3 ms·

Oh it's by Nature one of the beneficiaries of the corporate capture of publication metrics. This is like reading an article by DeBeers about how you can do a pr

by ftxbro 3y ago

Oh it's by Nature one of the beneficiaries of the corporate capture of publication metrics. This is like reading an article by DeBeers about how you can do a proposal without spending as much on diamonds as you are afraid that you might. Here's what you can do. Make a github account. Make an account on arxiv.org or biorxiv.org. Publish your work onto arxiv. Put all of your data onto your github account, including copies of whatever you put onto arxiv and including extensive markdown readme file that is a synopsis of the paper. Disseminate it by announcing it on your twitter or mastodon or rss blog or substack or research community discord and even put it to a site like hacker news if it's relevant. If you are with an affiliated institution then their press office will put a small release.

MavropaliasG 3y ago
Use OSF (osf.io) instead, which is made for open science
ISL 3y ago
This approach alone will not get you the peer-review necessary for colleagues to take you seriously nor the publication record necessary to get a job.
- ftxbro 3y ago
  It's true, you should eventually submit it to the most topical free journal after doing something like these steps to make your scientific data accessible, discoverable and useful. It won't get as many academia merit points as submitting to the journals that have lobbyists.
jkh1 3y ago
Can I put my 25 TB microscopy image data set on GitHub? Will they host it for free indefinitely? In the life sciences, there are dedicated public repositories (databases) where the data is hosted (free to the researcher), catalogued, standardized and curated to some extent. These repositories are searchable and often crossreference each other. So you can find a data set even if you didn't know about it before. Putting data all over the internet in dumps like Zenodo, Dryad and the like is just not very useful. Advertizing your work is probably good for your career but this is not what makes your data and work useful to others. It's how easy you make it for others to understand, access and combine your data with their own data. This means providing data and metadata using open community standards (there are already a bunch of these in life sciences even if there are gaps in coverage).
- ftxbro 3y ago
  > "Can I put my 25 TB microscopy image data set on GitHub? Will they host it for free indefinitely? In the life sciences, there are dedicated public repositories (databases) where the data is hosted (free to the researcher), catalogued, standardized and curated to some extent." Yes this is better. Like if you are a scientist and you find an amazing new cancer gene then you should probably put it in the actual gene repository and not randomly on github. Because you're this hypothetical scientist you probably know the exact niche place that is most appropriate for that already. Like GenBank or whatever is the one that there was a scandal about the pre-covid coronavirus genes were mysteriously deleted from it.
- pizza 3y ago
  bittorrent could be an interesting fallback distribution method. There's already academictorrents
- tetris11 3y ago
  https://zenodo.org https://zenodo.org
- dekhn 3y ago
  I talked with NIH program managers and leadership about this quite some time ago and tried to convince them to explicitly fund long-term data hosting for science publications. The budgeting got complicated quickly: paying for a bucket with 25TB isn't a huge expense. Does NIH cut a deal with AWS, or GCP, or Azure, or (shudder) Oracle so they get discounts (these can halve or even more reduce storage settings). Does it go in long-term storage or live storage? And that doesn't even include egress- which in my experience, when you have lots of downloaders, gets expensive fast. Does NIH cover the distribution costs, or do requesters pay? Do people running high throughput jobs in clusters near the S3 storage get to work directly against the data or do they make a duplicate? Their response in this instance was to fund SRA-in-the-cloud and other ventures, such as having PIs in well-connected locations like U.Chicago rent datacenter space in an exchange, negotiate very cheap hosting and bandwidth, and then give people access to compute and data either there, or in AWS (https://www.uchicagomedicine.org/forefront/news/university-of-chicago-launches-cloud-to-analyze-cancer-data https://www.uchicagomedicine.org/forefront/news/university-o...) This still doesn't address the "high quality metadata problem", which IMHO is the NP-complete problem of biology.

by ftxbro 3y ago

MavropaliasG 3y ago

Use OSF (osf.io) instead, which is made for open science

ISL 3y ago

This approach alone will not get you the peer-review necessary for colleagues to take you seriously nor the publication record necessary to get a job.

ftxbro 3y ago
It's true, you should eventually submit it to the most topical free journal after doing something like these steps to make your scientific data accessible, discoverable and useful. It won't get as many academia merit points as submitting to the journals that have lobbyists.

jkh1 3y ago

Can I put my 25 TB microscopy image data set on GitHub? Will they host it for free indefinitely? In the life sciences, there are dedicated public repositories (databases) where the data is hosted (free to the researcher), catalogued, standardized and curated to some extent. These repositories are searchable and often crossreference each other. So you can find a data set even if you didn't know about it before. Putting data all over the internet in dumps like Zenodo, Dryad and the like is just not very useful. Advertizing your work is probably good for your career but this is not what makes your data and work useful to others. It's how easy you make it for others to understand, access and combine your data with their own data. This means providing data and metadata using open community standards (there are already a bunch of these in life sciences even if there are gaps in coverage).

ftxbro 3y ago
> "Can I put my 25 TB microscopy image data set on GitHub? Will they host it for free indefinitely? In the life sciences, there are dedicated public repositories (databases) where the data is hosted (free to the researcher), catalogued, standardized and curated to some extent." Yes this is better. Like if you are a scientist and you find an amazing new cancer gene then you should probably put it in the actual gene repository and not randomly on github. Because you're this hypothetical scientist you probably know the exact niche place that is most appropriate for that already. Like GenBank or whatever is the one that there was a scandal about the pre-covid coronavirus genes were mysteriously deleted from it.
pizza 3y ago
bittorrent could be an interesting fallback distribution method. There's already academictorrents
tetris11 3y ago
https://zenodo.org https://zenodo.org
dekhn 3y ago
I talked with NIH program managers and leadership about this quite some time ago and tried to convince them to explicitly fund long-term data hosting for science publications. The budgeting got complicated quickly: paying for a bucket with 25TB isn't a huge expense. Does NIH cut a deal with AWS, or GCP, or Azure, or (shudder) Oracle so they get discounts (these can halve or even more reduce storage settings). Does it go in long-term storage or live storage? And that doesn't even include egress- which in my experience, when you have lots of downloaders, gets expensive fast. Does NIH cover the distribution costs, or do requesters pay? Do people running high throughput jobs in clusters near the S3 storage get to work directly against the data or do they make a duplicate? Their response in this instance was to fund SRA-in-the-cloud and other ventures, such as having PIs in well-connected locations like U.Chicago rent datacenter space in an exchange, negotiate very cheap hosting and bandwidth, and then give people access to compute and data either there, or in AWS (https://www.uchicagomedicine.org/forefront/news/university-of-chicago-launches-cloud-to-analyze-cancer-data https://www.uchicagomedicine.org/forefront/news/university-o...) This still doesn't address the "high quality metadata problem", which IMHO is the NP-complete problem of biology.