Discover and read the best of Twitter Threads about #openscience

Most recents (24)

My editorial paper entitled, "No raw data, no science: another possible source of the reproducibility crisis". When I feel the results are too beautiful, I requested raw data before sending it out for review. 40 out of 41 did not send me the right data.
molecularbrain.biomedcentral.com/articles/10.11…
21 of them were just withdrawn without providing raw data. 19 of them were rejected due to insufficient raw data (ex. just one sample per group provided) and/or to mismatches between raw data and the results shown. Mismatches are mostly huge, not subtle.
14 out of those 40 that were withdrawn or rejected were published in other journals (impact factor from 2.2 to 4.7; mean: 3.37). 12 journals had a policy requiring or encouraging raw data sharing upon request and so I requested raw data. None out of 12 gave me what I requested.
Read 18 tweets
@nytimes on our Wearable Microphone Jammer (see it in action here: ). it uses ultrasound to disable surrounding microphones from recording you; lead by Heather Zheng & @ravenben with Yuxin Chen, Huiying Li, @tengshanyuan, Steven Nagels and I ->#chi2020 1/N
@nytimes @ravenben @tengshanyuan Here's how it works: sandlab.cs.uchicago.edu/jammer/ The engineering behind it allows us to get an awesome jamming coverage by making it #wearable : (1) any small movement decreases the impact of the typical blind spots that ultrasonic jammers have; and, (2) it jams in many directions!
@nytimes @ravenben @tengshanyuan What happens when you activate the jammer and talk to someone while surrounded by microphones? Those microphones capture noise rather than your voice, but you don't hear any jamming (it's ultrasonic). This means you speak freely but speech recognizers will fail to spy on you.
Read 6 tweets
Extraordinarily glad that @GlobalYAcademy is co-organizing @WorldSciForum this year, streamlining young global voices (whether our members or nominated speakers) throughout the conference. Wohoo"

worldscienceforum.org

#wsfbp2019 #worldscienceforum #budapest #sciforum2019
Starting with the @GlobalYAcademy + @IAPartnership Science Leadership Workshop *right from the beginning*

#wsfbp2019 #worldscienceforum #budapest #sciforum2019
Then a wonderful @Junge_Akademie @GlobalYAcademy combination with Marion Schulte zu Berge @miliba01 @DrTolullah @DianaUrge on the responsibility of scientists

#wsfbp2019 #worldscienceforum #budapest #sciforum2019
Read 20 tweets
My #CSPC2019 live tweeting #THREAD starts here!

I'll reply to this tweet w/ each panel I attend, creating a thread under each w/ live notes

My schedule: 🔗cspc2019.sched.com/shawnmcguirk

And, ICYMI, see the new CSPC magazine for my op-ed about @DSP_SPE & #CapacityBuilding in #scipol!
I wasn't intending on tweeting the symposium, but 2 really good points on skills:

🔹 For communications, the ability to be brief (tweet length summaries!) is key

🔹 Universities should promote organic mentorship by leveraging alumni office, get alums to meet students over ☕!
🔹 Skills development has strong socio-economic dimension. Accessibility to good schooling even as early as Kindergarten can have large impacts later in life. The foundation of transferable (read: critical) skills stays with you as you later develop expertise.

#CSPC2019 #skills
Read 216 tweets
In a new study out in @nature, our researchers make a big step forward in our quest to map the brain. Study findings lay the groundwork to better understand brain disorders & diseases such as #Alzheimers and #schizophrenia.

alleninstitute.org/what-we-do/bra…
This new study describes a high-resolution expansion of our #openscience Allen Mouse Brain Connectivity Atlas-- the most detailed map of connections in a mammalian brain to date. Access via: connectivity.brain-map.org
Using a computational approach, our researchers found that different sections of the cortex and thalamus can be mapped into a hierarchy, much like a company’s org chart – although not all connections followed this hierarchical structure. #brainmapping
Read 5 tweets
In the past months, we at @GlobalYAcademy have started to improve the visibility of young global scientists. I'll starting sharing more about what I learned through this about #digitization #academies #wikipedia and the visibility of researchers. Here's a picture of NYAs
#gyawiki
NYAs are national young academies. There are around 50 of them, some have a long and prominent history, some have just started *this week*.

Have a look globalyoungacademy.net/national-young…
NYAs are great (*I'm biased, as Executive Member of the GYA... :):
- scientific excellence is understood both in conventional terms, but also in terms of societal impact
- terms are limited. You have 4-5 years to *really* do work
- are typically very diverse! (@WikiWomenInRed)
Read 22 tweets
Just taught two more seminars on learning to read science papers.

Some rambly thoughts (tired)

It is the most amazing thing to see the wonder in the students' eyes. That moment when they get it, especially when they SEE that who researchers are matters to the science they do.
We've been using a paper on baseball players to study the malleability of perception. When they first read it they take it at face value, then we deconstruct that the authors are American, living in the US & using an American activity about which they make universal claims. 🤢
We add time as a factor, and they realise the participant pool would have looked dramatically different just 100 years ago because of sexism and racism.

Then we discuss the decision-making process in the science & in how it was documented, the many choices made at both stages.
Read 7 tweets
At #FORCE2019 @npscience getting everyone warmed up for a panel on "Who will influence the success of #preprints in biology and to what end?"
@npscience . @npscience laid important foundations for the discussion: (1) be aware of stakeholders' cultural backgrounds and the influences on the their viewpoints; and (2) it's always a balance between individual vs collaborative gains. #Force2019
@npscience First panelist @ReaderMeter compared #preprints to a staging area, akin to how we would interact with an #opensource project, where all sorts of collaboration could happen and #openscience practised 🌟 #Force2019
Read 13 tweets
Helping the outcomes of 34% of patients w/ #cancer (who failed Rx) by whole genome sequencing and sharing data for off-label drug use: lessons from the Netherlands
nature.com/articles/s4158… @Nature #openscience #immunotherapy
@nature That was the 1st of a 3-fer on WGS for #cancer today
Value of whole genome sequencing for 254 patients w/ triple-negative breast cancer nature.com/articles/s4159… @NatureMedicine by @SerenaNikZainal @Cambridge_Uni @MRC_CU @lunduniversity and collaborators
@nature @NatureMedicine @SerenaNikZainal @Cambridge_Uni @MRC_CU @lunduniversity 3rd on paired tumor, germline DNA + RNAseq, clinical data in 500 patients to expand clinical trial options nature.com/articles/s4158… @NatureBiotech
Read 3 tweets
Been thinking about @mit @MIT_CSAIL #Stallman

I started at MIT in 1991 as a 18yo girl who'd coded in LISP for 4 years, gobbled up Society of Mind, competed in high school national science fairs with a neural net I'd trained to recognize emotions in music (kinda ;) ).

1/n
Needless to say, studying AI at MIT was a dream come true.

Then I dropped out of AI and CS by the end of my freshman year.

2/n
I've never been able to pinpoint why.

At the time I said it was because I found AI at school really boring -- I'd read the AI book already and the lecturer (Winston) just lectured to the book. Sure. But really???

3/n
Read 14 tweets
Currently in a Mechanisms Network of Expertise (MNoE) workshop/session at #SIRC2019 The room is packed (standing room only) so hopefully my live-tweeting will help folks that couldn't fit.
@ImplementCollab also has a webinar on this topic. More info at …plementationresearchcollaboration.org/past-webinars/ (but no link to the webinar that I could find)
@ImplementCollab Mechanisms help us understand the causal process by which an implementation strategy functions. Ex: provider knowledge deficit is a "determinant", education is a strategy, and adoption is the outcome. A mechanism is what explains how education leads to adoption #SIRC2019
Read 23 tweets
Been thinking about the connection between the publication/peer review process and the (toxic?) culture of defensiveness/combativeness in academia.

We’ve set up a system where scholars invests a lot in their ideas (e.g., run studies, write manuscripts)...
1/6
... and then are put in a position to defend those ideas from reviewers' critiques when the work is done.

Essentially, we incentivize them to be combatants and staunch defenders of their ideas, rewarding them for digging their heals in when faced with criticism or new ideas.
2/6
But #RegisteredReports are a game changer in the culture of scientific knowledge production. Since in this model researchers and reviewers work together prior to data collection, it incentivizes openness and collaboration to improve the work beforehand...
3/6
Read 6 tweets
1. PhD thesis 'Modelling BCG vaccination in the UK: What is the impact of changing policy?' submitted and everything is totally normal....

Written with #rstats, #bookdown, and #thesisdown.

Read here: bit.ly/seabbs-thesis

#phdchat #epitwitter #openscience #tuberculosis
2. Thanks to my supervisors @n3113n and @Christensen_H + my funders @HPRU_EI + @PHE_uk for the data.
3. Some results: 'getTBinR: an R package for accessing and summarising the World Health Organisation Tuberculosis data'

Code: github.com/seabbs/getTBinR

Paper: doi.org/10.21105/joss.…

#getTBinR
Read 13 tweets
1. First release of {#idmodelr} is now on CRAN. {idmodelr} is a library of #infectiousdisease models and utilities for using them. Use case is exploration/education/research + signposting.

bit.ly/idmodelr

#rstats #epitwitter #dynamics #opensource #openscience
2. Current status is WIP with more features - and additional models - planned. Contributions much appreciated!

Planned features: github.com/seabbs/idmodel…
3. {#idmodelr} has an accompanying #shiny app that demos some of the functionality and can be used as a standalone tool for exploring infectious disease models.

See here: github.com/seabbs/explore…
Read 9 tweets
So a few of us (@unhlangothi, @adantro, PeterLatham, @TPVogels, @JosephRaimondo) wrote a perspective piece for #PLOSCompBio entitled "Think: Theory for Africa" dx.plos.org/10.1371/journa…
here are some of the points
"we call for greater efforts to empower Africans to join the global neuroscience community and argue that the subfield of computational neuroscience is the ideal vehicle to do so"
neurotheory is super accessible!
just need #data and #expertise
Read 17 tweets
1. New (first) paper now available: Exploring the effects of BCG #vaccination in patients diagnosed with #tuberculosis: Observational study using the Enhanced Tuberculosis Surveillance system

Paper: doi.org/10.1016/j.vacc…
Preprint: doi.org/10.1101/366476

#phdchat #rstats
2. Highlights

Evidence of an association between BCG vaccination and reduced all-cause mortality in TB cases.

Weaker evidence of an association between BCG vaccination and reduced repeat TB episodes in TB cases.

Little evidence of an association with other TB outcomes.
3. Background: Bacillus Calmette–Guérin (BCG) is one of the most widely-used vaccines worldwide. BCG primarily reduces the progression from infection to disease, however, there is evidence that BCG may provide additional benefits.
Read 7 tweets
Choice history biases subsequent evidence accumulation
My latest with @jwdegee, @k_tsetsos and @donner_lab now out in @eLife!

paper: doi.org/10.7554/eLife.…
blog: tinyurl.com/y4g3rqa3
code: github.com/anne-urai/2019…
data: doi.org/10.6084/m9.fig…
story:👇
Ever noticed how your behavior is affected by the choices you've made in the past - even when you *know* it's better to just focus on the information in front of you?

You're not alone! Across many different experiments and tasks, people show choice history biases.
These biases vary between individuals - some people tend to repeat, others consistently switch from their previous decisions.

But *how* do previous choices affect the dynamics of a decision, from seeing a stimulus to reporting what you saw?
Read 10 tweets
I'm gonna do a small thread on: Why did I coin #bropenscience?

The shortest answer to the question is: because it’s amusing and seems to upset exactly the right people, while also drawing attention to behaviours and ideas that harm #openscience and its adoption in deep ways.
The bro-iest, wannabe macho-est (given context of course — we’re talking about scientists, so macho/bro-ism will manifest in very specific ways) people seem to get upset.
And that’s great, they are the ones that probably need to take a step back and understand that their aggressiveness and even their overrepresentation can push people away.
Read 9 tweets
Microscopy technique development's exploding, but core facilities still buy confocals. This ugly baby will end that.

Less phototoxicity, WAY faster than confocal. NO DRAWBACK.

Details here: andrewgyork.github.io/high_na_single…

Co-invented by @amsikking.

Get one from jon@asiimaging.com
I've heard there's "no free lunch" in microscopy; advantages come with tradeoffs. We take this as a personal challenge!

Our new microscope design gives the gentleness/speed of lightsheet microscopy, AND the high NA and simple sample prep you're used to with confocal microscopy.
We want this microscope in YOUR hands, ASAP. Traditional publication takes years, commercialization even longer. Even preprints take time to prepare.

Our fastest path is #OpenScience ; see
andrewgyork.github.io/high_na_single…
for up-to-date parts list, build instructions, & preliminary data
Read 13 tweets
TODAY IS THE DAY! Join us at the #MarchForScience at our main march in New York City or in 130+ locations around the world including Mexico, Chile, Guatemala, Malawi, Ghana, Germany, Croatia, Finland, India, Philippines, China, Australia & Antarctica: bit.ly/mfs2019
Xiamen, China joined the global #MarchForScience today to advocate for cleaner, healthier & more environmentally cities. Thank you!!!
The Phillipines marched for the preservation of their reefs and forests #MarchForScience
Read 15 tweets
#RM_Ott19 last panel @research_money on whole-of-govt initiatives to support #innovation. Moderated by @ChristineTrautt @CollegeCan, w/ Rob Wright ADM of @PSPC_SPAC, Wayne Moore @DFO_MPO, @NancyHamzawi ADM @environmentca, Andrea Johnston @ISED_CA, Gilles Saindon @AAFC_Canada
#RM_Ott19 RW says @PSPC_SPAC is looking beyond the usual vertical approach of governments, taking a more partnership view to drive success. WM @DFO_Science adds that bar has been set high for collab across departments, to get other ministers' / ADM's input and advice
#RM_Ott19 AJ @ISED_CA likes the "partnership" view, which aligns well with innovation portfolio of ISED. The federal family can be engaged in partnerships in one swoop (e.g. in Clean Growth Hub) rather than forcing external partners to reach out to depts separately
Read 18 tweets
A late-night thread on reproducibility and #openscience in cognitive neuroscience, including our upcoming series of (rather punchy) comment pieces at the journal Cortex. Gather round all ye.
Here is my editorial introducing the seven commentaries. I’m going to move through each of them here in turn, and stick around to the end of the thread to hear about two new initiatives we’re launching this year in response psyarxiv.com/shryx /1
First up, Huber et al . report how they tried to replicate a study published in @NatureNeuro. After being invited beforehand to run & submit the study by one editor, a different editor then desk rejected them once the (non-replication) results were in. /2
Read 19 tweets
Today I want to talk about a couple of things I dislike about my (sub)field.

🅰️ I hate closed sourced langs & the epitome: Matlab.
neuroplausible.com/matlab

🅱️ I hate how coding is (not) taught to people.
neuroplausible.com/programming
High-level point:

Everybody in psych/neuro should be taught to code & taught an #opensource #openscience programming language.
Before I dive in to saying what I dislike about closed source langs & Matlab esp, I would like to make some clarifications/caveats because the last thing I want is to add confusion to an already tricky issue since some people (e.g., women, PoC) are told they "can't code" often:
Read 47 tweets
Today I'd like to talk about issues with respect to #openscience and specifically sharing code.

But first an intro to what open science is...
I am sure you all know a bit about #openscience already but essentially it's a very broad community/movement that aims to make science more accessible, transparent, inclusive, etc.

@daniellecrobins and @rchampieux have this great umbrella infographic!

#Openscience boils down to making science more free and open in the same general ways that the related open source and free software movements/communities pushed for change by making the outputs of science more accessible to both the general public and to other scientists.
Read 58 tweets

Related hashtags

Did Thread Reader help you today?

Support us! We are indie developers!


This site is made by just three indie developers on a laptop doing marketing, support and development! Read more about the story.

Become a Premium Member ($3.00/month or $30.00/year) and get exclusive features!

Become Premium

Too expensive? Make a small donation by buying us coffee ($5) or help with server cost ($10)

Donate via Paypal Become our Patreon

Thank you for your support!