It was great to talk about reproducible workflows for @riotscienceclub @riotscience_wlv. You can watch the recording below, but if you don't want to listen to me talk for 40 minutes, I thought I would summarise my talk in a thread:
Thank you again @JamesEBartlett for a fantastic talk (with a really nice personal touch) on reproducible workflows!
— RIOT Science Club Wolverhampton (@riotscience_wlv) February 16, 2021
Thanks especially for the co-leads @IMLahart for co-hosting and @DrManiBhogal for nabbing James!
Slides: https://t.co/CNqxzOhch1
Video: https://t.co/YjHEHuRJlz
Why are lunch breaks important for #code?
— Dr Rebecca Hirst (@HirstRj) February 11, 2021
If you can't remember what your variable names refer to after lunch, you sure as hell won't remember in 3 months.
More from Science
@mugecevik is an excellent scientist and a responsible professional. She likely read the paper more carefully than most. She grasped some of its strengths and weaknesses that are not apparent from a cursory glance. Below, I will mention a few points some may have missed.
1/
The paper does NOT evaluate the effect of school closures. Instead it conflates all ‘educational settings' into a single category, which includes universities.
2/
The paper primarily evaluates data from March and April 2020. The article is not particularly clear about this limitation, but the information can be found in the hefty supplementary material.
3/
The authors applied four different regression methods (some fancier than others) to the same data. The outcomes of the different regression models are correlated (enough to reach statistical significance), but they vary a lot. (heat map on the right below).
4/
The effect of individual interventions is extremely difficult to disentangle as the authors stress themselves. There is a very large number of interventions considered and the model was run on 49 countries and 26 US States (and not >200 countries).
5/
1/
I've recently come across a disinformation around evidence relating to school closures and community transmission that's been platformed prominently. This arises from flawed understanding of the data that underlies this evidence, and the methodologies used in these studies. pic.twitter.com/VM7cVKghgj
— Deepti Gurdasani (@dgurdasani1) February 1, 2021
The paper does NOT evaluate the effect of school closures. Instead it conflates all ‘educational settings' into a single category, which includes universities.
2/
The paper primarily evaluates data from March and April 2020. The article is not particularly clear about this limitation, but the information can be found in the hefty supplementary material.
3/
The authors applied four different regression methods (some fancier than others) to the same data. The outcomes of the different regression models are correlated (enough to reach statistical significance), but they vary a lot. (heat map on the right below).
4/
The effect of individual interventions is extremely difficult to disentangle as the authors stress themselves. There is a very large number of interventions considered and the model was run on 49 countries and 26 US States (and not >200 countries).
5/
https://t.co/hXlo8qgkD0
Look like that they got a classical case of PCR Cross-Contamination.
They had 2 fabricated samples (SRX9714436 and SRX9714921) on the same PCR run. Alongside with Lung07. They did not perform metagenomic sequencing on the “feces” and they did not get
A positive oral or anal swab from anywhere in their sampling. Feces came from anus and if these were positive the anal swabs must also be positive. Clearly it got there after the NA have been extracted and were from the very low-level degraded RNA which were mutagenized from
The Taq. https://t.co/yKXCgiT29w to see SRX9714921 and SRX9714436.
Human+Mouse in the positive SRA, human in both of them. Seeing human+mouse in identical proportions across 3 different sequencers (PRJNA573298, A22, SEX9714436) are pretty straight indication that the originals
Were already contaminated with Human and mouse from the very beginning, and that this contamination is due to dishonesty in the sample handling process which prescribe a spiking of samples in ACE2-HEK293T/A549, VERO E6 and Human lung xenograft mouse.
The “lineages” they claimed to have found aren’t mutational lineages at all—all the mutations they see on these sequences were unique to that specific sequence, and are the result of RNA degradation and from the Taq polymerase errors accumulated from the nested PCR process
Look like that they got a classical case of PCR Cross-Contamination.
They had 2 fabricated samples (SRX9714436 and SRX9714921) on the same PCR run. Alongside with Lung07. They did not perform metagenomic sequencing on the “feces” and they did not get
A positive oral or anal swab from anywhere in their sampling. Feces came from anus and if these were positive the anal swabs must also be positive. Clearly it got there after the NA have been extracted and were from the very low-level degraded RNA which were mutagenized from
The Taq. https://t.co/yKXCgiT29w to see SRX9714921 and SRX9714436.
Human+Mouse in the positive SRA, human in both of them. Seeing human+mouse in identical proportions across 3 different sequencers (PRJNA573298, A22, SEX9714436) are pretty straight indication that the originals
Were already contaminated with Human and mouse from the very beginning, and that this contamination is due to dishonesty in the sample handling process which prescribe a spiking of samples in ACE2-HEK293T/A549, VERO E6 and Human lung xenograft mouse.
The “lineages” they claimed to have found aren’t mutational lineages at all—all the mutations they see on these sequences were unique to that specific sequence, and are the result of RNA degradation and from the Taq polymerase errors accumulated from the nested PCR process
What is going on at SWANSEA UNIVERSITY in Wales?
1.
https://t.co/d5NKtNlxxa
Sounds as if its connected to Bill Gates "LUCIFERASE" Vaccine?
2.
https://t.co/k0w1mjaPg0
"HILLARY RODHAM CLINTON SCHOOL OF LAW"
- AT SWANSEA UNIVERSITY!!!
3.
https://t.co/jifuWq6cGq
Remember all those FIRES, over the Summer!!!
4.
https://t.co/H3lstFyYx8
WUHAN PARTNERSHIP
"Links between Swansea & Wuhan date back to 1855 when Swansea missionary Griffith John founded the Wuhan Union Hospital.
This relationship was strengthened when representatives of the two cities signed an agreement".
5.
https://t.co/5b1JqiEQzi
Swansea University Strengthens Links with China
1.
https://t.co/d5NKtNlxxa
Sounds as if its connected to Bill Gates "LUCIFERASE" Vaccine?
2.
https://t.co/k0w1mjaPg0
"HILLARY RODHAM CLINTON SCHOOL OF LAW"
- AT SWANSEA UNIVERSITY!!!
3.
https://t.co/jifuWq6cGq
Remember all those FIRES, over the Summer!!!
4.
https://t.co/H3lstFyYx8
WUHAN PARTNERSHIP
"Links between Swansea & Wuhan date back to 1855 when Swansea missionary Griffith John founded the Wuhan Union Hospital.
This relationship was strengthened when representatives of the two cities signed an agreement".
5.
https://t.co/5b1JqiEQzi
Swansea University Strengthens Links with China
1/ Automobiles and Intake Fraction. Since cars are back in the news I thought I would retweet this model result I offered in early April 2020. I focused only on 1 micron particles & accounted for windows completely closed & cracked slightly open.
2/ Related air exchange rates were based on experimental results in literature for mid-sized sedans. Particle deposition to indoor surfaces were accounted for, as the surface to volume ratio in a 3 m3 cab is large. An important outcome was the intake fraction (IF)
3/ Here, IF is the number of particles (or virions in collective particles) inhaled by a receptor DIVIDED BY the number or particles (or virions in collective particles) emitted by an infector.
4/ Integrated over the two hour drive (in this example) the IF for all windows closed & a receptor at rest is 0.08 (8% of what comes out of the infectors respiratory system ends up in the respiratory system of the receptor). 8%! That is a very high intake factor.
5/ With additional ventilation from cracking a window open drops the IF to 0.012 (1.2%) still relatively high. Can get lower by opening more windows.
Simulation: Riding in car for 120 min w/ infected passenger who seems fine other than a cough every few mins. (1) a lot of SARS-CoV-2 virus (in fine aerosol particles) accumulation in car cabin w/ windows closed; (2) cracking window open slightly = dramatic reduction. #COVID19 pic.twitter.com/bCmrmnLUPG
— Dr. Richard Corsi (@CorsIAQ) April 4, 2020
2/ Related air exchange rates were based on experimental results in literature for mid-sized sedans. Particle deposition to indoor surfaces were accounted for, as the surface to volume ratio in a 3 m3 cab is large. An important outcome was the intake fraction (IF)
3/ Here, IF is the number of particles (or virions in collective particles) inhaled by a receptor DIVIDED BY the number or particles (or virions in collective particles) emitted by an infector.
4/ Integrated over the two hour drive (in this example) the IF for all windows closed & a receptor at rest is 0.08 (8% of what comes out of the infectors respiratory system ends up in the respiratory system of the receptor). 8%! That is a very high intake factor.
5/ With additional ventilation from cracking a window open drops the IF to 0.012 (1.2%) still relatively high. Can get lower by opening more windows.
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BREAKING: @CommonsCMS @DamianCollins just released previously sealed #Six4Three @Facebook documents:
Some random interesting tidbits:
1) Zuck approves shutting down platform API access for Twitter's when Vine is released #competition
2) Facebook engineered ways to access user's call history w/o alerting users:
Team considered access to call history considered 'high PR risk' but 'growth team will charge ahead'. @Facebook created upgrade path to access data w/o subjecting users to Android permissions dialogue.
3) The above also confirms @kashhill and other's suspicion that call history was used to improve PYMK (People You May Know) suggestions and newsfeed rankings.
4) Docs also shed more light into @dseetharaman's story on @Facebook monitoring users' @Onavo VPN activity to determine what competitors to mimic or acquire in 2013.
https://t.co/PwiRIL3v9x
Some random interesting tidbits:
1) Zuck approves shutting down platform API access for Twitter's when Vine is released #competition
2) Facebook engineered ways to access user's call history w/o alerting users:
Team considered access to call history considered 'high PR risk' but 'growth team will charge ahead'. @Facebook created upgrade path to access data w/o subjecting users to Android permissions dialogue.
3) The above also confirms @kashhill and other's suspicion that call history was used to improve PYMK (People You May Know) suggestions and newsfeed rankings.
4) Docs also shed more light into @dseetharaman's story on @Facebook monitoring users' @Onavo VPN activity to determine what competitors to mimic or acquire in 2013.
https://t.co/PwiRIL3v9x
