Clear all memory in R

There are several steps to clear all memory in R.

Step-1: Clear all variables from the workspace.
rm(list=ls(all=TRUE))

Note: if all=TRUE option ls function ensures to get all variables (even imported by other packages).

Step-2: Call garbage collector.

gc()

Bioinformatics Conferences and Journals

Top 10 Bioinformatics Conferences

1. ISMB - Intelligent Systems in Molecular Biology
2. RECOMB - Research in Computational Molecular Biology
3. ECCB - European Conference on Computational Biology
4. Pacific Symposium on Biocomputing
5. BMEI - International Conference on BioMedical Engineering and Informatics
6. CBMS - IEEE Symposium on Computer-Based Medical Systems
7. WABI - Algorithms in Bioinformatics
8. CMSB - Computational Methods in Systems Biology
9. ICNSC - International Conference on Networking, Sensing and Control
10. BIBE - IEEE International Conference on Bioinformatics and Bioengineering

Top 10 Bioinformatics Journals

1. BIOINFORMATICS - Bioinformatics/computer Applications in The Biosciences
2. PLOS COMPUT BIOL - PLOS Computational Biology
3. BMC Bioinformatics
4. BIB - Briefings in Bioinformatics
5. TITB - IEEE Transactions on Information Technology in Biomedicine
6. TCBB - IEEE/ACM Transactions on Computational Biology and Bioinformatics
7. JBI - Journal of Biomedical Informatics
8. BIOL DIRECT - Biology Direct
9. JCB - Journal of Computational Biology
10. CMPB - Computer Methods and Programs in Biomedicine

Source:  http://academic.research.microsoft.com/RankList?entitytype=3&topdomainid=2&subdomainid=21&last=5&orderby=6

R subsetting may convert a dataframe into a vector

The common way of subsetting in R is to give the row or column indexes inside brackets ([rows,cols]). One notable property of this type of
However, users generally

Protein folding, RMSD and Gibbs Energy

Today I was discussing with my friend Swakkhar Shatabda on the protein folding problem. Although I came to know about protein folding in one of my early courses, there is a lot more to explore.

Today, I got familiar with few metrics used to measure the distance between two conformations of protein - RMSD (Root Mean Square Deviation), cRMSD and dRMSD. One ppt file helped me understand it.  I got this file from Standord University website.

I also learned about Gibbs Free Energy.

I really enjoyed the discussion between us!

Install R in ubuntu from command line

 Steps to install R in ubuntu from command line:

1. add the following configuration in /etc/apt/sources.list file
   # configuration for R
   deb http://cran.nexr.com/bin/linux/ubuntu precise/
2. Command: sudo apt-get update
3. Command: sudo apt-get install r-base
4.  Command to start R: R
5. Command to quit R: q()

NOTE:

1) Step-1 is dependent on the version of ubuntu. You can find the ubuntu version using the following command:

 lsb_release -a

2) You can also different mirror site for step-1. The list is available here.

3) You may need to use secure apt. In that case, just after step-1 (before step-2), run the following commands:

gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E084DAB9

 gpg -a --export E084DAB9 | sudo apt-key add - 

 
Reference: http://cran.r-project.org/bin/linux/ubuntu/README

Continuous Query

Today I came to know a new concept in DB - Continuous Query. Traditionally, one query is run once over the current dataset and it is completed. Continuous query, in contrast, logically runs continuously over the database. Possible application of this type of query may be in Stock market, Traffic monitor etc.

Reference:
Shivnath Babu, Jennifer Widom, Continuous queries over data streams. http://ilpubs.stanford.edu:8090/527/1/2001-9.pdf