Processing 192 million reads in less than 5 minutes
In a recent BMC Bioinformatics paper, Feng et al. talks about their new Hadoop flavoured software PeakRanger, a peak caller for ChIP-seq data. I must admit paper is really fantastic, and it shows how powerful can Hadoop implementation be. On [...]
Class and Objects in R: S3 Style
When it comes to R Programming, I guess you can always consider me as a beginner. Although I have known basic R for quite some time now, I never tried object-oriented programming in R. Recently I started to explore some [...]
Disposable and Stressful Research
Some interesting (not so) new links, The disposable academic: Why doing a PhD is often a waste of time? Whining PhD students are nothing new, but there seem to be genuine problems with the system that produces research doctorates (the [...]
What characterizes successful computational biologists?
A latest survey report in Nature Biotechnology highlights some of notable computational biology advances in year 2010. Featured computational biology breakthroughs falls broadly in four categories, Emergence of next-generation computational methods for Next-generation sequence analysis such as de novo transcriptome assembly of [...]
Growth of Bioinformatics Databases
Latest Nucleic Acids Research (NAR) Database issue is out now. NAR Database 2011 issue features 96 new online databases covering a variety of biological data types and it also includes update on 83 data resources that have previously been published [...]
Getting cited
Just checked a recent BMC Bioinformatics paper covering the overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics. A very interesting read indeed. More interestingly, this peer reviewed paper by Ronald Taylor cites one of my favorite and [...]
Some interesting Big Data Links
Closing the gap between big data and people who need It According to Stefan Groschupf, the CEO of Datameer there is “a gap between the data and the people that want to get close to it”, particularly those who wants [...]
Dancing with data
The Economist has an interesting article about data visualization guru Hans Rosling. I will recommend everyone to read the whole story. In this article Dr Rosling points out that reluctance of big institutions to share the data, Most public data [...]
Progress is difficult to measure in the software realm
Interesting observation in Dilbert comics about progress in software world, Progress is difficult to measure in the software realm. You could measure the lines of code I produce, but that would reward inefficiency
Unhappy mind bubbles
A very interesting paper in journal science by Harvard University researchers Matthew Killingsworth and Daniel Gilbert suggests that wandering mind is an unhappy mind. In their research they found that “people are thinking about what is not happening almost as [...]
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