rOpenSci is a collaborative effort to develop R-based tools for facilitating Open Science

At rOpenSci we are creating packages that allow access to data repositories through the R statistical programming environment that is already a familiar part of the workflow of many scientists. We hope that our tools will not only facilitate drawing data into an environment where it can readily be manipulated, but also one in which those analyses and methods can be easily shared, replicated, and extended by other researchers. While all the pieces for connecting researchers with these data sources exist as disparate entities, our efforts will provide a unified framework that will be quickly connect researchers to open data.

http://ropensci.org/

rentrez - search or download data from various NCBI databases.

rentrez provides functions that work with the NCBI eutils to search or download data from various NCBI databases.

The package hasn't been thoroughly tested yet, but the functions for each of the Eutils functions are implimented. If you try the package and find bugs please let me know.

The Best Scientific Figures of 2012

http://www.wired.com/wiredscience/2012/12/science-figures-2012/?pid=5582&viewall=true

Humanity's Recent Evolution

It's easy to think that modern life has slowed human evolution, but the opposite is true. Most of humanity's genetic variation has accumulated in the last few thousand years during a period of extraordinary population growth. As a species, we're more evolvable than ever.

In the figure above, taken from an in-depth genetic analysis of 6,515 people, the amount of genetic variation collectively present at each location in the human genome is tabulated from before (left) and after (right) the population boom.

Citation: “Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants.” By Wenqing Fu, Timothy D. O’Connor, Goo Jun, Hyun Min Kang, Goncalo Abecasis, Suzanne M. Leal, Stacey Gabriel, David Altshuler, Jay Shendure, Deborah A. Nickerson, Michael J. Bamshad, NHLBI Exome Sequencing Project & Joshua M. Akey. Vol. 491, No. 7426, 29 November 2012

Install R and Rstudio in Ubuntu

http://blog.cloud-mes.com/2012/09/16/install-r-and-rstudio-in-ubuntu/

Install R in Ubuntu is extremely easy if you don’t meet any exception, but if you meet, then you’d better be a very advanced linux user :-)

Install R

Because the Ubuntu official source R version is usually half of years older than R-project official source, so it is recommanded to using r-project.org official source to install the latest R system.

vi /etc/apt/sources.list

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# append below line to end of sources.list # you can view mirror at http://cran.r-project.org/mirrors.html deb http://ftp.ctex.org/mirrors/CRAN/bin/linux/ubuntu precise/

import the GPG key and install r-base

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cd ~ gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E084DAB9 gpg -a --export E084DAB9 | sudo apt-key add - apt-get upgrade apt-get install r-base

Install Oracle DB access package

You can found new version of ROracle or DBI package in CRAN, it is also required you properly install the Oracle Instant Client.

manual install the ROracle

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wget http://cran.r-project.org/src/contrib/DBI_0.2-5.tar.gz R CMD INSTALL DBI_0.2-5.tar.gz wget http://cran.r-project.org/src/contrib/ROracle_1.1-5.tar.gz R CMD INSTALL --configure-args='--with-oci-inc=/opt/oracle/instantclient_11_2/sdk/include' ROracle_1.1-5.tar.gz

Install RStudio Server

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apt-get install libssl0.9.8 # must install even you have newer version apt-get install libapparmor1 apparmor-utils wget http://download2.rstudio.org/rstudio-server-0.96.331-i386.deb dpkg -i rstudio-server-0.96.331-i386.deb rstudio-server verify-installation

Do some RStudio Server setting

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echo 'rsession-memory-limit-mb=1000' > /etc/rstudio/rserver.conf echo 'rsession-stack-limit-mb=4' >> /etc/rstudio/rserver.conf echo 'rsession-process-limit=20' >> /etc/rstudio/rserver.conf # Only pass below if you will using proxy mode echo 'www-address=127.0.0.1' >> /etc/rstudio/rserver.conf groupadd rstudio

Setting the proxy server for RStudio server

This section is optional, assured already install nginx in server.

do not forgot link to /opt/nginx/conf/vhosts

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server { listen 80; server_name cvprstudio; location / { proxy_pass http://localhost:8787; proxy_redirect http://localhost:8787/ $scheme://$host/; } }

Setting auto restart and PATH

1 2	ln -s /usr/lib/rstudio-server/extras/init.d/debian/rstudio-server /etc/init.d/rstudio-server vi /etc/init.d/rstudio-server

append below line to /etc/init.d/rstudio-server SCRIPTNAME

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ORACLE_BASE=/opt/oracle ORACLE_HOME=/opt/oracle/instantclient_11_2 TNS_ADMIN=/opt/oracle/network/admin NLS_LANG=AMERICAN_AMERICA.AL32UTF8

Now you can restart/start via standard init.d service way

1	/etc/init.d/rstudio-server restart

Add a user in RStudio

1 2	adduser --ingroup rstudio cindy passwd cindy # setting password

Update package

Usually it is more good to upgrade the r-base in system wide packages instead of per user

really good ideas and guides on fast publication

go there to see the details, http://yihui.name/en/2012/03/a-really-fast-statistics-journal/

Followings are my comments:


Dear Yihui, Very Excellent Ideas and applicable tech guides. I agree well with you, though I am not working in pure stat area, but in Biology. The same issues you pointed out here, occurred also for Biology and for all other academic publishing areas (I guess). We definitely need some improvements in formatting, data/code sharing, and also peer review process.

In BioMed area, f1000research (http://f1000research.com/) has made the first step. "F1000 Research will offer immediate publication; open, post-publication peer review; open revisioning of work including ongoing updates;and encourage raw data deposition and publication. In addition, F1000Research will accept a broad range of article formats and content types." I think F1000research, by its post-publication peer-review rule, would be an ideal one fit your expectation (fast publication). Do you want to express any of your ideas on post-publication peer-review? I have not found them in this blog, though I have felt your passions on that.

应尊重植物学家的研究成果

http://www.cell.com/fulltext/S0092-8674(11)01501-7#bcor2

如何写申请 － 工作和项目

Funding: Got to get a grant

Nature Science Reports - a journal like PLoS from Nature

http://www.nature.com/srep/index.html

匹夫無罪，懷璧其罪

百姓本沒有罪，因身藏璧玉而獲罪。原指財寶能致禍。後亦比喻有才能、有理想而受害。


    “匹夫无罪，怀璧其罪”出自《春秋左传-桓公十年》，原文如下：“初，虞叔有玉，虞公求旃。弗献。既而悔之，曰：‘周谚有之：匹夫无罪，怀璧其罪。吾焉用此，其以贾害也？’乃献之。又求其宝剑。叔曰：‘是无厌也。无厌，将及我。’遂伐虞公。故虞公出奔共池。”

Air Pollution Linked to Heart and Brain Risks

研究表明：空气污染可能导致心脏和大脑疾病

关于生物统计学和统计遗传学的短文

Biostatistics: Revealing analysis

Mathematics in Biology

Mathematics in Biology

这是 Science 的生物数学专辑。8年前曾经给我触动，今天又偶然遇到它。

why we study phenotypic variations

the proteome is closer to the phenotype than the genome or the transcriptome, and as such may be more directly responsive to natural selection, and thus closely linked to adaptation. 


I just cite a sequence here.

a good plant research center - UZH Institute of plant biology

Molecular Plant Biology / Phytopathology
Prof. Beat Keller	Prof. Robert Dudler	PD Christoph Ringli
Plant Developmental Genetics
Prof. Ueli Grossniklaus
Evolutionary Functional Genomics
Prof. Kentaro Shimizu
Molecular Plant Physiology
Prof. Enrico Martinoia	Prof. Felix Keller	Prof. Stefan Hörtensteiner
Limnology and Limnological Station
Prof. Jakob Pernthaler
Microbiology
Prof. Leo Eberl		Dr. Laure Weisskopf
Administration / Library
Administration Library

course material on evolution and genomics

Evolution and Genomics, here collected many different courses on evolution and genomics.

find video of various courses in Khan academy

http://www.khanacademy.org/

I do not agree with him

Cultural history holds back Chinese research

We can not freely choose culture for ourself in China now. Everything has been controlled, especially those of culture. So how do you conclude as this, Peng Gong, a so-called intellectual in China? It is not the right time to think if cultural hold back research. It is the time for us to think how/at what level the communism politic depleted our freedom of ....

Do you know what happened in the period of the Cultural Evolution? We have already no culture for at least tens of years. 

important reference of computational/statistical application in Evo and Eco

These references are mostly recommended by my friend, Jinlong.

1. Phylogeography and Phylogenetics
http://www.utsc.utoronto.ca/~jweir/

2. Statistical method in Ecology
http://www.unc.edu/courses/2010fall/ecol/563/001/index.html
http://www.unc.edu/courses/2010fall/ecol/563/001/docs/lectures.html

3. principals of phylogenetics
http://ib.berkeley.edu/courses/ib200b/IB200B_SyllabusHandouts.shtml

4. phylogenetic comparative methods
http://www2.unil.ch/phylo/teaching/pmc.html

5. Bodega phylogenetic wiki
http://bodegaphylo.wikispot.org/Topics

6. wild evolution group
http://wildevolution.biology.ed.ac.uk/

7. Quantitative Methods in Ecology and Evolution
http://www.zoology.ubc.ca/~schluter/bio548/

8. how to a quantitative ecologist
http://greenmaths.st-andrews.ac.uk/index.aspx

The "impact factor" revisited - 影响因子的前生后世

你知道什么是杂志的影响因子吗？它的目的是什么？它和什么没关系？请看影响因子的前生后世。

a logical progression for scientific research 做科研的逻辑

the logical progression:


(1) identifying the research question,
(2) characterizing the data, 
(3) formulating the model,  
(4) drawing valid conclusions.