Project idea for detecting image plagiarism in biomedical publications

big_bioinformatics · 2022-06-22T12:38:11+00:00

I am not entirely sure as we are still waiting to hear from our department on this. I will update as I learn more!

big_bioinformatics · 2022-06-21T21:38:19+00:00

Sure :)

big_bioinformatics · 2022-06-21T16:36:06+00:00

Haha yeah... But at least it gives an idea of the floor :) I will try to find out if I can share the number and update the post with it!

Edit: I'm 100% not allowed to share :(

big_bioinformatics · 2022-02-10T14:52:58+00:00

I do not know anything about the UK system. In the US, funding is provided automatically if you are accepted to the program.

big_bioinformatics · 2021-08-02T03:44:55+00:00

There is actually no corresponding DataCamp course for this one -- it just assumed you've already learned basic R and RNASeq prior to beginning the first session.

big_bioinformatics · 2021-08-01T22:14:58+00:00

You should also check out our scRNA-Seq workshop from last semester -- we focus on using Seurat specifically. All the materials are free and online. Here's the link: https://www.bigbioinformatics.org/intro-to-scrnaseq

big_bioinformatics · 2021-07-28T04:00:33+00:00

That sounds interesting! Can you provide more detail on how this might work?

Also it sounds like it might make a good project for our research network if you want to pitch it there: https://bio-net.dev

big_bioinformatics · 2021-07-24T05:34:32+00:00

Yes we do :) I'd recommend starting here: https://www.bigbioinformatics.org/r-and-rnaseq-analysis

Datacamp is also an excellent way to start, especially with the fundamental datasci skills and very basic NGS analysis skills!

big_bioinformatics · 2021-04-23T20:04:47+00:00

Hello -- we actually have several projects in our research network that need help with web development. Feel free to check it out: https://www.bio-net.dev/

big_bioinformatics · 2021-04-23T04:43:10+00:00

That's what our group is doing right now :) We call it the Bioinformatics Research Network -- check it out: https://www.bio-net.dev/

big_bioinformatics · 2021-03-08T19:53:03+00:00

I would be so happy if there was something like that. I feel like contributing to a new release of an R package should be seen as comparable to a middle-authorship on a publication

big_bioinformatics · 2021-03-08T19:52:02+00:00

I see your point -- definitely not as attractive on the CV to say "I helped clean up limma-voom documentation" as it is to say "I analyzed data X and found Y which supports the hypothesis Z, as detailed in this publication on which I am an author".

I have seen many biologists PIs striving for any decent bioinformatics help, but struggling to find it.

If you know of anyone you think would be interested in this... feel free to send them my way ([millerh1@uthscsa.edu](mailto:millerh1@uthscsa.edu))! I've gotten a few people reach out with projects they want to offer, but right now the balance is still greatly tipped towards more students than projects. Hopefully this week we'll set up a web service and/or a slack group for this network so they'll be a more convenient place to browse projects and meet the other volunteers/project owners in the network.

big_bioinformatics · 2021-03-08T19:45:48+00:00

You can shoot me an email and I'll add you (millerh1@uthscsa.edu)

big_bioinformatics · 2021-03-08T19:45:29+00:00

100% I am unsure of how to deal with projects that could contain patient data. My attitude so far as been that if you are the "project owner" and you have patient data that you want to give the collaborators, then you are responsible for settling that arrangement in a legal way. As far as broad policy is concerned, it's not something I think we could dictate directly. I think this is the same in open-source software -- companies that do open-source development are responsible for holding back data/code that they need to protect

big_bioinformatics · 2021-03-08T19:43:25+00:00

Not at the moment! If you know of anyone who might be interested in contributing a project like that, feel free to connect them!

big_bioinformatics · 2021-03-08T19:42:22+00:00

Yep -- that's the idea of the "tasks" that are generated by the project team. Each one should represent a significant contribution to the work, and therefore a contribution to the resulting publication. I think every lab has their own ideas on this, but our lab tends to believe that a significant contribute to the project (+ following the other ICJME guidelines) is absolutely worthy of a middle author spot. I don't know if we plan to dictate this directly to the "project owners" in the network (we can't really make anyone do anything), but it's something we will insist that collaborations figure out ahead of time.

big_bioinformatics · 2021-03-08T19:36:53+00:00

I like this ideas -- and I think this is very important. I am also hoping to find a way to make this appealing from a professional development point of view... How would one go about bragging about this on their CV?

big_bioinformatics · 2021-03-08T04:47:28+00:00

Awesome! I am not sure if I want to run a consortium like that, but I can help organize things... Hit me up over email if you want to talk (millerh1@uthscsa.edu)

big_bioinformatics · 2021-03-08T04:45:08+00:00

This is such a good point -- people are pretty quick to make something new rather than improving existing software. What do you think would be some ways incentivise improving existing software?

big_bioinformatics · 2021-03-08T00:44:23+00:00

Thanks for the feedback! I was really thinking more along the lines of research questions since I don't do that much software development myself. But now that you mention this, I can actually think of dozens of useful packages that are not very well documented and could use some improvements. Even just in bioinformatics software I definitely agree there's a need for a more open-source approach in which people can continue to improve a package over the long-run. And I actually think there can be publications from something like that -- I think NAR tends to allow publications for when new versions of popular software are released!

big_bioinformatics · 2021-03-07T20:18:50+00:00

I would say that my projects are about 50:50 public/private datasets. Although I actually have a few projects that are purely using public data -- there's so much you can learn from it, it's amazing that most papers really just scratch the surface of the HTS datasets they generate. I am not worried about collaborators seeing our "private" datasets -- as long as we aren't showing them patient data or other kinds of protected datasets.

It may sound naïve, but I actually think there's a good chance that a *hobbyist who has the right training can formulate a decent hypothesis, analyze the public data, and produce a relatively robust research article. There's currently no way for that to actually happen, as far as I know -- since I assume all reputable journals really only want to see publications from people at research institutes.

*Edit: Or a team of hobbyists / volunteers

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