Discover and read the best of Twitter Threads about #openscience

Most recents (24)

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
9 Reasons to apply to EMCL8
sisu.ut.ee/emcl8tartu/ava…
👉Applications due Feb 28

1. Learn to integrate:

⭐️ #openscience into your workflow
⭐️ learn to write a #registeredreport BY DOING!!!
⭐️ all in an interdisciplinary setting focused on working together as a team
2. You'll also learn to keep an open lab notebook.

3. You'll help create a special journal issue focused on walking researchers through the steps of doing open science, from idea to open notebook to registered report.
4. Teachers are top caliber, diverse & international: 8 women 4 men.

5. Cheap! Tuition is free & travel to Estonia is cheap (+/- 200 Euros in Summer!)

6. #Greenscience event: Bring your own cups!
sisu.ut.ee/emcl8tartu/gre…
Read 8 tweets
This hasn't gotten much attention and I admit I'm disappointed.

There's a lot of talk about #inclusion and #diversity in #science, right along with countless heated discussions of #unconscious #bias permeating all of science. But talk and discussions won't solve the problem>
Taking steps to promote inclusivity & discourage bias will.

Why is it important to talk about this here if this is just a relatively small workshop?

1. To draw attention to what we can DO; talk is cheap.
2. to describe how a workshop like EMCL can contribute significantly to professional growth, making attendance to similar events typically accessible only to a privileged few .

Specifically:

3. Workshops like these are naturally tight-knit. Teams work closely for a week.>
Read 10 tweets
(1/n) Excited that final version of work led by @D4N__ studying evolutionary repeatability and collateral sensitivity is out. #mathevo #clecliniccancer nature.com/articles/s4146… @CCLRI @NatureComms @CWRUSOM
(2/n) This collab between @CompSciOxford @CCLRI @CWRUSOM & @MoffittPSOC is an extension of @D4N__ ‘s initial theory paper that proposed ‘steering evolution’ as a method of extending the use of existing drugs to control infection. #AntibioticResistance journals.plos.org/ploscompbiol/a…
(3/n) using the fitness landscape metaphor, we reasoned that instances of collateral sensitivity need not be repeatable, as evolutionary branch points could lead to multiple peaks - which could have different sensitivity profiles.
Read 11 tweets
Now accepting applications for:

EMCL8: Open Science & Transparency Methods Workshop
sisu.ut.ee/emcl8tartu/ava…

Focus: incorporate #OpenScience & #RegisteredReports into workflow

Faculty include:
@NeilLewisJr
@dagmardivjak
@Research_Tim
@MariannaBolog
@GernsbacherLAB

Pls Rtwt
Purpose: to provide research methods training in a hands-on, collaborative setting to researchers from different methodological backgrounds, i.e. linguists, psychologists, theorists, experimentalists, corpus linguists, etc.
Topics to be covered in a hand-on context include:

- Deciding on a research topic

- Transforming the research topic into a research question

- Developing experimental hypotheses

- Designing an experiment to test hypotheses

- Making clear predictions based on the design
Read 24 tweets
I am embarking on my own #PaperPerDayChallenge where I read at least one paper, well, per day for a whole year. To kick start, nature.com/articles/43573… inspired by @ukrepro Reproducibility Workshop @CumberlandLodge and a talk by @MarcusMunafo
Paper #2: Hard not be cynical about advocates of reproducibile science given most have careers built on the very questionable practices they wish to stamp out, so great to see @russpoldrack tackling this head on and offering great advice along the way 👍 ac.els-cdn.com/S0896627318310…
Paper #3 - false positives from multiple testing in anovas and importance of distinguishing exploratory and confirmatory hypotheses — also I thought anovas corrected for Multiple testing and this paper shows so too do many others, I’m not the only idiot! link.springer.com/content/pdf/10…
Read 159 tweets
Some thoughts regarding the suggestion to move SfN between (non-US) countries due to travel restrictions. I have organized some 20 scientific conferences in my career, half of them recurring in the same city, half of them in different countries around the globe.
Organizing a conference in a different country every year is an entirely different project than turning on the autopilot for [city] every three years, where you have your known venue, hotels, staff, infrastructure, and suppliers.
The business model changes completely due to things like labour laws, insurance issues, technical interoperability issues, staffing, local knowledge, and simple ol' human behavior. And about 200 other details ranging from contracts with 40 hotels to poster board pins.
Read 9 tweets
Got a seat right in the front at #CSPC2018 @sciencepolicy for the panel on #NextGenCanScience (science and the next generation) feat enablers of trainees getting involved in #scipol @ChiefSciCan @McGill_VPRI @katemoran Stacey Robinson and @DanWicklum
#CSPC2018 @ChiefSciCan mentions #Budget2018 reinvestments of 2.8B$ to create more collaborative infrastructure in govt labs and beyond. This is a once in a lifetime opportunity to get things right and elevate Canada in science leadership 🙌
📣 All major equipment in federal labs will be part of a registry and be accessible to everyone ➡️ democratizing the infrastructure of #cdnsci - @ChiefSciCan #CSPC2018 @sciencepolicy
Read 37 tweets
Panel 2, on granting agencies and #citizenscience w/ @mgfortin_rd @NSERC_CRSNG + Ted Hewitt @SSHRC_CRSH + Serge Marchand @FRQS1 + Louise Poissant @FRQSC + Michael Strong @CIHR_IRSC #CSPC2018
#CSPC2018 @mgfortin_rd says #citizenscience and participative science is incredibly important. This isn't only including public in research, it's engaging communities who have knowledge incl #indigenous traditional knowledge.
... Current project ongoing, is a northern community that wants to better document the status of their natural resources (air quality, water) and to analyze the impact of #climatechange & other human impacts on these. There is added value to including these communities. #CSPC2018
Read 36 tweets
#CSPC2018 panel on #scienceadvice starts!

@DLEKirkwood chief scientist of @NRCan says issue is not do much making sure science is valued in govt (seems it is) but to ensure evidence is used in policy. Plus, policy is inherently quicker than science.

#scipol #canpoli #cdnsci
... The challenge for new science advisors and chief scientists is to ensure that the need for #EBDM in policy is understood across the department, across govt. #CSPC2018
#CSPC2018 Sarah Gallagher @csa_asc says building relationships btw scientists and policymakers (#scicomm skills helpful here!) is key
Read 30 tweets
I've been thinking about #PlanS a lot since the announcement. I've been reflecting on my experience with the foundation's policy implementation. Random thoughts:
"Whether the plan succeeds or fizzles out hangs on how the funders implement the new policy." sciencebusiness.net/news/hope-and-…
I agree & think that there is enough funder experience in #openaccess policy implementation to successfully implement this. While it's important to critically review each new policy development the community that wants to see change really needs to support any effort to change
It can be scary being first in something - however it can also reaffirm that need for change. So far I haven't seen many examples of open access being a detriment to research. For PlanS this isn't a single entity, but an entire coalition, which is quite impressive.
Read 22 tweets
Finally out "Maps of Subjective Feelings" with @aivoAALTO @LNummenmaa and J. Hietanen. pnas.org/content/early/… 1/7
In this study we run three web experiment asking how we perceive 100 common feelings by assessing them i) over 5 dimensional scales, ii) similarity between them iii) how they map on the body and iv) collected similar terms from @neurosynth 2/7
Results showed 5 robust clusters with DBSCAN and visualization with tSNE gave clear components related to emotional valence as well as mental saliency. 3/7
Read 10 tweets
Proud to see published my first #openscience, collaborative and cumulative science project with great collaborators @jakewomick, @TobiasRothmund, @KinglaKing, and @JohnJost1.

A perfect start to #SIPS2018 in just a few days!

journals.sagepub.com/doi/pdf/10.117… #SPPS

Thread alert (1/12)
Methodologically, this work adds to the existing literature in a few meaningful ways. We used facets of established constructs to gain a more precise understanding of the psychological underpinnings of Trump supporters (2/12)
We analyzed psychological differences between politically relevant groups in the 2016 Election: Democrats, Republicans, and Trumpists in both primaries and general election. (3/12)
Read 13 tweets

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