Discover and read the best of Twitter Threads about #openscience

Most recents (24)

Flanker is a reference free tool to faciliate analysis of flanking regions around genes - it extracts sequences around genes of interest then clusters these based on mash distance thresholds (lots of tunable options to customise this)
There are lots of great tools for studying mobile genetic elements like TETyper/MEFinder/Galileo etc but these all rely on reference databases and specialist knowledge.
Read 9 tweets
To *animal researchers*, a must-read on a sensitive topic rdcu.bs/cfsk6: statistical power of #animalresearch and of the number of animals used. A thread of why-do-I-like-this-paper or watch a 10-min video bit.ly/2M0EyNm @NatureNeuro go.nature.com/3dopwwl
Disclaimer: own production with amazing collaborators @sarabdjitsingh@MathiasVSchimdt@KorosiAniko@z_baram@JelleKnop@JessicaLBolton@joeribordes & twitterless others
Red is bad, green is good. At best 12.5% of animal experiments are estimated to be sufficiently prospectively powered. ‘At best’ because the estimate is before any subsequent experimental bias, p-hacking/fishing, multiple testing…
Read 22 tweets
There is a highly instructive symposium on "Veil of Ignorance" #ProcessTracing in the new @APSAtweets QMMR publication qmmrpublication.com/uploads/1/1/4/… There is lots to say ab it. For now, I want to focus on whether (causal) qualitative research has a problem w/ confirmation bias that 1/
needs to be addressed.
In short, Veil of Ignorance process tracing aims to blindfold the data collectors and analysts to the hypotheses to reduce risk of confirmation bias.
Proposal receives a lot of criticism by all respondents, partly for valid reasons, partly not, IMO 2/
If there was no bigger issue with confirmation bias, there would not be much benefit in talking about blinding in qualitative research.
As Beach notes, the intro to the symposium does not present evidence that bias is a problem. This is correct, but there is also no evidence 3/
Read 15 tweets
Our paper about large-scale atmospheric flow patterns and extreme precipitation events over the Mediterranean is now available in the Int. J. Climatology #RMetSJournals #OpenAccess #OpenScience
rmets.onlinelibrary.wiley.com/doi/10.1002/jo…
Here follows a small thread about the main findings:
We analyzed the daily weather patterns over the Mediterranean and grouped them based on their variability in the lower and middle troposphere. We derived 9 patterns that represent distinct synoptic-scale atmospheric conditions over the area.
These patterns are related to the preferential occurrence of extreme precipitation over different subregions. Especially for the coast and highlands, the probability of extremes in the most relevant pattern is over 4x higher than the nominal probabilities .
Read 6 tweets
beste @haan_judith en @mariekeadria, in scienceguide.nl/2021/01/zonder… vertellen jullie over de rol van leiderschap. Het riep bij mij superveel vragen op. Ik wil een paar dingen terugspelen als commentaar, maar eindig met een central vraag. 1/
@haan_judith @mariekeadria voor mij staat #openscience compleet los van leiderschap. Als de associatie dat in beide gebieden veel kan en misschien moet gebeurden, daar kan ik in meegaan. Maar voor mij staan ze verder los van elkaar: voor #openscience heb je gewoon alle teamrollen nodig. 2/
@haan_judith @mariekeadria Ik zag 'getalenteerd amateurmodel' voorbijkomen. Dat is hard. Ik weet niet of dit helemaal te veranderen is. Ik heb wel een beeld met wat er bedoelt wordt. Het laat mooi zien dat middelen doelen worden. Want het aantal publicaties en subsidies staat niet los van leiderschap. 3/
Read 8 tweets
Vu mon grand intérêt pour les cultures #orphelines, je ne peux m'empêcher de partager ce bel article review fraîchement publié dans Molecular Plant, avec un focus sur les céréales et les nouvelles techniques d'amélioration.
#ThreadRésumé ! ⤵️⤵️⤵️ 1/
L'article complet est accessible sans paywall (vive l'#openscience) :

2/
sciencedirect.com/science/articl…
Petit rappel sur les cultures orphelines. Il s'agit d'espèces qui ont peu bénéficié de programmes d'amélioration et sont cultivées à échelle souvent locale. L'intérêt pour ces plantes prend beaucoup d'ampleur aujourd'hui, pour plusieurs raisons.
3/
Read 32 tweets
Hey twitter!
We are now live on r/science to discuss our preprint on the misuse of #OpenScience principles in #COVID19 research projects.

Our results are available as a preprint here: doi.org/10.1101/2020.0…

Come and discuss it here:
reddit.com/r/science/comm…

#AcademicChatter
Read 8 tweets
NEW EXPLAINER ATTACHED: why you should ignore people or articles saying there’s insufficient evidence of the link between Covid and Vitamin D and start taking 4000 IU (100 micrograms) / day NOW*. That’s 10x the RDA. Nothing to lose (except a few pennies) and everything to gain. ImageImageImageImage
*4000 IU / day for healthy adults with no contraindications (you’d probs already know if you have any). Some experts recommend taking 10,000 IU / day for few weeks to help build up levels. Liquid form best as it’s oil-soluble. Older kids 2000 IU / day, younger ones 1000 IU / day
IMPORTANT: New #OpenScience live meta-analysis of all #vitaminD studies by @CovidAnalysis concludes Vitamin D is effective for #COVID19.

Treatment studies - 75% improvement, p = 0.00012
Sufficiency studies - 58% improvement, p < 0.0001

vdmeta.com Take 4000 / day
Read 7 tweets
A thread on #research policy - maybe not good New Year fare, but #COVID19 has demonstrated how important it is to have it right. Really interested in a conversation around this. International best practice is to create a broad base of international quality research activity: 1/11
A broad base ensures we are as well prepared and well educated as we can be for whatever comes along. Excellent #research happens in both the private and public sectors and both should be encouraged. Tax policy incentivises the former: the challenge lies with the latter 2/11
For at least 10 yrs there has been confusion over the reason for funding public sector #research, and what the distinction is between this research and for-profit research: take a look at the @scienceirel annual reports to see the emphasis on commercialisation 3/11
Read 11 tweets
Why I think that $ocean datamarket & @oceanprotocol can be a gamechanger for #opendata & #openscience (with regard to the 1st round of DAO grant proposals). This is going to be a bit of a tweetstorm ... 🌊 ... lets dive in ... 🤿
Studies on open data and open science show us the main drivers of participation in #opendata & #openscience (this list will be incomplete).
In the following I will cite @AnnekeZuiderwyk and @H_Spiers a lot, as they summarized this brilliantly in "Sharing and re-using open data: A case study of motivations in astrophysics". sciencedirect.com/science/articl…
Read 19 tweets
Really excited to share a new In Press article at @PsychScience with @minzlicht and @ZoeLFrancis titled The Experience of Empathy in Everyday life! This is my first first-author publication and I'm thrilled to finally tell you about it😀! Preprint psyarxiv.com/hjuab, thread:
We used quota-sampling and experience sampling to examine everyday experiences of empathy and their connection with subjective well-being and prosocial behaviour in the everyday lives of a sample of U.S. adults that was representative of the population on key demographics 1/8.
Our sample of 246 adults answered 7,343 surveys, yielding a rich dataset we are happy to open to interested researchers (osf.io/y3ud7/). We found some really interesting findings that can inform our understanding of empathy moving forward. 2/8
Read 9 tweets
during my #PhD, i conducted a side project investigating what the barriers are towards making changes to the #academicpublishing system to reduce publication #bias

journals.plos.org/plosone/articl…

this showed me a rather dark side to #academia... 1/8

#AcademicTwitter #phdlife
i got about 50:50 praise and hate for this. weirdly enough, the praise and hate were often about the same thing: the (early) stage of my career.

praise: "it's great you're so keen and have grasped key issues and taken action so early..." 2/8
hate: "you're too early in your career and naïve to understand these issues. you shouldn't be researching this"

more worryingly, whilst i did get a lot of this feedback in person/by email, some of it was BEHIND MY BACK to my colleagues 3/8
Read 10 tweets
21 Tips on how to sound #openscience: in the last three weeks before x-mas, I will tweet on tip each day on how to sound like an open scientist, without actually doing open science. Enjoy! Image of a x-mas candle wit...
21 Tips on how to sound #openscience #1: provide temporary green #openaccess to paywalled literature without an open license during a global health crisis (only for one crisis is enough)
21 Tips on how to sound #openscience #2: host a website, tell everyone they can use it, allow everyone to use it in publication (free advertisement), but do not allow others to reuse it. Better ever, say: "but it is on the internet!"
Read 24 tweets
1/4
2013 yılından beri verdiğim "Araştırma Yöntemleri " derslerini " "İktisatta Araştırma Yöntemleri ve Bilim Ahlakı" adı altında Ankara Üniversitesi'nin Açık Ders Malzemeleri'ne yükledim. acikders.ankara.edu.tr/course/view.ph…
Bu adresten, konulara göre ayırdığım ders içeriklerine, derslerde kullandığım PP Slide'larına, çoğu açık erişim olan okumalara ve izlemelere, geçmiş yıllarda sorduğum sorulara özgür ve bedava ulaşabilirsiniz.Derslerin çoğunun İngilizce PP Slide'ları da yine bu adreste yer alıyor.
3/4
Önümüzdeki dönem "İktisat ve Felsefe Monologları"na bilim ahlakı videoları yükleyeceğim. Her video 5 dakikayı geçmeyen kayıtlardan oluşacak.Araştırmaya yeni başlayan iktisatçıların merak ettiği ama sormaya çekindiği bazı soruları yanıtlamayı düşünüyorum.
Read 5 tweets
🚨Highlight reel thread of today's talk.🚨

I spoke to students and faculty at @AbertayUni about how we do #edtech research at WGU Labs, and advice for psychology PhDs looking to land an #altac role.

[THREAD] with pics, links to posts, and the full presentation at the end 👇🏼 1/
The #edtech industry has been on the rise since 2018, but #COVID19 has acted as a catalyst for online learning at scale in 2020. Edtech adoption by educators has been a huge output of this pandemic & all the more reason that our work at Labs is super relevant right now. 2/
However, there are some three key problems that I see with #edtech research👇🏼

Edtech research should focus IMO on enhancing core learning processes. I've talked about some of this here: nicolebarbaro.com/2020/06/16/usi… 3/
Read 10 tweets
1/ 🥳🎉We won an academic award!
Today CoronaWatchNL received the Research Data Prize, an important academic award on making data available in a FAIR manner to improve and validate research. We contributed to this publication and are co-author on it. #OpenScience #AcademicTwitter
2/ CoronaWatchNL collects data on the COVID-19 disease in The Netherlands. The data is collected from various sources on a daily basis, like RIVM, LCPS, NICE and many more.
doi.org/10.5281/zenodo…
3/ The data can also be found on GitHub.
github.com/J535D165/Coron…
Read 5 tweets
we're going to have a big copyright law fight in science... putting scientific knowledge online, allows legal scraping in the USA. That means, putting data online, puts it out in the open. I am not sure if the scraped data falls under copyright (does it)? 1/
but that latter is not the point: by taking data from a licensed source that does not allow redistribution, and you put it online, you *are* distributing it. Similar thing we see with SPARQL end points. The scraping there is trivial. 2/
it nicely shows that most researches don't git a s***/f*** (depending on region) about copyright law (also why many happily give it for free to publishers). Few journals give a s***/f*** (depending on publisher) either. 3/
Read 13 tweets
Check out our new paper by @smartinezarbas et al. about #CRISPR mediated interactions within a wastewater #microbiome in @NatureMicrobiol! Exciting collaboration between @uni_lu @TGen @IUBloomington @isbsci @KU_Leuven. Funding by @FnrLux
nature.com/articles/s4156…

A 🧵👇

1/9
In parallel with recent work of @mhe345 @NatureComms nature.com/articles/s4146…, we explored the roles of #plasmids and #phages within a wastewater treatment plant microbial community, using longitudinal integrated #omics data 2/9
We identified 31 bacterial MAGs with complete #CRISPR-Cas systems from the 14-months data set. These MAGs served as the basis for downstream population-level analyses of #CRISPR interactions 3/9
Read 9 tweets
Daily Bookmarks to GAVNet 11/01/2020 greeneracresvaluenetwork.wordpress.com/2020/11/01/dai…
The next-generation bots interfering with the US election

nature.com/articles/d4158…

#election #bots
(Why) Philosophy Should Be a Foundation of Our World

medium.com/the-philosophe…

#philosophy #DecisionMaking #education #KnowledgeManagement
Read 8 tweets
1. La v2 de notre #preprint “Open Science Saves Lives: Lessons from the COVID-19 pandemic” est out.
Cosignée par 371 chercheurs. Résumé rapide de l'article.

doi.org/10.1101/2020.0…
#OpenScience
2. Les problèmes que nous avons trouvés sont également mis en évidence ici, avec le pipeline de publication classique.
Nous avons souligné le nombre élevé d'essais erronés ou redondants et la manière dont les registered reports et les preregistrations auraient pu aider
3. Environ 700 papiers étaient revus en un jour ou moins avant d'être acceptés.
Parmi ces articles, 224 présentaient de nouveaux résultats de recherche et ~32% d'entre eux présentaient des conflits d'intérêts éditoriaux (eCOI). eCOI + revue en un jour c'est, au mieux, louche.
Read 16 tweets
1. The v2 or our #preprint “Open Science Saves Lives: Lessons from the #COVID19 pandemic” is out.
It has been co-signed by 371 scientists. Here is a quick summary of our findings and solutions
doi.org/10.1101/2020.0…
#OpenScience #openaccess #OpenData @AcademicChatter
2. The problems that we have found are also highlighted here along with a classical publication pipeline.
We have highlighted the high number of flawed or redundant trials and how registered reports and thorough preregistrations could have helped
3. We have found approximately 700 papers being reviewed in a day or less before being accepted.
Among these 224 manuscripts presented new research results and ~32% of them had editorial conflicts of interests (eCOI). eCOI + review in a day is, at best, shady.
Read 16 tweets
We are thrilled to share our #preprint "Atlas of genetic effects in human #microglia transcriptome across brain regions, aging and #disease pathologies"!
Work led by @lopeskp @JackHumphrey_ #Gijsje and others from #deWitte and #Raj Lab (@towfiqueRaj)
t.ly/pZqQ 1/23
Here, we describe the Microglia Genomic Atlas (#MiGA) project. A genetic and transcriptomic resource of 255 primary human microglia isolated from 4 brain regions of 100 donors with neurodegenerative and psychiatric disease and controls. 2/23 Image
We performed the following analysis: I) age-related (the age of donors range from 21 to 103 y.o! II) brain regional heterogeneity ; III) expression and splicing quantitative trait loci #eQTL & #sQTL. 3/23
Read 23 tweets
Survived another ASHG plenary talk :)

In case you missed it, I presented results on behalf of @Regeneron from a trans-ancestry #COVID19 meta-analysis of common and rare variants + gene burden tests in >883k imputed samples and >592k exomes.
#ASHG20
Using REGENIE developed by @joellembatchou and @marchini (SAIGE gave us some bizarre results with rare variants) to run our common and rare variant GWASes, we found 2 loci associated with susceptibility and 3 loci with hospitalization. #ASHG20
Curiously, despite losing ~75% of the cases, we found more loci with hospitalization than using all COVID19 positive individuals - @covid19_hgi sees the same pattern.

One might suspect a severe COVID19 GWAS would be even more powerful at the same sample size
#ASHG20
Read 10 tweets
It appears the SNSI arguing that universities ought to install publisher spyware on their servers
bjoern.brembs.net/2020/10/is-the…
is just the tip of the iceberg.
There seems to be a clan of publisher-initiatives and companies that reinforce each other and create a disinformation and surveillance network: PSI, LibLynx etc.

Something is brewing that the #OpenScience community doesn't seem to have on their radar, yet.
Again, as so many times before, academics have to organize a defense against the onslaught of corporate interests against the public good.
Read 5 tweets

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