Jeffrey Perkel
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Articles by Jeffrey Perkel
Science fiction: nine lab-life novels for your holiday reading
Katabasis R. F. Kuang Harper Voyager (2025) Graduate studies can be hell — metaphorically. In Katabasis, it’s the literal truth. Katabasis is Greek for a descent to the underworld — think Dante’s Inferno. But in R. F. Kuang’s hands, these works are not literature but travel guides. Alice Law and Peter Murdoch are PhD students at the University of Cambridge, UK, the top institution in their field of analytical magick.
Got bugs? Here’s how to catch the errors in your scientific software
Science is becoming increasingly computational. Experimental data must be logged, cleaned, checked and analysed. Data analysis often involves iterative trial and error using ‘scripting’ programming languages such as Python and R. The outputs of such programs are then included in papers, presentations and grant applications. A typical piece of professional software contains up to 50 errors per 1,000 lines of code (D. A. W. Soergel F1000Research 3, 303; 2015).
Python, the movie! The origin story of the programming language comes to the silver screen
In 2005, Travis Oliphant was an information scientist working on medical and biological imaging at Brigham Young University in Provo, Utah, when he began work on NumPy, a library that has become a linchpin of scientific computing in the Python programming language. Oliphant came across Python as a graduate student in 1998 and, as he wrote in the Guide to NumPy (2006), “quickly fell in love” with it. That “is a remarkable statement to make about a programming language”, he acknowledged.
Beyond AlphaFold: how AI is decoding the grammar of the genome
In 1862, Victor Hugo reportedly wrote to his publisher to ask how his newly published novel Les Misérables was selling, with a single character query: “?” The response: “!” This story of one of the world’s most concise correspondences is apocryphal. But some genome-focused artificial intelligence (AI) systems can, like the French writer’s publisher, respond meaningfully to equally short prompts.
Which programming language should I use? A guide for early-career researchers
Each year, the code-sharing platform GitHub releases its ‘State of the Octoverse’ report, which among other things ranks the popularity of programming languages. The latest report, released in October 2024, had some good news for pythonistas, as Python programmers are called: for the first time in ten years, the language JavaScript had been bumped from the top of the leader board and replaced by Python.
85 million cells - and counting - at your fingertips
When it comes to single-cell gene-expression data, biologists face an embarrassment of riches. There are thousands of data sets to choose from. Unfortunately, those data sets have not all been processed in the same way; they might use different names for similar or identical cells or tissues; and they are scattered across the Internet — or available only on request. Smart software untangles gene regulation in cells Using any one data set is relatively straightforward.
No installation required: how WebAssembly is changing scientific computing
In late 2021, midway through the COVID-19 pandemic, George Stagg was preparing to give exams to his mathematics and statistics students at the University of Newcastle, UK. Some would use laptops, others would opt for tablets or mobile phones. Not all of them could even use the programming language that was the subject of the test: the statistical language R. “We had no control, really, over what devices those students were using,” says Stagg.
AI and science: what 1,600 researchers think
Nature (Nature) ISSN 1476-4687 (online) ISSN 0028-0836 (print)
From better bridges to more efficient cars: how pocket calculators changed the world
Empire of the Sum: The Rise and Reign of the Pocket Calculator Keith Houston W. W. Norton (2023) As a child during the late 1970s and early 1980s, I recall some of my classmates coming to school sporting digital watches with built-in calculators. With their microscopic buttons and tiny liquid-crystal displays, these devices were the acme of cool: as well as doing maths on their wrists, the kids could also play Space Invaders.
How to make your scientific data accessible, discoverable and useful
Miguel Acevedo typically gets two questions about his research on malaria in lizards. “Do lizards really get malaria?” (The answer is yes.) And, “Will I get malaria from a lizard?” (Not likely.) Lizard malaria is a model for vector-borne disease ecology and evolution1.
Six tips for better coding with ChatGPT
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The sleight-of-hand trick that can simplify scientific computing Original
Research software is like the tower-building game Jenga — tools atop tools atop tools. When developers tweak their individual pieces, this can change the function of the software that depends on them, potentially altering results — or causing the software to fail. Version 3.6.0 of the R programming language, for instance, introduced a replacement algorithm for generating random numbers. This and the older algorithm both work, but not in the same way.
Smart software untangles gene regulation in cells
When it comes to dissecting how a cell’s regulatory circuits are wired, some researchers turn to their pipettes. Emily Miraldi turns to her keyboard. A computational and systems biologist at Cincinnati Children’s Hospital in Ohio, Miraldi uses mathematics to understand what makes cell systems tick, and to predict how they respond to their environment. As a postdoc, she worked with computational biologist Richard Bonneau and immunologist Dan Littman at New York University in New York City.
A graphics toolkit for visualizing genome data
The genomics world has no shortage of visualization tools. But as new methods and data types emerge, existing techniques can struggle to cope. Now, a tool known as Gosling allows bioinformaticians to build apps that can display genomic information with the same level of flexibility that developers have come to expect from other graphics programming tools.
Example Quarto manuscript
Inline computation Imagine we are analyzing data from a clinical trial. We have grouped subjects in three bins and measured the concentration of some metabolite. (These data are simulated.) Rather than analyzing those data and then copying the results into our manuscript, we can use the programming language R to do that in the manuscript itself. Simply enclose the code inside backticks, with the letter r.
Six tips for better spreadsheets
As a data-science librarian at the University of California, San Diego, Stephanie Labou has seen her share of spreadsheet horror stories. The most haunting was a table of hand-entered GPS coordinates. “It was a complete mix,” Labou recalls. The spreadsheet was produced by citizen-scientists. Some had written the word ‘degrees’, some ‘0’ and some ‘o’; some had used superscripts, some hadn’t; others wrote ‘north’, ‘west’ or neither.
Cut the tyranny of copy-and-paste with these coding tools
If you’ve written a scientific manuscript, there’s a good chance you’re familiar with the app-switching two-step that happens when you copy your data from one program and paste them into another. That time-tested workflow does the job, but it isn’t always the most efficient process. Perhaps you receive new samples and need to update your numbers. Or maybe you have to fix an error you made when processing your data.
The giant plan to track diversity in research journals
Lerback, J. C., Hanson, B. & Wooden, P. Earth Space Sci. 7, e2019EA000946 (2020). Article Google Scholar Day, A. E., Corbett, P. & Boyle, J. Chem. Sci. 11, 2277–2301 (2020). Article PubMed Google Scholar Ye, J. et al. Proc. 2017 ACM Inf. Knowl. Mgmt 1897–1906 (2017). Article Google Scholar Le, T. T. et al. Cell Syst. 12, 900–906 (2021). Article PubMed Google Scholar Davidson, N. R. & Greene, C. S. Preprint at bioRxiv https://doi.org/10.1101/2021.06.21.449261 (2021). Freeman, R. B. & Huang, W. Nature 513, 305 (2014).
Terra takes the pain out of ‘omics’ computing in the cloud
Biomedical research produces massive amounts of data. But actually sharing them can be a challenge. “It doesn’t matter how enthusiastic you are about sharing data, actually sharing data is logistically a pain,” says Elinor Karlsson, a geneticist at the University of Massachusetts Chan Medical School in Worcester.
Finding Points to Possible Blood Test for Brain Tumors Original
By Jeffrey Perkel HealthDay Reporter MONDAY, Nov. 17 (HealthDay News) -- Researchers have stumbled across a novel mechanism by which brain tumors model their environment to nurture their own growth. The findings expose a fundamental biological process of which oncologists were previously unaware, and which may one day be exploited to combat glioblastoma, experts said.
Stem Cells Coaxed to Make Precursors to Egg, Sperm
By Jeffrey Perkel HealthDay Reporter WEDNESDAY, Oct. 28 (HealthDay News) -- In a step that might someday aid infertile couples, scientists have nudged stem cells to become human germ cells -- precursors to egg and sperm. "For the first time we have a human genome-based system for how to make a germ cell or not," said lead researcher Renee Reijo Pera, director of the Center for Human Embryonic Stem Cell Research and Education at Stanford University School of Medicine.
Single-cell proteomics takes centre stage
Claudia Ctortecka was both sceptical and intrigued when her thesis adviser told her in 2018 about a new method that uses mass spectrometry to analyse the protein contents of individual cells. When he said he was looking for someone to pursue this single-cell proteomics strategy in his laboratory at the Vienna BioCenter research institute, she decided to take a chance. “I was always very much interested in mass spectrometry,” she says.
Single-cell analysis enters the multiomics age
It takes about 20 days for a mouse to grow from fertilized egg to newborn pup. Ricard Argelaguet and his colleagues were interested in what exactly happens inside the cells of a mouse embryo between days 4.5 and 7.5, when the stem cells shift into three layers: the ectoderm, which develops into the nervous system; the mesoderm, which develops into muscle and bone; and the endoderm, which develops into the gut and internal organs.
Five reasons why researchers should learn to love the command line
Jennifer Johnson’s principal investigator had a simple request. Since 2018, their team had sequenced the DNA of some 1,300 silver fox (Vulpes vulpes) specimens, and the lab head wanted to know precisely how many bases it had collected, and how well those bases aligned to the reference genome. Johnson, a bioinformatician at the University of Illinois at Urbana-Champaign, had the necessary data. But they were scattered across her hard drive.
Ten Computer Codes That Transformed Science
AP Photo/Michel Spingler, File In 2019, the Event Horizon Telescope team gave the world the first glimpse of what a black hole actually looks like. But the image of a glowing, ring-shaped object that the group unveiled wasn’t a conventional photograph. Read Full Article » Show comments Hide Comments
Sliced, diced and digested: AI-generated science ready in minutes
One vision for the future use of AI in scientific publishing is to synthesise information from multiple journal articles. Credit: Shutterstock No matter how many months or years authors take to produce a scientific paper, Sabine Louët needs only a few seconds to generate a coherent 300-word summary of it.
Why scientists are turning to Rust
In 2015, bioinformatician Johannes Köster was what he called “kind of a full-time Python guy”. He had already written one popular tool — the workflow manager Snakemake — in the programming language. Now he was contemplating a project that required a level of computational performance that Python simply couldn’t deliver. So he began casting about for something new.
Challenge to scientists: does your ten-year-old code still run?
What Nicolas Rougier needed was a disk. Not a pocket-sized terabyte hard drive, not a compact disc — an actual floppy disk. For those who missed the 1980s, the original floppy disk was a flexible, flimsy disk inside a square sleeve with a hole in the centre and a notch in the corner, and a couple of hundred kilobytes of storage.
Alexa, do science! Voice-activated assistants hit the lab bench
Alexa-powered tools allow researchers to quickly access laboratory-specific information.Credit: Chloe Collyer/Bloomberg/Getty Funsho Fakuade has spent a lot of time in the dark. As a PhD student studying ion channels and cardiac arrhythmias at Georg August University in Göttingen, Germany, his work typically involves measuring the electrical output and fluorescence intensity of cells under a microscope.
The software that powers scientific illustration
Like many researchers, Rita Sattler is trained to conduct science, not to draw it. But papers still need writing — and illustrating. So, when the time came to document what her team had done for a journal article, Sattler did what her colleagues frequently do: she fired up PowerPoint. Microsoft’s tool for creating and displaying slideshow presentations is one of two popular options for creating scientific illustrations; the other is Adobe Illustrator.
Behind the Johns Hopkins University coronavirus dashboard
In December when the disease that now is known as COVID-19 emerged in China, Ensheng Dong was studying the worrying spread of measles. A first-year graduate student in civil and systems engineering with a focus on disease epidemiology at Johns Hopkins University in Baltimore, Maryland, Dong began tracking the new disease.
Synchronized editing: the future of collaborative writing
Draft scientific manuscripts are typically confidential. So, when Elana Fertig was asked to take a look at an in-development paper on a functional gene-annotation strategy, she expected to receive the file in a private e-mail. What she got was a public announcement, shared on Twitter. The paper had been written by Olga Botvinnik, a computational biologist at the Chan Zuckerberg Biohub in San Francisco, California, who is an advocate of the global movement to make research more accessible.
Mischief-making bots attacked my scientific survey
Credit: Melissa Simone Melissa Simone, a quantitative psychologist at the University of Minnesota in Minneapolis, uses surveys to study eating behaviours in people from sexual and gender minorities (LGBT+). In less than 24 hours of promoting one such survey on Twitter, she received 386 responses. But in most cases there was nobody at the keyboard.
PanLingua: a free online tool that makes bioRxiv multilingual
How to read English preprints in any of the 104 languages recognized by Google Translate. 6 March 2020 Jeffrey M. Perkel Nicolas Menijes Crego/Alamy Stock Photo Science may be a global enterprise, but it communicates mostly in one tongue - English. And that can be a problem if you’re not fluent in it. There is an enormous community of researchers who are not native English speakers, yet they are expected to write their articles in English to a very high standard.
Collaborative Writing with Manubot
This manuscript (permalink) was automatically generated from jperkel/mymanuscript@b2f0193 on March 31, 2020. Authors Jeffrey M. Perkel 0000-0001-5699-1008 · jperkel · j_perkel Technology Editor, Nature Abstract To provide a working example for an article on collaborative science writing platforms, we created this demonstration document. The article was published 31 March 2020 in Nature [1]. We encourage readers to explore and , as detailed in the Methods section below.
Just say "no" to manels
There’s an app for that. 7 February 2020 Jeffrey Perkel Bloomberg/Getty Images By one estimate, nearly three in 10 scientists around the world are women. In some disciplines, the ratio is higher. But you’d never know it from the speaker lists at many scientific meetings. Conferences across a range of disciplines routinely invite more men than women to speak.
Three ways to collaborate on writing
Document-sharing tools for scientists. 10 January 2020 Jeffrey M. Perkel Federico Caputo / Alamy Stock Photo Science is a collaborative exercise, and whether they are writing papers or grant applications, or soliciting feedback from their thesis committee, researchers frequently must author, edit, and share documents with their colleagues.
Xenotransplantation makes a comeback
Jeffrey M Perkel1 Nature Biotechnology volume 34, pages3–4(2016)Cite this article 104 Accesses 13 Citations 20 Altmetric Metrics details Subjects Author information Affiliations Pocatello, Idaho Jeffrey M Perkel Authors Search for Jeffrey M Perkel in: About this article Further reading Decellularization combined with enzymatic removal of N‐linked glycans and residual DNA reduces inflammatory response and improves performance of porcine xenogeneic pulmonary heart valves in an ovine in vivo...
The microscope makers putting ever-larger biological samples under the spotlight
Long-term functional imaging of an entire Drosophila embryo, captured using light-sheet microscopy.Credit: Raghav Chhetri and Philipp Keller/HHMI, Janelia Research Campus In a sunny third-floor office at the Howard Hughes Medical Institute’s Janelia Research Campus in Ashburn, Virginia, Philipp Keller is showing off the optics for his latest microscope. They’re not much to look at — yet. “What we have right now in the building is this,” Keller says, pointing to his computer screen.
The Quest for a Simple Cancer Test
Receive emails about upcoming NOVA programs and related content, as well as featured reporting about current events through a science lens. Embedded in a small translucent wafer measuring just under an inch a side, the spiraling coils—like neatly packed iPod earbuds—aren’t much to look at. But judging on appearance alone would sell short the brainchild of Chwee Teck Lim of National University Singapore and Jongyoon Han of the Massachusetts Institute of Technology.
Make code accessible with these cloud services
Murphy’s law for the digital age: anything that can go wrong, will go wrong during a live demonstration. For Ben Marwick, that happened in front of a roomful of landscape-archaeology students in Berlin. The topic: computational reproducibility using Docker. Docker is a software tool that generates ‘containers’ — standardized computational environments that can be shared and reused.
TechBlog: Need an instrument? Build it!
Naturejobs | Naturejobs Blog 19 Apr 2017 | 16:00 GMT | Posted by Jeffrey Perkel | Category: Blog, Technology The 6 April issue of Nature included a Toolbox feature on the growing use of DIY electronics in scientific research. Daniel Cressey writes: Arduinos and similar devices, such as the Raspberry Pi, pack considerable power on their diminutive boards, providing tremendous opportunities for automation, networking and data collection and analysis.
Workflow systems turn raw data into scientific knowledge
Reinventing the wheel is pointless, but for computational biologists it’s sometimes unavoidable. So when Rob Finn and Folker Meyer realized how much their work overlapped, they decided to try something different. Finn is head of the sequence-families team at the European Bioinformatics Institute (EBI) in Hinxton, UK; Meyer is a computer scientist at Argonne National Laboratory in Lemont, Illinois.
Desperately seeking scientists
When so many email addresses on journal articles don’t work, we have a problem. 12 August 2019 Jeffrey M. Perkel Malte Mueller/Getty Images Nearly one-in-five email addresses in the MEDLINE literature database are invalid, according to a report posted on the bioRxiv preprint server in May.
Julia: come for the syntax, stay for the speed
When it comes to climate modelling, every computational second counts. Designed to account for air, land, sun and sea, and the complicated physics that links them, these models can run to millions of lines of code, which are executed on the world’s most powerful computers.
The computational protein designers
By designing a protein from the ground up, researchers can create molecules with forms and functions not found in nature.Credit: Brian DalBalcon Cassie Bryan’s success at crafting a protein that worked as she intended was a long time coming. When it finally happened, after six long years, she hit the bar and celebrated with beers — and a karaoke rendition of Joan Jett’s ‘Bad Reputation’.
A “petting zoo for code” makes studies easier to reproduce
A new tool helps users to compose, compute and publish reproducible articles. 18 June 2019 Jeffrey M. Perkel Fanatic Studio / Alamy Stock Photo Will Ludington Ben Marwick When biophysicist Will Ludington came to write up a recent paper about what he calls “the algebra of the microbiome”, he and his coauthors specifically took computational complexity into account.
The new techniques revealing the varied shapes of chromatin
This multicoloured image of chromatin was created using multiplexed fluorescence in situ hybridization and super-resolution microscopy.Credit: Bogdan Bintu/The Xiaowei Zhuang Laboratory/The Alistair Boettiger Laboratory Molecular models suggest that chromosomes assemble in an ordered, hierarchical way: DNA wraps around proteins called histones to form nucleosomes, which fold into 30-nanometre fibres, then 120-nanometre ‘chromonema’, and further into larger chromatin structures until they...
Antibodies: will their star continue to rise?
Due to their high specificity and selectivity, antibodies hold great potential for use in the life sciences, in everything from basic research to diagnostics and therapeutics.
A simple approach to dating bones
TOOLBOX 23 April 2019 Forensic anthropologist Ann Ross describes the techniques she uses to determine the age of human skeletons. Forensic anthropologist Ann Ross identifying bone fragments in her laboratory.Credit: Marc Hall/NCSU In the late 1990s, as an anthropology PhD student at the University of Tennessee, Knoxville, Ann Ross travelled to Bosnia to help identify casualties of war.
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