🌟Hello #AcademicMastodon🌟

I'm Hannah and currently working on the research project to understand the role of #Mastodon in #academia during my internship here.

If you haven’t done so already, please consider participating in the project. I would love to hear from you:

🔗https://rug.eu.qualtrics.com/jfe/form/SV_9M1VEyMQ8k4xv94

A huge THANK YOU to everyone who has already participated in the survey! It is really insightful to read your opinions and experiences.

#AcademicChatter #OpenScience #Plushtodon #SocialMedia

Translate Science invites you to our September panel: In Conversation with Humberto Debat and Devang Mehta.

Date: September 22, 2024
Time: 12:00 PM EDT, 16:00 UTC

Hosting / RSVP: https://blog translatescience.org/translate-science-september-2024-panel/ JOIN CODE: multilingualaccess

🚀 Boosts appreciated!

#OpenScience #translation #LifeScience

This is important | Ten simple rules for recognizing data and software contributions in hiring, promotion, and tenure. This is an important #openscience issue that needs to be considered in hiring, promotion, and tenure. I hope it shows up #ploscomp soon!

https://osf.io/preprints/osf/u3c4y

TOMORROW! Monday April 22, 16:00 UTC!

Translate Science invites you to our first community event, "In conversation with Lynne Bowker and Emma Steigerwald." We'll be talking about how they incorporate open and multilingual science in their work.

More details and RSVP here: https://blog.translatescience.org/translate-science-april-2024-panel/

#OpenScience #translation #MultilingualResearch

We knew little about the presence of pharmaceuticals in river waters, despite a growing body of evidence about their harmful effects on the environment. A large group of scientists addressed this gap by sampling 258 rivers in 104 countries on all continents:

💊 https://doi.org/10.1073/pnas.2113947119

All samples were collected using the same equipment, with strict adherence to a single methodology + all samples were delivered and analysed in one place! 👏 This is what #openscience looks like today!

One of the (many) good sides of teaching: you get plenty of time to delve into topics and develop your own material (and code).

I now want to share part of my materials as a #DataScience textbook online:
https://florian-huber.github.io/data_science_course/book/cover.html
(work in progress)

All materials and source code is on #github: https://github.com/florian-huber/data_science_course

And a pdf version can be found on #zenodo: https://zenodo.org/records/10074475

#opensource #Openscience

Michael Eisen has been fired for
praising "one of The Onion’s fake news stories on [Xitter]. The story bore the headline “Dying Gazans Criticized For Not Using Last Words To Condemn Hamas.” Eisen said “The Onion speaks with more courage, insight and moral clarity than the leaders of every academic institution put together. I wish there were a @TheOnion university.”

https://www.science.org/content/article/prominent-journal-editor-fired-endorsing-satirical-article-israel-hamas

You can sign the petition in defense of free expression here: https://docs.google.com/forms/d/e/1FAIpQLSfdJyIQzIsTypmmZXIi-RfSjbe4Psp1RIvjXz-DxWJKA5hHIQ/viewform

#OpenScience

Open letter to HHMI and eLife, in defense of free expression

To the Board of Directors, eLife and Erin O’Shea, President, HHMI: We, the undersigned life scientists, are writing to express our view that Professor Michael Eisen's social media posts should not be grounds for removing him as eLife editor or otherw…

^{Google Docs}

2) #Metagenomics is now maturing to a point where large-scale worldwide meta-analyses become possible, with enough public data to study rare species in broad contexts. This is possible only if the raw data and, above all, the associated #metadata are public and accessible.

So please, do not keep the metadata behind closed doors, and adopt an #openscience policy whenever possible 😀

Scientists, RSEs, sysadmins: unite! And register for the Workshop on Reproducible Software Environments 👇
https://hpc.guix.info/blog/2023/09/first-workshop-on-reproducible-software-environments/

#OpenScience #ReproducibleResearch #HPC #Guix

Hello scientists in 🇫🇮 and 🌍 - @coderefinery starts next week, and everyone is invited. This isn't a programming course, but extra tools (#git, #testing, #reproducibility, #documentation, etc) needed for a scientist to do programming comfortably. T-Th, Sep 19-21 and 26-28, online.
https://coderefinery.github.io/2023-09-19-workshop/

If you're at Aalto, invite us to your research group to help put these tools into practice - we don't teach and leave you alone!
#teaching #course #RSEng #OpenScience #HPC

CodeRefinery workshop September 19-21 and 26-28, 2023

Free workshop on git, testing, documentation, and more in a workshop - for researchers and scientists.

^{coderefinery.github.io}

Our field experiment on code sharing behavior in the social sciences has been published in PLOS One 🥳 (co-authored by @laura_schaechtele and Andreas Schneck).

Read the full article open access https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0289380

(Main take-aways in the thread below)

#metaRep #openscience #opendata #opencode #replication

Hi again #Mastodon!
I joined the fediverse when a lot of my community had not migrated from the bird site, so could only partially reconstruct it here using automated tools. If I followed you there and don’t here, say hi and let’s reconnect!

For those who don’t know me, I am a #virologist by training with almost 20 years of experience as a #science #editor, a passion for #microbiology and all science really, #OpenScience #openaccess & people

Have a lovely day everyone

#introduction #fediverse

Been a busy past few days with work, travelling, and fighting off jet lag... but one thing that I am happy to announce is that an HPC community engineering team that I helped start is now officially a part of the Ubuntu project. If you are interested in using Ubuntu for HPC, or just interested in being involved with a community engineering team, you should totally check out this article below 👇

https://ubuntu.com/blog/introducing-ubuntus-new-hpc-community-team

#ubuntu #HPC #openscience #Community

Does anyone have any research software engineering (#RSEng) or #SciComp related graphics that can be used as stickers or general promotional material? (not tied to any one organization, CC-BY or better)
#HPC #OpenScience #ComputationalScience

Attached are some drafts I did a while ago following the tools metaphor, but I'm definitely not good at this...

For those that missed it here's our presentation for our graduation from the OLS-7 cohort. We're excited to keep building up our community with the direction we worked on formalizing during our time in the program.

https://youtu.be/NABzQGG-D6c?t=3360

#community #OpenScience

And now protocols.io goes the way of Mendely:

https://www.protocols.io/workspaces/protocolsio-news/news/the-next-chapter-for-protocolsio

If you don't want your personal data being sold or otherwise misused, stop using protocols.io!

Bit by bit, every useful tool in science is getting killed by the surveillance publishers.

#openscience

An #openscience question for earth scientists:

I'd like to know what standards earth scientists would use to store institution and coordinates of an experiment in an XML file?

Searching for metadata standards for geospatial data, I found, e.g.:

https://www.fgdc.gov/metadata/iso-standards

Which is waaaaay too detailed for me. Anybody able and willing to help me out?

Together, OLI and TIRS study all parts of Earth’s surface every 16 days.

From land to ice to sea, the open data provided by the #Landsat program has contributed to a deeper understanding of our changing planet. #OpenScience
#NASAEarth

Why we think every scholarly organization, but in particular scholarly societies, should not just migrate to #Mastodon, but host their own instances - and what that has to do with the journals many scholarly societies use to generate revenue:

https://royalsocietypublishing.org/doi/10.1098/rsos.230207

#fediverse #openscience #openaccess #infrastructure

After months of work I'm so happy that our new preprint is online!

Profiling the expression of #transportome genes in #cancer: a systematic approach.
https://www.biorxiv.org/content/10.1101/2023.07.18.549498v1

It's a bit unfinished but it's by design! We want and need #feedback from #bioinformatics and #physiology people to move forward. I've tried to follow #openscience principles, so the pipeline is completely autonomous, containerized and the code for the paper is there, included in the repos!

Profiling the Expression of Transportome Genes in cancer: A systematic approach

The transportome, the -omic layer encompassing all Ion Channels and Transporters (ICTs), is crucial for cell physiology. It is therefore reasonable to hypothesize a role of the transportome in disease, and in particular in cancer.

^bioRxiv

"We need to run away from metrics that are one dimensional. The temptation to reduce complex things to a number is tempting, but the problems and the toxicity that arise from this are problematic" - @fperez at #NASACERN #OpenScience summit

"We need to think of other ways to assess intellectual value, extending beyond the publication to sustain healthier scientific communities." - @fperez

(my interpretation of the quote due to some language and stream interruptions.. 😬)

"The number of people from Latin America in leadership positions is miniscule, especially compared to the userbase. I'm going to spend my sabbatical time to build capacity and work on problems that are relevant to Latin America. If #UNESCO wants to provide resources for that - I'd be happy to talk!" - @fperez

(answer to a question by Ana Persic on the involvements of the Global Majority in #OSS)

#OpenScience #NASACERN

edit: I found slides! https://docs.google.com/presentation/d/1k9i032ujwHSvH2kqDKia7xWB0lEO2sxk-YUMlTDms_Q/

2307-CERN-NASA-OpenScience-fperez

Scientific Open Source? Understanding and Supporting Software in Science Fernando Pérez, UC Berkeley These slides: bit.ly/cern23-oss-fperez

^{Google Docs}

I wanted to share with you a new thing I'm working on: https://biohandbook.me/

It's a resource for practical best practices and tips to use in bioinformatic analyses. The idea is to work together to define standards and workflows and write them down. I love the open science, FAIR data and FAIR code philosophy but there are not many easy-to-use and direct resources around to actually tell you how to do things in the bioinformatics world.

1/n

#bioinformatics #handbook #OpenScience

Glad to announce the 1st Workshop on Reproducible Software Environments for Research and High-Performance Computing!
https://hpc.guix.info/events/2023/workshop/

Consider submitting a talk or tutorial!

📅 Nov. 8–10, 2023
🗺 Montpellier, France

#OpenScience #ReproducibleResearch #HPC #Guix

Data incoming!

@nasa’s CPEX-CV mission flew off the coast of Cabo Verde in 2022 to study infant storms and how dust, moisture and other factors affect storm intensification. The data is now available to the public. #OpenScience https://go.nasa.gov/3BWzdNl
#NASAEarth

Only one week is left to register for our webinar on DOIs for Research Software.🗓️
Sign up & learn about:
- the importance of #ResearchSoftware & how DataCite supports it.
- A Zenodo–GitHub integration
- HERMES by @DLR
Please register & retweet:👇
https://datacite.zoom.us/webinar/register/8816832870820/WN_-K-zNcRIQOmxU3y1v-nEpQ

Please boost, if you love research software that has a DOI! 🚀 🙌

@zenodo_org
@researchsoft
@sdruskat
@gabioshka
@us_rse
@de_rse
#OpenResearch #Software #OpenScience #Citation #Metrics #ResearchMetrics

I've been playing with the idea of building a Digital Research Academy and I need your feedback!

The idea is to build a network of trainers in #OpenScience, software #RSEng, and #dataliteracy from different fields to be able to provide great training.

From the community for the community 🙌

What other cool initiative exist, that we could learn from?

What are your experiences?

What would be a good organisational form for this?

Let me know! (see article)
https://heidiseibold.ck.page/posts/feedback-wanted-building-a-digital-research-academy