a permanent member of the study section, I see and feel the pain as well on the other side. I have a different take on the funding crisis, some supported by data from Sally Rock. It is not so much the government cutting money (personally, I can't tell the government to get further into debt to fund science). I have reviewed grants for the EU, Germany, Canada, Ireland, Singapore, United Arab Emirates, Israel,... you name it. Except for young starting positions, nowhere else is the salary of a Professor depending on the grant. The crisis is caused by Universities hiring too many Professors with an explicit reliance on someone else paying - in the past 20 years, most of these were hired without tenure so they can get fired easily. It is this idea that you can hire someone and he is supposed to bring in their own salary on grants that kills the system. It also completely eliminates academic freedom, as I can only work on what I get funded to do. Another problem is that we have a lot of old folks in the system: The rate of NIH grants funded to PIs that are over 65 increased more than 6 fold in the past 20 years, from 1% to now nearly 7%. This isn't the majority, but such people usually have tenure and a higher salary, so they disproportionately take the small amount of funding Universities do have. I don't think asking NIH for more funding is the solution. We need to tell NIH that PI salaries should be limited, slowly from the current 95% to 50% (Francis Collins and Bruce Alberts have called for this before), and hopefully no salary for PIs except for transition positions like K99-00 which seemed to be a good idea. The Universities have to re-take responsibility for their faculty and support them. Which unfortunately also will mean even fewer jobs for the young like you, but at least some predictability. The current system is broke.

谢谢你的分享。我也想分享一个差不多的故事。作为一个还算比较不错的大学的有着终身教职的教授,我还是比较尊重那些能拿到终身教职的人。我现在的职位还算比较稳固的, 但我也会像你一样离开学术圈,在不久的将来。我打算提前退休,去做一些与众不同的事情。我的女儿,曾经在高中和大学任教过,就一直很确定要进入学术圈了,现在她是MIT的一名研究生。但是她现在必须要更换导师了,因为她以前的导师没能拿到终身教职,必须收拾东西走人了。像你这样如此优秀的年轻人离开学术圈,的确是一件让人很伤心的事情。但是作为一名学生委员会的永久理事,我也能理解你们的痛苦。关于这次的基金危机,我有一些不同的观点,主要是基于Sally Rock提供的数据。并不完全是政府部分削减了科学研究的资金投入。我查阅了很多国家的科研基金投入,包括英国,德国,加拿大,新加坡,伊朗,等等。除了那些刚开始做教授的那些人之外,其余的教授的资金状况都比较好。这次危机主要是因为在过去的二十年间,很多大学雇佣了过多的教授,而没有能增加对他们的资金投入,他们大多是被雇佣的时候并没有得到终身教职,所以很快就会被解聘。正是这种想法,我们可以雇佣更多的教授,而这些教授可以自己申请基金来平衡他们的开支,造成这次危机。也使得我们的学术研究失去了自由,只有在我得到基金资助的时候我才能做研究。另一个问题是,在我们的科研系统里面有着太多的老家伙,NIH所资助的那些PI中高于65岁的PI人数已经增加了6倍,从以前的1%增长到了现在的7%,他们的人数不多,但是这些人拿着终身教职,而且通常薪水很高。是他们让基金的分配比例失衡了。我不认为向NIH申请更多的基金额度是解决问题的办法。我们应该向NIH建议,限制部分PI的薪水。大学也应该重新考虑他们的教职工,并且给他们更好的支持。当然,于此同时有些不幸的事情也会发生,比如,很多像你这样的年轻人将压根就无法得到类似的工作了,更别提申请基金了。但是完全可以预测的是,现在的基金分配系统的确出了问题。

 

以下太多了,懒得翻译了

AnandMarch 2, 2014 at 9:14 AM

It's 8pm on a Sunday evening and I am still at my computer in my office...no, I am not working long hours but I am now living in Saudi Arabia, where I work as a Research Scientist. I did my postdoc in Houston at Rice University and after a couple of rejection, a wonderful offer from a good friend fell on my lap. He accepted a professor position here in KAUST and he decided to hire me and my wife to work in his lab. Unlike the situation in the US, we don't have any financial constraints (yet?) but of course there's a massive sacrifice in terms of living in the middle of a desert in a gated compound. I guess my point is that, if the US or any other first world nation does not take this deep dissatisfaction seriously, they will lose their talents to other countries that are willing to pay. Of course, not everyone will attempt this move but those really wanting to do science might bite the bullet. All the best for your startup and I wish I had the guts to do what you did and leave academia...the main problem for those of us in academia is that we are told from very early on that we are just not good enough to leave and this insecurity tends to inhibit our growth.

 

Patricia CabezasMarch 2, 2014 at 3:45 PM

Hi Lenny,
Thanks for the post. Being in academia has always been like a roller coaster for me. Some days I love it and I feel that I could be doing this forever, and other days it makes me feel so miserable. I moved from Europe 3 years ago for a first postdoc in the US and unfortunately the experience was traumatic... no project, non-existent advisor, non very friendly labmates... After my first year I was so lost and depressed that I decided to quit for a few months. All I wanted to do was quitting academia but my visa didnt allow me to find a regular job, so I decided to apply for another postdoc in Washington DC and I got it. This is a position for another 2 years with a good advisor in a really outstanding institute.... however dealing with uncertainty of "what's the next" is killing me. I feel lucky cause my couple has accepted to move with me to the east coast but of course taking the decision was a painful, tearful and stressful process. I love science but I cant handle all the sacrifices associated with it. I think I want to quit after this postdoc but the idea of sitting down in the computer and reformat my CV for the private setting is so discouraging... no idea about how to do it or even how to start. I am scared that if I try to quit I will not be able to find a job outside of academia. And... thats my story. Just wanted to say thanks for the post. Wish you the best and good luck with this new challenge!!

I think the motto "I am afraid I won't find any job out of academia because I don't have any other skills" is very common. That is my fear too, and one of the reason I haven't quit yet.

Kevin MooreMarch 3, 2014 at 8:54 PM

Lenny: Congratulations on a difficult but I think very wise decision. Whatever path you choose, I think you will do well.

The post-WWII model of academic labs training and spawning new professors who start their own labs and train more students who start...became unsustainable by the 1970s when the academic science community could no longer remain on its indefinite (geometric!) expansion binge. Those times won't come back, at least not in our lifetimes. Therefore, on average, each faculty member need train only ONE new professor during their entire career. The rest of their Ph.D. students will need to find their professional callings and creative outlets in other ways...of which there are plenty. It's an exciting world out there and there has never been a better or more stimulating time to work in the biological sciences. This will be the "Biology Century."

I've just retired from a 30+ year career in pharmaceutical biotechnology R&D (mostly R). This trend was already clear to me 35 years ago during my postdoc and I have never for an instant regretted the choice I made NOT to go into academic research. Fortunately both my Ph.D. and postdoctoral advisors encouraged me and others to pursue non-academic careers, I read here that many of you are not so fortunate in that regard.

I still am surprised and a little saddened by the number of grad students and postdocs who to this day drink the Kool-Aid served by their faculty advisors for so long before making other plans.

Edoardo VacchiMarch 4, 2014 at 3:16 AM

I don't think this Open Letter (not by me) has been posted before here http://crypto.junod.info/2013/09/09/an-aspiring-scientists-frustration-with-modern-day-academia-a-resignation/ I think it is enlightening in this regard.

I am an Italian PhD Student in CS at my last year and I made the decision not to pursue an academic career, once I'm done with this last year.

I've been wondering whether I'm making the right decision. I already know where I'll probably go to work; I'm already in touch with them, and I enjoy the place. Still, I sometimes still feel this is a defeat, rather than a successe, as I believed that a job in academia would have made me happier. I enjoy sharing knowledge, teaching people the things I love; but what I really see these days is too much politics, and very little science. I'm not really enjoying working in this field anymore. Besides, the road to reach a reasonably "secure" job position in this field is too steep, and I want certainties at this point in my life.

Again, I kind of like feel this is a defeat for me; but reading that so many people are sharing my very same concerns, is making me more convinced that I'm making the right choice.

Lenny TeytelmanMarch 4, 2014 at 11:19 AM

[By Chris Edwards]
You mention your love of teaching. When I was an undergrad, I was
pretty shocked by how put off my professors were by being forced to
teach. Seemed they couldn't get back to their research agenda fast
enough. That was interesting to me because I entertained the idea of
an academic career just so I could become a teaching professor. But
the world did a lot of changing and one day I had a realization - you
do not need a PhD to be a professor. If you truly love teaching, there
is only one excuse today to not do it and that is being terrible at
it. Sure, you can't strut in front of a class of undergrads who are
forced to pay the rent seeking guardians of "approved" knowledge, but
that model is collapsing fast. You can give lectures, write papers and
text books, help people who really want to learn, etc. all without any
humiliation from university politics, journal publishers, and funding
agencies. It's called the Internet. If you've got something valuable
to share, don't lament that the rotten university is keeping you from
sharing it; just do it. Putting education on the internet is really
showing a commitment to teaching and sharing. The precedent for this
is free software. Though its enormous contribution to civilization has
yet to be fully appreciated outside of the weird people involved, it
demonstrates another area that the old gatekeepers are still taxing
the gates while the walls fall away. As a bonus, this approach allows
crackpots to give it a shot (oh noes! say the horrified academics).
And with the crackpots will be the truly brilliant people with really
revolutionary ideas that would never have had a shot at academic life
by today's rules.

As an aside, my job (paying about 1/3 to 1/2 of industry) is providing
tech support to a pharmacology lab. Grovelling for funding and playing
games for "impact" is pretty much 90% of the mission.

Good luck to you!

Joshua NicholsonMarch 4, 2014 at 11:52 AM

This is a great post and so many great comments following it! Thanks for sparking a discussion. I am currently a 5th year PhD student at Virginia Tech in Cell Bio. I am scheduled to finish sometime in the late summer/early fall (+/- 5 years jk!)) so figuring out what I'll do next has been on my mind a lot.

My PI expects me to go on to do a postdoc, however as Michael Eisen so eloquently put it "it is a terrible time to be a scientist" and I realize this and simply don't think it is the life for me. Accepting this I have put on applications to different programs what my other aspirations are and instead of encouraging different paths my PI "corrected" MY "future goals" to doing a postdoc! Of course, I accepted the change and just moved on even though I disagreed. So it is not easy to openly express the desire to do something else.

Indeed, I consider myself quite successful having won numerous awards during grad school and having 10+ pubs but in the end think playing the lottery with my life in academia is just not worth it! Like you, I have started to pursue something independent yet very much related.

I successfully raised enough capital to start The Winnower (thewinnower.com), a science journal that hopes to fix many of the problems with peer review and access. It launches in a few weeks and I could not be more excited. I am rewarded by academic scientists for presenting the "best poster" or talk for 15 minutes but raising enough money to start an entire business that aims to HELP science is left completely without praise.

Anyways goodluck to you and ZappyLab and goodluck to the rest of our bunch!

HaroldMarch 4, 2014 at 6:51 PM

Hey Lenny,

This post definitely struck a chord for me. I went in to a PhD a few years ago hell bent on doing research that would, with luck, leave the world a better place, without much concern about financial compensation and, to be honest, without doing much, if any actual research into the realities or even possibilities of a career in academia.

As time went by though it became increasinly clear. or perhaps more accurately, dificult to avoid the reality of what lay before me. One of my Asociate Supervisor asked me how long I planned to stay in the research game - noting that it really wasnt much of a career and that in his case he was mostly supported by his wifes career choices. This was quite a shock to me at thee time because the only answer i had at the time was "forever". Another Supervisor left right at the end of my thesis to pursue something in the private sector, giving me a good rundown on everything he felt was broken about the current system. By this time i had seen enough dysfunction in my own rather pitiful attempts at adding to the sum total of human knowledge and most of the idealism I had was burned away.

Anwyay at any rate by the end of that PhD I found myself at a crossroad - whether to plunge forward with what looked like an increasingly not so great option that i had plowed years of my life into pursuing or to try and break out into something else where my qualifications might be more than a little rusty. Both seemed scary. I made the choice to try and switch back to my undergrad love of software development though. While it took longer than i woud have hoped to tun myself into an employable 2014 model developer i can say now that it was absolutely the right choice and for the most part i'm really happy in what i do.

At the same time i've seen a friend who stayed in acaedmia, who seemed best positioned of all of us to have a good career get treated abominably by her University, former Supervisor and colleagues in Research. A crazy smart person who bore the brunt of others gross incomeptence (the portion of the research grant that efectively compromised her salary was farcically spent on completely useless equipment), and was treated with all the professsional respect typically afforded to a 15 year old kid working at McDonalds.

Anwyay, long story short - life can be better out there. Its sad because i thikn the kind of basic, nuts and bolts research that can only really be done at Universtities is vital to society but theres no reason to put yourself through this kind of thing. Life is short and theres a lot of personally and socially rewarding things you can achieve in another arena.

All the best.

UnknownMarch 5, 2014 at 12:11 PM

Hi Lenny,

Thanks for your post and for being so open and honest about your experiences. I made the decision to leave bench research after my Ph.D., when I was offered a great job opportunity by my graduate advisor. I won't go into all the reasons behind this decision but many are similar to what others have already expressed in the comments. This decision was also made despite having excellent publications from graduate school, so I do not view this decision as a second choice or because I didn't "think I could make it". However, I do know that others view my decision this way, which is a frustrating perception, but just highlights how attitudes about other career options have got to change.

I wanted to bring everyone's attention to a live Q&A with Keith Yamamoto that is happening tomorrow on Google Hangouts on Air. He'll be answering questions from the audience about ways to change graduate education to give trainees more opportunities to explore other career options than academia. This might be a good forum to bring up some of the points about changing faculty perceptions and creating opportunities within institutions about non-academic-bench-research careers.

The Q&A can be joined here: https://plus.google.com/events/cn3j3lsgl6os7e7e0ch5n3sjvjc

khismetMarch 5, 2014 at 12:27 PM

I always knew I could be happy doing many different things, but got on the academia train, fell in love, and thought I'd follow it all the way...at least through a PhD. But I had such a horrible experience getting my M.S. that considering doing it all again for 3x as long was inconceivable. I tried to stick with it and interviewed and was accepted to my DREAM PhD (well-funded, multidisciplinary, cutting-edge, prestigious), but the spark and desire was just gone and I couldn't commit to 6ish years and a cross-country move to do something I wasn't sure about. I had fallen out of love. My M.S. story is all too common among grad students at both master's and doctoral levels: My adviser was essentially absent, funding I had been promised by my adviser was withdrawn, obtaining external funding was near impossible, I worked two jobs (TA and lab manager) in addition to my classes and research and was paid paltry sums, I was hard-pressed to find support from anyone especially my adviser. Now I have a lot of anger toward my adviser, but I also recognize it is as much the system at fault as it is him. He's expected to work ten or so jobs (prof, author, grant-writer, adviser, scientist, co-adviser, academic fellow, etc., etc.........father, husband) for paltry sums and with little support (or even training in the case of teaching). It was the realization that it was not parts of or people in the system that were broken but the system itself that led me to seek ex-academic opportunities. If the whole system is so broken that it commonly fosters the kinds of miserable experiences that friends, those here, and I experienced, it is not a system I want to be a part of for life.

As many young people do, I didn't place much value on pay, job security, place of residency, etc. because I thought if I really loved the job none of that would matter. The truth is ignoring the necessity of these aspects of a job is simply ignoring reality, results in exploitation, and sets people up to fail.

pdsMarch 5, 2014 at 2:28 PM

Here is my perspective as a tenured prof at an Ivy with 2 NIH grants funded, and my own lab for 20 years:

So many other people I’ve met along the way were smarter, harder workers, and had better hands than I. I don’t think that I have any more talent than the average scientist who provided comments here, and I don’t think I could land the job I have now in today’s competitive climate. The competition is very tough at every level, and I still worry about the next grant cycle. I’ve been very lucky.

My choice of career path was a deeply personal one, and I’m grateful and amazed that things worked out for me. Along the way, there were lots of times when projects went nowhere, frustrations swelled and I considered directions that would have taken me away from science. While I was a post doc, I volunteered tutoring remedial math to test the waters as a high school teacher; then my project began to work.

Some of my students and post docs became professors, but I never judged those who made the choice to leave academia or science. I would no sooner criticize their decisions about who to date or marry – the choices are equally personal. My job as a mentor is to be as supportive as I can to help trainees be successful on the path they choose, where ever it leads.

JenMarch 5, 2014 at 11:20 PM

I left academia almost 3 years ago, after 5 years of Ph.D. work and 6 years as a post-doc at Berkeley. As many have stated above, the system is broken, but how do we fix it? I ended up in a very tangentially related field -- working for an engineering and biomechanics legal consulting firm -- something I was never aware of as a possible career. My boss had the courage and foresight to hire me despite my cell and developmental biology background. I wish we could convince more companies to do the same - that Ph.D.'s may appear to be highly specialized, but they are also extremely bright, trainable, analytical, and hard-working people who have a lot to contribute.

As for my back story - I see it's already listed on your Google doc, but here it is again: http://willblog4food.wordpress.com/2011/06/26/once-a-scientist-always-a-scientist/

Good luck with your startup!

Mike BarnettMarch 7, 2014 at 3:07 PM

Best of luck. I left astrophysics a while ago but not a professor of science education and having a wonderful time where I get to teach and engage kids in learning science skills.

I do wonder about two things, since I spend a lot of my time in policy now. First, there was a massive boost in NIH funding from the late 90s to the early 2000s, till about 2003 the NIH budget was way above the expected rate of increase. This lead to a massive increase in the number of faculty positions and graduate students. It was something like a 150% increase in the number of graduate students. This was just unsustainable and it feels like the housing bubble... it will just keep going...

Now we are on a downward trend... seems like there was a bubble as many of those students and faculty are looking for funding and jobs... so now we have this bust in funding after a massive boost... Now we have more people going after funding and with decreases in funding (though not as much as the increases during that 8 year window).

I rarely see discussions of this on most blogs like this. I would love to hear some thoughts

Brad GulkoMarch 7, 2014 at 5:36 PM

As I understand it, a key issue is not so much the modest decline in funding, from sources like the NIH but researcher demography. As senior researchers opt not to retire, and instead extend their careers into (and past) their 80's, they retain the bulk of the funding as most experienced (thus judged most qualified according to grant scoring criteria).

A recent speaker from the NIH showed statistics on PI age and funding rates indicating that the number of absolute dollars has only declined modestly since 2008. However, due to the indicated increase in older PI’s, the pool of funds practically available to researchers just past their "young investigator" phase would have to drop dramatically.

This effect should diminish over the next 20 years or so as mortality ultimately removes older researchers from the pool of applicants, but may also cost us generation of young investigators that are likely seek employment elsewhere. I provide this without any sense of malice or injustice; it’s just how the numbers work out.

William RayMarch 8, 2014 at 6:59 PM

In almost all ways, I'm in complete agreement with your synopsis of the current situation and its alarming portents. It's been crystal clear to everyone, except seemingly the funding agencies and the institutions that expect the NIH and NSF to be bottomless cash cows, that we were heading for a serious crisis for at least the last 10 years.

The only significant insight I'd offer, that I don't think I've seen mentioned in other posts, is that the current world is even more terrifying for those of use who made it into junior faculty positions just as the magnitude of the crisis became fully apparent. For a postdoc to leave academia is sad, but, while there might be a bit of a social stigma attached by the still-in-academia peer group, leaving academia after doing a stint as a postdoc, isn't "failure", it's a decision. A junior faculty member who fails to get tenure for lack of funding - even if they're scoring far better on their unfunded grant proposals than the tenured faculty who are voting them out ever did on their funded ones - has just failed their final exam. Leaving isn't a decision, it's a dismissal, and it's a far larger black mark in terms of future employability in the field.

So - if you're a postdoc, be smart. Look at today's funding and tenure climate, and run like hell.

Or, if you're the stubborn type, take the faculty position, find out whether you're as good as you think you are, and even if you don't get tenure, force the people who are responsible for this mess to look you in the eye and accept their culpability as they show you out the door. I can't for a moment fault you for running while you can, but, the institutional establishment is never going to accept responsibility and change the culture, if we all let them off the hook by leaving of our own volition.

Me, they're going to have to drag out the door kicking and screaming.

GarciApril 24, 2014 at 12:46 AM

I am 43 now and just took your same decision last year...It has been rewarding, even having been one year on my own "sabbatical" terms (no salary, plenty of new stimulating inputs in science and culture..as a European I moved to yet another new country). I have recently started to work on an International Organization. Higher salary, not so new exciting research, but on the other hand I feel my work finally has a purpose that people recognise...and the level of stress is way reduced (even if my colleagues think they are very stressed...but then again..they haven't spent their previous 15 years trying to build a path towards academia!)

So welcome to NON-Academia..Í think you won't regret it!

ScottApril 28, 2014 at 7:12 AM

I agree that academia has its flaws. The funding situation is dire, tenure is tenuous, and 70-80 hours per week at work can put a stress on personal wants and desires. Even the hiring process is incredibly slanted and difficult to predict. That said, it reads to me like Lenny wasn't 100% sold on the academic life. He laments about moving to new cities to pursue his profession. He had started a side business, presumably during his post doc. I also chuckled at the thought that... "work should be something one desires to come back to after a weekend." That is assuming one was able to get one's head outside of work in the first place. Finding a work / life balance is important, but different quotients are required for different paths. Those people who are on the 'academic track' or who are already in faculty positions know this, and make the sacrifices to make it work.

Joanna BlueberryJanuary 9, 2015 at 1:33 AM

It is sad. I love science, enjoyed my M.Sc., my Ph.D. and first fellow but now I struggle to find a job in academia. I've published and evolved but still it seems that if I don't have connections there is no way of getting a postdoc. I don't want to use connections, I want to be judge by my own achievements. I've always believed in science being 'the pure field' of work, where the fairness and accomplishments are rewarded. The truth is that if you are not one of the sharks then most probably you will forever be just another cheap tool in their hands. If you are a woman, that's even worse. Unless you like being called the B word by everyone around. I still love science and can't think of anything else I could do instead. Becoming a monk maybe.

20

一个MIT的博士要离开学术圈,结果引发了上千人的热烈讨论(中)

的确是上千人进行讨论,我这里分两次翻译网友们的讨论结果:

Lenny TeytelmanFebruary 15, 2014 at 7:53 AM

The reason I did not want to publish this - a single voice is invariably dismissed. So, I want to assemble in a central place as many essays like this from students, postdocs, and professors. The funding crisis will not be addressed until the severity of it is acknowledged and NIH, politicians, and scientists are alarmed enough. Please e-mail me your stories to lenny at zappylab dot com (whether new or published elsewhere). I will put together a site aggregating all of them.

以前我不发表这个观点的原因是-势单力孤。所以我希望等到足够多的类似的观点由不同的学生,博士后,甚至教授提出来之后,把它们整合在一起。学术圈的资金危机很难解决,除非NIH本身意识到问题的严重性,而且最好是政客,科学家们也对此有着足够的警醒。所以请把你的经历发邮件给我,不管你以前是否也在其它什么场合抱怨过,我将对他们做一个汇总,统一发表出来。

BioluminessaFebruary 17, 2014 at 10:55 AM

Hi Lenny. Thank you for sharing your perspective! Here is another to add to your collection of essays. I wrote this piece the other day coming to similar conclusions. http://bioluminate.blogspot.com/2014/02/the-seven-stages-of-grief-for-academic.html

谢谢你分享你的观点,这里有个故事可能比较符合你的要求。

sheiselsewhereFebruary 25, 2014 at 11:54 AM

I often get told that I shouldn't be so negative and that things will get better. Unfortunately, I don't have the time to wait. Here is my contribution.

http://sheiselsewhere.mosdave.com/2014/02/16/singing-for-supper/

长久以来,人们就告诉我我不应该如此的悲观,一切都会好起来的。不幸的是,我已经没有足够的时间去等待事情好转了。下面是我的经历。

Dregev21February 28, 2014 at 2:13 PM

Wow, thank you for posting this! I have gone through a very similar situation and have also decided to quit pursuing this dream. I was a 4th year PhD student at the University of Florida (where I had already had to change labs since my first mentor moved to UAB) and my project was going nowhere fast. I also started seeing academia for what it has become; an industry of cheap labor and false hopes. But like you, I stayed in it for as long as I could because of my love for science, learning and teaching. I quit and got out with a MS degree this past November and I am very happy with my decision. I began working as a research coordinator at UF, making more money and like you felt liberated and free from the constant stress of graduate work and research. I believe most students come in to graduate scholl for the same reasons, but it has become so disheartening and scary, that it didn't seem worth it to me anymore. I think it is important for current students to know and understand that there are other things to do in life that are more fruitfull, less stressful and just as intelectually stimulating and rewarding. In any case, thank you for sharing!

哇,谢谢你的分享!我有着同样的经历,也准备放弃一直追寻的梦想了。我是佛罗里达大学的一名在读博士生,这是我博士生涯的第四年,而博士期间,我已经换过一次导师了,因为我的前导师去了UAB,所以我的博士课题也换了。就我的经历来看,我也认为学生圈现在充斥着廉价劳动力和虚假的期望。然而就像你一样,凭着对科学的一腔热血,我坚持了很长时间。直到去年十一月,我辍学了,就拿到了一个硕士学位,并且我非常开心我做了这样的决定。我的第一份工作是在UF做一个研究协调员,可以挣很多钱了,也终于从无止境的毕业研究课题压力中解放出来了,跟你一样的自由了。我觉得是时候让现在的学生知道在我们的生命中还有这非常多的更有意义,会收获更大,但却压力更小的事情可以做。

Travels with Moby March 1, 2014 at 12:58 PM

Good Luck to you. I made this choice for many similar reasons about 6 years ago. But I was a college professor at a small college. You have aptly described the scenario. Even without the added stress of the grant machine, the choices that we are forces to make that divorce ourselves from family, friends to pursue this academic dream are incredibly costly. What I did find after a year in industry, is that I was not alone, I met former academics in industry and elsewhere that have expressed the same concerns. I wish you the best, and you are not alone.

祝你好运!我也做了同样的决定,在六年前。但是我曾经是一个小学院的一名教授。你非常精准的描述了我们这样的教授的状态。即使没有基金方面的压力,我们这样的选择也使得我们无法兼顾家庭,朋友。追求学术的道理牺牲真的好大。当我离开学术圈,进入产业界的第一年,我终于不再觉得孤单了,我遇到以前学术圈的好友的时候也听到过他们有着类似的抱怨。不管怎么样,还是希望你能好好的,毕竟,我们都不孤单。

Kevin ZelnioMarch 3, 2014 at 8:51 AM

Good luck! Life is better outside academia lol. I left 2 phds (got my masters after first one) and a decade long research career with 12 and then a 5+ year science communication career, left the country and started a microbrewery in Sweden. My skills as a scientist have been instrumental in my new profession as a beer maker (serious lab and sanitation skills here!) and a business person (improved and more diverse funding sources! AKA investors and people who drink BEER - which is like everybody). I cried a lot, I won't lie. Almost wrecked my marriage and the stress turned me into a horrible father for a while. Its just not a sustainable career for some types of people. Which is a shame, because the career is selecting for the same type of people and missing out on a diversity of life styles which could most likely benefit the scientific community in a number of ways. Here was my story: http://deepseanews.com/2013/02/19294/

祝你好运!学术圈外面的世界更精彩,O(∩_∩)O哈哈哈~我有着长达12年的科学研究经历和多于5年的科学普及经历,终于离开了我的祖国,来到了瑞典开始酿酒。在我还是科学家的时候掌握的各种技能对我现在作为一个啤酒酿造师还是蛮有帮助的,尤其是严肃认真的实验习惯以及无菌操作技巧。那时候申请各种稀奇古怪的基金所锻炼出来的沟通技巧也特别适合自己现在转行做商人。我曾经为这样的转变哭泣过,我承认。这几乎摧毁了我的婚姻生活,也在一段时间让我变成了一个糟糕的父亲。对某些人来说,这样的职业不是一辈子的事情,而且是某种意义上的丢脸。以下是我的故事。

UnknownMarch 3, 2014 at 2:10 PM

I don't see why I should view your departure as
a bad sign for the life sciences. As an engineer,
we celebrate when our students graduate, go
start a company or join an existing one, and
create products that make the world a better
place. Or, go work at a national laboratory,
the FCC, a non-profit, or any of the other types of
jobs where engineers make a contribution.

我不认为,应该把你的离开看作是科学界的损失。作为工程师,我们欢迎毕业了的同学开公司或者加入已有的公司,去创造一些让人们生活更美好的产品。或者,干脆去国家实验室工作,或者FCC也行,一个非盈利组织,或者可以参加很多其它类似的,对工程师有需求的工作

Lenny TeytelmanMarch 3, 2014 at 2:26 PM

First of all, it is terrific that you are supportive of graduate students who go on to be productive outside of academia! Unfortunately, in life sciences, you often lose support of your mentor the second you say that you do not plan to be a tenure track professor.
Second, and most importantly - the reason our departures and anxieties are cause for concern - being a professor, in the current funding climate, requires a level of sacrifice for science that fewer and fewer of the most talented and brightest scientists will make. Our taxpayers spend an extraordinary amount funding research. If the best scientists leave academia, research will suffer. Training of the future scientists will suffer. Science, inside and outside of academia will suffer.

首先,像你这样的毕业生,走出学术圈之后还能创造如此多的产品,必然是非常了不起的。不幸的是,在生命科学领域,你经常就会失去你导师的资助,就像你博文里面提到的第二点那样,你也不打算去争取一个终身教职了。

其次,最重要的是我们的离开仅仅是因为焦虑,在如今的基金资助条件下,成为一个教授,需要一定程度的牺牲,只有极少数的非常聪明,非常有才智的科学家能做到了。我们的纳税人还是投入了大笔资金在科学研究的,如果大量的优秀科学家都离开了学术圈,那谈何学术成果呢。一个科学家的训练是需要耗费大量时间和金钱的,他们都将因此受损,同时,不管是学术圈里面还是外面都会蒙受巨大的损失。

gregMarch 3, 2014 at 3:07 PM

Your story collection is a great idea. I hope you'll keep the sources of the site open? I bet a lot of people would like to contribute to making that project stand out - I would certainly be helping out.

Thanks a ton for your blog post. Your last point about leaving your wife if she'd treated you as badly as science does is awesome. I'm just coming to the realization that you seem to already have: the notion that "If you can see yourself possibly loving any profession as much as you love science, you're not cut out for science" is unhealthy - it's a mark of the sort of brainwashing that academia does to you.

Best wishes on your future path.

你这个想把所有类似的学术圈失意的故事收集起来的想法很棒。我希望你能持续收集,并且保持开放。我也确信会有非常多的人参与进来贡献他们的故事,让这个计划传播开来。我也会尽我的努力去推动它。

能看到你这个博文真的是三生有幸。你最后那句话(如果你妻子对你像科学对你那样你肯定把她给甩了)简直是太精彩了。我也开始有着你曾经有过的想法了,如果你对追求科学还抱有疑问,是因为你的爱不够坚定,这样的想法是不对的,这只是学术圈对你的洗脑。

Jessica WilsonMarch 6, 2014 at 11:43 AM

This is fantastic writing, despite the sadness. I sympathize (finishing PhD in neuroscience, considering heading out).

I'd love to try and make a video with some of the stories you've accumulated. I'm already looking through that Google Doc you posted right now, and my heart is breaking.

文章写的真棒,尽管让人感到莫名的悲伤和失望。作为一个刚刚结束了神经科学学习课程的博士生,我深有同感。

我很乐意为你收集的这些故事拍一个video,我也看完了你在google doc里面所表达的观点,实在是太震撼了。

CBMarch 12, 2014 at 6:09 PM

Really great stuff. I have reread this post a dozen times over the past couple weeks, as I am a postdoc currently on the precipice of throwing in the towel on my academic career. I find the last sentence particularly meaningful. I can't shake the feeling that giving up on this career that I have been laser-focused on for ten years feels an awful lot like a traumatic breakup. But the simple truth is exactly as you described, academic science simply doesn't respect its professionals nearly enough for the best of us to stick around.

Ugh, breakups suck!

 

Michael RuddyMarch 14, 2014 at 1:55 PM

How appropriate for a Valentine post ... if you do not love everything about what you are doing – move on until you find it!

O(∩_∩)O哈哈~在情人节发表这样的观点实在是太适合不过了。如果你实在是不喜欢你正在做的事情,果断的放弃,持续寻找直到找到你所爱的。

Nick EffordFebruary 15, 2014 at 8:53 AM

I sympathise and wish you a successful and fulfilling future, wherever that takes you. The pressures in UK academia are much the same, as is the relatively low pay. We've seen our pay fall 13% taking into account inflation over the last 5 or 6 years, and universities refuse to offer a decent pay increase despite increasing their income from students and despite the fact that they are sitting on huge cash reserves. My own institution would rather spend £50 million on new buildings than reward its staff for their dedication.

Like you and countless others, I'm reluctant to leave a job that can be very exciting and stimulating. But the truth is that the stress levels make it increasingly unsustainable. There is constant pressure to write papers and secure research funding and simultaneous pressure to improve teaching quality, but there is a failure to recognise that time is a finite resource, so one activity must inevitably be traded off against the other.

I don't expect to receive the same remuneration as I would in industry, but I do need one of two things to happen: either working conditions need to improve or the pay needs to improve to reflect the real pressures of the job. I've sacrificed too many evenings and weekends over the years, and that has had a negative impact on personal physical and mental health as well as family relationships. If something doesn't give soon, I could well end up following you out of academia.

The trade union for academics in the UK is currently locked in a bitter pay dispute with the universities. You can find out more about it at http://fairpay.web.ucu.org.uk/

Good luck!

Nick

我也深有同感,也期望你有个成功而且精彩的未来,不管你走向哪个领域。英国的学术圈压力也很类似,因为相对来说基金资助量都很小。在过去的5到6年间,我们的资金总量,考虑到通货膨胀,反而缩减了13%,大学却拒绝对研究基金做一个比较像样的提高,尽管他们向学生收取的学费更多了,而且他们的现金流也非常健康。我所在的研究所情愿花五千万欧元区修建一个大楼,也不会去奖励那些辛辛苦苦奉献着的教职工。

像你以及无数的其他类似经历的人一样,我也不情愿离开这个即兴奋又刺激的研究工作。但是压力的与日俱增让我的研究工作越来越难以为继。我们既要保证发表足够的文章,还要争取研究基金的支持,同时还要提高我们的教学质量,但是我们不得不承认,一个人的时间是有限的,所以我们必然会在有些方面做得不够。

我不期望能得到与工业界相当的报酬,我仅仅是期望我们的工作条件能得到改善,并且我们的报酬水平应该能对得住我们实际上所承受的工作压力。长年以来,我已经付出了无数个夜晚和周末,而这对我个人的身心健康是一个很大的影响,同时也极大的影响了我的家庭关系。如果这一切不尽快改善的话,我想,我应该马上就会追寻你的脚步,离开这学术圈了。

16

最全面的转录组研究软件收集

能看到这个网站真的是一个意外,现在看来,还是外国人比较认真呀, 这份软件清单,能看出作者的确是花了大力气的,满满的都是诚意。from: https://en.wiki2.org/wiki/List_of_RNA-Seq_bioinformatics_tools
https://en.wiki2.org/wiki/List_of_RNA-Seq_bioinformatics_tools软件主要涵盖了转录组分析的以下18个方向,看我我才明白自己的水平的确没到家,印象中的转录组分析也就是差异表达,然后注释以下,最多分析一下融合基因,要不然就看看那些miRNA,和lncRNA咯,没想到里面的学问也大着呢,怪不得生物是一个大坑,来再多的学者也不怕,咱有的是研究方向给你。

    1 Quality control and pre-processing data
        1.1 Quality control and filtering data
        1.2 Detection of chimeric reads
        1.3 Errors Correction
        1.4 Pre-processing data
    2 Alignment Tools
        2.1 Short (Unspliced) aligners
        2.2 Spliced aligners
            2.2.1 Aligners based on known splice junctions (annotation-guided aligners)
            2.2.2 De novo Splice Aligners
                2.2.2.1 De novo Splice Aligners that also use annotation optionally
                2.2.2.2 Other Spliced Aligners
    3 Normalization, Quantitative analysis and Differential Expression
        3.1 Multi-tool solutions
    4 Workbench (analysis pipeline / integrated solutions)
        4.1 Commercial Solutions
        4.2 Open (free) Source Solutions
    5 Alternative Splicing Analysis
        5.1 General Tools
        5.2 Intron Retention Analysis
    6 Bias Correction
    7 Fusion genes/chimeras/translocation finders/structural variations
    8 Copy Number Variation identification
    9 RNA-Seq simulators
    10 Transcriptome assemblers
        10.1 Genome-Guided assemblers
        10.2 Genome-Independent (de novo) assemblers
            10.2.1 Assembly evaluation tools
    11 Co-expression networks
    12 miRNA prediction
    13 Visualization tools
    14 Functional, Network & Pathway Analysis Tools
    15 Further annotation tools for RNA-Seq data
    16 RNA-Seq Databases
    17 Webinars and Presentations
    18 References