Discover and read the best of Twitter Threads about #OpenScience

Most recents (24)

Feels very timely today to be on the way to the #Nobel Symposium in Stockholm: The First Great Pandemic of the 21st Century.
Though I do not believe the #monkeypox outbreak will be a pandemic, it's a reminder there are many pathogens that can rear their heads in different ways.
Tomorrow, I'll talk about how phylogenetics played a critical role in #COVID19 #SARSCoV2 - but also outline what challenges we face when we look to tomorrow's pandemics. In particular we have to ensure: sequencing, sharing, software & sufficient background.
A lot of pandemic preparedness focuses on detecting a new pathogen, or what to do once we know it's bad news. But a lot of the critical work is a little more boring: encouraging #openscience, ensuring credit, maintaining & advancing software & building up our virus knowledge.
Read 8 tweets
A little thread on biodiversity #datasharing #openaccess #openscience. On sharing data on #rainforest birds and habitat that @gundupoo and I collected during 1997-99 in the Kalakad-Mundathurai Tiger Reserve #WesternGhats... a retrospective from a quarter century later 1/n In KMTR, March 1999; Photo by P JeganathanIn KMTR, Dec 2018; Photo by Kalyan Varma
Field biologists need not just collect or hoard biodiversity data for their own use. Sharing under a CC-BY or public domain (CC0) license enables better and wider use and adds value to science and scholarship, students and citizens. 2/n Illustration @dasaptaerwin @WikiCommons
For a start, our doctoral research data from KMTR, used in a couple of papers, is now @datadryad (CC0/Public Domain license). Bird and vegetation/habitat data from 21 transects in rainforests along an elevation gradient and from abandoned plantations. 3/n
datadryad.org/stash/dataset/…
Read 14 tweets
mich nervt doch nicht, dass #weltgesellschaft andere organisation als nationalstaatlichkeit sucht. GANZ IM GEGENTEIL. mich nervt, dieses revival von nationalstaat auf diesem dummen niveau 🙁 an @kobich #LiberalerPaternalismus sucks dissent.is/Liberaleratern…
DIE METAPHER VOM MYZEL
ist besser, als
DIE METAPHER VOM RHIZOM
ist besser, als
DIE METAPHER VOM SYSTEM

fiasta-da-bulius.ch #agree2disagree #how2disasgree und die suche nach #CriticalMass (so?)
wrnn ich erklären müsste, woran ich aktuell arbeite.

DIE GRENZEN VON #Polsprung 1

#KatharinaVonZimmern
#bsggt
#FiastaDaBulius
#Q102014 Q102014.xyz Image
Read 9 tweets
A *brutal* snapshot of #COVID19
in cancer patients
⚠️75 of 416 patients died
*⃣ 61.3% of these deaths were due to
COVID-related complications
mdpi.com/2072-6694/14/9… #scicomm #snrtg #openscience #immunology #oncology #immunocompromised
Please 💉get vaccinated💉
to protect yourself
AND the immunocompromised
from Sars-Cov-2.
The immunocompromised, immunosuppressed, and immunodeficient are taking a beating from this virus.
A f-cking beating.
Read 4 tweets
🦠#COVID19 infection
*⃣ and reinfection *⃣
in a young⚠️immunocompromised ⚠️boy
fighting rare cancer
A 4⃣5⃣0⃣ battle for survival - he died
journals.lww.com/pidj/Fulltext/… #bioinformatics #openscience #snrtg #scicomm #immunology #raredisease Image
Immunocompromised patients,
- like kids fighting cancer,
are depending on *you* for protection.
Please💉get vaccinated💉
I meant to write a '450 DAY' battle for survival.
Read 4 tweets
More #inclusive #openscience can help solve society’s most pressing problems—and at a faster pace—but making it mainstream requires systemic institutional change. Our new article: issues.org/opening-up-ope…
@libcce @cekroeger @theNASciences @theNASEM @AAUniversities
A thread🧵 (1/8)
"The whole enterprise has to change to truly realize the full benefits of open science..... Technology has not only improved the speed at which science is carried out, but many of the problems scientists study, from climate change to #COVID19, demand urgency."🧵 (2/8)
The type of knowledge-sharing and collaboration exemplified by #CMIP and @pangeo_data must become standard, which requires institutionalizing these practices.🧵 (3/8)

gallery.pangeo.io/repos/pangeo-g…
Read 8 tweets
Very excited about @Fermilab seminar tomorrow!

It will present a new measurement of the W boson mass to be published soon, no #openscience article yet.

There are already articles appearing, but in this thread, I try to explain why this is important with one (famous) plot Image
Why? Because the W boson is really important for the standard model, particularly for checking its consistency. I'm really excited!
The standard model, the physics theory that particle physics use is great at predicting things. This plot checks its internal consistency by comparing different ways to determine the mass of two particles: the W boson (connected to the weak interaction) and the top quark Image
Read 18 tweets
Most people don't realise that academic science is a very long way from healthy.

In fact, all good academic scientists must, at some point, go through a reckoning. When they awaken from the 'dream of science' to realise just how broken things are.

🧵 1/11
#ScienceInCrisis
My own crisis happened during my PhD. It was gradual, but at some point I realised academic science wasn't driven by truth, quality, or collectivism, but ego, opportunism, and exploitation. I couldn't believe it. It seemed so wrong and unfair.

2/11
#ScienceInCrisis
It hit me like grief. Anger, depression, bargaining. Years later & I'm still struggling. It hurts when I see bad science or a bad scientist getting celebrated.

I've been been told my 'problem' is I 'care about doing good science'. But I refuse to give in.

3/11
#ScienceInCrisis
Read 12 tweets
Hey #ACC22 presenters, especially late breaking studies of consequence. If you don't have simultaneous peer-reviewed pub, consider #preprint what you presented so it's archived & accessible. Let’s make it normative. @medrxivpreprint @yaleHFdoc #LBCT @EricTopol @CMichaelGibson
@medrxivpreprint @yaleHFdoc @EricTopol @CMichaelGibson For all #ACC22 presenters, preprinting is easy; we accept scientific studies, screen rapidly, post quickly. Non-profit. It is of the community-available throughout the world, understood as pre-peer reviewed, and citable. Almost all reputable journals are fine with it, incl @NEJM.
@medrxivpreprint @yaleHFdoc @EricTopol @CMichaelGibson @NEJM In the pandemic @medrxivpreprint stimulated discussions about research in progress, & many examples of advancing research. Cardiology has not yet fully embraced it, yet is this work any less important? All fields should accelerate public scientific communication & #openscience.
Read 6 tweets
An increasingly hot topic in #openscience is the degree to which OS strategies are applicable (or desirable) for qualitative methods. A hopefully provocative thread: 1/x
Much of my thinking here is influenced by my colleagues @MattMakel @thegrumblybuns @alongerbmarie @MchenryMelaniew who wrote this recent piece with me (should be free to download) 2/x

tandfonline.com/eprint/VJAJIAY…
I'm generally sympathetic to colleagues who think basic OS principles and strategies have considerable value regardless of whether you're primarily using quan or qual methods (or mixed-methods, for that matter). 3/x
Read 8 tweets
@larswillighagen and I are looking into registering things in the @NWONieuws ISAAC system. the forms is non-trivial. For scholarly articles NL asks for "nummer", EN ask for "Issue number"... so, where does the volume number go? And what's the "magazine URL"?
@larswillighagen @NWONieuws we're making progress and starting to feel confident to tweet this screenshot, knowing we might have something releasable today :) Even adding authors is getting close :)
@larswillighagen @NWONieuws just successfully used this to add DOI to the @NWONieuws ISAAC system, with autoadding of authors and all! :)

Near your Google Chrome Store soon.
Read 14 tweets
Over the last few days, I have seen posts advocating @RoySocChem, @AmerChemSociety to #boycott Russian scientists at conferences/from publications. Some Universities in Europe have already done so. I am very, very strongly against the boycott!
Here is a🧵with my reasons 1/11
For disclosure - I am Russian, born in the USSR, with my family currently in Russia and in Ukraine
I have been living in the UK alone since 16yo, when I went to @DurhamChemistry for my UG
*I will use male pronouns for leaders due to the gender bias in power 2/11
I'm sad to receive full face criticism for the actions of the 'president' neither I nor my family/friends ever voted. I know he still totals 146% & an absolute 'support'. I was lucky to have been in a position to 'vote with my legs out of Russia', but most people could not! 3/11
Read 12 tweets
@EthereumDenver was a superspreader of spores for the new social fabric of #Web3.

#DigitalCredentials and #ReputationProtocols entangle into a symbiotic relationship - online and offline. 🧬

ICYMI: 5 #OpenRecognition moments into a single thread ⬇️ 🧵
/1 the Keynote. @provenauthority hypnotic narrative connects the above (#OnChain) with the below (#OffChain), the present (#Web2) with the future (#Web3) across one rainbow of Use Cases 🌈

See you on the dancefloor ! 🕺 @discoxyz

#VC #DIDs #W3C

/2 #P2P Reward systems. #Praise to @tokengineering research and #hail to #OpenScience. 🙏

Inverting the "Get cited or die" dark and toxic mantra of research.

#DAO #DeSci

@NEARProtocol @oceanprotocol @SputnikDAO

Read 7 tweets
"Paris Call on Research Assessment" osec2022.eu/paris-call/

1. "Recognises that openness improves the quality, efficiency and impact of research, and fosters team science;"

Duh... you cannot peer review what you are not allowed to see

1/
2. "Reaffirms the need to align what we assess with what we value;"

Yes, very important. And likely evaluate. Why assess X which aims to quantify Y, if assessing Z has the same aim. That is, if your aim is good peer review, measure good peer review, and not the JIF.

2/
3, "Calls for an assessment system where research proposals, researchers, research units and research institutions are evaluated on the basis of their intrinsic merits and impact [..]"

This is hard, but since when do scholars shy away from hard problems?

3/
Read 23 tweets
I am delighted that, after years of collaborative and interdisciplinary efforts, our work is finally out nature.com/articles/s4146…
A joint effort with a wonderful team of colleagues (@ico2s , @portabolomics) spanning software engineering (@nocoffeenocode), synthetic biology & environmental microbiology (@vdlorenzo_CNB) and social sciences (@LPelechova , @PEALSncl )
We take a small but important step in developing tools for #OpenScience and more #reproducible strain engineering.
Read 8 tweets
Brain mapping requires thorough synaptic measurements with diverse subclasses of neurons. Check out our latest #neuroscience publication: “Synaptic connectivity to L2/3 of primary visual cortex measured by two-photon #optogenetic stimulation”
📄 elifesciences.org/articles/71103 🧵 1
Our team [including @trav_ha, @timjarsky, @HongkuiZeng & @lukecampagnola] + @bakermind combined optogenetic stimulation with simultaneous multicellular recording to measure synaptic connections within cortical microcircuits. #optogenetics🧵 2
The reliability of multiphoton optogenetic stimulation was measured across Cre lines & connectivity measurements were verified by #patchclamp recordings 🧵 3
Read 8 tweets
Our paper is live! Can fMRI measure well-being? Can the "positive-negative axis" from @fmrib_steve et al. be seen in a larger, independent dataset w/younger subs collected across sites and scanners? Want it as a preregistered replication? Read on! doi.org/10.1098/rsos.2… 1/14 Smith et al 2015 results fi...
Using code made publicly available by @fmrib_steve, we first did an exact computational replications of their 2015 Nature Neuroscience paper. It worked! You can read about that at BioRxiv: doi.org/10.1101/2020.0… 2/14
Next, we wondered if this same relationship would show up in a totally independent, younger, cross-scanner dataset like the ABCD study funded by @NIAAAnews @NIDAnews @NIMHgov @NICHD_NIH @NINDSfunding @NIHOBSSR @NIMHD @NIH 3/14 Image
Read 14 tweets
📢 Welcome to ar5iv.org

Change the "X" in any arXiv article link to the "5" in ar5iv to get a modern HTML5 document.

Thread: what is included, why now, and how we hope to merge back into arXiv.

#OA #OpenScience #preprints

1/10
What to expect?

A collection of 1.75 million preprints, readable today.
That measures at ~97% of the available sources.

Most documents mostly read well (~80%).
Few are perfect.
Almost all have a clear path to support.

2/10
Our own e-journal CSS:

- optimized for large screens, best in Firefox
- decent on mobile, in any browser
- justified text, with hyphenation
- dark/light themes (toggle with 🌙/☀️)
- highlighted notes
- basic figure zoom
- 1000+ lines of misc CSS elbow grease

3/10
Read 11 tweets
Serratus is now published in @Nature :) nature.com/articles/s4158…

We searched 5.7M seq libraries (10.2 petabases) for all 15,000 known RNA viruses. In 11 days, we uncovered 130,000+ new RNA viruses (incl 9 new CoV, with a twist). That’s near an order of magnitude bump.
[1/N] 🧵👇
[2] For the Scientific Conclusions, @rayanchikhi has a great thread from the preprint:
👉 👈
[3] As the pandemic hit, like many scientists we wanted to help. The idea was simple: analyze all public sequencing data to ensure every possible Coronavirus sequence ever sampled is identified and freely available. And do it fast.

(aka Eye of SRAn)
Read 13 tweets
Different cell types in the brain have their own connectivity rules and patterns. In a recently published study, our #neuroscience researchers took a deep dive into the connectomics of an important but enigmatic cell type, the chandelier cell. 🧵1

📄 elifesciences.org/articles/73783
🔬 💻 Using large-scale #electronmicroscopy with automated segmentation, we mapped the complete axo-axonic input onto pyramidal neurons (1,929 synapses in total, 1,127 from chandelier cells) in a volume of layer 2/3 of mouse visual cortex. #ImagingTheFuture #BrainMapping🧵2
By completely reconstructing the presynaptic chandelier cells, we found a novel principle of connectivity, where a group of interneurons are essentially interchangeable, but their postsynaptic targets individually regulate the amount of input they receive from the population. 🧵3
Read 7 tweets
in light of the worrying Elsevier Pilot that was discussed this week, what Pilots do @tweetsunl have with #Elsevier? Is this information online? What are Dutch universities paying Elsevier for? Is that making knowledge dissemination better? How?
@tweetsunl ah, thx for the DM I got.. more info here: universiteitenvannederland.nl/en_GB/open-sci… I'll look at the current pilots today and what they mean for Open Science, which they are meant to serve...
the first Pilot I'll look at is "Description Data Monitoring support service": universiteitenvannederland.nl/files/Descript… The description is brief, so there is not much to go on... that's quite ironic indeed...
Read 74 tweets
Happy to announce that our article "Temperature effects on crop yields in heat index #insurance" with @tobi_dal and @RobertFinger1 is now online and #openaccess in @_Food_Policy. A short 🧵about the article that is available here:
sciencedirect.com/science/articl…
#Heat drives crop yield volatility. Index #insurance can reduce the resulting financial losses suffered by farmers and support #adaptation to #climatechange. Yet, there remains a protection gap for heat risks in most of European #agriculture. (1/🧵)
We introduce a payout function into heat (weather) index insurance design that integrates a cutting-edge method to empirically estimate nonlinear temperature effects on crop yields. We apply and evaluate this novel function for German winter wheat and rapeseed producers. (2/🧵)
Read 11 tweets
Peer review and accepting constructive feedback is critical in research; however, criticizing someone's work to everyone BUT them is not peer review. If you don't suspect something strongly enough to tell the author, you shouldn't be saying it. It's unprofessional and toxic.
Whatever our work is, it's not about us, but contributing to something bigger than ourselves. We should want our contribution to be as valuable as possible. Feedback gets you there. Toxic behaviors don't. People can't fix something they can't see. Tell them.
If you have a concern, voice it. Explain your rationale; support it. Don't be vague. "Well, I don't really get it," or "your study has problems," are both useless except for hurting people who have done nothing but try to contribute. That's a vulnerable position. Be better.
Read 5 tweets

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