TechBlog: Jupyter powers bioinformatics, again
Bioinformatics isn’t easy for newbies. It’s typically done on the Linux command line, where users direct the computer using text-based instructions rather than clicking a mouse. Read more
TechBlog: HiPiler simplifies chromatin structure analysis
For my recent Toolbox on 3D genome visualization tools, Nils Gehlenborg at Harvard Medical School clued me into two interesting pieces of software. One, HiGlass,was included in my article; a related tool, HiPiler, was not. But that doesn’t mean it’s not worth talking about. Read more
TechBlog: Mike Goodstadt: A circuitous route to bioinformatics
Most coders come to bioinformatics by one of two routes. They’re either biologists skilled in programming, or programmers with an interest in biology. Mike Goodstadt, the programmer behind the genome-visualization tool TADkit, took a different approach. Read more
TechBlog: Building synthetic circuits from RNA
As my recent Technology Feature made clear, the technology to synthesize large genomes is advancing at a remarkable pace. So too are technologies for wiring genetic circuits to endow those genomes with novel properties. In the 3 August issue of Nature, researchers at Arizona State University in Tempe describe a new technology to do just that. Read more
TechBlog: Jupyter Joins the Galaxy
There’s a galaxy of tools in the Galaxy bioinformatics environment — 4,807 at last count. With them, researchers can do just about anything, computationally speaking. One thing they couldn’t do was work with their data programmatically. Now, thanks to a recent software update, that gap has been filled. Read more
TechBlog: How to build long DNA
My most recent Technology Feature, on the technology of genome synthesis, describes advances in the field of large-scale genome hacking. Researchers are rewriting the genomes of organisms from E. coli to yeast, with millions of bases written from scratch. Now, through projects like Genome Project-write, they are turning their attention to even more complex organisms, with concomitantly larger genomes. Read more
TechBlog: The sound of DNA
With an alphabet comprising just four letters, DNA sequence isn’t much to look at. So, when sequence analysis tools want to highlight key elements, they typically do so using colour, font, or by overlaying other types of information. In the not-too-distant future, there may be another option: Audio. Read more
TechBlog: C. Titus Brown: Predicting the paper of the future
C. Titus Brown, a bioinformatician at the University of California, Davis, participated in a January workshop at Caltech on “The Paper of the Future,” and wrote about the experience on his blog. Here, he expands on how academic publishing may change in the years to come. Read more
TechBlog: My digital toolbox: Julia Stewart Lowndes
Julia Stewart Lowndes, a marine data scientist at the National Center for Ecological Analysis and Synthesis (NCEAS) at the University of California at Santa Barbara, published a paper this week laying out the challenges her team faces as they try to share and reuse data on the world’s oceans. Here, some key lessons. Read more
TechBlog: Smartphone science, no programming required
In the 4 May Nature technology feature, I explore the growing use of smartphones to drive scientific research. Today’s phones are so full-featured, they’re often ready for use out-of-the-box. Sometimes, though, a custom app is required, and that can be a sticking point, as programming a mobile app isn’t easy. Read more
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