Road Plan for half of 2018 - Read please

[lpantano]

@lpantano @gurgese @ThomasDesvignes @mhalushka @mlhack @keilbeck @BastianFromm @ivlachos @TJU-CMC @sbb25 @phillipeloher

Hi all,

It will be a little long email, but please take 15 min to go over. It will help to decide how we start spreading the word about this.

• BOSC was great, people got a lot of question and it was accepted with open hands.
• I got a lot of good ideas to help with the format and get people using it:
  • make a logo, we are having the competition during this week, so we are almost there.
  • create a separated repository with the format only, see here
  • submit to EDAM ontology and FAIRsharing, they are database that keep track of formats and databases, (I submitted to both), we are waiting to be reviewed. @BastianFromm maybe you want to submit mirGeneDB to FAIRSharing.org?
  • publish a very small paper with the format only. This actually, I am in favor to do it. We can publish on F1000. It is open and they allow very short papers. The main idea is to have something out soon so we get people aware, without a paper it is more difficult, and the current work with tewari data is great but it will need time. Can you tell me what do you think?

The deadline for important modifications to the first version of the format is in 1 week (07/08/2018). Just to be sure we spread the word with the very first usable format.

For that I need all of you to go to the definition and open an issue with anything you think it is important to have and we don't have it. Anything, you would need to have if I want to develop something over this format, in term of query, visualization, re-mapping, anything you would need to know.

As final idea, all people recommend to try to present this as in many place as possible, but I cannot do it alone. So even if it is a slide in a talk, just do it. Having a paper will help. But you still can do this at any time. If you go to a conference and have a poster, as well, mention this to people, so we can create an ecosystem of mirna data analysis tools.

In summary:

• need your thoughts about publishing the format in F1000 (very short paper), leaving the python tool and tewari data for the next publication.
• need your feedback to make the format useful for everybody.

Thanks!

#18

[lpantano]

I forgot to mention to click on watch on this https://github.com/miRTop/mirGFF3 so you know what is going on when the file is modified, please! and Like it with an star as well :)

[lpantano]

Hi all,

Did anyone have a chance to go through this, I would love to have your inputs.

Thanks!

[mhalushka]

I think this is a great plan. Please let me know how I can better engage and help out. I might have a trainee who can do some analysis of the Tewari data, if you need help there.

[lpantano]

Thanks @mhalushka , having more people would help. I am trying to get as well a trainee.

I'll wait until have a couple of more comments, and if everybody agrees, work on the draft for the GFF paper, so we have it for August.

Cheers

[ThomasDesvignes]

Hi Lorena,
yes, I agree too that this is a great plan.
Logo, independent repository to make this format independent of miRTOP, submission to file format databases, all that sounds great to me and seems like efficient new steps towards for a solid global format. Also, having an initial very short publication of the format before doing the more extensive study is likely a good move. This initial publication may attract more people to the group and this may lead to novel ideas which could improve the solid bases we already have.
I really like the quote you wrote down from Tracy Teal ("If you want to go fast, go alone; If you want to go far, go together"), I think it summarize very well our situation and our common interest in making things happen as a group.
I will try and get more data out soon and comment on the format definition . Please let me know if I can help on this short note you want to write or if I can help in any other way!
I will also add a slide about the group in all my miRNA related talk from now on!
Cheers,

[mlhack]

Hi all, Lorena, thx for your continuous effort to move this forward. publishing is certainly always a good idea. maybe we can have a teleco next week to discuss the scope of this paper? right now i am not sure if a format only paper would be very short. it might be important to motivate the new format by discussing current methods and formats in order to make clear that this new format is something useful. you are thinking in publishing the conversion/downstream analysis tools separately or together with the tewari analysis? maybe the conversion tool(s) could go with the format paper and the downstream analysis (getting statistics out of the gff format) with the tewari data? Best, Mic

…

On 2 July 2018 at 21:08, Lorena Pantano ***@***.***> wrote: @lpantano <https://github.com/lpantano> @gurgese <https://github.com/gurgese> @ThomasDesvignes <https://github.com/ThomasDesvignes> @mhalushka <https://github.com/mhalushka> @mlhack <https://github.com/mlhack> @keilbeck <https://github.com/keilbeck> @BastianFromm <https://github.com/BastianFromm> @ivlachos <https://github.com/ivlachos> @TJU-CMC <https://github.com/TJU-CMC> @sbb25 <https://github.com/sbb25> @phillipeloher <https://github.com/phillipeloher> Hi all, It will be a little long email, but please take 15 min to go over. It will help to decide how we start spreading the word about this. - BOSC was great, people got a lot of question and it was accepted with open hands. - I got a lot of good ideas to help with the format and get people using it: - make a logo, we are having the competition during this week, so we are almost there. - create a separated repository with the format only, see here <https://github.com/miRTop/mirGFF3> - submit to EDAM ontology and FAIRsharing, they are database that keep track of formats and databases, (I submitted to both), we are waiting to be reviewed. @BastianFromm <https://github.com/BastianFromm> maybe you want to submit mirGeneDB to FAIRSharing.org? - publish a very small paper with the format only. This actually, I am in favor to do it. We can publish on F1000 <https://f1000research.com>. It is open and they allow very short papers. The main idea is to have something out soon so we get people aware, without a paper it is more difficult, and the current work with tewari data is great but it will need time. Can you tell me what do you think? The deadline for important modifications to the first version of the format is in 1 week (07/08/2018). Just to be sure we spread the word with the very first usable format. For that I need all of you to go to the definition <https://github.com/miRTop/mirGFF3/blob/master/definition.md> and open an issue with anything you think it is important to have and we don't have it. Anything, you would need to have if I want to develop something over this format, in term of query, visualization, re-mapping, anything you would need to know. As final idea, all people recommend to try to present this as in many place as possible, but I cannot do it alone. So even if it is a slide in a talk, just do it. Having a paper will help. But you still can do this at any time. If you go to a conference and have a poster, as well, mention this to people, so we can create an ecosystem of mirna data analysis tools. In summary: - need your thoughts about publishing the format in F1000 (very short paper), leaving the python tool and tewari data for the next publication. - need your feedback to make the format useful for everybody. Thanks! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#21>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AI2iM7enGtGfZ-8SfpkjcWNEzJvGp3OEks5uCm-VgaJpZM4U_zRs> .

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[mhalushka]

I am happy to jump on a conference call. I'd like to figure out what to assign my trainee to work on.

[lpantano]

Thanks Thomas for chiming in.

Thanks Michael for the input.

I proposed to leave the tool and tewari data for a future paper because the tool needs a lot of work if you want to have all the most important features added. For instance, querying the file is not implemented yet.

I think as well that working on the format for a publication will produce some changes for the better and that will affect the tool.

So my current plan is to publish the format, and we can make it long but then I need more contribution for that because I won’t be able to come with all the perspective. I think it would be great to have a good discussion for the paper, if everybody is on board. As well, there is actually no a wide used format, so that makes easier to promote the work we are doing.

If this plan goes ahead, I think mentioning that there is an open community developing the tool can bring more collaborators and make the tool better for the publication with the tewari data, plus we’d use the data to make the point the tool helps integrating big amount of samples and tools.

Here it is the doodle to try to make a conference call:

https://doodle.com/poll/ufinbin4fv772eee

Thanks all for ur feedback!

[lpantano]

sorry, I added times to the pool. Remember, ET time. Thanks

[lpantano]

Thanks for choosing your time:

I'll set up the meeting for Thursday 19, from 9-11am ET zone time. Some of you can at 9 and others at 10, so I'll be the two hours there and I can update Thomas who can only at 10am (sorry Thomas I totally forgot you are 3h behind me :( , we can meet even later that day if that is ok). I will send minutes at the end with the plan that we hopefully can agree on.

I'll send invitation on Monday!

Thanks!

[phillipeloher]

The plan looks good to me and Thursday works great.

[lpantano]

Hi all,

this is the invitation:

Topic: Mirtop - road plan 2018
Time: Jul 19, 2018 9:00 AM Eastern Time (US and Canada)

Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/221604941

Or iPhone one-tap :
US: +16699006833,,221604941# or +16468769923,,221604941#
Or Telephone:
Dial(for higher quality, dial a number based on your current location):
US: +1 669 900 6833 or +1 646 876 9923
Meeting ID: 221 604 941
International numbers available: https://zoom.us/u/eu3Ib7wO5

[mhalushka]

Thank you. I will be on the call. Also, the Tewari paper came out in Nat Biotech. So there is nothing holding us back from moving forward with their data now and getting our findings published. https://www.ncbi.nlm.nih.gov/pubmed/30010675