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#figshare

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Open Science Pasteur

La newsletter #ScienceOuverte de l'#InstitutPasteur a compilé cette semaine une sélection d'articles autour des #EntrepôtsDeDonnées
­👉 #OnVousExplique : Les entrepôts de données
👉 Comment trouver un entrepôt de données dans le domaine biomédical ?
👉 Le répertoire d’entrepôts de données #re3data
👉 Les différences entre plusieurs entrepôts de données généralistes : #RechercheDataGouv, #Zenodo, #Dryad et #Figshare
👉 Déposer des données dans un entrepôt, que doit-on anticiper ? L’exemple de #GEO
👉 Disparition de certains entrepôts de données : quel impact sur l’accès aux #DonnéesDeRecherche ?

➡️ 4682g.r.sp1-brevo.net/mk/mr/sh

4682g.r.sp1-brevo.netLettre d'information Science Ouverte
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Open Science Pasteur

Nous avons comparé plusieurs #EntrepôtsDeDonnées pluridisciplinaires : #RechercheDataGouv, #Zenodo, #Dryad et #Figshare
Au-delà du point commun de simplicité d'utilisation, quelles différences ?
#OpenData #OnVousExplique

➡️ openscience.pasteur.fr/2025/02

Open science : évolutions, enjeux et pratiques · Les différences entre plusieurs entrepôts de données généralistes : Recherche Data Gouv, Zenodo, Dryad et FigsharePour ouvrir ses données de recherche, il existe de très nombreux entrepôts de données. Parmi eux, les entrepôts dits « généralistes » ou « pluridisciplinaires » permettent le partage de tous types …
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El Duvelle

Looking at the size of some of the articles I have in my Zotero library. Some of these are massive! 20 Mb, 60 Mb, come on!

We need to be a bit more careful with our article file sizes... High-res pics can be uploaded to a separate storage if needed, and maybe normal resolution versions can be in the paper?

I also found out that for some reason #Zotero grabs the explanatory video that sometimes comes with papers (e.g. in Neuron). These can be massive too and for some reason are not shown in the Zotero library, but they are there in your disk.

Edit: removed mention of #Figshare because it is apparently owned by one of the giant publishing companies..

#Academia#ResearchArticles
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Simon porter

Had a great #pidfest After presenting a RAiD like workflow doi.org/10.6084/m9.figshare.25, we got access to the demo version of the RAiD API. …so here is a demo with an actual RAiD workflow: overleaf.com/read/vnpvrdkbqswr maybe the first RAid to Author and Author contribution statement demo? #overleaf #figshare #ORCid #RAiD

figshareExploring ‘RAiD like’ workflows with figshare and OverleafThe demonstration supports the following presentation:One of the promising functions of RAiD identifiers is their ability to represent a research activities as they evolve. As research activities develop over time, RAid workflows shift from structured definition, to providing structure for new research outputs that the activity creates, and then finally to contributing to the discovery and provenance infrastructure necessary to build trust in research. Using the figshare project as a proxy for a RAiD activity definition, we propose to demonstrate how RAid can facilitate the flow of metadata from creation through to publication - automatically creating publication authorship details from associated ORCiDs, and providing incentives for researchers to improve their ORCiD records in the process. Finally, by linking publication outputs to RAiD identifiers (our stand in figshare project), we demonstrate the advantages of leaving a RAiD id provenance trail in your research publication - making it easier to distinguish research that has been created over time vs fabricated outputs that may have been created by Paper Mills using generative AI.
Continued thread
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Tim Fallon, PhD :verified:(jk)

@datadryad I used #FigShare in the past, but switched to DataDryad once I realized FigShare was a for-profit repository, and DataDryad had a standing partnership with my institution. But it's frustrating as FigShare had a solution for (1) and (3), and (2) was less painful since you could introspect into archive files like .tar.gz . For someone who wants to upload datasets and analyses in an incremental way (10-20 DOIs per paper?) feels like the repos instead push you to 1 DOI per paper.

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Dr. Robert M Flight

We've been using #figshare and #zenodo for code / data repositories for manuscripts for a few years now. But I just went back to look at a student's repo from 4 years ago, and I think our research group needs a better checklist around the creation of these repositories.

Data in a file.rar?? And an actual directory structure? Ideally, this should have been a single `zip` or `tar.gz` file that could be easily extracted and everything would be ready to go.

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IGB Library

in der

-Forschende sind an einer Nature-Publikation zur Artenvielfalt in europäischen Flüssen beteiligt.

igb-berlin.de/news/kaum-noch-e

Die Aufnahme des -Artikels in unsere mit dem bedarf aufgrund hoher Autor*innenanzahl einiger Improvisation, aber nichts ist unmöglich.

Interessant auch das file sowie die Daten- und Codeverfügbarkeit auf und .

www.igb-berlin.deKaum noch Erholung: Artenvielfalt in europäischen Flüssen stagniert  | IGB
Continued thread
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Jere Odell

Software like, #Figshare, is part of “a general trend of deskilling library staff, leaving them only with ‘softer’ skills. … [B]y making data management ‘cheap’ in terms of funding and staff required ... [these] platforms place [repository management] at the bottom of budget priorities. Making the scarcity of resources more manageable transforms a situation of precarity into a normal state of functioning.” #scholcomm #repositories

Replied in thread
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Sebastian Karcher

@polka I don't think this will turn out as well with #protocols.io, but #figshare was bought and is part of Digital Science which used to be part of Nature & is now majority held by the same holding company as SN.

I have a preference for some of figshare's non-profit & FLOSS competitors (Zenodo, Dataverse), but I think it's fair to say they've kept doing what they were doing prior to acquisition, are doing it well, and overall benefit open science (they make $ by selling repos to institutions).

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Sebastian Karcher

Oh, great -- I just found that #figshare has broken a potentially huge number of #DOI links (they've broken an internally re-redirect, so it's fixable, but still). I'm not quite sure under what condition, but it appears a fair number of DOIs ending in .v1 for projects with only a single version are affected.

Try e.g. the DOI under "Cite" here: figshare.com/articles/journal_
#dataLibs

figshareLeadership in Times of Populism: Selected Examples of Italian Political LeadersThe issue of leadership is becoming increasingly a phenomenon studied by specialists in political sciences. However, the emerging theoretical concepts call for constant changes and updates due to the political practice. This is supported by the changes in the political scene observed in many countries, generally referred to as the “populist revolution”. This phenomenon, with varying intensity, has been present on the Italian political scene for almost a quarter of a century.The specificity of Italian populism should be expressed concerning three political leaders: Silvio Berlusconi, Beppe Grillo and Matteo Renzi. Although, there are many differences between them – the time of appearance, the scope of power and political culture, there are also common formal references regarding personal image and applied rhetoric. The distinct approach of leadership to populism has been further strengthened by the increasing use of new means of social communication. As a result, the intersection of technology and social change has had and will have a significant impact on the perception of politics in the future.
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Rob Edwards

Phages... So many #phage and they are all #prophage integrated into a #bacteria #genome

A few million prophages from > million bacterial genomes

Are prophages good or bad for bacteria? The data shows they provide heaps of benefits

The paper is in #biorxiv and the data is on #figshare

biorxiv.org/content/10.1101/20

open.flinders.edu.au/projects/

bioRxivThe Promise and Pitfalls of ProphagesPhages dominate every ecosystem on the planet. While virulent phages sculpt the microbiome by killing their bacterial hosts, temperate phages provide unique growth advantages to their hosts through lysogenic conversion. Many prophages benefit their host, and prophages are responsible for genotypic and phenotypic differences that separate individual microbial strains. However, the microbes also endure a cost to maintain those phages: additional DNA to replicate and proteins to transcribe and translate. We have never quantified those benefits and costs. Here, we analysed over two and a half million prophages from over half a million bacterial genome assemblies. Analysis of the whole dataset and a representative subset of taxonomically diverse bacterial genomes demonstrated that the normalised prophage density was uniform across all bacterial genomes above 2 Mbp. We identified a constant carrying capacity of phage DNA per bacterial DNA. We estimated that each prophage provides cellular services equivalent to approximately 2.4 % of the cell’s energy or 0.9 ATP per bp per hour. We demonstrate analytical, taxonomic, geographic, and temporal disparities in identifying prophages in bacterial genomes that provide novel targets for identifying new phages. We anticipate that the benefits bacteria accrue from the presence of prophages balance the energetics involved in supporting prophages. Furthermore, our data will provide a new framework for identifying phages in environmental datasets, diverse bacterial phyla, and from different locations. ### Competing Interest Statement The authors have declared no competing interest.
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