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Article
| Open AccessProgressive Cactus is a multiple-genome aligner for the thousand-genome era
The Progressive Cactus program can create reference-free alignments of hundreds of large vertebrate genomes efficiently, and is used for the alignment of more than 600 amniote genomes.
- Joel Armstrong
- , Glenn Hickey
- & Benedict Paten
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Review Article
| Open AccessArray programming with NumPy
NumPy is the primary array programming library for Python; here its fundamental concepts are reviewed and its evolution into a flexible interoperability layer between increasingly specialized computational libraries is discussed.
- Charles R. Harris
- , K. Jarrod Millman
- & Travis E. Oliphant
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Career Column |
How we learnt to stop worrying and love web scraping
For Nicholas DeVito, Georgia Richards and Peter Inglesby, custom webscrapers have driven their research — and their collaborations.
- Nicholas J. DeVito
- , Georgia C. Richards
- & Peter Inglesby
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Technology Feature |
Challenge to scientists: does your ten-year-old code still run?
Missing documentation and obsolete environments force participants in the Ten Years Reproducibility Challenge to get creative.
- Jeffrey M. Perkel
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News Round-Up |
Coronavirus in pets, French research strategy and a duplication detector
The latest science news, in brief.
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Technology Feature |
Four tools that help researchers working in collaborations to see the big picture
What project-management software can do for scientists.
- Julian Nowogrodzki
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Technology Feature |
Alexa, do science! Voice-activated assistants hit the lab bench
Research-optimized tools can take notes, dictate instructions and answer questions, allowing researchers to work hands-free.
- Jeffrey M. Perkel
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News |
Publishers launch joint effort to tackle altered images in research papers
Industry group aims to agree shared standards for software able to detect issues during peer review.
- Richard Van Noorden
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News Feature |
Meet this super-spotter of duplicated images in science papers
Elisabeth Bik quit her job to spot errors in research papers — and has become the public face of image sleuthing.
- Helen Shen
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Technology Feature |
Sound bytes: sightless coding
For visually impaired researchers, learning to program can be challenging. A tool called CuriO offers a multisensory route.
- Constance Clare
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Technology Feature |
Synchronized editing: the future of collaborative writing
A growing suite of tools allows teams of researchers to work collectively to edit scientific documents.
- Jeffrey M. Perkel
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Article |
Gene expression cartography
A new computational framework, novoSpaRc, leverages single-cell data to reconstruct spatial context for cells and spatial expression across tissues and organisms, on the basis of an organization principle for gene expression.
- Mor Nitzan
- , Nikos Karaiskos
- & Nikolaus Rajewsky
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Technology Feature |
Make code accessible with these cloud services
Container platforms let researchers run each other’s software — and check the results.
- Jeffrey M. Perkel
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Correspondence |
Challenge to test reproducibility of old computer code
- Konrad Hinsen
- & Nicolas Rougier
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News Feature |
Quantum gold rush: the private funding pouring into quantum start-ups
A Nature analysis explores the investors betting on quantum technology.
- Elizabeth Gibney
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Outlook |
An operating system for the biology lab
Laboratory-automation start-ups are borrowing a page from the software industry.
- Michael Segal
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Outlook |
The emerging world of digital therapeutics
The treatment of many physical and mental-health conditions is going digital.
- Simon Makin
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Outlook |
An AI boost for clinical trials
Big data and artificial intelligence could help to accelerate clinical testing.
- Marcus Woo
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Outlook |
The future of electronic health records
The digitisation of medical records in the United States has brought benefits, but not everyone is content with how they have been implemented.
- Jeff Hecht
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Toolbox |
Workflow systems turn raw data into scientific knowledge
How workflow tools can make your computational methods portable, maintainable, reproducible and shareable.
- Jeffrey M. Perkel
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Toolbox |
Julia: come for the syntax, stay for the speed
Researchers often find themselves coding algorithms in one programming language, only to have to rewrite them in a faster one. An up-and-coming language could be the answer.
- Jeffrey M. Perkel
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Comment |
Three pitfalls to avoid in machine learning
As scientists from myriad fields rush to perform algorithmic analyses, Google’s Patrick Riley calls for clear standards in research and reporting.
- Patrick Riley
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Toolbox |
How to support open-source software and stay sane
Releasing lab-built open-source software often involves a mountain of unforeseen work for the developers.
- Julian Nowogrodzki
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Toolbox |
Craft beautiful equations in Word with LaTeX
Manufacturers are ditching equation editors in word-processing software in favour of the LaTeX typesetting language. Here’s how to get started.
- David Matthews
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Nature Careers Podcast |
Working scientist podcast: Love science, loathe coding? Research software engineers to the rescue
Simon Hettrick tells Julie Gould about the role of research software engineers, what they do and how you can become one.
- Julie Gould
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News |
GPS glitch threatens thousands of scientific instruments
A quirk in how Global Positioning System signals are time-stamped risks messing up devices’ data from 6 April.
- Declan Butler
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Letter |
Particle robotics based on statistical mechanics of loosely coupled components
A stochastic robotic system shows deterministic behaviour—such as locomotion, object transport and phototaxis—from the collective motion of many loosely coupled disk-shaped ‘particles’ that perform only volumetric oscillations.
- Shuguang Li
- , Richa Batra
- & Hod Lipson
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News |
Pioneering ‘live-code’ article allows scientists to play with each other’s results
eLife’s prototype lets scientists modify the software underlying figures to validate, build on, or better understand the work.
- Jeffrey M. Perkel
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Career Feature |
How scientists can team up with big tech
Technology companies are attracting researchers through funding and partnership opportunities.
- Gabriel Popkin
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News |
Peer-reviewed homeopathy study sparks uproar in Italy
Advocates of homeopathy say that the rat study is evidence of the practice’s efficacy, but some scientists have cast doubt on the paper.
- Giorgia Guglielmi
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Outlook |
Simulated labs are booming
Blowing up your lab is usually discouraged, but it’s part of the experience when you’re learning online.
- Nicola Jones
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Toolbox |
Supercharge your data wrangling with a graphics card
Graphics processing units aren’t just of interest to gamers and cryptocurrency miners. Increasingly, they’re being used to turbocharge academic research, too.
- David Matthews
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Toolbox |
How AI technology can tame the scientific literature
As artificially intelligent tools for literature and data exploration evolve, developers seek to automate how hypotheses are generated and validated.
- Andy Extance
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News |
How Unpaywall is transforming open science
Unpaywall has become indispensable to many academics, and tie-ins with established scientific search engines could broaden its reach.
- Holly Else
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News |
Software beats animal tests at predicting toxicity of chemicals
Machine learning on mountain of safety data improves automated assessments.
- Richard Van Noorden
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Toolbox |
Speaking in code: how to program by voice
Some computer scientists turn to voice-command tools to avoid the pain of typing.
- Julian Nowogrodzki
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News |
Microsoft’s purchase of GitHub leaves some scientists uneasy
They fear the online platform will become less open, but other researchers say the buyout could make GitHub more useful.
- Andrew Silver
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Article |
Renewing Felsenstein’s phylogenetic bootstrap in the era of big data
A new version of the phylogenetic bootstrap method enables assessment of the robustness of phylogenies that are based on large datasets of hundreds or thousands of taxa.
- F. Lemoine
- , J.-B. Domelevo Entfellner
- & O. Gascuel
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News Q&A |
How I scraped data from Google Scholar
A researcher explains how — and why — he spent a whole summer harvesting information from the platform, which is notoriously hard to mine.
- Holly Else
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News |
Web of Science owner buys tool that offers one-click access to journal articles
Kopernio’s web-browser extension simplifies process of finding and legally downloading scholarly publications.
- Holly Else
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News |
Need to make a molecule? Ask this AI for instructions
Artificial-intelligence tool that has digested nearly every reaction ever performed could transform chemistry.
- Holly Else
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Comment |
Cybersecurity needs women
Safeguarding our lives online requires skills and experiences that lie beyond masculine stereotypes of the hacker and soldier, says Winifred R. Poster.
- Winifred R. Poster
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News |
Deluge of astronomical data will soon hit South Africa
The expansion of a telescope network creates a thirst for more data-handling expertise and infrastructure.
- Sarah Wild
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Career Guide |
China’s AI dreams
Why China’s plan to become a world leader in the field of artificial intelligence just might work.
- Owen Churchill
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News |
Science search engine links papers to grants and patents
The Dimensions database promises a financial perspective on scholarly literature.
- Richard Van Noorden
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Toolbox |
The research hardware in your video-game system
Motion sensors don’t just drive gameplay. With the right software, they can scan dinosaur skulls, monitor glaciers and help robots to see.
- Anna Nowogrodzki
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Toolbox |
A test drive of a DNA-analysis toolkit in the cloud
The Bioconductor project gathers genomics tools and data into a handy package that can run in the cloud.
- W. Wayt Gibbs
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News Feature |
Supercomputing poised for a massive speed boost
Plans to build ‘exascale’ machines are moving forward, but still face major technological challenges.
- Katherine Bourzac
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Review Article |
Programming languages and compiler design for realistic quantum hardware
To enable a quantum computer to solve practical problems more efficiently than classical computers, quantum programming languages and compilers are required to translate quantum algorithms into machine code; here the currently available software is reviewed.
- Frederic T. Chong
- , Diana Franklin
- & Margaret Martonosi