Submit work to BOSC2018

[lpantano]

Hi all

I plan to submit abstract for BOSC2018: https://gccbosc2018.sched.com. I will send the draft and incorporate the feedback but probably after submitting because the deadline is on Friday. I need to know if somebody oppose to this. I’ll add all people that have been involved from the beginning in order of contribution. BTW, all of you can present this whenever you want.

I'll use the affiliation here to add you as authors: http://mirtop.github.io. If you are not there, or want to change something let me know.

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

[BastianFromm]

Hi Lorena,

I would be very happy to see the direction the abstract would go before you submit it. Thanks Bastian

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Dr. Bastian Fromm (PhD)

PostDoc Department of Tumor Biology Institute for Cancer Research Norwegian Radium Hospital Oslo University Hospital PO Box 4950 Nydalen 0424 Oslo Norway

Room: K05, 072

tel: +47 22 78 18 73 cell: +47 94 12 29 55 eMail: bastianfromm@gmail.com, bastian.fromm@rr-research.no DB: http://www.mirgenedb.org/

profiles Linkedin https://www.linkedin.com/in/bastian-fromm-90286843/ Loop http://loop.frontiersin.org/people/399448/overview Mendeley https://www.mendeley.com/profiles/bastian-fromm/ ORCID http://orcid.org/0000-0003-0352-3037 Publons https://publons.com/author/306130/bastian-fromm#profile Researchgate https://www.researchgate.net/profile/Bastian_Fromm2 Scopus https://www.scopus.com/authid/detail.uri?authorId=25030115200 Twitter https://twitter.com/@BastianFromm Xing https://www.xing.com/profile/Bastian_Fromm?sc_o=mxb_p

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On Tue, Mar 13, 2018 at 5:58 PM, Lorena Pantano notifications@github.com wrote:

Hi all

I plan to submit abstract for BOSC2018: https://gccbosc2018.sched.com. I will send the draft and incorporate the feedback but probably after submitting because the deadline is on Friday. I need to know if somebody oppose to this. I’ll add all people that have been involved from the beginning in order of contribution. BTW, all of you can present this whenever you want.

I'll use the affiliation here to add you as authors: http://mirtop.github.io. If you are not there, or want to change something let me know.

cc:@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 @phillipeloher https://github.com/phillipeloher

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/miRTop/incubator/issues/18, or mute the thread https://github.com/notifications/unsubscribe-auth/AaAi34XMsX7d3xUk7MSPVtsiSp5JB6nKks5td_qjgaJpZM4SpE5b .

[lpantano]

This is a preliminary version, feel free to comment in any thing:

https://docs.google.com/document/d/1F6wuOSzQb-waIHILnxtf95HmdxfUpVCjBMRgWoBn-zw/edit

On Mar 16, 2018, at 6:43 AM, BastianFromm notifications@github.com wrote:

Hi Lorena,

I would be very happy to see the direction the abstract would go before you submit it. Thanks Bastian

---

Dr. Bastian Fromm (PhD)

PostDoc Department of Tumor Biology Institute for Cancer Research Norwegian Radium Hospital Oslo University Hospital PO Box 4950 Nydalen 0424 Oslo Norway

Room: K05, 072

tel: +47 22 78 18 73 cell: +47 94 12 29 55 eMail: bastianfromm@gmail.com, bastian.fromm@rr-research.no DB: http://www.mirgenedb.org/

profiles Linkedin https://www.linkedin.com/in/bastian-fromm-90286843/ Loop http://loop.frontiersin.org/people/399448/overview Mendeley https://www.mendeley.com/profiles/bastian-fromm/ ORCID http://orcid.org/0000-0003-0352-3037 Publons https://publons.com/author/306130/bastian-fromm#profile Researchgate https://www.researchgate.net/profile/Bastian_Fromm2 Scopus https://www.scopus.com/authid/detail.uri?authorId=25030115200 Twitter https://twitter.com/@BastianFromm Xing https://www.xing.com/profile/Bastian_Fromm?sc_o=mxb_p

---

On Tue, Mar 13, 2018 at 5:58 PM, Lorena Pantano notifications@github.com wrote:

Hi all

I plan to submit abstract for BOSC2018: https://gccbosc2018.sched.com. I will send the draft and incorporate the feedback but probably after submitting because the deadline is on Friday. I need to know if somebody oppose to this. I’ll add all people that have been involved from the beginning in order of contribution. BTW, all of you can present this whenever you want.

I'll use the affiliation here to add you as authors: http://mirtop.github.io. If you are not there, or want to change something let me know.

cc:@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 @phillipeloher https://github.com/phillipeloher

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/miRTop/incubator/issues/18, or mute the thread https://github.com/notifications/unsubscribe-auth/AaAi34XMsX7d3xUk7MSPVtsiSp5JB6nKks5td_qjgaJpZM4SpE5b .

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[lpantano]

The work has been accepted for long talk: 17min + 3m questions.

Thanks a lot.

I'll try to post the slides here with enough times for you to review. Probably, early June.

Please, post here the logo you want me to use in the acknowledgement slide.

[keilbeck]

Great news Lorena

From: Lorena Pantano notifications@github.com Reply-To: miRTop/incubator reply@reply.github.com Date: Friday, April 20, 2018 at 1:05 PM To: miRTop/incubator incubator@noreply.github.com Cc: Karen Eilbeck keilbeck@genetics.utah.edu, Mention mention@noreply.github.com Subject: Re: [miRTop/incubator] Submit work to BOSC2018 (#18)

The work has been accepted for long talk: 17min + 3m questions.

Thanks a lot.

I'll try to post the slides here with enough times for you to review. Probably, early June.

Please, post here the logo you want me to use in the acknowledgement slide.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/miRTop/incubator/issues/18#issuecomment-383192623, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AKXgF6PvPDW3PusrUTH5DkOz3z0ZLU-Gks5tqjFNgaJpZM4SpE5b.

[ivlachos]

Congrats Lorena!

[BastianFromm]

excellent!

---

Dr. Bastian Fromm (PhD)

PostDoc Department of Tumor Biology Institute for Cancer Research Norwegian Radium Hospital Oslo University Hospital PO Box 4950 Nydalen 0424 Oslo Norway

Room: K05, 072

tel: +47 22 78 18 73 cell: +47 94 12 29 55 eMail: bastianfromm@gmail.com, bastian.fromm@rr-research.no DB: http://www.mirgenedb.org/

profiles Linkedin https://www.linkedin.com/in/bastian-fromm-90286843/ Loop http://loop.frontiersin.org/people/399448/overview Mendeley https://www.mendeley.com/profiles/bastian-fromm/ ORCID http://orcid.org/0000-0003-0352-3037 Publons https://publons.com/author/306130/bastian-fromm#profile Researchgate https://www.researchgate.net/profile/Bastian_Fromm2 Scopus https://www.scopus.com/authid/detail.uri?authorId=25030115200 Twitter https://twitter.com/@BastianFromm Xing https://www.xing.com/profile/Bastian_Fromm?sc_o=mxb_p

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On Fri, Apr 20, 2018 at 9:12 PM, ivlachos notifications@github.com wrote:

Congrats Lorena!

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[ThomasDesvignes]

Congrats Lorena!

[lpantano]

Hi all,

I am preparing the slides for next week talk:

https://docs.google.com/presentation/d/1Nyk6xHL80pHglLYrv5XJ9a8FExjpHpnGAdkVhZSbJrk/edit?usp=sharing

Right now is just the skeleton of the talk, but if you visit in a couple of days, it should be fairly done.

Thanks in advance!

[keilbeck]

Thanks for sharing. It looks good. Let me know if you need help with anything. Maybe figures? Cheers, K

From: Lorena Pantano notifications@github.com Reply-To: miRTop/incubator reply@reply.github.com Date: Monday, June 18, 2018 at 5:22 PM To: miRTop/incubator incubator@noreply.github.com Cc: Karen Eilbeck keilbeck@genetics.utah.edu, Mention mention@noreply.github.com Subject: Re: [miRTop/incubator] Submit work to BOSC2018 (#18)

Hi all,

I am preparing the slides for next week talk:

https://docs.google.com/presentation/d/1Nyk6xHL80pHglLYrv5XJ9a8FExjpHpnGAdkVhZSbJrk/edit?usp=sharing

Right now is just the skeleton of the talk, but if you visit in a couple of days, it should be fairly done.

Thanks in advance!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/miRTop/incubator/issues/18#issuecomment-398214188, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AKXgF7fEaNchWHj098usWpyMAHDdoKIsks5t-CgUgaJpZM4SpE5b.

[mhalushka]

If I can be of any help, let me know.

[ivlachos]

The outline makes sense and seems to cover everything.

I'll keep an eye on the google doc.

Let me know if there is anything I can do to help.

[ivlachos]

Sorry! my bad. Closed it by mistake.

[lpantano]

Hi all again, cc @phillipeloher

I updated the slides, I don't think I would move a lot from this, but I made some comments and happy to accept any comments or slides. Just modify directly using the link:

https://docs.google.com/presentation/d/1Nyk6xHL80pHglLYrv5XJ9a8FExjpHpnGAdkVhZSbJrk/edit?usp=sharing

@keilbeck don't know if you want to explain better the GFF3 slide

If somebody wants to make a better figure for isomiRs scheme go ahead please. Maybe just reply here to say you'll do it.

The talk is on Jun 27, 1:44pm, so I'll freeze slides the day before that, on Jun 26, 8pm PST.

Please add at the end the logo of your institution, or the name and a picture of you, if you want.

I think this is all for now.

Thanks!

[mhalushka]

Lorena, You did a great job on this. I added and commented on a few things. I don't know if you can make the font bigger on slides 17-19. They won't project well. Thanks for doing all of this. Marc

[xbdr86]

Hi!

Nice job! My suggestion is that slides 18:20 are pretty information dense, maybe you want to add some animations or comments to focus the attention of the audience to certain aspects of the multiple plots.

Good luck!

Xavi

[ThomasDesvignes]

Hi Lorena! I'm back from Antarctica so I now have a better connection and also more time! I've made a few minor comments and I think it's looking good! Thanks for getting all this together and being the driver of this great project! Cheers! Thomas PS: contact me if you end up visiting Oregon after the meeting!

[lpantano]

Thanks all for the comments, I'll try to address all of them and try to add some notes to explain better the figures. If somebody didn't add the logo, please do :) @phillipeloher?

@ThomasDesvignes, I'll be in Portland downtown Saturday afternoon until 8pm, mainly in the powell book store :P

[phillipeloher]

Looks good @lpantano , good job! Added Jefferson's logo. Not sure when we need the develop the details of the isomiR annotations (e.g. slide 10) - where is the most appropriate place (email?) for suggestions there?

[lpantano]

Awesome! You can discuss in GitHub using an issue, this is the main document for now: https://github.com/miRTop/incubator/blob/master/format/definition.md

On Jun 26, 2018, at 8:16 AM, phillipeloher notifications@github.com wrote:

Looks good @lpantano https://github.com/lpantano , good job! Added Jefferson's logo. Not sure when we need the develop the details of the isomiR annotations (e.g. slide 10) - where is the most appropriate place (email?) for suggestions there?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/miRTop/incubator/issues/18#issuecomment-400347795, or mute the thread https://github.com/notifications/unsubscribe-auth/ABi_HFP5YrueRhWxcXUMX4H8RlaTfLzvks5uAlBlgaJpZM4SpE5b.

[lpantano]

Slides are done, I am submitting to F1000 to have it as a record and all of you can cite. I'll post the link one is up there.

[lpantano]

Hi,

All of you can cite the talk using this: http://dx.doi.org/10.7490/f1000research.1115724.1

Please, help to spread the word about this format and encourage developers to help to support a conversion from the current output to GFF3.

Remember that any of you can mention this project at any talk, and submit it to any conference.

Cheers