Moving atoms For some reason a paper copy of “Chemical and Engineering News” (November 11, 2019 – Vol 97 Issue 44) ended up in my hands, and I almost missed this fun section named: “30 years of moving atoms: How scanning probe microscopes revolutionized nanoscience” (link.) The article is progressing over time from 1993 til… Read More »
I use grep very often, and I made-up and acronym that made sense to me: Get REgular ExPression But I discovered this YouTube video that gives an accurate historical recounting of its birth and where its name came from. See video below, titled “Where GREP Came From – Computerphile” Summary: this comes from the command g/re/p… Read More »
Even though I have been using computers all my life there are still many aspects of computing that are mysterious to me, and I am sure many others… One of my favorite quotes is “A leads to B leads to C” (“Future’sEnd” – StarTrek:Voyager, Season 3, episodes 50 & 51) and so my last post being… Read More »
Binder 2.0 As just an “end-user” of software for data analysis it is sometimes difficult to just catch up with what’s available, and I end-up discovering new things simply browsing the web looking for something specific, and ending up finding something else… that was the case for Docker a couple years ago. Today (Dec 30,2019)… Read More »
Recently I was testing a Docker image to run a container for Next Gen sequencing, a way to test an existing “pipeline” on the first published study of the effect of the Zika virus. (https://hub.docker.com/r/maayanlab/zika/) Running a docker container may provide some ease in reproducibility, but sometimes there are also hardware barrier that need to… Read More »
Downsampling I have performed a search for creating a set of down-sampled data from an actual large dataset, and while there are many creative information on BioStar and other forums, I find that the most versatile and easy to use tool would be one recommended on the forums: seqtk which is available on Github: github.com/lh3/seqtk Quoting… Read More »
SRA: Sequence Read Archive The Sequence Read Archive (SRA) makes biological sequence data available to the research community to enhance reproducibility and allow for new discoveries by comparing data sets. The SRA stores raw sequencing data and alignment information from high-throughput sequencing platforms, […] However, it is rather difficult to even find the download links… and even… Read More »
I have started a series of tutorials that I am writing from the perspective of a biologist wanting to use a Docker container for a specific application. An easy example could be using EMBOSS, the molecular biology open suite for analysis. The tutorials are online at the Biochemistry department here: Docker tutorials (general page) Docker… Read More »
The recent update on enterotypes1 was an important read. Yes, we desperately need to reduce the dimensionality of the gut microbiome data and discover the stable “archetypes” of the microbiome functional states. The concept of genera-based enterotypes is a step in this direction. However, one may feel a “sense of fragility” while reading the 2017… Read More »
Deep neural networks are everywhere. They are revolutionizing our day-to-day lives, and this phenomenon no longer needs any introduction or description. Deep learning is especially suitable to find structures in overwhelming amounts of data. Recently, biological data became exactly that – overwhelming, and application of deep learning toolsets to it indeed looks very natural. You… Read More »