7d Hologram

3 dimensional position or space
+ 2 dimensional angle
+ light perception (depth and intensity)
+ Time


Elysia chlorotica

1. A draft genome assembly of the solar-powered sea slug Elysia chlorotica. 2019.2.19 scientific data

2. Genome Analysis of Elysia chlorotica Egg DNA Provides No Evidence for Horizontal Gene Transfer into the Germ Line of This Kleptoplastic Mollusc. 2013.8 molecular biology and evolution




windows 网络配置



1. netsh winsock reset:【原理待续】

2. 网络连接:重置网络:【原理待续】


R_LANG on MS Windows

1. Suits: R, RTools & Rstudio

2. environment variables:
Modify the variable  BINPREF in the file “/R-3.6.0/etc/x64/Makeconf” to “/path/to/Rtools/mingw_64/bin/” to solve a compiling error.

3. configure R environment:~/.Rprofile, R/R-x.x.x/etc/Rprofile.site



将ttf或者otf文件直接复制粘贴到文件夹:C:\Windows\Fonts,系统就会自动安装该字体。然后打开word或者adobe acrobat pro等软件就可以看到新的字体了。

2. 修改字体的名称

  • 使用font creator软件打开字体,然后点击“Font->Properties”;
  • 软件里面显示的字体名称:在identification标签页里面修改“font family”“Full font name”;
  • Font文件夹处的显示:在extended标签页里面修改“typographical family”“typographic subfamily”;



-u: 最大进程数

-n: 最大文件句柄数目

2.soft limit vs hard limit

ulimit -S -a view all soft limits

ulimit -H -a view all hard limits




gcc compile options


LD_LIBRARY_PATH=”/path/to/lib”: 寻找.so文件,对应于-lz等(小写的L)
C_INCLUDE_PATH=”-I/path/to/include”: 寻找.h文件,对应于代码中的#include<>


-L: 给定动态链接库的路径,给到.so文件所在的文件夹
-l(L的小写): 表示本次编译所需要的动态链接库
-Werror: 视警告为错误;出现任何警告即放弃编译.
-Wl,-rpath: 向ld传递-rpath参数,add a direcory to the runtime library search path. This is used when linking an ELF executable with shared objects. All -rpath arguments are concatenated and passed to the runtime linker, which uses them to locate shared objects at runtime.

python 单元测试



A testcase is created by subclassing unittest.TestCase. The three individual tests are defined with methods whose names start with the letters test. This naming convention informs the test runner about which methods represent tests.

The crux of each test is a call to assertEqual() to check for an expected result; assertTrue() or assertFalse() to verify a condition; or assertRaises() to verify that a specific exception gets raised. These methods are used instead of the assert statement so the test runner can accumulate all test results and produce a report.

The setUp() and tearDown() methods allow you to define instructions that will be executed before and after each test method. They are covered in more detail in the section Organizing test code.

The final block shows a simple way to run the tests. unittest.main() provides a command-line interface to the test script. When run from the command line, the above script produces an output that looks like this:

PCA – 数据降维


新数据,2维:(5,0), (10,0)

最终简化为一维:5, 10



related posts:

1. http://www.iro.umontreal.ca/~pift6080/H09/documents/papers/pca_tutorial.pdf

2. https://stats.stackexchange.com/questions/90331/step-by-step-implementation-of-pca-in-r-using-lindsay-smiths-tutorial

3. http://www.cnblogs.com/pangxiaodong/archive/2011/10/15/2212786.html



Good place

1.Stanford Medical School:斯坦福医学院

(http://med.stanford.edu/: logo encrypted)

2.harvard medical school: 哈佛医学院

Purcell lab: in Department of Psychiatry at Brigham & Women’s Hospital, an affiliate of Harvard Medical School.(plink)

3.Division of Statistical Genetics, Department of Human Genetics, University of Pittsburgh: 匹兹堡大学,人类遗传学院,统计遗传所

4.ecole polytechnique federale de lausanne: 洛桑联邦理工学院

5.Stowers Institute for Medical Research: 斯托瓦斯医学研究所


eigensoft 7.2.1



3.smartpca 结果

eigenvector1 eigenvector2
eigenvalue 9 0
YC1.YC_snp -0.3162 -0.3162
YC2.YC_snp -0.3162 -0.3162
YC3.YC_snp -0.3162 -0.3162
YC4.YC_snp -0.3162 -0.3162
YC5.YC_snp -0.3162 -0.3162
ZC1.ZC_snp 0.3162 0.3162
ZC2.ZC_snp 0.3162 0.3162
ZC3.ZC_snp 0.3162 0.3162
ZC4.ZC_snp 0.3162 0.3162
ZC5.ZC_snp 0.3162 0.3162


PCA summary


1. 使用的population scale SNPs





2014 – Whole-genome sequencing of Berkshire (European native pig) provides insights into its origin and domestication

BMC genomics – 2017 – Oreochromis niloticus (Nile Tilapia) – sex determination regions

Sex determination regions

The new O_niloticus_UMD1 assembly was used to study sequence differentiation across two sex-determining regions in tilapias. The first region is an XX/XY sex-determination region on LG1 found in many strains of til-apia [9, 34, 44–47]. We previously characterized this region by whole genome Illumina re-sequencing of pooled DNA from males and females [48]. We realigned these sequences to the new O_niloticus_UMD1 assembly and searched for variants that were fixed in the XX female pool and poly-morphic in the XY male pool. Figure 4 shows the FST and the sex-patterned variant alle le frequencies for the XX/XY O. niloticus comparison across the complete Orenil1.1 and O_niloticus_UMD1 assemblies, while Fig. 5 focuses on the highly differentiated ~9Mbp region on LG1 with a substantial number of sex-patterned variants, indicative of a reduction in recombination in a sex determination region that hasexistedforsometime[48].

The second sex comparison is for an ZZ/WZ sex-determination region on LG3 in a strain of O. aureus [11,49]. This region has not previously been characterized using whole genome sequencing. For this comparison we identified variant alleles fixed in the ZZ male pool and polymorphic in the WZ female pool. Figure 6 shows the FST and the sex-patterned variant allele frequencies for this comparison across the whole O_niloticus_UMD1 assembly, while Fig. 7 focuses on the differentiated region on LG3. O. aureus LG3 contains a large ~50Mbp region of differentiated sex-patterned variants, also indicative of a reduction in recombination in the sex determination region. Figure 6 also shows this differentiation pattern on several other LGs (LG7, LG9, LG14, LG16, LG18, LG22 and LG23). It is possible that these smaller regions of sex-patterned differentiation are actually translocations in O.aureus relative to the O. niloticus genome assembly.