Posts Tagged ‘i0gpwrite’

List of collaboration tools

July 3, 2017

Thought the below was an interesting snippet from a dialogue I had….

QT:{{”

Collaboration tools: Even a small group…will quickly get unwieldy if we coordinate using long CC-chains on email threads.

I think the minimum requirements are central management, email lists, and document sharing.

Options that come to mind are:
– Google G-suite, Drive, and Groups (free for nonprofits, robust features, integrate with existing login…)
– Slack plus Dropbox (more suited for teams who are actively collaborating, but it could be a great framework)
– Yammer (looks great, but I’ve never really used it)
– Office365 (it’s heavyweight and costs money, but it’ll give us all the features we could ever imagine)
– Basecamp (I haven’t used it in years, and it’s more about project management than collaboration)

“}}

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First, design for data sharing : Nature Biotechnology : Nature Research

June 20, 2017

Design for data sharing
http://www.Nature.com/nbt/journal/v34/n4/full/nbt.3516.html Issues in distributing mPower mobile dataset – no DAC, allowing donors to change preferences

QT:{{”
“This March, Sage Bionetworks (Seattle) began sharing curated data collected from >9,000 participants of mPower, a smartphone-enabled health research study for Parkinson’s disease. The mPower study is notable as one of the first observational assessments of human health to rapidly achieve scale as a result of its design and execution purely through a smartphone interface. To support this unique study design, we developed a novel electronic informed consent process that includes participant-determined data-sharing preferences. It is through these preferences that the new data—including self-reported outcomes and quantitative sensor data—are shared broadly for secondary analysis. Our hope is that by sharing these data immediately, prior even to our own complete analysis, we will shorten the time to harnessing any utility that this study’s data may hold to improve the condition of patients who suffer from this disease.

Turbulent times for data sharing

Our release of mPower comes at a turbulent time in data sharing. The power of data for secondary research is top of mind for many these days. Vice President Joe Biden, in heading President Barack Obama’s ambitious cancer ‘moonshot’, describes data sharing as second only to funding to the success of the effort. However, this powerful support for data sharing stands in opposition to the opinions of many within the research establishment. To wit, the august New England Journal of Medicine (NEJM)’s recent editorial suggesting that those who wish to reuse clinical trial data without the direct participation and approval of the original study team are “research parasites”. In the wake of colliding perspectives on data sharing, we must not lose sight of the scientific and societal ends served by such efforts.” “}}

CATO score

May 28, 2017

Seq. variants influencing…TF occupancy
http://www.Nature.com/ng/journal/v47/n12/full/ng.3432.html Uses allelic analysis to develop the CATO score, how variants alter binding

QT:{{”
This approach resulted in a simple scoring scheme, termed contextual analysis of transcription factor occupancy (CATO), that provides a recalibrated probability of affecting the binding of any transcription factor, as well as a quantitatively ranked list of transcription factor families whose binding might be altered.
“}}

JEPricer Studio | animated abstractions of human data

May 27, 2017

https://jepricer.com/

Thoughts on last week’s conferences GP-Write & BoG ’17

May 15, 2017

TWEETS

https://storify.com/markgerstein/favorite-tweets-from-bog-17-gp-write-ib.html

TAGGED ITEMS

https://linkstream2.gerstein.info/tag/i0gpwrite/

SLIDES

http://lectures.gersteinlab.org/summary/Scaling-Computation-to-Keep-Pace-w-Data-Gen–20170510-i0gpwrite/

An Economic Framework of Microbial Trade

May 15, 2017

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0132907

Biogeography and individuality shape function in the human skin metagenome : Nature : Nature Research

May 15, 2017

http://www.nature.com/nature/journal/v514/n7520/abs/nature13786.html

Money still missing as the plan to synthesize a human genome takes another step forward | Science | AAAS

May 15, 2017

http://www.sciencemag.org/news/2017/05/money-still-missing-plan-synthesize-human-genome-takes-another-step-forward

Brainstorming is not the way to discuss scientific issues : Nature News & Comment

May 15, 2017

http://www.nature.com/news/brainstorming-is-not-the-way-to-discuss-scientific-issues-1.21951

With all due respect to Maholo, lab automation isn’t anthropomorphic : Nature Biotechnology : Nature Research

May 15, 2017

http://www.nature.com/nbt/journal/v35/n4/full/nbt.3795.html?WT.feed_name=subjects_animal-biotechnology