gmod-devel — GMOD developer's mailing list

Re: [GMOD-devel] All GMOD mail lists should be migrated from sourceforge

[Chris M. <cjm...@lb...>]

OK, so it seems the options are

 1. do our own thing on AWS
 2. bionet, Don's suggestion
 3. google groups

I worry about taking too long deciding as SF may start auto-booting people
off the different lists soon. I worry particularly about 1 as this will
take additional effort and it will be easy for this to fall through the
cracks. I'm also not sure how much maintenance is required.

I haven't heard any objection to 2.

There seems to be sufficient voices against 3 to veto it (though personally
I have had none of the mentioned issues, and for the OBO lists we're using
this because it's the path of least resistance)

On Wed, Jul 5, 2017 at 12:28 PM, Don Gilbert <gil...@gm...>
wrote:

> Dear all,
>
> Bionet still is running at http://www.bio.net/
> providing open discussion/news for biology groups, including still some of
> the model organisms (arabidopis, zebrafish, and add-ons like corn,
> medicago, annelida, ..).  This is GNU-Mailman mailing list software (same
> as sourceforge was/is).  It is self-service mostly, I maintain the
> hardware/software, keep spammers at bay, moderaters manage accounts and
> moderation :)
>
> While this is now low-key, not many new folks find it in this age of
> twitter/facebook/googroups, it continues to work and serve mail for those
> who continue to use it (it still has Usenet cross links but not many still
> use Usenet, ie. twitter without ads or owners).
>
> Genbank/NCBI folks still use their bionet.genbank to announce data
> updates.  Bionet was created/funed by Human Genome project way back (1988?)
> so it has been up and running a while now .. longer than Google,
> Sourceforge, or even NCBI.
>
> This isn't a push for GMOD to use, but if any among you want to look and
> try, there is a "new group" form
> http://net.bio.net/biomail/create
> and you can look around at other groups traffic.
>
> About 100 messages / month spread over about 25 still active groups.
> Flybase, Wormbase, Yeastbase (sorry mike) opted to run their own a while
> back but those bionet.dros, bionet.celegans, bionet.yeast lists still exist.
>
> I own the  bio.net domain (handed on from stanford, then in uk), and
> could work out with Indiana U netowkr folks a gmod.org domain linkage if
> you need that.
>
> - Don Gilbert
>
>
> On Wed, Jul 5, 2017 at 2:33 PM, Scott Cain <sc...@sc...> wrote:
>
>> Thanks for the feedback about Google Groups.  I had some vague uneasiness
>> about using it anyway, but since it was "free" I was willing to at least
>> entertain the idea.  No more entertaining.
>>
>> While I'm sure I could set up mailman on an AWS instance (and it probably
>> wouldn't even need to be that big), I am worried about such things as
>> security and the need for on going maintenance--I already don't have as
>> much time as I would like to work on GMOD stuff.  If mailman becomes a time
>> sink, that would be a real drag.  I guess I'll have to spend a little time
>> thinking/reading about it.
>>
>> Thanks,
>> Scott
>>
>>
>> On Wed, Jul 5, 2017 at 2:01 PM, Dave Clements <cle...@ga...
>> > wrote:
>>
>>> Hi All,
>>>
>>> I recommend strongly against migrating to Google Groups.  We tried
>>> Google Groups for the GCC2015 Mailing lists and we had lots of trouble with
>>> academic institutions silently blocking emails from google groups. The only
>>> workaround we could find was to also subscribe people with a non-work email
>>> address.  That was an enormous pain and it wasn't what people wanted.
>>>
>>> January-July 2015 is the only time I've used Google Groups extensively,
>>> and that experience led me to conclude that I won't try it again.
>>>
>>> Unfortunately, I don't have a recommended alternative.  GMOD and Galaxy
>>> have been using Nabble for years to archive lists, but I don't have any
>>> experience with them hosting email lists.
>>>
>>> Does anyone know how hard it is to maintain our own mailman installation
>>> on GMOD.org.
>>>
>>> *In summary: Google Groups: Don't do it.*
>>>
>>> Dave C
>>>
>>> On Wed, Jul 5, 2017 at 10:37 AM, Scott Cain <sc...@sc...> wrote:
>>>
>>>> Ah, I hadn't even thought about the idea of going the G suite for
>>>> education route.  I'll make a few queries about it, since I would really
>>>> rather have the "gmod.org" branding on whatever we migrate to.
>>>>
>>>> On Wed, Jul 5, 2017 at 1:28 PM, Todd Harris <tod...@gm...>
>>>> wrote:
>>>>
>>>>> Agreed. I saw then ignored that email from SF.
>>>>>
>>>>> Google Groups can be a little finicky sometimes but generally works
>>>>> well for most users.
>>>>>
>>>>> If we want to corral lists under the gmod.org domain, someone would
>>>>> need to petition Google for a G Suite for Education account.  That might be
>>>>> more overhead than is necessary to just get some core lists up and running
>>>>> before the end of the month.
>>>>>
>>>>> Todd
>>>>>
>>>>> > On Jun 19, 2017, at 2:51 PM, Chris Mungall <cjm...@lb...>
>>>>> wrote:
>>>>> >
>>>>> > I think it's time to ditch sourceforge altogether.
>>>>> >
>>>>> > Of course, we ditched them some time ago as a hosted VCS and ticket
>>>>> system, moving to github, but we left the mail lists in place. Now it's
>>>>> time to move these too:
>>>>> >
>>>>> >       • Recently I got an email from sourceforge asking me to
>>>>> confirm I wanted to remain on all sf mailing lists (non-confirmation
>>>>> resulting in automatic unsubscription within the month). It looked a bit
>>>>> phishy and I suspect many people will either not click or will not see the
>>>>> email, and will silently drop off the lists.
>>>>> >       • it is now no longer possible for list admins to manage
>>>>> members!
>>>>> >       • more spam seems to have been getting through
>>>>> > Unless anyone has a better suggestion, it seems like migrating to
>>>>> google groups is the best solution. This is what we're doing with the OBO
>>>>> lists: https://github.com/OBOFoundry/OBOFoundry.github.io/issues/435
>>>>> >
>>>>> > This may be a good time to do some spring cleaning, consolidate some
>>>>> groups, formally abandon some others. And perhaps we can breathe some life
>>>>> into some existing ones? gmod-architecture seems to get no love - yet this
>>>>> is at a time when the model organism databases are consolidating their
>>>>> architecture and community discussions would be most welcome!
>>>>> >
>>>>> > Here is the list of lists on SF:
>>>>> >
>>>>> > <PastedImage.png>
>>>>> >
>>>>> > A lot of these are either dead or were never really alive
>>>>> >
>>>>> > A curated list of GMOD lists:
>>>>> > http://gmod.org/wiki/GMOD_Mailing_Lists
>>>>> >
>>>>> > ------------------------------------------------------------
>>>>> ------------------
>>>>> > Check out the vibrant tech community on one of the world's most
>>>>> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
>>>>> _________________________________________
>>>>> > Gmod-devel mailing list
>>>>> > Gmo...@li...
>>>>> > https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>>>>
>>>>>
>>>>> ------------------------------------------------------------
>>>>> ------------------
>>>>> Check out the vibrant tech community on one of the world's most
>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>> _______________________________________________
>>>>> Gmod-devel mailing list
>>>>> Gmo...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> ------------------------------------------------------------
>>>> ------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain
>>>> dot net
>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> <(216)%20392-3087>
>>>> Ontario Institute for Cancer Research
>>>>
>>>> ------------------------------------------------------------
>>>> ------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>> _______________________________________________
>>>> Gmod-devel mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>>>
>>>>
>>>
>>>
>>> --
>>> https://galaxyproject.org/
>>> https://getgalaxy.org/
>>> https://usegalaxy.org/
>>> https://gcc2017.sciencesconf.org/
>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> <(216)%20392-3087>
>> Ontario Institute for Cancer Research
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Gmod-devel mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>
>>
>
>
> --
> don gilbert - www.bio.net - bioinformatics - indiana.u.
>

Re: [GMOD-devel] Gmod-devel Digest, Vol 109, Issue 2

[Nathan D. <nat...@lb...>]

I think these are great.  Do you think, in addition, having standard gitter
channels underneath GMOD might also make sense?

Not sure if that is overkill or not.

On Wed, Jul 5, 2017 at 10:46 AM, <gmo...@li...>
wrote:

> Send Gmod-devel mailing list submissions to
>         gmo...@li...
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         https://lists.sourceforge.net/lists/listinfo/gmod-devel
> or, via email, send a message with subject or body 'help' to
>         gmo...@li...
>
> You can reach the person managing the list at
>         gmo...@li...
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Gmod-devel digest..."
>
>
> Today's Topics:
>
>    1. Re: All GMOD mail lists should be migrated from sourceforge
>       (Todd Harris)
>    2. Re: All GMOD mail lists should be migrated from sourceforge
>       (Scott Cain)
>    3. Re: All GMOD mail lists should be migrated from sourceforge
>       (Scott Cain)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 5 Jul 2017 11:28:40 -0600
> From: Todd Harris <tod...@gm...>
> To: Chris Mungall <cjm...@lb...>
> Cc: gmod-devel list <gmo...@li...>
> Subject: Re: [GMOD-devel] All GMOD mail lists should be migrated from
>         sourceforge
> Message-ID: <B0D...@gm...>
> Content-Type: text/plain; charset=utf-8
>
> Agreed. I saw then ignored that email from SF.
>
> Google Groups can be a little finicky sometimes but generally works well
> for most users.
>
> If we want to corral lists under the gmod.org domain, someone would need
> to petition Google for a G Suite for Education account.  That might be more
> overhead than is necessary to just get some core lists up and running
> before the end of the month.
>
> Todd
>
> > On Jun 19, 2017, at 2:51 PM, Chris Mungall <cjm...@lb...> wrote:
> >
> > I think it's time to ditch sourceforge altogether.
> >
> > Of course, we ditched them some time ago as a hosted VCS and ticket
> system, moving to github, but we left the mail lists in place. Now it's
> time to move these too:
> >
> >       ? Recently I got an email from sourceforge asking me to confirm I
> wanted to remain on all sf mailing lists (non-confirmation resulting in
> automatic unsubscription within the month). It looked a bit phishy and I
> suspect many people will either not click or will not see the email, and
> will silently drop off the lists.
> >       ? it is now no longer possible for list admins to manage members!
> >       ? more spam seems to have been getting through
> > Unless anyone has a better suggestion, it seems like migrating to google
> groups is the best solution. This is what we're doing with the OBO lists:
> https://github.com/OBOFoundry/OBOFoundry.github.io/issues/435
> >
> > This may be a good time to do some spring cleaning, consolidate some
> groups, formally abandon some others. And perhaps we can breathe some life
> into some existing ones? gmod-architecture seems to get no love - yet this
> is at a time when the model organism databases are consolidating their
> architecture and community discussions would be most welcome!
> >
> > Here is the list of lists on SF:
> >
> > <PastedImage.png>
> >
> > A lot of these are either dead or were never really alive
> >
> > A curated list of GMOD lists:
> > http://gmod.org/wiki/GMOD_Mailing_Lists
> >
> > ------------------------------------------------------------
> ------------------
> > Check out the vibrant tech community on one of the world's most
> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
> _________________________________________
> > Gmod-devel mailing list
> > Gmo...@li...
> > https://lists.sourceforge.net/lists/listinfo/gmod-devel
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 5 Jul 2017 13:37:20 -0400
> From: Scott Cain <sc...@sc...>
> To: Todd Harris <tod...@gm...>
> Cc: Chris Mungall <cjm...@lb...>,  gmod-devel list
>         <gmo...@li...>
> Subject: Re: [GMOD-devel] All GMOD mail lists should be migrated from
>         sourceforge
> Message-ID:
>         <CA+JTaozRYEN4aX_9wzeZHmvbDY-37tfY6xNRSfrpOzKK2hXmuw@mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Ah, I hadn't even thought about the idea of going the G suite for education
> route.  I'll make a few queries about it, since I would really rather have
> the "gmod.org" branding on whatever we migrate to.
>
> On Wed, Jul 5, 2017 at 1:28 PM, Todd Harris <tod...@gm...> wrote:
>
> > Agreed. I saw then ignored that email from SF.
> >
> > Google Groups can be a little finicky sometimes but generally works well
> > for most users.
> >
> > If we want to corral lists under the gmod.org domain, someone would need
> > to petition Google for a G Suite for Education account.  That might be
> more
> > overhead than is necessary to just get some core lists up and running
> > before the end of the month.
> >
> > Todd
> >
> > > On Jun 19, 2017, at 2:51 PM, Chris Mungall <cjm...@lb...> wrote:
> > >
> > > I think it's time to ditch sourceforge altogether.
> > >
> > > Of course, we ditched them some time ago as a hosted VCS and ticket
> > system, moving to github, but we left the mail lists in place. Now it's
> > time to move these too:
> > >
> > >       ? Recently I got an email from sourceforge asking me to confirm I
> > wanted to remain on all sf mailing lists (non-confirmation resulting in
> > automatic unsubscription within the month). It looked a bit phishy and I
> > suspect many people will either not click or will not see the email, and
> > will silently drop off the lists.
> > >       ? it is now no longer possible for list admins to manage members!
> > >       ? more spam seems to have been getting through
> > > Unless anyone has a better suggestion, it seems like migrating to
> google
> > groups is the best solution. This is what we're doing with the OBO lists:
> > https://github.com/OBOFoundry/OBOFoundry.github.io/issues/435
> > >
> > > This may be a good time to do some spring cleaning, consolidate some
> > groups, formally abandon some others. And perhaps we can breathe some
> life
> > into some existing ones? gmod-architecture seems to get no love - yet
> this
> > is at a time when the model organism databases are consolidating their
> > architecture and community discussions would be most welcome!
> > >
> > > Here is the list of lists on SF:
> > >
> > > <PastedImage.png>
> > >
> > > A lot of these are either dead or were never really alive
> > >
> > > A curated list of GMOD lists:
> > > http://gmod.org/wiki/GMOD_Mailing_Lists
> > >
> > > ------------------------------------------------------------
> > ------------------
> > > Check out the vibrant tech community on one of the world's most
> > > engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
> > _________________________________________
> > > Gmod-devel mailing list
> > > Gmo...@li...
> > > https://lists.sourceforge.net/lists/listinfo/gmod-devel
> >
> >
> > ------------------------------------------------------------
> > ------------------
> > Check out the vibrant tech community on one of the world's most
> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> > _______________________________________________
> > Gmod-devel mailing list
> > Gmo...@li...
> > https://lists.sourceforge.net/lists/listinfo/gmod-devel
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 3
> Date: Wed, 5 Jul 2017 13:46:27 -0400
> From: Scott Cain <sc...@sc...>
> To: Todd Harris <tod...@gm...>
> Cc: Chris Mungall <cjm...@lb...>,  gmod-devel list
>         <gmo...@li...>
> Subject: Re: [GMOD-devel] All GMOD mail lists should be migrated from
>         sourceforge
> Message-ID:
>         <CA+JTaoz=QHUse+7iGN9iyOpFqDoT-ddeTydtWcd6i56y7HBidw@mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> OH! I totally forgot about this: gmod.org already has a free google apps
> account from before they started charging for it.  I suspect that's all we
> needed to make groups under the gmod.org domain.
>
> On Wed, Jul 5, 2017 at 1:37 PM, Scott Cain <sc...@sc...> wrote:
>
> > Ah, I hadn't even thought about the idea of going the G suite for
> > education route.  I'll make a few queries about it, since I would really
> > rather have the "gmod.org" branding on whatever we migrate to.
> >
> > On Wed, Jul 5, 2017 at 1:28 PM, Todd Harris <tod...@gm...>
> wrote:
> >
> >> Agreed. I saw then ignored that email from SF.
> >>
> >> Google Groups can be a little finicky sometimes but generally works well
> >> for most users.
> >>
> >> If we want to corral lists under the gmod.org domain, someone would
> need
> >> to petition Google for a G Suite for Education account.  That might be
> more
> >> overhead than is necessary to just get some core lists up and running
> >> before the end of the month.
> >>
> >> Todd
> >>
> >> > On Jun 19, 2017, at 2:51 PM, Chris Mungall <cjm...@lb...> wrote:
> >> >
> >> > I think it's time to ditch sourceforge altogether.
> >> >
> >> > Of course, we ditched them some time ago as a hosted VCS and ticket
> >> system, moving to github, but we left the mail lists in place. Now it's
> >> time to move these too:
> >> >
> >> >       ? Recently I got an email from sourceforge asking me to confirm
> I
> >> wanted to remain on all sf mailing lists (non-confirmation resulting in
> >> automatic unsubscription within the month). It looked a bit phishy and I
> >> suspect many people will either not click or will not see the email, and
> >> will silently drop off the lists.
> >> >       ? it is now no longer possible for list admins to manage
> members!
> >> >       ? more spam seems to have been getting through
> >> > Unless anyone has a better suggestion, it seems like migrating to
> >> google groups is the best solution. This is what we're doing with the
> OBO
> >> lists: https://github.com/OBOFoundry/OBOFoundry.github.io/issues/435
> >> >
> >> > This may be a good time to do some spring cleaning, consolidate some
> >> groups, formally abandon some others. And perhaps we can breathe some
> life
> >> into some existing ones? gmod-architecture seems to get no love - yet
> this
> >> is at a time when the model organism databases are consolidating their
> >> architecture and community discussions would be most welcome!
> >> >
> >> > Here is the list of lists on SF:
> >> >
> >> > <PastedImage.png>
> >> >
> >> > A lot of these are either dead or were never really alive
> >> >
> >> > A curated list of GMOD lists:
> >> > http://gmod.org/wiki/GMOD_Mailing_Lists
> >> >
> >> > ------------------------------------------------------------
> >> ------------------
> >> > Check out the vibrant tech community on one of the world's most
> >> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
> >> _________________________________________
> >> > Gmod-devel mailing list
> >> > Gmo...@li...
> >> > https://lists.sourceforge.net/lists/listinfo/gmod-devel
> >>
> >>
> >> ------------------------------------------------------------
> >> ------------------
> >> Check out the vibrant tech community on one of the world's most
> >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> >> _______________________________________________
> >> Gmod-devel mailing list
> >> Gmo...@li...
> >> https://lists.sourceforge.net/lists/listinfo/gmod-devel
> >>
> >
> >
> >
> > --
> > ------------------------------------------------------------------------
> > Scott Cain, Ph. D.                                   scott at scottcain
> > dot net
> > GMOD Coordinator (http://gmod.org/)                     216-392-3087
> > <(216)%20392-3087>
> > Ontario Institute for Cancer Research
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> Gmod-devel mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>
>
> ------------------------------
>
> End of Gmod-devel Digest, Vol 109, Issue 2
> ******************************************
>

Re: [GMOD-devel] All GMOD mail lists should be migrated from sourceforge

[Don G. <gil...@gm...>]

Dear all,

Bionet still is running at http://www.bio.net/
providing open discussion/news for biology groups, including still some of
the model organisms (arabidopis, zebrafish, and add-ons like corn,
medicago, annelida, ..).  This is GNU-Mailman mailing list software (same
as sourceforge was/is).  It is self-service mostly, I maintain the
hardware/software, keep spammers at bay, moderaters manage accounts and
moderation :)

While this is now low-key, not many new folks find it in this age of
twitter/facebook/googroups, it continues to work and serve mail for those
who continue to use it (it still has Usenet cross links but not many still
use Usenet, ie. twitter without ads or owners).

Genbank/NCBI folks still use their bionet.genbank to announce data
updates.  Bionet was created/funed by Human Genome project way back (1988?)
so it has been up and running a while now .. longer than Google,
Sourceforge, or even NCBI.

This isn't a push for GMOD to use, but if any among you want to look and
try, there is a "new group" form
http://net.bio.net/biomail/create
and you can look around at other groups traffic.

About 100 messages / month spread over about 25 still active groups.
Flybase, Wormbase, Yeastbase (sorry mike) opted to run their own a while
back but those bionet.dros, bionet.celegans, bionet.yeast lists still exist.

I own the  bio.net domain (handed on from stanford, then in uk), and could
work out with Indiana U netowkr folks a gmod.org domain linkage if you need
that.

- Don Gilbert


On Wed, Jul 5, 2017 at 2:33 PM, Scott Cain <sc...@sc...> wrote:

> Thanks for the feedback about Google Groups.  I had some vague uneasiness
> about using it anyway, but since it was "free" I was willing to at least
> entertain the idea.  No more entertaining.
>
> While I'm sure I could set up mailman on an AWS instance (and it probably
> wouldn't even need to be that big), I am worried about such things as
> security and the need for on going maintenance--I already don't have as
> much time as I would like to work on GMOD stuff.  If mailman becomes a time
> sink, that would be a real drag.  I guess I'll have to spend a little time
> thinking/reading about it.
>
> Thanks,
> Scott
>
>
> On Wed, Jul 5, 2017 at 2:01 PM, Dave Clements <cle...@ga...>
> wrote:
>
>> Hi All,
>>
>> I recommend strongly against migrating to Google Groups.  We tried Google
>> Groups for the GCC2015 Mailing lists and we had lots of trouble with
>> academic institutions silently blocking emails from google groups. The only
>> workaround we could find was to also subscribe people with a non-work email
>> address.  That was an enormous pain and it wasn't what people wanted.
>>
>> January-July 2015 is the only time I've used Google Groups extensively,
>> and that experience led me to conclude that I won't try it again.
>>
>> Unfortunately, I don't have a recommended alternative.  GMOD and Galaxy
>> have been using Nabble for years to archive lists, but I don't have any
>> experience with them hosting email lists.
>>
>> Does anyone know how hard it is to maintain our own mailman installation
>> on GMOD.org.
>>
>> *In summary: Google Groups: Don't do it.*
>>
>> Dave C
>>
>> On Wed, Jul 5, 2017 at 10:37 AM, Scott Cain <sc...@sc...> wrote:
>>
>>> Ah, I hadn't even thought about the idea of going the G suite for
>>> education route.  I'll make a few queries about it, since I would really
>>> rather have the "gmod.org" branding on whatever we migrate to.
>>>
>>> On Wed, Jul 5, 2017 at 1:28 PM, Todd Harris <tod...@gm...>
>>> wrote:
>>>
>>>> Agreed. I saw then ignored that email from SF.
>>>>
>>>> Google Groups can be a little finicky sometimes but generally works
>>>> well for most users.
>>>>
>>>> If we want to corral lists under the gmod.org domain, someone would
>>>> need to petition Google for a G Suite for Education account.  That might be
>>>> more overhead than is necessary to just get some core lists up and running
>>>> before the end of the month.
>>>>
>>>> Todd
>>>>
>>>> > On Jun 19, 2017, at 2:51 PM, Chris Mungall <cjm...@lb...> wrote:
>>>> >
>>>> > I think it's time to ditch sourceforge altogether.
>>>> >
>>>> > Of course, we ditched them some time ago as a hosted VCS and ticket
>>>> system, moving to github, but we left the mail lists in place. Now it's
>>>> time to move these too:
>>>> >
>>>> >       • Recently I got an email from sourceforge asking me to confirm
>>>> I wanted to remain on all sf mailing lists (non-confirmation resulting in
>>>> automatic unsubscription within the month). It looked a bit phishy and I
>>>> suspect many people will either not click or will not see the email, and
>>>> will silently drop off the lists.
>>>> >       • it is now no longer possible for list admins to manage
>>>> members!
>>>> >       • more spam seems to have been getting through
>>>> > Unless anyone has a better suggestion, it seems like migrating to
>>>> google groups is the best solution. This is what we're doing with the OBO
>>>> lists: https://github.com/OBOFoundry/OBOFoundry.github.io/issues/435
>>>> >
>>>> > This may be a good time to do some spring cleaning, consolidate some
>>>> groups, formally abandon some others. And perhaps we can breathe some life
>>>> into some existing ones? gmod-architecture seems to get no love - yet this
>>>> is at a time when the model organism databases are consolidating their
>>>> architecture and community discussions would be most welcome!
>>>> >
>>>> > Here is the list of lists on SF:
>>>> >
>>>> > <PastedImage.png>
>>>> >
>>>> > A lot of these are either dead or were never really alive
>>>> >
>>>> > A curated list of GMOD lists:
>>>> > http://gmod.org/wiki/GMOD_Mailing_Lists
>>>> >
>>>> > ------------------------------------------------------------
>>>> ------------------
>>>> > Check out the vibrant tech community on one of the world's most
>>>> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
>>>> _________________________________________
>>>> > Gmod-devel mailing list
>>>> > Gmo...@li...
>>>> > https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>>>
>>>>
>>>> ------------------------------------------------------------
>>>> ------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>> _______________________________________________
>>>> Gmod-devel mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>>>
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain
>>> dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> <(216)%20392-3087>
>>> Ontario Institute for Cancer Research
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> Gmod-devel mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>>
>>>
>>
>>
>> --
>> https://galaxyproject.org/
>> https://getgalaxy.org/
>> https://usegalaxy.org/
>> https://gcc2017.sciencesconf.org/
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> <(216)%20392-3087>
> Ontario Institute for Cancer Research
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-devel mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>
>


-- 
don gilbert - www.bio.net - bioinformatics - indiana.u.

Re: [GMOD-devel] All GMOD mail lists should be migrated from sourceforge

[Scott C. <sc...@sc...>]

Thanks for the feedback about Google Groups.  I had some vague uneasiness
about using it anyway, but since it was "free" I was willing to at least
entertain the idea.  No more entertaining.

While I'm sure I could set up mailman on an AWS instance (and it probably
wouldn't even need to be that big), I am worried about such things as
security and the need for on going maintenance--I already don't have as
much time as I would like to work on GMOD stuff.  If mailman becomes a time
sink, that would be a real drag.  I guess I'll have to spend a little time
thinking/reading about it.

Thanks,
Scott


On Wed, Jul 5, 2017 at 2:01 PM, Dave Clements <cle...@ga...>
wrote:

> Hi All,
>
> I recommend strongly against migrating to Google Groups.  We tried Google
> Groups for the GCC2015 Mailing lists and we had lots of trouble with
> academic institutions silently blocking emails from google groups. The only
> workaround we could find was to also subscribe people with a non-work email
> address.  That was an enormous pain and it wasn't what people wanted.
>
> January-July 2015 is the only time I've used Google Groups extensively,
> and that experience led me to conclude that I won't try it again.
>
> Unfortunately, I don't have a recommended alternative.  GMOD and Galaxy
> have been using Nabble for years to archive lists, but I don't have any
> experience with them hosting email lists.
>
> Does anyone know how hard it is to maintain our own mailman installation
> on GMOD.org.
>
> *In summary: Google Groups: Don't do it.*
>
> Dave C
>
> On Wed, Jul 5, 2017 at 10:37 AM, Scott Cain <sc...@sc...> wrote:
>
>> Ah, I hadn't even thought about the idea of going the G suite for
>> education route.  I'll make a few queries about it, since I would really
>> rather have the "gmod.org" branding on whatever we migrate to.
>>
>> On Wed, Jul 5, 2017 at 1:28 PM, Todd Harris <tod...@gm...>
>> wrote:
>>
>>> Agreed. I saw then ignored that email from SF.
>>>
>>> Google Groups can be a little finicky sometimes but generally works well
>>> for most users.
>>>
>>> If we want to corral lists under the gmod.org domain, someone would
>>> need to petition Google for a G Suite for Education account.  That might be
>>> more overhead than is necessary to just get some core lists up and running
>>> before the end of the month.
>>>
>>> Todd
>>>
>>> > On Jun 19, 2017, at 2:51 PM, Chris Mungall <cjm...@lb...> wrote:
>>> >
>>> > I think it's time to ditch sourceforge altogether.
>>> >
>>> > Of course, we ditched them some time ago as a hosted VCS and ticket
>>> system, moving to github, but we left the mail lists in place. Now it's
>>> time to move these too:
>>> >
>>> >       • Recently I got an email from sourceforge asking me to confirm
>>> I wanted to remain on all sf mailing lists (non-confirmation resulting in
>>> automatic unsubscription within the month). It looked a bit phishy and I
>>> suspect many people will either not click or will not see the email, and
>>> will silently drop off the lists.
>>> >       • it is now no longer possible for list admins to manage members!
>>> >       • more spam seems to have been getting through
>>> > Unless anyone has a better suggestion, it seems like migrating to
>>> google groups is the best solution. This is what we're doing with the OBO
>>> lists: https://github.com/OBOFoundry/OBOFoundry.github.io/issues/435
>>> >
>>> > This may be a good time to do some spring cleaning, consolidate some
>>> groups, formally abandon some others. And perhaps we can breathe some life
>>> into some existing ones? gmod-architecture seems to get no love - yet this
>>> is at a time when the model organism databases are consolidating their
>>> architecture and community discussions would be most welcome!
>>> >
>>> > Here is the list of lists on SF:
>>> >
>>> > <PastedImage.png>
>>> >
>>> > A lot of these are either dead or were never really alive
>>> >
>>> > A curated list of GMOD lists:
>>> > http://gmod.org/wiki/GMOD_Mailing_Lists
>>> >
>>> > ------------------------------------------------------------
>>> ------------------
>>> > Check out the vibrant tech community on one of the world's most
>>> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
>>> _________________________________________
>>> > Gmod-devel mailing list
>>> > Gmo...@li...
>>> > https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>>
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> Gmod-devel mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> <(216)%20392-3087>
>> Ontario Institute for Cancer Research
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Gmod-devel mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>
>>
>
>
> --
> https://galaxyproject.org/
> https://getgalaxy.org/
> https://usegalaxy.org/
> https://gcc2017.sciencesconf.org/
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

Re: [GMOD-devel] All GMOD mail lists should be migrated from sourceforge

[Dave C. <cle...@ga...>]

Hi All,

I recommend strongly against migrating to Google Groups.  We tried Google
Groups for the GCC2015 Mailing lists and we had lots of trouble with
academic institutions silently blocking emails from google groups. The only
workaround we could find was to also subscribe people with a non-work email
address.  That was an enormous pain and it wasn't what people wanted.

January-July 2015 is the only time I've used Google Groups extensively, and
that experience led me to conclude that I won't try it again.

Unfortunately, I don't have a recommended alternative.  GMOD and Galaxy
have been using Nabble for years to archive lists, but I don't have any
experience with them hosting email lists.

Does anyone know how hard it is to maintain our own mailman installation on
GMOD.org.

*In summary: Google Groups: Don't do it.*

Dave C

On Wed, Jul 5, 2017 at 10:37 AM, Scott Cain <sc...@sc...> wrote:

> Ah, I hadn't even thought about the idea of going the G suite for
> education route.  I'll make a few queries about it, since I would really
> rather have the "gmod.org" branding on whatever we migrate to.
>
> On Wed, Jul 5, 2017 at 1:28 PM, Todd Harris <tod...@gm...> wrote:
>
>> Agreed. I saw then ignored that email from SF.
>>
>> Google Groups can be a little finicky sometimes but generally works well
>> for most users.
>>
>> If we want to corral lists under the gmod.org domain, someone would need
>> to petition Google for a G Suite for Education account.  That might be more
>> overhead than is necessary to just get some core lists up and running
>> before the end of the month.
>>
>> Todd
>>
>> > On Jun 19, 2017, at 2:51 PM, Chris Mungall <cjm...@lb...> wrote:
>> >
>> > I think it's time to ditch sourceforge altogether.
>> >
>> > Of course, we ditched them some time ago as a hosted VCS and ticket
>> system, moving to github, but we left the mail lists in place. Now it's
>> time to move these too:
>> >
>> >       • Recently I got an email from sourceforge asking me to confirm I
>> wanted to remain on all sf mailing lists (non-confirmation resulting in
>> automatic unsubscription within the month). It looked a bit phishy and I
>> suspect many people will either not click or will not see the email, and
>> will silently drop off the lists.
>> >       • it is now no longer possible for list admins to manage members!
>> >       • more spam seems to have been getting through
>> > Unless anyone has a better suggestion, it seems like migrating to
>> google groups is the best solution. This is what we're doing with the OBO
>> lists: https://github.com/OBOFoundry/OBOFoundry.github.io/issues/435
>> >
>> > This may be a good time to do some spring cleaning, consolidate some
>> groups, formally abandon some others. And perhaps we can breathe some life
>> into some existing ones? gmod-architecture seems to get no love - yet this
>> is at a time when the model organism databases are consolidating their
>> architecture and community discussions would be most welcome!
>> >
>> > Here is the list of lists on SF:
>> >
>> > <PastedImage.png>
>> >
>> > A lot of these are either dead or were never really alive
>> >
>> > A curated list of GMOD lists:
>> > http://gmod.org/wiki/GMOD_Mailing_Lists
>> >
>> > ------------------------------------------------------------
>> ------------------
>> > Check out the vibrant tech community on one of the world's most
>> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
>> _________________________________________
>> > Gmod-devel mailing list
>> > Gmo...@li...
>> > https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Gmod-devel mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-devel mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>
>


-- 
https://galaxyproject.org/
https://getgalaxy.org/
https://usegalaxy.org/
https://gcc2017.sciencesconf.org/

Re: [GMOD-devel] All GMOD mail lists should be migrated from sourceforge

[Scott C. <sc...@sc...>]

OH! I totally forgot about this: gmod.org already has a free google apps
account from before they started charging for it.  I suspect that's all we
needed to make groups under the gmod.org domain.

On Wed, Jul 5, 2017 at 1:37 PM, Scott Cain <sc...@sc...> wrote:

> Ah, I hadn't even thought about the idea of going the G suite for
> education route.  I'll make a few queries about it, since I would really
> rather have the "gmod.org" branding on whatever we migrate to.
>
> On Wed, Jul 5, 2017 at 1:28 PM, Todd Harris <tod...@gm...> wrote:
>
>> Agreed. I saw then ignored that email from SF.
>>
>> Google Groups can be a little finicky sometimes but generally works well
>> for most users.
>>
>> If we want to corral lists under the gmod.org domain, someone would need
>> to petition Google for a G Suite for Education account.  That might be more
>> overhead than is necessary to just get some core lists up and running
>> before the end of the month.
>>
>> Todd
>>
>> > On Jun 19, 2017, at 2:51 PM, Chris Mungall <cjm...@lb...> wrote:
>> >
>> > I think it's time to ditch sourceforge altogether.
>> >
>> > Of course, we ditched them some time ago as a hosted VCS and ticket
>> system, moving to github, but we left the mail lists in place. Now it's
>> time to move these too:
>> >
>> >       • Recently I got an email from sourceforge asking me to confirm I
>> wanted to remain on all sf mailing lists (non-confirmation resulting in
>> automatic unsubscription within the month). It looked a bit phishy and I
>> suspect many people will either not click or will not see the email, and
>> will silently drop off the lists.
>> >       • it is now no longer possible for list admins to manage members!
>> >       • more spam seems to have been getting through
>> > Unless anyone has a better suggestion, it seems like migrating to
>> google groups is the best solution. This is what we're doing with the OBO
>> lists: https://github.com/OBOFoundry/OBOFoundry.github.io/issues/435
>> >
>> > This may be a good time to do some spring cleaning, consolidate some
>> groups, formally abandon some others. And perhaps we can breathe some life
>> into some existing ones? gmod-architecture seems to get no love - yet this
>> is at a time when the model organism databases are consolidating their
>> architecture and community discussions would be most welcome!
>> >
>> > Here is the list of lists on SF:
>> >
>> > <PastedImage.png>
>> >
>> > A lot of these are either dead or were never really alive
>> >
>> > A curated list of GMOD lists:
>> > http://gmod.org/wiki/GMOD_Mailing_Lists
>> >
>> > ------------------------------------------------------------
>> ------------------
>> > Check out the vibrant tech community on one of the world's most
>> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
>> _________________________________________
>> > Gmod-devel mailing list
>> > Gmo...@li...
>> > https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Gmod-devel mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> <(216)%20392-3087>
> Ontario Institute for Cancer Research
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

Re: [GMOD-devel] All GMOD mail lists should be migrated from sourceforge

[Scott C. <sc...@sc...>]

Ah, I hadn't even thought about the idea of going the G suite for education
route.  I'll make a few queries about it, since I would really rather have
the "gmod.org" branding on whatever we migrate to.

On Wed, Jul 5, 2017 at 1:28 PM, Todd Harris <tod...@gm...> wrote:

> Agreed. I saw then ignored that email from SF.
>
> Google Groups can be a little finicky sometimes but generally works well
> for most users.
>
> If we want to corral lists under the gmod.org domain, someone would need
> to petition Google for a G Suite for Education account.  That might be more
> overhead than is necessary to just get some core lists up and running
> before the end of the month.
>
> Todd
>
> > On Jun 19, 2017, at 2:51 PM, Chris Mungall <cjm...@lb...> wrote:
> >
> > I think it's time to ditch sourceforge altogether.
> >
> > Of course, we ditched them some time ago as a hosted VCS and ticket
> system, moving to github, but we left the mail lists in place. Now it's
> time to move these too:
> >
> >       • Recently I got an email from sourceforge asking me to confirm I
> wanted to remain on all sf mailing lists (non-confirmation resulting in
> automatic unsubscription within the month). It looked a bit phishy and I
> suspect many people will either not click or will not see the email, and
> will silently drop off the lists.
> >       • it is now no longer possible for list admins to manage members!
> >       • more spam seems to have been getting through
> > Unless anyone has a better suggestion, it seems like migrating to google
> groups is the best solution. This is what we're doing with the OBO lists:
> https://github.com/OBOFoundry/OBOFoundry.github.io/issues/435
> >
> > This may be a good time to do some spring cleaning, consolidate some
> groups, formally abandon some others. And perhaps we can breathe some life
> into some existing ones? gmod-architecture seems to get no love - yet this
> is at a time when the model organism databases are consolidating their
> architecture and community discussions would be most welcome!
> >
> > Here is the list of lists on SF:
> >
> > <PastedImage.png>
> >
> > A lot of these are either dead or were never really alive
> >
> > A curated list of GMOD lists:
> > http://gmod.org/wiki/GMOD_Mailing_Lists
> >
> > ------------------------------------------------------------
> ------------------
> > Check out the vibrant tech community on one of the world's most
> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
> _________________________________________
> > Gmod-devel mailing list
> > Gmo...@li...
> > https://lists.sourceforge.net/lists/listinfo/gmod-devel
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-devel mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

Re: [GMOD-devel] All GMOD mail lists should be migrated from sourceforge

[Todd H. <tod...@gm...>]

Agreed. I saw then ignored that email from SF.

Google Groups can be a little finicky sometimes but generally works well for most users.

If we want to corral lists under the gmod.org domain, someone would need to petition Google for a G Suite for Education account.  That might be more overhead than is necessary to just get some core lists up and running before the end of the month.

Todd

> On Jun 19, 2017, at 2:51 PM, Chris Mungall <cjm...@lb...> wrote:
> 
> I think it's time to ditch sourceforge altogether.
> 
> Of course, we ditched them some time ago as a hosted VCS and ticket system, moving to github, but we left the mail lists in place. Now it's time to move these too:
> 
> 	• Recently I got an email from sourceforge asking me to confirm I wanted to remain on all sf mailing lists (non-confirmation resulting in automatic unsubscription within the month). It looked a bit phishy and I suspect many people will either not click or will not see the email, and will silently drop off the lists.
> 	• it is now no longer possible for list admins to manage members!
> 	• more spam seems to have been getting through
> Unless anyone has a better suggestion, it seems like migrating to google groups is the best solution. This is what we're doing with the OBO lists: https://github.com/OBOFoundry/OBOFoundry.github.io/issues/435
> 
> This may be a good time to do some spring cleaning, consolidate some groups, formally abandon some others. And perhaps we can breathe some life into some existing ones? gmod-architecture seems to get no love - yet this is at a time when the model organism databases are consolidating their architecture and community discussions would be most welcome!
> 
> Here is the list of lists on SF:
> 
> <PastedImage.png>
> 
> A lot of these are either dead or were never really alive
> 
> A curated list of GMOD lists:
> http://gmod.org/wiki/GMOD_Mailing_Lists
> 
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________
> Gmod-devel mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-devel

[GMOD-devel] Announcing development of a new tool: CMap-js

[Andrew W. <aw...@ia...>]

Dear GMOD community,

This is to announce an alpha version of a new genetic map viewer, CMap-js.
We intend this as a replacement for CMap, which has served researchers well
for a long time, but which lacks the kind of interactivity that modern
client-side web technologies allow – and which won’t scale well with larger
datasets.

With the caveat (again) that this is an early-release version, and not
feature-complete ...

Check out the look-and-feel of the application here:
https://legumefederation.org (from the "CMap-js" button). Try clicking and
dragging over the blue map background and on the marker lists or the QTL
features on the right.

Get the code here: https://github.com/LegumeFederation/cmap-js. We welcome
developers to join in - or users to send feature requests.

Some of our design objectives are: flexible configuration; simple data
formats (accepting CMap tabular data for backward compatibility), ability
to pass in data via API (no database requirement and including cross-site
or user generated maps), minimal use of external libraries, ease of
installation, high interactivity (panning, zooming, clicking, adding or
removing maps, etc.), and scalability to a very large number of markers.
Theses structural goals are in addition to the ability to compare maps,
ability to display region data (QTLs, GWAS, etc.), the ability to
represent genetic-genomic comparisons (both within and cross-species), and
the ability to represent relations between features for any given map. We
still have quite a large set of features to add, but please let us know if
there are things that you would particularly like to see.

This is primarily the work of Andrew Wilkey and Alex Rice, and has been
funded by the NSF Legume Federation project, https://www.nsf.gov/
awardsearch/showAward?AWD_ID=1444806.


-- 
- Andrew Wilkey

T: +1-515-203-3774
E: aw...@ia...
O: 0023 CGIL

[GMOD-devel] All GMOD mail lists should be migrated from sourceforge

[Chris M. <cjm...@lb...>]

I think it's time to ditch sourceforge altogether.

Of course, we ditched them some time ago as a hosted VCS and ticket 
system, moving to github, but we left the mail lists in place. Now it's 
time to move these too:

  - Recently I got an email from sourceforge asking me to confirm I 
wanted to remain on all sf mailing lists (non-confirmation resulting in 
automatic unsubscription within the month). It looked a bit phishy and I 
suspect many people will either not click or will not see the email, and 
will silently drop off the lists.
  - it is now no longer possible for list admins to manage members!
  - more spam seems to have been getting through

Unless anyone has a better suggestion, it seems like migrating to google 
groups is the best solution. This is what we're doing with the OBO 
lists: https://github.com/OBOFoundry/OBOFoundry.github.io/issues/435

This may be a good time to do some spring cleaning, consolidate some 
groups, formally abandon some others. And perhaps we can breathe some 
life into some existing ones? gmod-architecture seems to get no love - 
yet this is at a time when the model organism databases are 
consolidating their architecture and community discussions would be most 
welcome!

Here is the list of lists on SF:

![](cid:0EE...@lb... "PastedImage.png")

A lot of these are either dead or were never really alive

A curated list of GMOD lists:
http://gmod.org/wiki/GMOD_Mailing_Lists

[GMOD-devel] Galaxy Community Conference: Register by 16 June

[Dave C. <cle...@ga...>]

Hello all,


A few GCC2017 <https://gcc2017.sciencesconf.org/> things since the previous
announcement:

1) The presentation schedule <https://gcc2017.sched.com/> has been posted.
(In particular, see

http://sched.co/B59G, http://sched.co/B5x9, http://sched.co/B57M)

2) The poster and demo schedule will likely be posted later today

(And some of these are GMOD related as well.)

3) Lightning talk <https://gcc2017.sciencesconf.org/page/submit> and
birds-of-a-feather
<https://docs.google.com/forms/d/e/1FAIpQLSdRCs97OWt47qmMxWZAtSV3TTLJ24IhW0m2lHGPLiqJU0Xkzw/viewform>
submission are still open

4) There is still limited space available for late poster and computer demo
submissions <https://gcc2017.sciencesconf.org/page/submit>

5) Register by 16 June <https://gcc2017.sciencesconf.org/page/registration>


This is the last announcement we'll post to the GMOD Lists. Please forward
it to anyone who you think might be interested.


And, we do hope to see you in Montpellier!


Dave C on behalf of the GCC2017 Organizing Committee


--

2017 Galaxy Community Conference (GCC2017)

26-30 June 2017

Montpellier, France

https://gcc2017.sciencesconf.org/

https://gcc2017.sched.com/

--



The Galaxy Community Conference (GCC) <https://gcc2017.sciencesconf.org/>
brings together researchers working in and supporting data intensive life
science research. There is no better place to share your work and learn
from others that are addressing diverse questions and facing common
challenges in data intensive biology. GCC participants work across the tree
of life, around the world, and represent universities, research
organizations, industry, medical schools and research hospitals.



GCC2017 will be in Montpellier, France, 26-30 June and features two days of
presentations, discussions, poster sessions, lightning talks, computer
demos, keynotes, and birds-of-a-feather meetups
<https://gcc2017.sched.com/overview/type/Conference>, all about
data-intensive biology and the tools that support it. GCC2017 also
features data
and coding hackathons <https://gcc2017.sciencesconf.org/page/hackathon>,
and two days of training <https://gcc2017.sched.com/overview/type/Training>
covering 16 different topics.  GCC2017 will be held at Le Corum Conference
Centre <http://www.montpellier-events.com/en/The-Corum/Presentation> in the
heart of Montpellier <https://gcc2017.sciencesconf.org/resource/page/id/2>,
just 10km from the Mediterranean.



Registration closes 16 June
<https://gcc2017.sciencesconf.org/page/registration>.  Costs start at 75€
per day for postdocs and students.



If you work in data intensive life science research then GCC2017 is an
ideal opportunity to present your work. Lightning talk
<https://gcc2017.sciencesconf.org/page/submit> and birds-of-a-feather
<https://docs.google.com/forms/d/e/1FAIpQLSdRCs97OWt47qmMxWZAtSV3TTLJ24IhW0m2lHGPLiqJU0Xkzw/viewform>
submission are still open, and there is limited space available for late
poster and computer demo submissions
<https://gcc2017.sciencesconf.org/page/submit>.



About Galaxy

Galaxy <https://galaxyproject.org/> is an open, web-based platform for
data-intensive biomedical analysis used by tens of thousands of researchers
around the world.  It supports ad hoc exploration and analysis through
scalable and repeatable data analysis pipelines for large research studies.
Galaxy is available in over 90 free and publicly accessible web servers, on
public and national cloud infrastructures, and is locally installed at
hundreds, if not thousands, of research organisations around the world.



We hope to see you in Montpellier!



Au revoir,



The GCC2017 Organising Committee

-- 
https://galaxyproject.org/
https://getgalaxy.org/
https://usegalaxy.org/
https://gcc2017.sciencesconf.org/

Re: [GMOD-devel] [gsoc2017-papers] [galaxy-dev] Project Publication Reference Tracking Tool -- are you interested in?

[Dave C. <cle...@ga...>]

Hi Anton,

We've already got folks from the Galaxy Project, Reactome, InterMine, and
BioPython on board.  And now several more folks are on the Gitter channel
as well.  I think we may end up with too many people involved.  *(But
that's the kind of problem I want to have!  :-)*

Also, the project isn't about biology per se. It's about finding papers
that reference software projects often in indirect ways.  The software can
be from any domain.

And I would argue that identifying where to search and what to search for
is up to the people using the software (for example, me), rather than the
person developing the software (Chris).

Questions?  I suggest continuing this conversation on gitter
<https://gitter.im/references-tracking/Lobby>.

Cheers,

Dave C


On Mon, May 15, 2017 at 6:00 AM, Anton Nekrutenko <an...@ne...> wrote:

> Krzysztof:
>
> This can be very interesting potentially. However, to be useful such a
> tool needs to take into account how real-world researchers (biologists)
> perform literature searches. Do you have someone who can guide in
> understanding this "very non-linear" process?
>
>
> a.
>
> Anton Nekrutenko
> Professor of Biochemistry
> and Molecular Biology
> Penn State University
> http://nekrut.bx.psu.edu
> (814) 826-9628
>
>
> On Mon, May 15, 2017 at 1:14 AM, Krzysztof Kutt <krz...@gm...>
> wrote:
> >
> > Hi!
> >
> > We do not know each other yet, so I will briefly introduce myself.
> >
> > I'm Chris, a Polish PhD candidate in Computer Science field at AGH
> University of Science and Technology in Krakow. In my work I deal with the
> broad concept of artificial intelligence. In particular the semantic web
> technologies (RDF, SPARQL, Linked Data) and the ability to support a group
> of knowledge engineers who create knowledge inside (semantic) wiki systems
> - in my PhD I propose some methods and prototypical tools for quality
> management, change management and motivation. I have also finished the
> Master's degree in Psychology and as a result I also deal with Affective
> Computing field.
> >
> > I know, I'm quite far away from bioinformatics :) so, what I am doing
> here?
> > As a part of Google Summer of Code program I will prepare a tool to keep
> track of publications that reference a specific project (project's papers,
> tools, etc). I think that at the end it will be a quite good tool that any
> researcher can use for dealing with the task, regardless of the research
> field.
> >
> > Specifically, it will be a set of Python scripts + GUI that will do four
> tasks:
> > 1) performs database search for new projects (search terms),
> > 2) handles alerts for updating the results later,
> > 3) gives the user the possibility to manually annotate results (e.g. as
> irrelevant),
> > 4) generates citation reports (e.g. list of papers that cite our project
> during last year).
> >
> > If you are interested in such a tool, do not hesitate to:
> > * read the more detailed description placed in the project's github
> wiki: https://github.com/kkutt/references-tracking/wiki/Tool-Description
> > * discuss it on the Gitter channel: https://gitter.im/references-
> tracking/Lobby or simply write me an e-mail
> > We already have interest from members of the Galaxy, Reactome,
> InterMine, and BioPython communities.
> > I am waiting for your comments :)
> >
> > If you are not interested in a project, maybe your colleagues are? :)
> >
> > Best regards,
> > Chris Kutt
> >
> > ___________________________________________________________
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> >   https://lists.galaxyproject.org/
> >
> > To search Galaxy mailing lists use the unified search at:
> >   http://galaxyproject.org/search/
>
> _______________________________________________
> gsoc2017-papers mailing list
> gso...@li...
> https://lists.galaxyproject.org/listinfo/gsoc2017-papers
>
>


-- 
https://galaxyproject.org/
https://getgalaxy.org/
https://usegalaxy.org/
https://gcc2017.sciencesconf.org/

Re: [GMOD-devel] [galaxy-dev] Project Publication Reference Tracking Tool -- are you interested in?

[Anton N. <an...@ne...>]

Krzysztof:

This can be very interesting potentially. However, to be useful such a tool
needs to take into account how real-world researchers (biologists) perform
literature searches. Do you have someone who can guide in understanding
this "very non-linear" process?


a.

Anton Nekrutenko
Professor of Biochemistry
and Molecular Biology
Penn State University
http://nekrut.bx.psu.edu
(814) 826-9628

On Mon, May 15, 2017 at 1:14 AM, Krzysztof Kutt <krz...@gm...>
wrote:
>
> Hi!
>
> We do not know each other yet, so I will briefly introduce myself.
>
> I'm Chris, a Polish PhD candidate in Computer Science field at AGH
University of Science and Technology in Krakow. In my work I deal with the
broad concept of artificial intelligence. In particular the semantic web
technologies (RDF, SPARQL, Linked Data) and the ability to support a group
of knowledge engineers who create knowledge inside (semantic) wiki systems
- in my PhD I propose some methods and prototypical tools for quality
management, change management and motivation. I have also finished the
Master's degree in Psychology and as a result I also deal with Affective
Computing field.
>
> I know, I'm quite far away from bioinformatics :) so, what I am doing
here?
> As a part of Google Summer of Code program I will prepare a tool to keep
track of publications that reference a specific project (project's papers,
tools, etc). I think that at the end it will be a quite good tool that any
researcher can use for dealing with the task, regardless of the research
field.
>
> Specifically, it will be a set of Python scripts + GUI that will do four
tasks:
> 1) performs database search for new projects (search terms),
> 2) handles alerts for updating the results later,
> 3) gives the user the possibility to manually annotate results (e.g. as
irrelevant),
> 4) generates citation reports (e.g. list of papers that cite our project
during last year).
>
> If you are interested in such a tool, do not hesitate to:
> * read the more detailed description placed in the project's github wiki:
https://github.com/kkutt/references-tracking/wiki/Tool-Description
> * discuss it on the Gitter channel:
https://gitter.im/references-tracking/Lobby or simply write me an e-mail
> We already have interest from members of the Galaxy, Reactome, InterMine,
and BioPython communities.
> I am waiting for your comments :)
>
> If you are not interested in a project, maybe your colleagues are? :)
>
> Best regards,
> Chris Kutt
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/

[GMOD-devel] Project Publication Reference Tracking Tool -- are you interested in?

[Krzysztof K. <krz...@gm...>]

Hi!

We do not know each other yet, so I will briefly introduce myself.

I'm Chris, a Polish PhD candidate in Computer Science field at AGH
University of Science and Technology in Krakow. In my work I deal with the
broad concept of artificial intelligence. In particular the semantic web
technologies (RDF, SPARQL, Linked Data) and the ability to support a group
of knowledge engineers who create knowledge inside (semantic) wiki systems
- in my PhD I propose some methods and prototypical tools for quality
management, change management and motivation. I have also finished the
Master's degree in Psychology and as a result I also deal with Affective
Computing field.

I know, I'm quite far away from bioinformatics :) so, what I am doing here?
As a part of Google Summer of Code <https://summerofcode.withgoogle.com/>
program I will prepare a tool to keep track of publications that reference
a specific project (project's papers, tools, etc). I think that at the end
it will be a quite good tool that any researcher can use for dealing with
the task, regardless of the research field.

Specifically, it will be a set of Python scripts + GUI that will do four
tasks:
1) performs database search for new projects (search terms),
2) handles alerts for updating the results later,
3) gives the user the possibility to manually annotate results (e.g. as
irrelevant),
4) generates citation reports (e.g. list of papers that cite our project
during last year).

If you are interested in such a tool, do not hesitate to:
* read the more detailed description placed in the project's github wiki:
https://github.com/kkutt/references-tracking/wiki/Tool-Description
* discuss it on the Gitter channel: https://gitter.im/references-
tracking/Lobby or simply write me an e-mail
We already have interest from members of the Galaxy, Reactome, InterMine,
and BioPython communities.
I am waiting for your comments :)

If you are not interested in a project, maybe your colleagues are? :)

Best regards,
Chris Kutt

[GMOD-devel] Galaxy Community Conference (GCC2017) talk deadline extended

[Dave C. <cle...@ga...>]

*2017 Galaxy Community Conference (GCC2017)*
26-30 June 2017
Montpellier, France
https://gcc2017.sciencesconf.org/
--

*The deadline for submitting oral presentation abstracts for the 2017
Galaxy Community Conference <https://gcc2017.sciencesconf.org/> has been
extended to 29 April.* If you work in data intensive life science research
then GCC2017 is an ideal opportunity to present your work. Posters and
computer demonstration submission closes on 27 May and the lightning talk
submission deadline is 23 June.

The 2017 Galaxy Community Conference will bring together several hundred
researchers working in and supporting data intensive life science research.
There is no better place to share your work and learn from others that are
addressing diverse questions and facing common challenges in data intensive
biology. GCC participants work across the tree of life, come from around
the world, and represent universities, research organizations, industry,
medical schools and research hospitals.

GCC2017 will be in Montpellier, France, 26-30 June and will feature two
days of presentations, discussions, poster sessions, lightning talks,
computer demos, keynotes, and birds-of-a-feather meetups, all about
data-intensive biology and the tools that support it. GCC2017 also
includes data
and coding hackathons <https://gcc2017.sciencesconf.org/page/hackathon>,
and two days of training
<https://gcc2017.sched.com/overview/type/Training> covering
16 different topics.  GCC2017 will be held at Le Corum Conference Centre
<http://www.montpellier-events.com/en/The-Corum/Presentation> in the heart
of Montpellier <https://gcc2017.sciencesconf.org/resource/page/id/2>, just
10km from the Mediterranean.

Early registration <https://gcc2017.sciencesconf.org/resource/page/id/6> is
now open and starts at less than 55€ / day for post-docs and students. You
can also book low cost conference housing when you register. Travel
fellowships are being offered by the Galaxy Community Fund for early career
researchers that are travelling from afar.

*About Galaxy*
Galaxy <https://galaxyproject.org/> is an open, web-based platform for
data-intensive biomedical analysis used by tens of thousands of researchers
around the world.  It supports ad hoc exploration and analysis through
scalable and repeatable data analysis pipelines for large research studies.
Galaxy is available in over 90 free and publicly accessible web servers, on
public and national cloud infrastructures, and is locally installed at
hundreds, if not thousands, of research organisations around the world.

We hope to see you this summer in Montpellier!

Au revoir,

The GCC2017 Organising Committee

-- 
https://galaxyproject.org/
https://getgalaxy.org/
https://usegalaxy.org/
https://gcc2017.sciencesconf.org/

[GMOD-devel] SEMANTiCS 2017, Amsterdam, Sep 11-14, open Calls

[Sebastian H. <pr...@in...>]

Apologies for cross-posting

Call for Papers, Posters & Workshops and Tutorials
SEMANTiCS 2017 - The Linked Data Conference
13th International Conference on Semantic Systems

Amsterdam, Netherlands
September 11 -14, 2017
http://2017.semantics.cc

For details please go to: https://2017.semantics.cc/calls

Important Dates (Research & Innovation Track):
*Abstract Submission Deadline:May 17, 2017 (11:59 pm, Hawaii time)
*Paper Submission Deadline:      May 24, 2017 (11:59 pm, Hawaii time)
*Notification of Acceptance:     July 3, 2017 (11:59 pm, Hawaii time)
*Camera-Ready Paper:             August 14, 2017 (11:59 pm, Hawaii time)

Important Dates (Posters & Demos Track):
*Submission Deadline:            July 10, 2017 (11:59 pm, Hawaii time)
*Notification of Acceptance:     August 10, 2017 (11:59 pm, Hawaii time)
*Camera-Ready Paper:             August 18, 2017 (11:59 pm, Hawaii time)

Important Dates (Workshops & Tutorials):
*Proposals for Tutorials and Workshops without Call for Papers: June 30, 
2017 (23:59 Hawaii Time)
*Notification of Acceptance:                 April 13, 2017 (23:59 
Hawaii Time)
*Workshop Website/Call for Papers Online:    April 30, 2017 (23:59 
Hawaii Time)
*Camera-Ready Proceedings:                   September 4, 2017 (23:59 
Hawaii Time)
*SEMANTiCS 2017 Workshop & Tutorial Days:    September 11 and 14, 2017

Important Dates (Industry & Use Case Presentations):
*Submission Deadline June 23, 2017
*Notification of Acceptance July 4, 2017
*Presentation Ready August 15, 2017

As in the previous years, SEMANTiCS’17 proceedings will be published by 
ACM ICPS (pending) and CEUR WS proceedings.

SEMANTiCS 2017 will especially welcome submissions for the following hot 
topics:
*Data Science (special track, see below)
*Web Semantics, Linked (Open) Data & schema.org
*Corporate Knowledge Graphs
*Knowledge Integration and Language Technologies
*Data Quality Management
*Economics of Data, Data Services and Data Ecosystems


Following the success of previous years, the ‘horizontals’ (research) 
and ‘verticals’ (industries) below are of interest for the conference:

Horizontals:
*Enterprise Linked Data & Data Integration
*Knowledge Discovery & Intelligent Search
*Business Models, Governance & Data Strategies
*Semantics in Big Data
*Text Analytics
*Data Portals & Knowledge Visualization
*Semantic Information Management
*Document Management & Content Management
*Terminology, Thesaurus & Ontology Management
*Smart Connectivity, Networking & Interlinking
*Smart Data & Semantics in IoT
*Semantics for IT Safety & Security
*Semantic Rules, Policies & Licensing
*Community, Social & Societal Aspects

Data Science Special Track Horizontals:
*Large-Scale Data Processing (stream processing, handling large-scale 
graphs)
*Data Analytics (Machine Learning, Predictive Analytics, Network Analytics)
*Communicating Data (Data Visualization, UX & Interaction Design, 
Crowdsourcing)
*Cross-cutting Issues (Ethics, Privacy, Security, Provenance)

Verticals:
*Industry & Engineering
*Life Sciences & Health Care
*Public Administration
*e-Science
*Digital Humanities
*Galleries, Libraries, Archives & Museums (GLAM)
*Education & eLearning
*Media & Data Journalism
*Publishing, Marketing & Advertising
*Tourism & Recreation
*Financial & Insurance Industry
*Telecommunication & Mobile Services
*Sustainable Development: Climate, Water, Air, Ecology
*Energy, Smart Homes & Smart Grids
*Food, Agriculture & Farming
*Safety, Security & Privacy
*Transport, Environment & Geospatial

[GMOD-devel] GSoC 2017: Project Publication Reference Tracking: Building a community

[Dave C. <cle...@ga...>]

Hi All,

As you may have heard the Open Genome Informatics proposal
<http://gmod.org/wiki/GSoC> was accepted for GSoC 2017.  That proposal
covers all the GMOD projects, including Galaxy.  One of projects in the
proposal was:

*Project Publication Reference Tracking (Galaxy/Reactome)
<http://gmod.org/wiki/GSOC_Project_Ideas_2017>*

Assuming that this item gets prioritized for funding, and that we find a
great student, then this will be worked on this summer.  *Hopefully we'll
end up with a great tool that any open source community can use to keep
track of publications that reference it.*

*If having a tool that helps you track publications that use your resource
interests you then please keep reading below.  *

If not, then thanks for your time,

Dave C


*Building a community*

I've been reading the GSoC Mentoring Manual
<http://write.flossmanuals.net/gsoc-mentoring/> (one of the authors is Duke
Leto) and one of the things it suggests is getting the student engaged with
the community.  The community for this proposal isn't Galaxy or Reactome or
GMOD per se (although GMOD is pretty close).  The community is folks at
open source projects that want to track references to their projects (which
includes those who run bio DBs, public Galaxy Servers, and the various GMOD
component projects).

I'd like to build that community now.  *If you are interested in this
topic, and maybe in helping to provide guidance for a GSoC student then
please let me know.** If I hear from enough people I'll create a mailing
list.  If not, we'll just use email (and probably a Gitter channel).

Also, if anyone knows of tool that already does this, please let me know.
I don't want to reinvent the wheel this summer.  Galaxy does this using
lots of email alerts, CiteULike, and some custom scripts (they work sort
of, but oh the horror!).  I've got a 6 page doc describing the current
process that I've sent to every potential GSoC student who has contacted
me.  First thing I'll do is send that to those that are interested.

Thanks,

Dave C.

* You can also post to the whole list, but I'm trying to cut down on noise
in people's email.


-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/

[GMOD-devel] Galaxy Community Conference (GCC2017), Montpellier, France, 26-30 June

[Dave C. <cle...@ga...>]

*2017 Galaxy Community Conference (GCC2017)*

26-30 June 2017

Montpellier, France

https://gcc2017.sciencesconf.org/

--


The 2017 Galaxy Community Conference <https://gcc2017.sciencesconf.org/>
will bring together several hundred researchers working in and supporting
data intensive life science research. There is no better place to share
your work and learn from others that are addressing diverse questions and
facing common challenges in data intensive biology. GCC participants work
across the tree of life, come from around the world, and represent
universities, research organizations, industry, medical schools and
research hospitals.


GCC2017 will be in Montpellier, France, 26-30 June and will feature two
days of presentations, discussions, poster sessions, lightning talks,
computer demos, keynotes, and birds-of-a-feather meetups, all about
data-intensive biology and the tools that support it. GCC2017 also includes
data and coding hackathons <https://gcc2017.sciencesconf.org/page/hackathon>,
and two days of training <https://gcc2017.sched.com/overview/type/Training>
covering 16 different topics.  GCC2017 will be held at Le Corum Conference
Centre <http://www.montpellier-events.com/en/The-Corum/Presentation>
in the heart
of Montpellier <https://gcc2017.sciencesconf.org/page/location>, just 10km
from the Mediterranean.


Abstract submission <https://gcc2017.sciencesconf.org/page/submit> is now
open.  If you work in or support data intensive life science research then
GCC2017 is an ideal opportunity to present your work. The deadline for oral
presentations is Apr 15 (23:59 Paris local time), and posters and computer
demonstration submission closes on May 27 (23:59 Paris local time). The
Lightning talk submission deadline is June 23 (23:59 Paris time).


Early registration <https://gcc2017.sciencesconf.org/page/registration> is
also open and starts at less than 55€ / day for post-docs and students. You
can also book low cost conference housing
<https://gcc2017.sciencesconf.org/page/lodging> when you register. Travel
fellowships
<https://new.galaxyproject.org/news/2017-03-gcc2017-fellowships/> are being
offered by the Galaxy Community Fund for early career researchers that are
travelling from afar.


About Galaxy

Galaxy <https://galaxyproject.org/> is an open, web-based platform for
data-intensive biomedical analysis used by tens of thousands of researchers
around the world.  It supports ad hoc exploration and analysis through
scalable and repeatable data analysis pipelines for large research studies.
Galaxy is available in over 90 free and publicly accessible web servers, on
public and national cloud infrastructures, and is locally installed at
hundreds, if not thousands, of research organisations around the world.


We hope to see you this summer in Montpellier!


Au revoir,


The GCC2017 Organising Committee


PS: Please redistribute this announcement to any interested groups.

-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/

[GMOD-devel] [GSOC 2017] Open Genome Informatics Accepted as Mentoring Organization -- Welcome Mentors!

[Robin H. <Rob...@oi...>]

Reactome, Intermine, Galaxy, GMOD, and others will be participating in Google Summer of Code (GSoC) 2017 as part of the Open Genome Informatics mentoring organization.

Learn more about the event: https://summerofcode.withgoogle.com<http://www.nrnb.org/gsoc.html>
Check out our project ideas:  http://gmod.org/wiki/GSoC

If you have a project idea that you’d like to mentor, contact me asap.

Cheers,
Robin, Marc and Scott

[GMOD-devel] DBpedia Newsletter

[Sebastian H. <pr...@in...>]

Dear all,

please find below the first edition of the DBpedia Newsletter, which 
will be sent to all subscribers in a three month interval. Of course, we 
would welcome any people who are interested to sign up 
(_http://eepurl.com/crrrkz_). We decided to use the newsletter as the 
major outlet for updates on DBpedia, so no further Newsletter edition 
will be sent to this list. Smaller and concise announcements will be 
posted on our _blog_ <http://blog.dbpedia.org/>.

Also we would welcome anyone to contribute to the Newsletter with 
DBpedia (and Linked Open Data) related announcements by sending an email 
to _dbpedia@infai.org_ <mailto:db...@in...>. Announcement/News can 
include links and should be less than 100 words and are subject to 
moderation and editorial editing (mostly shortening).

Newsletter sign up form:<http://eepurl.com/crrrkz>_http://eepurl.com/crrrkz_

Thank you very much,

Sebastian


    *(Belated) Happy New Year to all DBpedians!*

We are a proud to look retrospectively at a successful year 2016 and 
would like to welcome 2017 with our new newsletter (~4 times per year), 
which will allow you to stay up to date and provide feedback, e.g. via 
the included survey and the planned events in 2017.

*New members *- We kickstarted 
the<http://wiki.dbpedia.org/dbpedia-association>_DBpedia Association_ 
<http://wiki.dbpedia.org/dbpedia-association> with a first wave of new 
members: OpenLink Software, Semantic Web Company, Ontotext, FIZ 
Karlsruhe, Mannheim University, Poznań University of Economics and 
Business, the Business Information Systems Institute Ltd and the Open 
Knowledge Foundation Greece joined the DBpedia Association in 2016. We 
created two web pages that summarize reasons 
to<http://wiki.dbpedia.org/why-is-dbpedia-so-important>_support DBpedia 
via donations_ <http://wiki.dbpedia.org/why-is-dbpedia-so-important> 
and<http://wiki.dbpedia.org/membership>_become a member_ 
<http://wiki.dbpedia.org/membership>.

*DBpedia in Dutch* (_http://nl.dbpedia.org_ <http://nl.dbpedia.org/>) is 
the first chapter which formalized an official DBpedia Chapter 
consortium. The cooperation was initiated by Koninklijke Bibliotheek 
(National Library of the Netherlands) and Huygens ING (research 
institute of History and Culture). Other partners like imec/Ghent 
University, the Netherlands Institute of Sound and Vision and the 
Network Institute (Vrije Universiteit) joined as well. This cooperation 
will strengthen the DBpedia Dutch chapter and community of contributors 
as well improve the cooperation with the Dutch research infrastructure 
and the Dutch Digital Heritage.

We are in intensive contact with the Japanese, the German and the 
Italian chapters to form official chapters and gain institutional 
support for DBpedia. You would like to know how to start a DBpedia 
chapter? Please check 
here:<http://wiki.dbpedia.org/about/language-chapters>_http://wiki.dbpedia.org/about/language-chapters_

*DBpedia Releases *- Since 2015 we provide bi-annual DBpedia releases. 
The latest 
one,<http://wiki.dbpedia.org/dbpedia-version-2016-04>_2016-04_ 
<http://wiki.dbpedia.org/dbpedia-version-2016-04>, featured a new 
Wikipedia references & citation dataset for the English Wikipedia. In 
addition, we separated the data which we received from heuristic-based 
infobox extractors from the already mapped and quality-controlled data 
to remove low quality data and avoid duplicates & low quality 
information. We improved on 
our<http://www.semantic-web-journal.net/content/wikidata-through-eyes-dbpedia-1>_Wikidata 
extraction_ 
<http://www.semantic-web-journal.net/content/wikidata-through-eyes-dbpedia-1> 
and mapped all our data to Wikidata-based DBpedia IRIs. Wikidata will 
become more and more the core of future extractions.

*Consortium partners for EU and national projects - *Since its 
conception DBpedia has never been funded directly, but was supported 
only by individual tasks in different projects and by the spirit of 
volunteers. With the establishment of the DBpedia Association, we are 
now in a position to receive direct funding and are eligible as a full 
consortium partner for EU and International projects. Furthermore, we 
are able to mediate trusted partners - who have worked with us in the 
past and contributed greatly to DBpedia - for national proposals in over 
30 countries worldwide (contact via reply to this email.)

*Events - *In addition to our participation in the 12th edition of the 
SEMANTiCS, in the 19th International Conference on Business Information 
Systems and in the Google Summer of Code project, we arranged three 
DBpedia community meetings, in The Hague, Leipzig and Sunnyvale, 
California. In order to get updates on our events and projects, stay 
tuned and check the<http://blog.dbpedia.org/>_DBpedia blog_ 
<http://blog.dbpedia.org/>. Please check out the dates to the two new 
DBpedia meetings below.

*Links - *We have revived the portal, that allows the LOD community to 
contribute their links, so we can include them in DBpedia Releases. If 
your database links to DBpedia, you can submit your links 
here:<https://github.com/dbpedia/links>_https://github.com/dbpedia/links_ 
. We provide additional support for this and also provide a service, 
that - once you have contributed your links - will tell you which data 
is linking to your knowledge base via 
DBpedia<http://downloads.dbpedia.org/links/backlinks/>_http://downloads.dbpedia.org/links/backlinks/_, 
available only for Association members.

/We would like to thank again all people who were involved to enable this!/


    *2017 - New Year - New Opportunities*

To make 2017 as great as 2016 we have already reviewed community 
feedback and worked out some plans to bring the DBpedia community closer 
together whereas we attain our goals and follow our visions. Below are 
the most important points for 2017.

*User Survey - *Sören Auer and the DBpedia Board prepared a survey to 
assess the direction of DBpedia and the DBpedia Association. We would 
like to know what you think should be our priorities. Please take a 
minute and vote 
here:<https://goo.gl/forms/NQxrMWskcKlZJAU63>_https://goo.gl/forms/NQxrMWskcKlZJAU63_

*User support *- We set up a new portal to streamline support requests 
for DBpedia. We would encourage you to submit all questions 
to<http://wiki.dbpedia.org/support>_http://wiki.dbpedia.org/support_.

And … if you are already an experienced DBpedia user, you can sign up 
and answer questions and get kudos. Upon request, we can issue a 
certificate for your CV. During the course of 2017 we will also provide 
a priority support channel for members and Chapters.

*Save the Date* *- Galway 21 Jun and Amsterdam 14 Sep*. DBpedia will be 
part of the_Language, Data and Knowledge (LDK) conference_ 
<http://ldk2017.org/> in Galway, Ireland (*Submission open until Feb 
16th*). This new biennial conference series aims at bringing together 
researchers from across disciplines. The DBpedia community will have a 
full day event on 21th of June 2017. Also during 
the<http://2017.semantics.cc/>_SEMANTiCS 2017 in Amsterdam_ 
<http://2017.semantics.cc/>, Sep 11-14 (*Submission open until May 17th 
or June 23rd*), the DBpedia community will get together on the 14th of 
September for a DBpedia community meeting. Updates will be posted in the 
respective<http://wiki.dbpedia.org/events>_events section_ 
<http://wiki.dbpedia.org/events> and the<http://blog.dbpedia.org/>_blog_ 
<http://blog.dbpedia.org/>.

*TextExt: DBpedia’s Open Text Extraction Challenge -* 
(_http://wiki.dbpedia.org/textext_) As DBpedia and Wikidata currently 
focus primarily on representing factual knowledge as contained in 
Wikipedia infoboxes, we created the DBpedia Open Text Extraction 
Challenge. Participants are asked to submit their engines that extract 
facts and knowledge from Wikipedia article texts to dramatically broaden 
and deepen the amount of structured DBpedia/Wikipedia data.

*Community coordination* - *You'd like to get involved in DBpedia? *We 
set up a new Get Involved section. If you are interested in details or 
would like to get in touch with the DBpedia community, please read 
here:<http://wiki.dbpedia.org/get-involved>_http://wiki.dbpedia.org/get-involved_

*Community chairs *- The active community of developers and engineers 
comes together in the DBpedia community committee. We will build up this 
committee with the help of Pablo Mendes and Magnus Knuth who will serve 
as provisional chairs. The committee can be joined by recommendation 
only based on merit. If you would like to get in contact with the 
community committee please check 
here:<http://wiki.dbpedia.org/about/contact>_http://wiki.dbpedia.org/about/contact_

Two delegates from the community committee are elected chairs and will 
take seats at the Board of Trustees. This board is the main 
decision-making body of the DBpedia Association and oversees the 
association and its work, as its ultimate corporate authority. There are 
four board meetings per year, please have a look at the public minutes 
here:<http://wiki.dbpedia.org/board-minutes>_http://wiki.dbpedia.org/board-minutes_

*Technical development I: Wikidata - *Many DBpedians are excited about 
the progress<https://www.wikidata.org/>_Wikidata_ 
<https://www.wikidata.org/> is making and we are planning to use 
Wikidata’s data as the new core for our extraction and fusion. This 
means that in future releases we will fuse data from Wikidata with the 
usual data we extract from over 100 Wikipedia language editions with 
additional data from other high quality LOD sources and do the usual 
refinement, typing and quality-control. We hope that this will provide 
an unprecedented knowledge graph with superior coverage, completeness 
and correctness.

*Technical development II: UnifiedViews - *our plan to achieve the above 
mentioned fusion will be realized by an active collaboration with 
the<https://www.semantic-web.at/>_Semantic Web Company (SWC)_ 
<https://www.semantic-web.at/>, where DBpedia developers work side by 
side with the<http://www.poolparty.biz/>_PoolParty Semantic Suite_ 
<http://www.poolparty.biz/> technical team to add scalability, 
provenance tracking and linking/fusion capabilities into the Data 
Processing Units of 
the<https://www.poolparty.biz/unifiedviews/>_UnifiedViews_ 
<https://www.poolparty.biz/unifiedviews/> workflows.

*Technical development III - *For 2017, we hope to establish further 
hands-on collaboration with companies and organisations to push all 
aspects of DBpedia, in particular: search and visualisation, ontology 
maintenance, querying and indexing crawling data from web and social 
media. We also work together with our members to prioritize on 
integrating data that they think useful.

*Membership* - If you would like to become a member of the DBpedia 
Association, please check all benefits 
here:<http://wiki.dbpedia.org/membership>_http://wiki.dbpedia.org/membership_.

If you require any further information, feel free to contact us by 
replying to this email. We are already very excited to spend time with 
you on further community meetings and to publish new DBpedia releases.

All the best,

Julia, Dimitris & Sebastian

DBpedia Association

[GMOD-devel] SEMANTiCS 2017, Amsterdam, Sep 11-14, Open Calls

[Sebastian H. <pr...@in...>]

Apologies for cross-posting

Call for Papers, Posters & Workshops
SEMANTiCS 2017 - The Linked Data Conference
13th International Conference on Semantic Systems

Amsterdam, Netherlands
September 11 -14, 2017
http://2017.semantics.cc

For details please go to: https://2017.semantics.cc/calls

Important Dates (Research & Innovation):
*Abstract Submission Deadline:       May 17, 2017 (11:59 pm, Hawaii time)
*Paper Submission Deadline:          May 24, 2017 (11:59 pm, Hawaii time)
*Notification of Acceptance:         July 3, 2017 (11:59 pm, Hawaii time)
*Camera-Ready Paper:                 August 14, 2017 (11:59 pm, Hawaii time)

Important Dates (Workshops & Tutorials):
*Submission of Proposals for Workshops with Call for Papers: March 31, 
2017 (23:59 Hawaii Time)
*Submission of Proposals for Tutorials and Workshops without Call for 
Papers: June 30, 2017 (23:59 Hawaii Time)
*Workshop Proposals Notification of Acceptance: April 13, 2017 (23:59 
Hawaii Time)
*Workshop Website/Call for Papers Online: April 30, 2017 (23:59 Hawaii Time)
*Workshop Camera-Ready Proceedings:  September 4, 2017 (23:59 Hawaii Time)
*SEMANTiCS 2017 Workshop & Tutorial Days: September 11 and 14, 2017

As in the previous years, SEMANTiCS’17 proceedings will be published by 
ACM ICPS (pending) and CEUR WS proceedings.

SEMANTiCS 2017 will especially welcome submissions for the following hot 
topics:
*Data Science (special track, see below)
*Web Semantics, Linked (Open) Data & schema.org
*Corporate Knowledge Graphs
*Knowledge Integration and Language Technologies
*Data Quality Management
*Economics of Data, Data Services and Data Ecosystems

Following the success of previous years, the ‘horizontals’ (research) 
and ‘verticals’ (industries) below are of interest for the conference:

Horizontals:
*Enterprise Linked Data & Data Integration
*Knowledge Discovery & Intelligent Search
*Business Models, Governance & Data Strategies
*Semantics in Big Data
*Text Analytics
*Data Portals & Knowledge Visualization
*Semantic Information Management
*Document Management & Content Management
*Terminology, Thesaurus & Ontology Management
*Smart Connectivity, Networking & Interlinking
*Smart Data & Semantics in IoT
*Semantics for IT Safety & Security
*Semantic Rules, Policies & Licensing
*Community, Social & Societal Aspects

Data Science Special Track Horizontals:
*Large-Scale Data Processing (stream processing, handling large-scale 
graphs)
*Data Analytics (Machine Learning, Predictive Analytics, Network Analytics)
*Communicating Data (Data Visualization, UX & Interaction Design, 
Crowdsourcing)
*Cross-cutting Issues (Ethics, Privacy, Security, Provenance)

Verticals:
*Industry & Engineering
*Life Sciences & Health Care
*Public Administration
*e-Science
*Digital Humanities
*Galleries, Libraries, Archives & Museums (GLAM)
*Education & eLearning
*Media & Data Journalism
*Publishing, Marketing & Advertising
*Tourism & Recreation
*Financial & Insurance Industry
*Telecommunication & Mobile Services
*Sustainable Development: Climate, Water, Air, Ecology
*Energy, Smart Homes & Smart Grids
*Food, Agriculture & Farming
*Safety, Security & Privacy
*Transport, Environment & Geospatial

For call details please go to: https://2017.semantics.cc/calls

[GMOD-devel] New Apollo Release 2.0.6(JB#29795a1bbb)

[Monica Munoz-T. <mcm...@lb...>]

*We announce our latest release: Apollo 2.0.6*


*Download our latest release*:
https://github.com/GMOD/Apollo/releases/latest


*New features include: *

   - Improved workflow for optional display of JBrowse native tracks.
   - Improved options to navigate to annotations listed in the *Annotations*
   tab.


*A couple of important bug fixes:  *

   - Fixes problems loading the list of available tracks (*Tracks *tab)
   when switching organisms, specially for slower connections.
   - Fixes naming for annotated genomic elements (other than protein coding
   genes) in the *User-created Annotations* area under various scenarios.


*Apollo for Docker, AMIs:*

   - Our* Docker release* has been updated and is available for download
   at: https://github.com/GMOD/docker-apollo/releases
   - *Amazon Machine Images* for Apollo 2.0.6 (Java 8, Tomcat 8, and Ubuntu
   16.04) are being updated and will be available on AWS in most regions next
   week.


*Thank you!*

We are very thankful to our community of users, admins, and developers who
contribute daily to the improvement of our genome annotation editing tool.

Contribute to this project by visiting our *GitHub tracker* or writing to
the *Mailing List*:

   - Open a GitHub issue at https://github.com/GMOD/Apollo/issues/
   - Post your questions on our mailing list at ap...@li...



*Learn More*

* *Detailed, searchable documentation:* pre-requisites, configuration, and
installation guides: http://genomearchitect.readthedocs.io/

* *Detailed account of all changes* available in the Apollo ChangeLog:
https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

* *Quick-Start Guide for Apollo 2.0.x*: If you already have Apollo
instances running, you can use your current JBrowse data directories. The
quick-start guide is available at: http://genomearchitect.rea
dthedocs.io/en/stable/Apollo2Build.html

* *Migrating existing annotations:* Please find detailed information about
migrating existing installations and their annotations at
http://genomearchitect.readthedocs.io/en/latest/Migration.html

** Troubleshooting* guide available at
http://genomearchitect.readthedocs.io/en/stable/Troubleshooting.html

** Apollo User Guide* is available at http://genomearchitect.org/use
rs-guide/

** Public Demo: If you are new to Apollo we encourage you to learn more
about our software and its functionality by taking a tour of our Apollo
Demo at http://genomearchitect.org/demo/ <http://genomearchitect.org/demo/>*

* More information available on the Apollo Website
<http://genomearchitect.org/> and the Apollo repository
<https://github.com/GMOD/Apollo/blob/master/README.md>.


We look forward to hearing from you.

Sincerely,
The Apollo Development Team <http://genomearchitect.org/about/>


[image: Inline image 1]

It is very likely you will receive this message more than once; we offer
our sincere apologies for the redundancy.





-- 
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720

[GMOD-devel] [GSoC 2017] [Open Genome Informatics] Google Summer of Code 2017 Participation

[Robin H. <Rob...@oi...>]

All,

We will again be putting forward an application to be a mentoring organization for Google Summer of Code 2017 students.

"Google Summer of Code is a global program that offers student developers stipends to write code for various open source software projects. Through Google Summer of Code, accepted student applicants are paired with a mentor or mentors from the participating projects, thus gaining exposure to real-world software development scenarios and the opportunity for employment in areas related to their academic pursuits. In turn, the participating projects are able to more easily identify and bring in new developers. Best of all, more source code is created and released for the use and benefit of all.” https://developers.google.com/open-source/gsoc/

Our team name since 2011 has been Open Genome Informatics. Since 2011, the Open Genome Informatics team has served as an "umbrella organization" to a variety of open bioinformatics projects, including GMOD and its software projects -- GBrowse, JBrowse, etc.; Galaxy; PortEco; Reactome; SeqWare; WormBase; DockStore and others. I’ll update the Open Genome Informatics page: http://gmod.org/wiki/GSoC, in preparation for applying for this year’s Google Summer of Code.

Call for 2017 Project Ideas and Mentors:  We are seeking project ideas to post and attract talented students to this year’s Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact Robin Haw, cc’ing Scott Cain and Marc Gillespie (emails above).

Mentoring organization application deadline: February 9, 2017

If you have any questions please let me, Scott and Marc know.

Thanks,
Robin Haw

[GMOD-devel] SEMANTiCS 2017, Amsterdam, Sep 11-14, 2nd Call for Research & Innovation Papers

[Sebastian H. <pr...@in...>]

Apologies for cross-posting

2nd Call for Research & Innovation Papers
SEMANTiCS 2017 - The Linked Data Conference
13th International Conference on Semantic Systems

Amsterdam, Netherlands
September 11 -14, 2017
http://2017.semantics.cc

The Research & Innovation track at SEMANTiCS welcomes the submission of 
papers on novel scientific research and/or innovations relevant to the 
topics of the conference. Submissions must be original and must not have 
been submitted for publication elsewhere. Papers should follow the ACM 
ICPS guidelines for formatting 
(http://www.acm.org/sigs/publications/proceedings-templates) and must 
not exceed 8 pages in lenght for full papers and 4 pages for short 
papers, including references and optional appendices.
Research & Innovation Papers are published within ACM ICP Series.

Important Dates (Research & Innovation)
     Abstract Submission Deadline:           May 17, 2017 (11:59 pm, 
Hawaii time)
     Paper Submission Deadline:            May 24, 2017 (11:59 pm, 
Hawaii time)
     Notification of Acceptance:             July 3, 2017 (11:59 pm, 
Hawaii time)
     Camera-Ready Paper:                     August 14, 2017 (11:59 pm, 
Hawaii time)

For details please go to: https://2017.semantics.cc/calls
or contact the Research and Innovation Chairs:
     Catherine Faron Zucker, faron [@] i3s.unice.fr, Université Nice 
Sophia Antipolis
     Rinke Hoekstra, rinke.hoekstra [@] vu.nl, Vrije Universiteit 
Amsterdam/University of Amsterdam

As in the previous years, SEMANTiCS’17 proceedings will be published by 
ACM ICP (pending).

SEMANTiCS 2017 will especially welcome submissions for the following hot 
topics:
*Data Science (special track, see below)
*Web Semantics, Linked (Open) Data & schema.org
*Corporate Knowledge Graphs
*Knowledge Integration and Language Technologies
*Data Quality Management
*Economics of Data, Data Services and Data Ecosystems

Following the success of previous years, the ‘horizontals’ (research) 
and ‘verticals’ (industries) below are of interest for the conference:

Horizontals
*Enterprise Linked Data & Data Integration
*Knowledge Discovery & Intelligent Search
*Business Models, Governance & Data Strategies
*Semantics in Big Data
*Text Analytics
*Data Portals & Knowledge Visualization
*Semantic Information Management
*Document Management & Content Management
*Terminology, Thesaurus & Ontology Management
*Smart Connectivity, Networking & Interlinking
*Smart Data & Semantics in IoT
*Semantics for IT Safety & Security
*Semantic Rules, Policies & Licensing
*Community, Social & Societal Aspects

Data Science Special Track Horizontals
*arge-Scale Data Processing (stream processing, handling large-scale graphs)
*Data Analytics (Machine Learning, Predictive Analytics, Network Analytics)
*Communicating Data (Data Visualization, UX & Interaction Design, 
Crowdsourcing)
*Cross-cutting Issues (Ethics, Privacy, Security, Provenance)

Verticals
*Industry & Engineering
*Life Sciences & Health Care
*Public Administration
*e-Science
*Digital Humanities
*Galleries, Libraries, Archives & Museums (GLAM)
*Education & eLearning
*Media & Data Journalism
*Publishing, Marketing & Advertising
*Tourism & Recreation
*Financial & Insurance Industry
*Telecommunication & Mobile Services
*Sustainable Development: Climate, Water, Air, Ecology
*Energy, Smart Homes & Smart Grids
*Food, Agriculture & Farming
*Safety, Security & Privacy
*Transport, Environment & Geospatial

For details please go to: https://2017.semantics.cc/calls

[GMOD-devel] Galaxy Event News: Melbourne & Montpellier France

[Dave C. <cle...@ga...>]

Hi All,

There are two big things going on in Galaxy right now:

1) *There's a big Galaxy gathering in Melbourne Australia next month*.
This includes a two day meeting, a day of user training, and a 4 day Galaxy
Administrator Training workshop (only the 2nd time we've offered
that). The announcement
is here
<http://dev.list.galaxyproject.org/Galaxy-Australasia-Meeting-Update-Register-now-Poster-Abstracts-Training-td4670424.html>.
 (And please help spread the word about this, even if you don't go.)

2) *Training topic nominations for the 2017 Galaxy Community Conference are
now open*.  If you have a topic you would like to see covered (or that you
would like to present), then please nominate it here
<https://docs.google.com/forms/d/e/1FAIpQLSe6IeP655G0JXB4pHoSXY6A9brZ6kfiRbC1n6Wx9vylk6fKyA/viewform>.
We are in the South of France this year.*

And, if you want to keep up on what's going on in the Galaxy, I recommend
subscribing to the Galaxy Announce mailing list
<https://lists.galaxyproject.org/listinfo/galaxy-announce>.

Thanks,

Dave C

*   Don't let this affect your decision to attend at all. :-)
-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/