Posts Tagged ‘x78qtcore’

Biology begins to tangle with quantum computing | Nature Methods

July 16, 2021

Technology Feature
Published: 23 June 2021
Biology begins to tangle with quantum computing
Vivien Marx
Nature Methods volume 18, pages715–719 (2021)

QT:{{”

“There’s a lot of buzz about quantum computing,” says Yale University researcher Mark Gerstein, whose projects traverse biology and informatics. Enthusiasm among his colleagues about the prospects of quantum computing is especially high in the physical sciences, and interest is growing in computational biology and biology more generally.


Gerstein co-authored a paper4 that grew from a series of discussions at the National Institute of Mental Health (NIMH), part of the US National Institutes of Health (NIH). It’s part of the NIH’s way of exploring how to support biologists interested and involved in quantum computing, he says. The wider neuroscience community, for example, is interested in how quantum approaches can be applied to deep learning and machine learning.

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https://www.nature.com/articles/s41592-021-01199-z

Digital secrets of successful lab management

July 16, 2021

QT:{{”
“Ironically, a lot of these tools are about not having people sit in front of a screen all the time,” says computational biologist Mark Gerstein at Yale University in New Haven, Connecticut. “I don’t think that helps people think.” Instead, he says, researchers spawn creativity when talking and scribbling down ideas together, be that on a phone, tablet, laptop or in person.

Like Brown, Gerstein prizes face-to-face conversation and
collaboration in his group, which works on large-scale analyses of biosensor and wearable data. As such, it attracts “hard-core computer geeks”, he says, so he’s thought deeply about how to entice them out from behind their screens.

“Computers now let us dictate, write and draw with our hands in much more relaxing and natural ways,” he says. Gerstein sets his phone on a nearby table, then uses Google Recorder to capture discussions, and the app (which is available only on Pixel phones) transcribes it in real time. The transcript is coupled to the audio and can be searched by keyword. Another dictation app, known as Rev, offers
quick-turnaround manual transcriptions for $1.25 per minute of recording. Gerstein also uses the app Grammarly to “take the yucky voice-to-text transcript and fix the language up quickly”.

Gerstein describes his group’s use of these tools together as a “stack” to go from conversation to a rough draft of a manuscript in just a few clicks, he says. He estimates that the tools cut the time they spent on that task in half.

Gerstein has also investigated tools that digitally recreate the experience of scientists gathered around a whiteboard. Zoom’s Annotate feature is one option, which he has deployed during remote meetings both before and during the pandemic. Another is Rocketbook, a reusable physical notebook ($16–45) that has whiteboard-like paper paired with a mobile-phone app that converts photos of notebook scribbles, cartoons and diagrams into digital files. Both Rocketbook and Google Lens use optical character recognition to interpret handwriting and translate it into searchable text. “I’ve saved thousands of sheets of paper this way,” says Gerstein.

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https://www.nature.com/articles/d41586-021-01752-y

BBC Media Request = Data Sanitisation

December 22, 2020

The Naked Scientists

Data sanitisation tool plugs privacy gap

Functional genomics data is vulnerable to de-anonymising attacks… 17 December 2020
Interview with
Mark Gerstein, Yale University

Part of the show RNA Vaccines, Privacy, and Penguins

part of the Naked Genetics podcast, on all podcast platforms and o
site here: https://www.thenakedscientists.com/podcasts/naked-genetics/rna-vaccines-privacy-and-penguins

direct link: https://www.thenakedscientists.com/articles/interviews/data-sanitisation-tool-plugs-privacy-gap

Desperately seeking scientists | Nature Index

August 12, 2019

Reunion coverage + Useful suggestion for ORCID that can be done with a secondary email

https://www.natureindex.com/news-blog/one-in-five-email-addresses-researcher-journal-articles-invalid-problem

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Mark Gerstein, the Albert Williams Professor of Biomedical Informatics at Yale University in New Haven, Connecticut, lists over 200 members on his lab’s alumni page, about half of whom were PhD students and postdocs. Recently, he invited many of them to a lab reunion. But first, he had to find them.
“It’s a nontrivial thing keeping track of peoples’ emails,” he says. The lab maintains a database of past members, but he’s now established a LinkedIn group, which has been particularly useful, he says. Former lab members who are on the social network can associate themselves with the lab, thus providing a mechanism for staying in touch. If nothing else, Gerstein notes, he likes to be able to contact lab expats in case there’s ever a question about an old project – for instance, to clarify a protocol or locate a file.

A third solution would be for a third-party ‘scientific directory’ service such as ORCID to add a mechanism for contacting authors, such as a button or form to send a message.
Laure Haak, Executive Director of ORCID, says, “At the current time, ORCID does not have these features on our roadmap.”
In the meantime, it is possible to make the email addresses in an ORCID profile public; go to Account Settings > Email and Notification Preferences, and change “who can see this” from “only me” to “everyone”.
Of course, even were the organization to add a messaging feature, overtaxed researchers may not read them.
“People get so much email,” Gerstein says. “I suspect people would ignore the messages.”
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What the Yale team studied – Marketplace – CBC News

January 19, 2019

https://www.cbc.ca/marketplace/blog/what-the-yale-team-studied

Twins get some ‘mystifying’ results when they put 5 DNA ancestry kits to the test | CBC News

January 19, 2019

https://www.cbc.ca/news/technology/dna-ancestry-kits-twins-marketplace-1.4980976

(4) Twins get ‘mystifying’ DNA ancestry test results (Marketplace) – YouTube

January 19, 2019

https://www.youtube.com/watch?v=Isa5c1p6aC0&feature=youtu.be

Massive analysis refines map of autism’s genetic roots | Spectrum | Autism Research News

December 23, 2018

https://www.spectrumnews.org/news/massive-analysis-refines-map-autisms-genetic-roots/

Mapping the Brain’s Genetic Landscape – The New York Times

December 17, 2018

https://www.nytimes.com/2018/12/13/health/genetics-brain-autism-schizophrenia.html

Analysis of 2,000 Brains Provides Clues to Schizophrenia, Autism | The Scientist Magazine(R)

December 15, 2018

https://www.the-scientist.com/news-opinion/analysis-of-2-000-brains-provides-clues-to-schizophrenia–autism-65210