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hackseq / vasco

Visualization of single cell RNA-seq data from tens of thousands of cells in real time
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status update #42

Open gracezheng opened 8 years ago

gracezheng commented 8 years ago

Hi everyone,

It was great to work with all of you on this project.

I just want to send a quick update on some thoughts:

10x is having a project planning meeting on Friday, and I will provide another update after that.

Thanks, Grace

oganm commented 8 years ago

To contact everyone you probably want to send mails as not everyone are active github users.

I am interested though I am unsure about the amount of time I can assign. On weekends, I am available this weekend (29-30 Oct) then 26-27 November. I can arrange weekends after those as needed. Other than that I can put some hours irregularly on weekdays. That depends on how everything else goes.

For publication, I am unsure, I'll consult my lab to see what they think.

We probably want to decide what is the exact end-product will be before implementing anything else so next weekend seems like a good time to talk.

esmason commented 8 years ago

I can work on it a few hours a week, usually I have more time on weekends. I can chat about it this weekend too,

szhan commented 8 years ago

I am more interested in integration with gene ontology. I would be interested in working on it on weekends mostly.

szhan commented 8 years ago

In terms of potential publication, maybe PLoS ONE? Possibly Bioinformatics App Note (novel enough)? Maybe IEEE BioVis (which recommends papers to be published in BMC Bioinformatics)?

oganm commented 8 years ago

Plos one is probably not a step up from F1k so it might not worth it to discard the discount for it. BMC Bioinformatics would be nice though we might not make it there. Maybe as a first attempt. What is Bioinformatics App Note? I couldn't find anything about it

szhan commented 8 years ago

I meant Application Note in Bioinformatics (which is probably a long shot anyway). If we can't make it to BMC, then we can't make it to Bioinformatics... I am not too familiar with F1000, as I haven't really read any articles published there. There are also PeerJ and eLife, but I am not too familiar with them either.

1234jc4321 commented 8 years ago

I found these two papers recently published in Bioinformatics as Application Notes. I think they are similar to VASCO. It could be a good place to publish.

Alla Mikheenko, Gleb Valin, Andrey Prjibelski, Vladislav Saveliev, and Alexey Gurevich Icarus: visualizer for de novo assembly evaluation Bioinformatics (2016) 32 (21): 3321-3323 doi:10.1093/bioinformatics/btw379

Hamid Younesy, Cydney B. Nielsen, Matthew C. Lorincz, Steven J.M. Jones, Mohammad M. Karimi, and Torsten Möller ChAsE: chromatin analysis and exploration tool Bioinformatics (2016) 32 (21): 3324-3326 doi:10.1093/bioinformatics/btw382

I'm also not familiar with F1000 research. The good point is that there is a hackathon channel and that one of the advisor of the channel is Ben Busby, one of the team leader at the Hackseq event.

I'm also interested to put a couple of hours per week in this project.

oganm commented 8 years ago

Any input from 10x? @gracezheng

esmason commented 8 years ago

What software quality does a visualization tool that is published in a peer reviewed journal have to be?

Because right now our code quality, robustness and maintainability is pretty low . Would we need to write unit tests, docstrings etc. ?

oganm commented 8 years ago

the main issue would be what exactly to put in the final product. then we can deal with making it maintainable. Though from my experience, code quality isn't a principle requirement for publication. It would make our lives better without a doubt though.