What’s in a number? Small numbers are roguish capsules of triple meaning. The number 7 is the date you were married; it’s the exact number of teaspoons of sugar in a halwa recipe your mom sent you; it’s the age of your eldest son on his next birthday. As we get older, we become acquainted … Continue reading “The tyranny of large numbers: mutations in breast cancer”
In certain circles, asking why speed is good is tantamount to heresy. I once submitted a paper with the phrase “computational performance is not an explicit goal of this work” in the abstract. It was rejected; in his explanatory note, the reviewer had said that my approach was “unlikely to yield great speedups,” and that … Continue reading “Accuracy puts the there in speed: DNA-Seq stuff!”
Getting things to “just work” is hard. Getting them to just work and be good is harder. With StrandNGS 3.0, we believe we’ve done both. A quarter year’s labour of love, three dot oh feels different because it is different; it feels good because it is. RNA alignment is faster. If you’re using transcriptome + genome alignment, you … Continue reading “It’s pronounced three dot oh”
Ploidy is a funny old Greek word for a modern, almost modish concept: data backups. Ploidy is the number of copies of an organism’s DNA. Certain kinds of algae, for instance, don’t buy into backups; they’re haploid, and contain only a single copy of DNA. Plants, on the other hand, are polyploidal; paranoiacs of the … Continue reading “Rare diseases: or, what happens when backups fail”
Retinoblastoma is an “oma” named for its surface effect, its “presentation”: it’s a cancer that attacks the eye. Worse, because 80% of retinoblastoma diagnoses occur before the age of 3, it’s a cancer that attacks the eyes—almost exclusively—of little children. Retinoblastoma is a “good cancer”: 90% of all RB cases survive into adulthood. … Continue reading “The clinical workflow, retinoblastoma and split alignment”