Last week I attend to the CSH Asia 2012 conference:High Throughput Biology- Genomics & Epigenomics.

This is the first time I go to a such big conference. I also apply to be a volunteer.

On the five days conference, I saw many core-people of this field, such as BingRen, Lucy Shapiro, Sunny Xie , and a lot of young scientists. they are creative and passionate people. What I learned from them are keep thinking, keep asking, keep working.

On next diary I will show you some interesting works on the conference.

I think creating github pages are not difficult, however when I realized that gp-pages are not a single branch it may belongs to a master branch. Problems are revealing.

I didn’t know how to create a Project Pages on a new folder. The following manual you may found on github.com. It said that, you may want to remove all files from the old working tree. But when you use the command, all file on your disk folder will be deleted ;(.

git rm -rf . # Remove all files from the old working tree

So please pay attention to the command if you have many files which didn’t want to be deleted.

####How to create a gh-pages without a master branch?#### This page will help you. Remember, using

git push origin :master

And using git push origin --delete gh-pages you can delete the gh-pages branch.

Today, I started the new blog on Github. All pages transferred from html to markdown.

This is a new start of my blog.

I use some css from the other’s blog. The most helpful jekyll blog are yihui.name, pingmygeek.com, huangzhimin.com and freemind.pluskid.org.

I use a label and a <q> tag from freemind.pluskid.org,

Because some pages will write using \(\LaTeX\) (I don’t know why the five letters are too close one to another ), I change the Markdown processor from rdiscount to kramdown.

When using Mathjax, I should avoid highlight.css mixing between Mathjax and Pygments

pygmentize -S friendly -f html | sed 's/^/.highlight code /g' > assets/css/highlight.css

0000 – Install an Linux system on your computer.

0001 – Follow the 10000 things all ICS students should do before graduating

0010 – Learn Cell, Molecular Biology, Genomic, Genetics by yourself.

0011 – Learn Computational mathematics, Applied mathematics and Statistics.

0100 – Try create a bioinformatics tool. Belief in your ability.

When I read DRACO paper, my adviser ask me the question (on the title).

My primitive idea is the following text. (2011.08)

On the beginning, I also send a letter to Dr. Rider, but I didn’t receive his reply T_T (2011.08.21)

This question can be divided into two parts: one is why viruses produce long dsRNAs, the other is why endogenous dsRNAs are short.

In August,I guess endogenous long dsRNA is unstable in cells.Dicer can cleaves endogenous dsRNAs to produce siRNA. Long endogenous dsRNAs can induce complete Gene silencing in mammalian cells and primary cultures. So endogenous dsRNA are shorter than exogenous dsRNA.

But, there are some questions on my guess.

What RNA belong to dsRNA?

As we know, mircoRNA is not siRNA, though it as little as siRNA. So, what RNA is dsRNA? tRNA and rRNA has some hairpin structure (cloverleaf structure). Does this structure is double strand structure? All RNA viruses must produce at least a transient dsRNA intermediate. In replicating + or - RNA, you have to produce the opposite sense RNA, thus forming a dsRNA molecule. tRNA has only one strand, and the hairpin structure isn’t made of double strands.

I think dsRNA must made of two strands perfectly complementary, the secondary structure isn’t reflect strand type.

On the molecular biology class, I learn mircoRNA is single strand. (2011.10.14)

Why endogenous dsRNAs are short?

In the DRACO paper, it said that uninfected mammalian cells don’t produce long dsRNA. Information generally transfer from DNA to RNA (central dogma). RNA can not replication in human cells.So endogenous dsRNAs are not existence in human cells.

Why viruses produce long dsRNAs but not short ones?

RNA viruses’ genetic information are all in the RNA, so it longer.

However, I think I have misunderstanding the question. (2011.10.09)

Why viruses produce dsRNAs?

Positive-strand RNA, dsRNA, or DNA viruses produce dsRNA.

RNA polymerase synthesizes an RNA strand complementary to the genome. This produces a dsRNA. RNA can not replication in human cells.So endogenous dsRNAs are not existence in human cells.

Negative-strand RNA viruses doesn’t produce dsRNA. (Double-Stranded RNA Is Produced by Positive-Strand RNA Viruses and DNA Viruses but Not in Detectable Amounts by Negative-Strand RNA Viruses)