Sabhrina Aninta

25 Followers
6 Following
30 Posts
Biodiversity informatician. Conservation geneticist. A bioinformatis, genomics, and popgen enthusiast. Mostly mammals. She/her.
LocationLondon, UK
Our latest #preprint https://ecoevorxiv.org/repository/view/6959/ explains why fitness can be defined in so many ways, and which version(s) you should use when. Fitness quantifies what #NaturalSelection favors. @gdoulcier #EvolGenPaper #Evolution 1/
Why there are so many definitions of fitness in models

Release 1.20 · samtools/samtools

Download the source code here: samtools-1.20.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.) New w...

GitHub

How to keep up with literature and develop good habits? Try the Journal Club Blitz!

A common problem we all face is that we don’t get to those “important non urgent” tasks. One such task for us scientists is to read papers. We all have our constantly filling pile of interesting papers to read. Yet even as students we already struggle to get to those and PIs I talk with commonly complain they don’t get to read papers anymore.

https://biociphers.wordpress.com/2024/04/28/how-to-keep-up-with-literature-and-develop-good-habits-try-the-journal-club-blitz/

How to keep up with literature and develop good habits? Try the Journal Club Blitz!

A common problem we all face is that we don’t get to those “important non urgent” tasks. One such task for us scientists is to read papers. We all have our constantly filling pile of interesting pa…

The BioCiphers Lab Blog

Superinteresting discussion here on biostars: how would you show that a dataset on SRA has been doctored?

https://www.biostars.org/p/9593647/

tbh i don't really buy OP's argument but could be convinced with more details. seems a mishmash of two arguments

NGS forensics: how to know if data is fabricated

A #p2p future for the web is the radical idea that its bad to put all data in a single place owned by 3 companies and rented by a few hundred. The internet wasnt a mistake, the cloud was a mistake. Platforms were a mistake. A mistake where its not only possible but routine for "everyone's health data" to get stolen. https://infosec.exchange/@patrickcmiller/112341111375581551

I need to share my health data with like 3 people that arent me. Why on earth is that data in the same pile as literally everyone else's.

Patrick C Miller :donor: (@[email protected])

UnitedHealth admits IT security breach could 'cover substantial proportion of people in America' https://go.theregister.com/feed/www.theregister.com/2024/04/23/unitedhealth_admits_breach_substantial/

Infosec Exchange

‘We need to slow down scientific publishing’

'We focus on metrics to evaluate a scientist’s career: how many articles they have published, how many times they were cited, what was the impact factor of all these articles. '

https://english.elpais.com/science-tech/2024-04-26/elisabeth-bik-expert-in-scientific-integrity-we-need-to-slow-down-scientific-publishing.html

#publishing #science #stem #academicchatter

Elisabeth Bik, expert in scientific integrity: ‘We need to slow down scientific publishing’

The Dutch microbiologist has been voluntarily searching for duplicate, erroneous or retouched academic images for more than 10 years and warning universities and scientific journals about it

EL PAÍS English
Finding the actual needle in a virtual haystack
by Christoph : :
...by glo­bal se­quenc­ing of en­vi­ron­men­tal DNA (eDNA) col­lect­ed from a sam­pling site and its ta­xo­nom­ic clas­si­fi­ca­tion and quan­ti­fi­ca­tion by bio­in­for­matics. When an­a­lyz­ing such vo­lu­min­ous da­ta­sets, ope­ra­tion­al ta­xo­nom­ic units (OTUs) often pop up that cor­res­pond ...
Read more → https://schaechter.asmblog.org/schaechter/2023/08/finding-the-actual-needle-in-a-virtual-haystack.html
#microbiology #ecology
Finding the actual needle in a virtual haystack

<p>by Christoph&nbsp:&nbsp:<br /> ...by glo­bal se­quenc­ing of en­vi­ron­men­tal DNA (eDNA) col­lect­ed from a sam­pling site and its ta­xo­nom­ic clas­si­fi­ca­tion and quan­ti­fi­ca­tion by bio­in­for­matics. When an­a­lyz­ing such vo­lu­min­ous da­ta­sets, ope­ra­tion­al ta­xo­nom­ic units (OTUs) often pop up that cor­res­pond to known ta­xa/spe­cies never found at the samp­ling site − the to­pic that brought you here − in ad­di­tion to... 

Small Things Considered
This might be a super long shot: anyone has any info of vacant affordable #housing for a family of three in #Copenhagen?

If you know of any #philosophy #postdoc opportunities, please let me know. Being unemployed is really... horrible. It's not even about the money, it's just so boring not to have a community, structure, a place to go to and work, and to feel as if you're a part of something 😔

#academia #academicchatter @academicchatter

Just had to explain to an editor why I would not review for Nature (mostly, Springer-Nature is a parasite on public resources meant for research and humankind interest). Good articles to back-up my claims and have less sweaty hands:

https://zenodo.org/record/6289488

https://www.molbiolcell.org/doi/10.1091/mbc.E19-03-0147

@DAFNEE

Ethical publishing: how do we get there?

The scientific journal publishing model is deeply unethical: today, a few major for-profit conglomerates control more than 50% of all articles in the natural sciences and social sciences, driving subscription and open-access publishing fees above levels that can be sustainably maintained by publicly funded universities, libraries and research institutions worldwide. About a third of the costs paid for publishing papers is profit for these dominant publishers’ shareholders, and about half of them covers costs to maintain the system running, including lobbying, marketing fees and paywalls, which in turn restrict access of scientific outputs from being freely shared to the public and other researchers. Thus, money that the public is told goes into science is actually being funneled away from it, or used to limit its access. Alternatives to this model exist and have increased in popularity in recent years, including diamond open-access journals and community-driven recommendation models that are free of charge for authors and minimize costs for institutions and agencies, while making peer-reviewed scientific results publicly accessible. However, for-profit publishing agents have made change difficult, by co-opting open-access schemes and creating journal-driven incentives that prevent an effective collective transition away from profiteering. Here, we give a brief overview of the current state of the academic publishing system, including its most important systemic problems. We then describe alternative systems. We explain the reasons why the move towards them can be perceived as costly to individual researchers, and demystify common roadblocks to change. Finally, in view of the above, we provide a set of guidelines and recommendations that academics at all levels can implement, in order to enable a more rapid and effective transition towards ethical publishing.

Zenodo