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:

My inspiration was making open science accessible. I wanted to outline the mistakes I've made along the way so people would feel empowered to give it a go. Increased accountability is seen as a barrier to adopting open science practices as an ECR https://t.co/bNK6poNpzx
It also comes across as all or nothing. You are either fully open science or your research won't get anywhere. However, that can be quite intimidating, so I wanted to emphasise this incremental approach to adapting your workflow https://t.co/HS3dx5qJL3
There are two sides to why you should work towards reproducibility. The first is communal. It's going to help the field if you or someone else can reproduce your whole pipeline.
There is also the selfish element of it's just going to help you do your work. If you can't remember what your work means after a lunch break, you're not going to remember months or years down the line https://t.co/iRSXISI5NE
Pre-registration is super helpful, but it takes time to learn how to do it effectively. I had no support for my first attempt and it was awful. https://t.co/o0QgrtBFfJ
But I learnt from my mistakes and eventually got to a point where I'm happy with my approach.
Some aspects of open science can't be added at the end. If you want to share your data, it has to be planned from the ethics stage and your participants have to consent to it. Just remember not all data can be shared openly for ethical reasons.
Sharing materials is one of the easiest things you can do, but very few researchers do it. You can share your stimuli (providing there's no copyright issues) and your task scripts. If you use @GorillaPsyc, there is an open materials function making it super easy.
Double check your analysis pipeline, especially when the results support your hypotheses. I caught an error in my first PhD study before it was too late, but it could have been super embarrassing.
You don't have to go the full R Markdown manuscript route, but I recommend at least scripting any data processing. If you do make a mistake, at least that error is reproducible. You can also use intermediaries like @tidystats to embed results from R into your Word file.
Finally, if you can't read the article in the first place, you can't reproduce it. Most journals allow you to post pre/post-prints and you can upload your dissertation/thesis to Thesis commons. Just double check it's permitted by your target journal: https://t.co/iIIw1VDHdC
Hopefully, this seminar shows people fuck up from time to time. It's about learning from those mistakes and doing what you can to minimise them in future. Try making your workflow more reproducible one step at a time. It'll be worth it in the long-run for you and the community.

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"The new answer to a 77-year-old problem"

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JUST ONE PERSON—UK 🇬🇧 scientists think one immunocompromised person who cleared virus slowly & only partially wiped out an infection, leaving behind genetically-hardier viruses that rebound & learn how to survive better. That’s likely how #B117 started. 🧵 https://t.co/bMMjM8Hiuz


2) The leading hypothesis is that the new variant evolved within just one person, chronically infected with the virus for so long it was able to evolve into a new, more infectious form.

same thing happened in Boston in another immunocompromised person that was sick for 155 days.

3) What happened in Boston with one 45 year old man who was highly infectious for 155 days straight before he died... is exactly what scientists think happened in Kent, England that gave rise to #B117.


4) Doctors were shocked to find virus has evolved many different forms inside of this one immunocompromised man. 20 new mutations in one virus, akin to the #B117. This is possibly how #B1351 in South Africa 🇿🇦 and #P1 in Brazil 🇧🇷 also evolved.


5) “On its own, the appearance of a new variant in genomic databases doesn’t tell us much. “That’s just one genome amongst thousands every week. It wouldn’t necessarily stick out,” says Oliver Pybus, a professor of evolution and infectious disease at Oxford.

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The UN just voted to condemn Israel 9 times, and the rest of the world 0.

View the resolutions and voting results here:

The resolution titled "The occupied Syrian Golan," which condemns Israel for "repressive measures" against Syrian citizens in the Golan Heights, was adopted by a vote of 151 - 2 - 14.

Israel and the U.S. voted 'No'
https://t.co/HoO7oz0dwr


The resolution titled "Israeli practices affecting the human rights of the Palestinian people..." was adopted by a vote of 153 - 6 - 9.

Australia, Canada, Israel, Marshall Islands, Micronesia, and the U.S. voted 'No' https://t.co/1Ntpi7Vqab


The resolution titled "Israeli settlements in the Occupied Palestinian Territory, including East Jerusalem, and the occupied Syrian Golan" was adopted by a vote of 153 – 5 – 10.

Canada, Israel, Marshall Islands, Micronesia, and the U.S. voted 'No'
https://t.co/REumYgyRuF


The resolution titled "Applicability of the Geneva Convention... to the
Occupied Palestinian Territory..." was adopted by a vote of 154 - 5 - 8.

Canada, Israel, Marshall Islands, Micronesia, and the U.S. voted 'No'
https://t.co/xDAeS9K1kW