5 days to the BioHackathon! Attribution and mini-publications
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Pjotr Prins
Mar 31, 2020, 1:43:39 PM3/31/20
to virtual biohackathon COVID-19 2020
For the BioHackathons we have created a publishing model that allows
contributors to get credit for work executed during and around
BioHackathons:
1. We have a pre-publishing server https://BioHackrXiv.org/ hosted
by the Open Science Foundation (OSF)
2. A published paper is a mini-publication and gets a (citeable) DOI
Mind: these mini-publications are not meant to be full scientific
papers (though they can grow into one).
Mini-publications are meant to describe what the group achieved so the reader
gets a sense of the 'state-of-the-art' and what was produced. It not only
allows getting credit for work (attribution), it also allows people to find
you and your work.
For the Japanese Biohackathon in Fukuoka we created the following
author instructions: https://github.com/dbcls/bh19/wiki/Author-instructions
We wrote a script that converts markdown into a suitable PDF using
pandoc. Attached are worked out examples of two working groups so you
get an idea. The PDF generator can be found at
https://github.com/journal-of-research-objects/bhxiv-gen-pdf
We'll also announce an online version that does not require installing
tools.
An example for the markdown of first attached paper can be found in
https://github.com/journal-of-research-objects/bhxiv-gen-pdf/tree/master/example/logic
During the BioHackathon we'll ask group coordinators to start on their
mini-publications. Ideally they are written up during the hackathon and
published right after! Instant gratification is what we aim for ;)
The organisers
contributors to get credit for work executed during and around
BioHackathons:
1. We have a pre-publishing server https://BioHackrXiv.org/ hosted
by the Open Science Foundation (OSF)
2. A published paper is a mini-publication and gets a (citeable) DOI
Mind: these mini-publications are not meant to be full scientific
papers (though they can grow into one).
Mini-publications are meant to describe what the group achieved so the reader
gets a sense of the 'state-of-the-art' and what was produced. It not only
allows getting credit for work (attribution), it also allows people to find
you and your work.
For the Japanese Biohackathon in Fukuoka we created the following
author instructions: https://github.com/dbcls/bh19/wiki/Author-instructions
We wrote a script that converts markdown into a suitable PDF using
pandoc. Attached are worked out examples of two working groups so you
get an idea. The PDF generator can be found at
https://github.com/journal-of-research-objects/bhxiv-gen-pdf
We'll also announce an online version that does not require installing
tools.
An example for the markdown of first attached paper can be found in
https://github.com/journal-of-research-objects/bhxiv-gen-pdf/tree/master/example/logic
During the BioHackathon we'll ask group coordinators to start on their
mini-publications. Ideally they are written up during the hackathon and
published right after! Instant gratification is what we aim for ;)
The organisers
ababaian
Mar 31, 2020, 10:12:11 PM3/31/20
to virtual biohackathon COVID-19 2020
This is a fantastic idea! I'll definitely promote this among the NCBI hackathons and Co.
There's also the F1000 hackathon channel if you'd like to take it to the next step and go for peer review: https://f1000research.com/collections/hackathons
=D =D =D
Artem
Pjotr Prins
Apr 2, 2020, 2:53:02 PM4/2/20
to virtual biohackathon COVID-19 2020
Dear all,
We have 342 members on this mailing list.
Only a few days left and it is important to get organised!
We are preparing presentations and a program. Stay posted!
What you can do now is join groups/topics on
https://github.com/virtual-biohackathons/covid-19-bh20/wiki
by adding your name. If there is no coordinator, do sign up as a
coordinator and put instructions in how to connect with you on Slack
or whatever. A coordinator does not have to be a supreme leader - you
can find out as you go along who fits the bill best.
Sunday and Monday, the first days of the BioHackathon we will spend
time deciding what to do. Mind, a BioHackathon is not only about what
is produced. It is also about connecting people and building up
(future) collaborations.
I have heard quite a few scientists complain that they are busier than
ever spending time in meetings, on papers and proposals! For me, where
I thought I could go into hibernation for a while, the opposite is
happening! Let the BioHackathon therefore be a choice to work on
something concrete and close to your heart and spend time with people
who are interested in the same things. Use it as an excuse to focus.
I'll tell my boss:
Hey, I can not this week, I am in a BioHackathon fighting COVID-19!
Two days ago we wrote we will have citable group publications on our
BioHackrXiv.org server. Let me add that the BioHackathon is
merit-based. If you contribute and participate you should get a
publication out of it. Not bad for a weeks worth of work!
We are ready!
> --
> You received this message because you are subscribed to the Google Groups "virtual biohackathon COVID-19 2020" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to virtual-biohacka...@googlegroups.com.
> To view this discussion on the web, visit https://groups.google.com/d/msgid/virtual-biohackathon/20200331174335.rcg7qoajknxeesyd%40thebird.nl.
We have 342 members on this mailing list.
Only a few days left and it is important to get organised!
We are preparing presentations and a program. Stay posted!
What you can do now is join groups/topics on
https://github.com/virtual-biohackathons/covid-19-bh20/wiki
by adding your name. If there is no coordinator, do sign up as a
coordinator and put instructions in how to connect with you on Slack
or whatever. A coordinator does not have to be a supreme leader - you
can find out as you go along who fits the bill best.
Sunday and Monday, the first days of the BioHackathon we will spend
time deciding what to do. Mind, a BioHackathon is not only about what
is produced. It is also about connecting people and building up
(future) collaborations.
I have heard quite a few scientists complain that they are busier than
ever spending time in meetings, on papers and proposals! For me, where
I thought I could go into hibernation for a while, the opposite is
happening! Let the BioHackathon therefore be a choice to work on
something concrete and close to your heart and spend time with people
who are interested in the same things. Use it as an excuse to focus.
I'll tell my boss:
Hey, I can not this week, I am in a BioHackathon fighting COVID-19!
Two days ago we wrote we will have citable group publications on our
BioHackrXiv.org server. Let me add that the BioHackathon is
merit-based. If you contribute and participate you should get a
publication out of it. Not bad for a weeks worth of work!
We are ready!
> You received this message because you are subscribed to the Google Groups "virtual biohackathon COVID-19 2020" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to virtual-biohacka...@googlegroups.com.
> To view this discussion on the web, visit https://groups.google.com/d/msgid/virtual-biohackathon/20200331174335.rcg7qoajknxeesyd%40thebird.nl.
LJ.Garcia
Apr 3, 2020, 11:56:02 AM4/3/20
to Pjotr Prins, virtual biohackathon COVID-19 2020
Dear COVID-19 Virtual BioHackathon topic coordinators,
Thanks a lot for taking the task on coordinating a hacking group. If you are not part yet of the #coordination slack channel, please join. If you have not added yet the coordination role to your topic wiki page, please do so. If you have not created a Slack channel yet, please do so and let us know its name.
We will host a kick-off meeting via a webinar (which one still under discussion) on the first day of the BioHackathon, Sunday 5th of April at 12:00 UTC. Apologies for those early in the morning or late at night. You can find the agenda for this video conference meeting and others during the week on the wiki at Video conference meetings - Agenda for the week [1]
We have prepared a Google slide master presentation [2]. We kindly ask you to add one slide for your topic/group there, you will have 1-3 minutes to describe aims, skills and potential outcomes; please also add another topic yours is potentially linked to. Questions will be done via Slack, channel #qa, please join it. We suggest you to name a delegate to help answer questions posted there in relation to your topic/group.
Many thanks for your collaboration. Should you have any questions or comments, please let us know.
Kind regards,
[2] https://docs.google.com/presentation/d/1QOR3G1yK8VtdbQzb-uj9GV_Qw1xTKRSrjwdtOpB1jbQ
Jaideep Sundaram
Apr 4, 2020, 1:42:18 PM4/4/20
to virtual biohackathon COVID-19 2020
Hello,
Please advise: how does a person sign-up (today is April 4)?
If it is too late to sign-up, can the section be updated to indicate that?
I do not see the option to do so here:
Participants section does not include such info.
Instead it provides a link to a Google sheet that lists participants and a link to this Google Group
Could someone update the Participants section to include information on how we can sign-up?
Excerpt from that section:
The following people have signed up. You can no longer add your name, but you can still participate! Use the mailing list and join a group/topic next week. To scale we have to split up in groups.
If it is too late to sign-up, can the section be updated to indicate that?
Thank you,
Jay
> To unsubscribe from this group and stop receiving emails from it, send an email to virtual-biohackathon+unsub...@googlegroups.com.
Pjotr Prins
Apr 4, 2020, 1:47:31 PM4/4/20
to Jaideep Sundaram, virtual biohackathon COVID-19 2020
At this point the best way is to sign up on Slack and join a group.
https://join.slack.com/t/virtualbiohac-xt62674/shared_invite/zt-cuur40oj-wdrVz50NocwVrH7vgKTdPg
the coordinators are there. I think all groups are on Slack right now.
Correct me if I am wrong.
Pj.
On Sat, Apr 04, 2020 at 10:42:18AM -0700, Jaideep Sundaram wrote:
> Hello,
> Please advise: how does a person sign-up (today is April 4)?
> I do not see the option to do so here:
> [1]https://github.com/virtual-biohackathons/covid-19-bh20/wiki
> name, but you can still participate! Use the [3]mailing list and join a
> > 1. We have a pre-publishing server [5]https://BioHackrXiv.org/
> [10]https://groups.google.com/d/msgid/virtual-biohackathon/
> 20200331174335.rcg7qoajknxeesyd%40thebird.nl.
> 4-4744-96a3-7b98d30a7da2%40googlegroups.com.
>
> References
>
> 1. https://github.com/virtual-biohackathons/covid-19-bh20/wiki
> 2. https://docs.google.com/spreadsheets/d/1auS0C58W0KHuqPg7-qKzgO4QjvcXpRg2NxhPu9EcWfI/edit#gid=0
> 3. https://groups.google.com/forum/#!forum/virtual-biohackathon
> 4. https://github.com/virtual-biohackathons/covid-19-bh20/wiki
> 5. https://BioHackrXiv.org/
> 6. https://github.com/dbcls/bh19/wiki/Author-instructions
> 7. https://github.com/journal-of-research-objects/bhxiv-gen-pdf
> 8. https://github.com/journal-of-research-objects/bhxiv-gen-pdf/tree/master/example/logic
> 9. javascript:/
> 10. https://groups.google.com/d/msgid/virtual-biohackathon/20200331174335....@thebird.nl
> 11. mailto:virtual-biohacka...@googlegroups.com
> 12. https://groups.google.com/d/msgid/virtual-biohackathon/902b1c6a-0fb4-4744...@googlegroups.com?utm_medium=email&utm_source=footer
https://join.slack.com/t/virtualbiohac-xt62674/shared_invite/zt-cuur40oj-wdrVz50NocwVrH7vgKTdPg
the coordinators are there. I think all groups are on Slack right now.
Correct me if I am wrong.
Pj.
On Sat, Apr 04, 2020 at 10:42:18AM -0700, Jaideep Sundaram wrote:
> Hello,
> Please advise: how does a person sign-up (today is April 4)?
> I do not see the option to do so here:
> Participants section does not include such info.
> Instead it provides a link to a Google sheet that lists participants
> and a link to this Google Group
> Could someone update the Participants section to include information on
> how we can sign-up?
> Excerpt from that section:
> The following people have [2]signed up. You can no longer add your
> Instead it provides a link to a Google sheet that lists participants
> and a link to this Google Group
> Could someone update the Participants section to include information on
> how we can sign-up?
> Excerpt from that section:
> name, but you can still participate! Use the [3]mailing list and join a
> group/topic next week. To scale we have to split up in groups.
> If it is too late to sign-up, can the section be updated to indicate
> that?
> Thank you,
> Jay
> On Thursday, April 2, 2020 at 2:53:02 PM UTC-4, pjotrp wrote:
>
> Dear all,
> We have 342 members on this mailing list.
> Only a few days left and it is important to get organised!
> We are preparing presentations and a program. Stay posted!
> What you can do now is join groups/topics on
> [4]https://github.com/virtual-biohackathons/covid-19-bh20/wiki
> If it is too late to sign-up, can the section be updated to indicate
> that?
> Thank you,
> Jay
> On Thursday, April 2, 2020 at 2:53:02 PM UTC-4, pjotrp wrote:
>
> Dear all,
> We have 342 members on this mailing list.
> Only a few days left and it is important to get organised!
> We are preparing presentations and a program. Stay posted!
> What you can do now is join groups/topics on
> hosted
> > by the Open Science Foundation (OSF)
> > 2. A published paper is a mini-publication and gets a (citeable)
> DOI
> >
> > Mind: these mini-publications are not meant to be full scientific
> > papers (though they can grow into one).
> >
> > Mini-publications are meant to describe what the group achieved so
> the reader
> > gets a sense of the 'state-of-the-art' and what was produced. It
> not only
> > allows getting credit for work (attribution), it also allows
> people to find
> > you and your work.
> >
> > For the Japanese Biohackathon in Fukuoka we created the following
> > author instructions: [6]https://github.com/dbcls/bh19/
> > by the Open Science Foundation (OSF)
> > 2. A published paper is a mini-publication and gets a (citeable)
> DOI
> >
> > Mind: these mini-publications are not meant to be full scientific
> > papers (though they can grow into one).
> >
> > Mini-publications are meant to describe what the group achieved so
> the reader
> > gets a sense of the 'state-of-the-art' and what was produced. It
> not only
> > allows getting credit for work (attribution), it also allows
> people to find
> > you and your work.
> >
> > For the Japanese Biohackathon in Fukuoka we created the following
> wiki/Author-instructions
> >
> > We wrote a script that converts markdown into a suitable PDF using
> > pandoc. Attached are worked out examples of two working groups so
> you
> > get an idea. The PDF generator can be found at
> >
> > [7]https://github.com/journal-of-research-objects/bhxiv-gen-pdf
> >
> > We wrote a script that converts markdown into a suitable PDF using
> > pandoc. Attached are worked out examples of two working groups so
> you
> > get an idea. The PDF generator can be found at
> >
> >
> > We'll also announce an online version that does not require
> installing
> > tools.
> >
> > An example for the markdown of first attached paper can be found
> in
> >
> > [8]https://github.com/journal-of-research-objects/bhxiv-gen-
> > We'll also announce an online version that does not require
> installing
> > tools.
> >
> > An example for the markdown of first attached paper can be found
> in
> >
> pdf/tree/master/example/logic
> >
> > During the BioHackathon we'll ask group coordinators to start on
> their
> > mini-publications. Ideally they are written up during the
> hackathon and
> > published right after! Instant gratification is what we aim for ;)
> >
> > The organisers
> >
> > --
> > You received this message because you are subscribed to the Google
> Groups "virtual biohackathon COVID-19 2020" group.
> > To unsubscribe from this group and stop receiving emails from it,
> send an email to [9]virtual-biohackathon+
> >
> > During the BioHackathon we'll ask group coordinators to start on
> their
> > mini-publications. Ideally they are written up during the
> hackathon and
> > published right after! Instant gratification is what we aim for ;)
> >
> > The organisers
> >
> > --
> > You received this message because you are subscribed to the Google
> Groups "virtual biohackathon COVID-19 2020" group.
> > To unsubscribe from this group and stop receiving emails from it,
> [10]https://groups.google.com/d/msgid/virtual-biohackathon/
> 20200331174335.rcg7qoajknxeesyd%40thebird.nl.
>
> --
> You received this message because you are subscribed to the Google
> Groups "virtual biohackathon COVID-19 2020" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to [11]virtual-biohacka...@googlegroups.com.
> --
> You received this message because you are subscribed to the Google
> Groups "virtual biohackathon COVID-19 2020" group.
> To unsubscribe from this group and stop receiving emails from it, send
> To view this discussion on the web, visit
> [12]https://groups.google.com/d/msgid/virtual-biohackathon/902b1c6a-0fb
> 4-4744-96a3-7b98d30a7da2%40googlegroups.com.
>
> References
>
> 1. https://github.com/virtual-biohackathons/covid-19-bh20/wiki
> 2. https://docs.google.com/spreadsheets/d/1auS0C58W0KHuqPg7-qKzgO4QjvcXpRg2NxhPu9EcWfI/edit#gid=0
> 3. https://groups.google.com/forum/#!forum/virtual-biohackathon
> 4. https://github.com/virtual-biohackathons/covid-19-bh20/wiki
> 5. https://BioHackrXiv.org/
> 6. https://github.com/dbcls/bh19/wiki/Author-instructions
> 7. https://github.com/journal-of-research-objects/bhxiv-gen-pdf
> 8. https://github.com/journal-of-research-objects/bhxiv-gen-pdf/tree/master/example/logic
> 9. javascript:/
> 10. https://groups.google.com/d/msgid/virtual-biohackathon/20200331174335....@thebird.nl
> 11. mailto:virtual-biohacka...@googlegroups.com
> 12. https://groups.google.com/d/msgid/virtual-biohackathon/902b1c6a-0fb4-4744...@googlegroups.com?utm_medium=email&utm_source=footer
Noushin Nabavi
Apr 4, 2020, 1:54:31 PM4/4/20
to Jaideep Sundaram, virtual biohackathon COVID-19 2020
Hi there, could I get an invitation to slack channel? here's my email nabavi...@gmail.com
Hello,
> To unsubscribe from this group and stop receiving emails from it, send an email to virtual-biohacka...@googlegroups.com.
> To view this discussion on the web, visit https://groups.google.com/d/msgid/virtual-biohackathon/20200331174335.rcg7qoajknxeesyd%40thebird.nl.
--
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I respectfully acknowledge that I live, work, and play on the traditional territory of Lekwungen, the Songhees and Esquimalt First Nations.
Noushin Nabavi, PhD | Tel.: +1 778-999-1982
Email: nabavi...@gmail.com | Webpage: https://noushinn.github.io
LJ.Garcia
Apr 4, 2020, 1:58:19 PM4/4/20
to Noushin Nabavi, Jaideep Sundaram, virtual biohackathon COVID-19 2020
Hi Noushin, all,
Here it goes https://virtualbiohac-xt62674.slack.com/join/shared_invite/zt-cuur40oj-wdrVz50NocwVrH7vgKTdPg
More information on communication/contribution channels at
https://github.com/virtual-biohackathons/covid-19-bh20/blob/master/CONTRIBUTING.md
Regards,
To view this discussion on the web, visit https://groups.google.com/d/msgid/virtual-biohackathon/CAN12VZmr4HX3%3DAa5e8iZkn%3DBwYHGMA%2BELOpTY0b6AxgA0AOGiw%40mail.gmail.com.
Yagoub Ali Ibrahim
Apr 4, 2020, 1:59:16 PM4/4/20
to Noushin Nabavi, Jaideep Sundaram, virtual biohackathon COVID-19 2020
Hello Noushin,
I have sent you an invitation to join the text-mining group.
------------
Sent from my mobile device.
Sent from my mobile device.
To view this discussion on the web, visit https://groups.google.com/d/msgid/virtual-biohackathon/CAN12VZmr4HX3%3DAa5e8iZkn%3DBwYHGMA%2BELOpTY0b6AxgA0AOGiw%40mail.gmail.com.
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