# What do I use?

Almost two years ago, I found this Q&A series on Biostars that asks well-known bioinformaticians what tools they use for their work:

1. What hardware do you use?
2. What is your text editor?
3. What software do you use for your work?
4. What do you use to create plots and charts?
5. What do you consider the best language to do bioinformatics with?
6. What bioinformatics tools/software do not get enough recognition?

# Thesis cover art

I was recommended to have some sort of cover art on my thesis, so I decided to make my cover using the awesome Gviz package. Below is all the code for how I generated my thesis cover art. Suggestions and comments most welcome!

# Back to the basics

As the first post of this year, I'd like to wish everyone a Happy New Year. 2014 was a year where I focused much more on reading papers, hence the lack of posts on this blog (for those interested in what I have been reading, you can check out my incomplete notes on my second wiki). In addition, I thought now would be a good time to share my 2014 Jetpack annual report for this blog:

For those who are really keen, here's the full report.

# 4th anniversary

I started this blog quite unspectacularly four years ago on this exact day. The real motivation behind starting this blog was that I wanted to do something (anything!) with the web space I purchased over a year ago in 2009. I had egotistically purchased the domain davetang.org1 because it was on my list-of-things-to-do-in-life2. But that was it; I had no plans on what to do with it.

# Calculating the h-index

Updated 2014 September 19th to include a method that does not require sorting.

The h-index is an index that is calculated by measuring the number of articles, say $n$, that has at least $n$ citations. If you published 10 articles, and each of them had four citations, your h-index would be four, since there are four articles with at least four citations. I'm not interested in what this number represents or measures but instead I'm interested in how one would calculate the h-index given an array of numbers.

# Querying PubMed using R

I've seen talks over the years where the speaker shows a bar chart with the number of articles in PubMed that contain a certain keyword and tallied per year. In most of the cases the speaker was trying to illustrate the growing number of articles that contain the keyword. Here I try to do the same by querying PubMed using R.

#install the RISmed package
install.packages("RISmed")
library(RISmed)

#now let's look up this dude called Dave Tang
res <- EUtilsSummary('dave tang', type='esearch', db='pubmed')

summary(res)
Query:
Tang, Dave[Full Author Name]

Result count:  10

#what are the PubMed ids for the Author Dave Tang?
QueryId(res)
[1] "23180801" "22976001" "22722852" "21888672" "21386911" "20510229" "19648138" "19501082" "19393063"
[10] "19270757"

#limit by date
res2 <- EUtilsSummary('dave tang', type='esearch', db='pubmed', mindate='2012', maxdate='2012')

summary(res2)
Query:
Tang, Dave[Full Author Name] AND 2012[EDAT] : 2012[EDAT]

Result count:  3

#three publications in 2012
QueryId(res2)
[1] "23180801" "22976001" "22722852"


# 10,000 monthly visitors, apparently

I created davetang.org on the 24th of April 2009 just for the sake of buying a domain with my name in it. Realising that I was and am paying for a service, I decided to actually make use of my web space. But it really started to become handy when I decided to pursue a PhD in April 2010; initially I just dumped everything I was learning onto my wiki and this blog. 4 years after creating davetang.org, I'm getting ~10,000 unique visitors to my domain each month according to AWStats, which my web hosting company has conveniently provided.

The dip around April, May and June in 2012 was due to the removal of AWStats by my web host. I guess enough people complained, so they brought it back. And if this trend continues, I will need to pay for more bandwidth.

I'm guessing the increase in visitors each month is due to the growing interest in RNA sequencing. Using Google Trends (formerly known as Google insight), we observe the growing web interest into the term RNA-Seq:

Of course I am doing a much better job (in my opinion) of writing better and more useful posts. To celebrate, I changed the header image to a photo I took while playing around with long exposure times. I took the photo near the Tokyo station in Japan; it looks cool so I thought I'll make it the header. I also changed the background to black because it's easier on the eyes.