linkstream2 microblog

http://sciencehill-cryoem.yale.edu/
cryoem.yale.edu
https://medicine.yale.edu/ccmi/

Webinar Invitation
General Data Science Overview
Date: November 1st
Time: 11:00 a.m. EDT

QT:{{”

How can we effectively and efficiently teach statistical thinking and computation to students with little to no background in either? How can we equip them with the skills and tools for reasoning with various types of data and leave them wanting to learn more?

In this talk we describe an introductory data science course that is our (working) answer to these questions. ….

Webinar Recordings:

We try to record every webinar we host and post all materials on our website. http://www.rstudio.com/resources/webinars/
“}}

http://nyer.cm/V1AcIwk

QT:{{”
But it’s the very specificity of genomic data that threatens privacy. Although most genomic databases strip away any information linking a name to a genome, such information is very hard to keep anonymous. “I’m not convinced you can truly de-identify the data,” says Mark Gerstein, a Yale professor who studies large genetic databases and is a fierce privacy advocate. He is concerned about whether even the most cutting-edge protections can safeguard personal data. “I am not a believer that large-scale technical solutions or ‘super-encryption’ will solely work,” he says. “There also needs to be a process for credentialing the individuals who access this data.”
…
Threats to privacy could multiply once there is an active market for genetic data. Wood speculates that it could be valuable to life insurance companies, which could use it to raise your premiums; or it could become a tool for those who want to prove or disprove paternity. White nationalist groups, who have become preoccupied with genetic testing, might find a way to weaponize the ancestry data the tests can show. It would not be the first time genetic information was used against a race or races. “Genetics has a very troubled history, from Darwin on,” says Yale’s Mark Gerstein.
…
Yet Columbia’s Yaniv Erlich and others, including Church, fear differential privacy could compromise biomedical research, with smudged data making it harder to get clear results. Mark Gerstein at Yale believes that scientists would be better off testing hypotheses on small amounts of publicly available but pure data, even if it’s not representative of the overall population, rather than using larger quantities of imperfect data.
“}}

Is Genetic Privacy a Myth?
http://protomag.com/articles/genetic-privacy-myth
Genetic tests and genome sequencing are generating terabytes of sensitive private data. How can they be kept safe?

QT:{{”
“The 4D Nucleome, a major research consortium funded by the US National Institutes of Health (NIH), is now requiring that all manuscripts related to its US$120-million, five-year programme are posted to an online preprint server ahead of peer review. And a privately funded, US$600-million biomedical research initiative in California is considering whether to demand its investigators do the same.”
“}}

http://www.nature.com/news/big-biology-projects-warm-up-to-preprints-1.21074

QT{{”
“Early on, the cells in an embryo can turn into any tissue. As these stem cells divide, they can lose this flexibility, committing to becoming one kind of cell or another. After that, cells typically shut down their viral genes.
Viral proteins appear to help keep stem cells from losing this potential. …
Viruses might have exploited embryos to make more copies of
themselves. By keeping their hosts as stem cells for longer, the viruses were able to invade more parts of the embryo’s body.” “}}

Ancient Viruses Are Buried in Your DNA, by @CarlZimmer
https://www.NYTimes.com/2017/10/04/science/ancient-viruses-dna-genome.html Nice #intuition on why they may promote the stem-cell state

QT:{{"

“The Advanced Protection Program incorporates a physical security key (a small USB or wireless device that costs around $25) to protect against phishing. The key, which participants need to buy themselves, uses public-key cryptography and digital signatures. Without the key, even someone with your password would be unable to access your account. Advanced Protection limits your Google data access to only Google apps and adds additional safeguards in the account recovery process to prevent someone from social engineering their way into your account. It also performs additional scans on files and attachments to ensure no malware is piggybacking on the download.”
"}}

#Google’s New Super-Secure Email Is Designed For High-Profile Targets http://www.Slate.com/blogs/future_tense/2017/10/17/google_introduces_super_secure_email_to_prevent_high_profile_hacks_could.html Appears to be open to all. Anyone tried this?

http://ymm.yale.edu/winter2014/people/faculty/181689/

materials in http://meetings.gersteinlab.org/2017/10.28/i0gi2017/

QT:{{"
"Wikipedia is one of the world’s most popular websites, but scientists rarely cite it in their papers. Despite this, the online encyclopedia seems to be shaping the language that researchers use in papers, according to an experiment showing that words and phrases in recently published Wikipedia articles subsequently appeared more frequently in scientific papers"
…
“Thompson and co-author Douglas Hanley, an economist at the University of Pittsburgh in Pennsylvania, commissioned PhD students to write 43 chemistry articles on topics that weren’t yet on Wikipedia. In January 2015, they published a randomized set of half of the articles to the site. The other half, which served as control articles, weren’t uploaded.
…
Using text-mining techniques to measure the frequency of words, they found that the language in the scientific papers drifted over the study period as new terms were introduced into the field. This natural drift equated to roughly one new term for every 250 words, Thompson told Nature. On top of those natural changes in language over time, the authors found that, on average, another 1 in every 300 words in a scientific paper was influenced by language in the Wikipedia article.”

"}}

#Wikipedia shapes lang. in science https://www.Nature.com/news/wikipedia-shapes-language-in-science-papers-1.22656 Seeding it with new pages & watching them evolve (v ctrls) as a type of soc. expt