NatureTech

Nature technology editor Jeffrey Perkel blogs regularly on Naturejobs about emerging technologies and how they are being applied in the workplace. We will update this page as new posts are published. You can read more blog posts from other authors at this link. The Nature Methods team also blogs about technology, at Methagora.

Latest Naturejobs Technology blog posts

Pacbios are hackable, too

Sometimes, a DNA sequencer is more than it seems. In this month’s Technology Feature, I talk to the researchers who have figured out ways to squeeze new life from an outdated DNA sequencer, the Illumina GAIIx. That’s a popular choice for sequencer-hackers, but not the only one. Stanford structural biologist Joseph Puglisi uses a PacBio RSII from Pacific Biosciences to plumb the biochemistry of protein translation. Read more

Git: The reproducibility tool researchers love to hate

Early in his graduate career, John Blischak found himself creating figures for his advisor’s grant application. Blischak was using the programming language R to generate the figures, and as he iterated and optimized his code, he ran into a familiar problem: Determined not to lose his work, he gave each new version a different filename — analysis_1, analysis_2, and so on, for instance — but failed to document how they had evolved. Read more

Lattice light-sheet microscopy gets an AO upgrade

In late 2014, just a month after learning he had won that year’s Nobel Prize in Chemistry for superresolution microscopy, Eric Betzig and colleagues described a technique that has taken the microscopy world by storm. Lattice light-sheet microscopy (LLSM) projects ultrathin, low-intensity planes of light into a biological sample, boosting image clarity while reducing phototoxicity and photobleaching, thus allowing researchers to image live cells at high resolution for extended periods. But LLSM also had a significant drawback. Read more

Machine learning gets a journal for interactive figures

Sometimes it’s hard to understand someone else’s research through a static scientific paper. Across countless universities and companies, at whiteboards and cafeteria tables, you’ll find scientists in animated conversations explaining their research to one another, asking questions, playing around with each other’s data: in short, interacting. Across the internet in recent years, people have extended these explanations to include interactive graphics and code. Read more

Put your email inbox on a low-spam diet

Mark Clemons has published over 250 papers over the past two-plus decades, nearly all of them involving breast cancer. So imagine his surprise when Clemons, a medical oncologist at the University of Ottawa, Canada, received a flattering email inviting him to submit his work to, of all places, a journal focusing on yoga research. Read more

Software quality tests yield best practices

Life science research increasingly runs on software. A good fraction, perhaps even most of it, is made by academics, for academics: Rough around the edges, perhaps, but effective — not to mention free. But, is it of high quality Alexandros Stamatakis decided to find out. Read more

‘Manubot’ powers a crowdsourced ‘deep-learning’ review

In Nature‘s February technology feature on ‘deep learning‘, a kind of artificial intelligence whose usage is spiking in life science research, author Sarah Webb points readers to a ‘comprehensive, crowd-sourced’ review of the field.

Available as a preprint on bioRxiv, the review is indeed comprehensive: the PDF runs to 123 pages and 552 references, and has been downloaded nearly 27,500 times since May 2017. But it was an intriguing footnote on the article’s title page that really piqued my interest: “Author order was determined with a randomized algorithm”. Read more

eLife replaces commenting system with Hypothesis annotations

he next time you feel moved to comment on an article in the open-access online journal eLife, be prepared for a different user experience.

On 31 January, eLife announced it had adopted the open-source annotation service, Hypothesis, replacing its traditional commenting system. That’s the result of a year-long effort between the two services to make Hypothesis more amenable to the scholarly publishing community. Read more

Interactive figures, a mea culpa

For the 1 February issue of Nature magazine, I wrote a Toolbox article on interactive figures. Unlike static PDFs or JPEGs, these figures allow users to explore the underlying data and code used to create them, for instance to zoom in on a crowded region of interest, or to probe the robustness of a computational model.

It’s an exceptionally broad and growing field of tech development, and my article name-checks more than a dozen tools. Inevitably, omissions were made, one of which was pointed out within hours of the article going live. Read more

‘Carbon rainbow’ enables highly multiplexed microscopy

Fluorescence microscopy has transformed the life sciences. By attaching fluorescent dyes or proteins to cellular structures, researchers can image fine cellular morphology; track molecular localization, motion, and dynamics; and more. But fluorescence microscopy also presents significant obstacles. One of those is multiplexing. Read more

eMAGE extends the gene-editing toolkit

The term “genome-editing” has become synonymous with CRISPR-Cas. But there’s more than one way to edit a genome, and each has its pros and cons. Read more

New instruments advance mass spec imaging

The current focus on single-cell biology reflects the growing awareness among life scientists that all cells are not alike. In the genomics world, methods such as scRNA-seq and Drop-seq allow researchers to probe cellular heterogeneity at the genetic level using next-gen DNA sequencing. Mass spectrometry imaging (MSI) does likewise for protein and metabolite studies. Read more

New tools track article buzz online

“How’s my paper doing?” It’s such a simple question, and in today’s hyperconnected world it’s relatively easy to work out who’s reading and talking about your scientific publications. But are there conversations you might be overlooking? Read more

Augmented reality makes protein structures appear

Scientific publications represent years of work. It’d be nice if somebody read them. That’s the problem Allister Crow faced as his postdoctoral work was published in early November. Crow, a structural biologist at the University of Cambridge, UK, was part of a team, led by Vassilis Koronakis, that solved the structure of a bacterial protein called MacB, a pump protein that is involved in antibiotic resistance and toxin secretion. The paper went online November 6 in the Proceedings of the National Academy of Sciences. But how to get people — and especially those outside his immediate field — to notice? Read more

MODs get a unified search portal

For decades, the research communities surrounding the major model organisms have each had an online place to call home. There’s the SGD, MGD, and RGD — the Saccharomyces, mouse, and rat genome databases, respectively; FlyBase and WormBase for Drosophila and C. elegans; and ZFIN, the Zebrafish Information Network. Read more

Timothée Poisot: Data science for the rest of us

Timothée Poisot recently travelled to London for MozFest 2017, “The world’s leading festival for the open Internet movement.” There, the quantitative and computational ecologist at the University of Montréal in Canada ran a session entitled “Scientific computing for the terabyte-less.” Here, he tells Naturejobs why life science research needn’t necessarily follow the Big Data model.  Read more

Bioconda promises to ease bioinformatics software installation woes

Bioinformatics is notoriously complicated, what with its arcane command-line interface, complex workflows, and massive datasets. For the uninitiated, simply installing the software can present a problem. Read more

Interactive figures address data reproducibility

Data reproducibility and transparency mean different things to different people, but one aspect involves allowing scientists to view and manipulate the data or code underlying published figures, both to double-check others’ work, and to replicate those analyses with custom data. Over the past year, for instance, the open-access journal F1000Research has implemented integrations with Code Ocean and Plotly for viewing and manipulating programming code and figures, respectively. Now, a new publication showcases interactive figures for 3D genome analysis, too. Read more

The nanopore toolbox

For this week’s Technology Feature, Michael Eisenstein wrote about the technology, applications, and challenges of nanopore DNA sequencing. In brief, the technology involves threading intact pieces of DNA through a tiny aperture in a membrane or other barrier, through which a current flows. As each base passes, it disrupts that current in a characteristic way, allowing the sequence to be determined. Read more

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. But there are alternatives. One popular choice is Galaxy; another is GenePattern. Both allow researchers to execute complex bioinformatics tools via open-source, point-and-click, web-based interfaces, freeing them from the burdens of the command line, programming, and software installation. As such, they make bioinformatics workflows relatively user-friendly. And that trend is continuing. Read more

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. HiPiler, says Gehlenborg, “is a tool to visualize individual features in [Hi-C] maps.” Think of it like a digital photo application that can find and extract all the faces in your image library*. Read more

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

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

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. In a paper published on 25 May in PLoS Computational Biology, the Galaxy team describes a plug-in that provides access to both Jupyter (neé IPython notebook) and RStudio. Read more

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

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

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

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

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

Create the perfect bibliography with the CSL Editor

Have you ever stumbled across a tool you never knew existed, then wondered how you ever lived without it? Happened to me the other day. The tool in question? CSL Editor, a search tool and editor for bibliographic styles. Read more

Need an instrument? Build it!

The 6 April issue of Nature included a Toolbox feature on the growing use of DIY electronics in scientific research. A recent article on the bioRxiv preprint server provides a case in point. Read more

My digital toolbox: Lorena Barba

Lorena Barba, a mechanical and aerospace engineer at George Washington University in Washington, DC, has long championed research reproducibility. In January, she traveled to Chile to run a weeklong course on reproducible research computing; the month before, she was awarded a 2016 Leamer-Rosenthal Prize, which celebrates those “working to forward the values of openness and transparency in research.” Here, she talks about flying snakes, “repro-packs,” and copyright. Read more

JOSS gives computational scientists their academic due

The currency of science is–duh!–publication. You do the work, you write a paper. Acceptance advances a researcher’s career in every way that counts: tenure, promotion, reputation, and funding. But what if your research output isn’t a research publication? For programmers who labor in the trenches to advance their and their colleagues’ science, that’s not a hypothetical question. Read more

My digital toolbox: Santiago Perez De Rosso on Git, reimagined

Santiago Perez De Rosso, a PhD student in the Software Design Group at MIT’s Computer Science and Artificial Intelligence Laboratory, talks about Gitless—a kinder, gentler form of version control software. Read more

Convey simplifies conflicts of interest disclosure

Every time a researcher submits an article or grant application, or fulfils their institution’s annual disclosure requirement, they must submit a new financial interests statement. The problem is, each entity may request slightly different information, or define conflicts slightly differently. For researchers that publish or give presentations frequently, the paperwork can quickly add up — as can the likelihood of embarrassing (or worse) oversights. Read more

Genome editing meets version control

Consider for a moment the logistics of rewriting a genome from scratch. Starting from a reference genome sequence, you nip and tuck, recode and reorganize. Changes to any one element changes the genetic coordinates of every element downstream, meaning the process requires consider genetic bookkeeping. Read more

Painting with yeast

An international research team led by Jef Boeke of New York University Langone Medical Center and Joel Bader at Johns Hopkins University in Baltimore, Maryland, report a remarkable feat – the complete de novo synthesis and redesign of five yeast chromosomes, a first step towards a completely synthetic model eukaryote. Read more

Escape gene name-mangling with "Escape Excel"

Excel tries to be helpful but sometimes makes the wrong choice and ends up corrupting the data. Here's a workaround. Read more

Science meets Netflix with data streaming

In today’s web-connected world, we’ve come to expect instant gratification. When you select a video on Netflix, you don’t wait for the file to finish downloading. Thanks to ever-increasing bandwidth, video can stream to your computer, playing as it arrives. Data streaming is being used in the life sciences too. Read more

Omnity opens multilingual semantic searches up to academia

When preparing a grant or publication, where can you turn for new ideas? it’s difficult to get outside one’s particular area of expertise — to mine the opportunities at cross-disciplinary boundaries  unless you know what you’re looking for. The developers of a new document search engine hope to make such cognitive leaps easier. Read more

Cell Atlas launch puts spatial proteomics online

As scientific career goals go, being digitized into a 3D game avatar probably rarely cracks researchers’ top 10. But for Emma Lundberg, it’s an achievement unlocked. Read more