Ramblings of a Bioinformatician

So, I tried installing Sleuth along with Kallisto for RNA-seq data analysis. Getting Kallisto to work was no big deal but Sleuth required a couple of dependencies even before installation. Following instructions on github and on other online tutorials which seemed pretty straightforward as in any R-Bioconductor based installation, I expected this to go smooth. Much to my surprise, it wasn't a cake walk! Sleuth requires us to install 'devtools' and 'rhdf5' from within biocLite in R (I think we could google a little about what these packages do). I had a fresh 64-bit BioLinux-8 installation which is basically a Linux Ubuntu 14.04 based OS, comes bundled with many preconfigured bioinformatics packages including a R version 3.2.0. Initially running biocLite('rhdf5') didn't throw any error and went all the way with just a couple of minor version warnings but biocLite('devtools') threw numerous errors and just wouldn't work. After a few

So we all have spent some quality time googling for an easy way to upgrade our R installation to the latest version on Ubuntu! Else why would you be here?! right?! Here are some quick steps to upgrade your R to latest version!  R-installations are tied up to their Ubuntu versions and hence are connected to the Ubuntu Distribution name like Trusty Tahr or Precise Pangolin. The trick here is to send a message to the repository with your latest Ubuntu distribution name, so it will pick up the latest version and update whatever is the new one out!  Just follow these steps, (simply copy-paste these commands in sequence, it will work, fingers crossed!)   1. Get the Ubuntu distribution name matching your current Version of ubuntu  distname=$(lsb_release -c -s)   2. Select the nearest CRAN mirror to you  echo "deb http://mirrors.ebi.ac.uk/CRAN/bin/linux/ubuntu $distname/" | sudo tee -a /etc/apt/sources.list > /dev/null  3. Authenticate download from the CRAN mir

MH370 A different point of view Here are the excerpts from an article by a pilot called Chris Goodfellow which make sense in my head and I thought it would make sense to many of my friends with a similar wavelength! Here we go! A lot of speculation about MH370. Terrorism, hijack, meteors. I cannot believe the analysis on CNN - almost disturbing. There could be a more simple explanation of this event. Loaded 777 departs midnight from Kuala to Beijing. Hot night. Heavy aircraft. About an hour out across the gulf towards Vietnam the plane goes dark meaning the transponder goes off and secondary radar tracking goes off.  Two days later we hear of reports that Malaysian military radar (which is a primary radar meaning the plane is being tracked by reflection rather than by transponder interrogation response) has tracked the plane on a southwesterly course back across the Malay Peninsula into the straits of Malacca. When I heard this I immediately brought up Google Earth and I

What is Clinical Genomics? What's the difference between precision medicine and personalised medicine? Genomics is the study of an organism's entire genome (all the DNA for the discussion lets say)! Clinical Genomics is the study of: – the correlation between diseases and human genome – the interaction of medication and human genome – developing disease diagnostic methods from human genome - Finally - coming up with ways to treat that disease based on all this knowledge built with the help of genomics. When we think about genomics in treating a disease like cancer, we consider two aspects. First is the patient’s own genome, which is in every cell in their body. In their genome, they may have mutations that make them more susceptible to a particular type of cancer than someone who doesn’t have that particular type of mutation. For example, we know that individuals with specific inherited mutations in BRCA1 and BRCA2 genes are at a greater risk for bre

What advice would you give to any aspiring candidate who is seeking to become a veterinarian? As we have seen in the recent past, Boromir tends to be pessimistic about most of the things we could do and say. But do not let Boromir discourage you. Here are some tips for you to prepare yourself to start a career as a Vet. Future Vet Website is an excellent place to start if you are looking for organised information. They advise you briefly about the necessary steps while you are in High School and as a College undergraduate. They also have lots of other interesting materials to read. Otherwise here are my simple tips -  Firstly ask yourself whether you are an animal lover - there's no point in being scared of animals, hate animals or indifferent about animals if you want to be their guardian angel for the rest of your life! Secondly be sure you want to be a vet for the right reason - to care, nurture, protect and save! and not for that Maserati you always wanted to

My dog is laying here on the couch and I noticed she just contracted hiccups and within 3 hiccups was back to normal again. Its not the first time I noticed, just the first time I noticed while browsing Quora. Humans will go to the ends of the earth trying every homeopathic cure known or suggested and can struggle for a considerable length of time to rid themselves of them.  The answer is in our anatomy.. our epiglottis is perpendicular to the axis of the trachea and is almost vertical due to our upright pose while it is slightly tilted in case of dogs! Venkatesh Chellappa (BVSc. &AH, MSc.)