gmod-devel — GMOD developer's mailing list

[GMOD-devel] Call to discuss hackathon topics/organization

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

Hi All,

I thought it would be a good idea to chat about the pre-PAG GMOD hackathon
to get close to the same page on what we want to attempt and accomplish.
The nice Apollo folks have set up a call for us on Thursday the 14th at 10
am PT/1 pm ET (in a few days):

https://lbnl.zoom.us/j/4161956725

Attendance is by no means mandatory.  If you'd like to take a look at
suggested topics as they stand now, please see:

http://gmod.org/wiki/2018_PAG_Hackathon

And the hackathon registration page is at:

https://www.eventbrite.com/e/gmod-2018-pag-hackathon-tickets-39700164260

Talk to you in a few days,
Scott

--
------------------------------------------------------------------------
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] GMOD hackathon before PAG San Diego in January

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

Hello,

This is an update on the hackathon.  It is a go; the hackathon page is up
on GMOD.org:

 http://gmod.org/wiki/2018_PAG_Hackathon

And the EventBrite page is up at

  https://www.eventbrite.com/e/gmod-2018-pag-hackathon-tickets-39700164260

Tickets are $50 which covers the costs associated with the room and lunch
on the first day.  Please feel free to add suggested topics to the wiki
page, or send the suggestions to me to add.

Thanks,
Scott


On Thursday, October 12, 2017, Scott Cain <sc...@sc...> wrote:

> Hi all,
>
> This January before PAG on the Wednesday and Thursday before PAG (January
> 10-11) in San Diego we are planning a GMOD hackathon.  We expect that
> participants will be interested in solving problems/creating solutions
> related to Tripal, JBrowse, Apollo, and Galaxy but if you're interested in
> another GMOD project, by all means, let us know!  We expect this hackathon
> to overlap with the Tripal hackathon that is on January 11 (I'm pretty
> sure; right Stephen?)
>
> If you are interested in attending this hackathon, please let me know so I
> can be sure we have an appropriately sized space.  And if you're coming for
> the pre-PAG hackathon, consider staying for PAG, since there is always a
> lot of GMOD-related content at the meeting!
>
> Thanks,
> Scott
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> 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

[GMOD-devel] European Galaxy Administrator Workshop, 8-12 January 2018, Oslo. FREE

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

*We are pleased to announce that registration
<https://skjema.uio.no/galaxy-admin-workshop-2018> is now open for
the European Galaxy Administrator Workshop
<https://www.elixir-europe.org/events/european-galaxy-administrator-workshop>*
.

   - Mon 8 January 2018 to Fri 12 January 2018 CET
   - Python room, Blindern, UiO campus, Ole Johan Dahls hus
   <https://www.uio.no/english/about/getting-around/areas/gaustad/ga06/>,
   Gaustadalléen 23B, Oslo, 0373, Norway

Participants will learn how to install, configure, customize, and extend
their own Galaxy servers. Topics include tool configuration, authentication
and user management, using heterogeneous storage and compute services, and
many other topics that will enable you to get your own Galaxy server up and
running, performing well, and used by your community. Have a look at the
programme
<https://github.com/elixir-no-nels/dagobah-training/blob/2018-oslo/README.md>
to
see more details on the planned content of the workshop.

*Maximum number of participants is limited to 30, and we will manage
registrations to allow for geographical distribution and proritize
participants with responsibility of administrating galaxy servers.* After
registering you will get a second confirmation if/when a slot has been
allocated to you.

Although located in Europe, and named to reflect this, the workshop is
definitely *open to a world-wide audience.* The workshop is a result of the
collaboration between the Elixir Galaxy WG
<https://www.elixir-europe.org/about/groups/galaxy-wg> and the Galaxy
Project, and so far known, this is the only Galaxy Admin workshop planned
for 2018.

*Participants are to cover their own travel and accomodation, while the
workshop participation is free of charge.*

*Instructors*

   - Björn Grüning <https://github.com/bgruening> (Elixir Galaxy WG
   <https://www.elixir-europe.org/about/groups/galaxy-wg>, Elixir Germany
   <https://www.elixir-europe.org/about-us/who-we-are/nodes/germany>,
University
   of Freiburg <https://www.uni-freiburg.de/?set_language=en>)
   - Marius van den Beek <https://github.com/mvdbeek> (Elixir Galaxy WG
   <https://www.elixir-europe.org/about/groups/galaxy-wg>, Institute Curie
   <https://science.institut-curie.org/>, France)
   - Nicola Soranzo <http://www.earlham.ac.uk/nicola-soranzo> (Elixir
   Galaxy WG <https://www.elixir-europe.org/about/groups/galaxy-wg>, Earlham
   Institute <http://www.earlham.ac.uk/>, UK)
   - Enis Afgan <https://galaxyproject.org/people/enis-afgan/> (Galaxy
   Project <https://galaxyproject.org/>, Johns Hopkins University
   <https://jhu.edu/>, USA)
   - Abdulrahman Azab
   <http://www.usit.uio.no/om/organisasjon/itf/ft/ansatte/azab/index.html>
(Elixir
   Norway <https://www.elixir-europe.org/about-us/who-we-are/nodes/norway>,
   USIT <http://www.usit.uio.no/>, University of Oslo <http://www.uio.no/>,
   Norway)

*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 a GMOD component. and is available in over 90 free and publicly
accessible web servers, on commercial and national cloud infrastructures,
and is locally installed at hundreds, if not thousands, of research
organizations around the world.


-- 
https://galaxyproject.org/
https://usegalaxy.org/

[GMOD-devel] Reminder: Tripal events at PAG XXVI

[Cannon, E. K [C. S] <ekc...@ia...>]

This is a reminder that abstract submission for the Tripal workshop at PAG is due this Friday, October 27th.

The Tripal session at PAG (http://www.intlpag.org/) will be the same time and place this year - Sunday January 14th 2018 from 4pm-6:10pm in San Diego, CA.  We are now requesting abstracts for oral presentations, due October 27th.  Anyone who is attending the conference is welcome to submit an abstract, and we are particularly encouraging groups that are new to Tripal or haven’t presented in this session in previous years to submit.  A variety of topics are welcome: new databases, custom extensions, integration with other tools, or any other Tripal related projects.  Abstracts should be limited to 250 words, and  can be submitted by email in MS Word or PDF, please send to both Meg Staton at mst...@ut...<mailto:mst...@ut...> and Ethy Cannon at ekc...@ia...<mailto:ekc...@ia...>. We look forward to hearing from you!

(Poster abstracts for the PAG conference are handled separately and due the same day, please see https://pag.confex.com/pag/xxvi/cfp.cgi)

Also, in case you missed it, there will be a Tripal hackathon and user meeting before PAG, on January 11th and 12th. If you are planning to attend and have already done so, please add your name to this google doc so we can be sure to have a big enough room. We are also soliciting feedback from the community on any topics or break out groups you would like to see.

Doc: https://docs.google.com/document/d/1klQwUqaT_KxPKIfGYy_3rtGnOMVhJxEoD9dZ4PGc4yg/edit?usp=sharing

In addition, if there is enough interest, we will offer a class of 8-16 students to learn the basics of Tripal during the morning of January 11th (in parallel with the hackathon). Each student will be able to use their own laptop or a free session on the cloud computing platform Jetstream to go through the materials. The class will guide the installation of all required software for a web server with Drupal, installing the Tripal core and extension modules, and loading data into standard modules (Organism, Feature, etc). Please share this with any interested colleagues, and anyone who wants to attend and has not already done so, sign up here: https://goo.gl/forms/FfOlYiCcUOdd3fx83. We’ll make a decision about offering the course based on number of interested people and announce to this mailing list in early December, so please sign up by then.

Feel free to reply with any questions and we will do our best to answer. Hope to see you in San Diego!

Ethy and Meg

[GMOD-devel] Call for presentations at GMOD workshop at PAG

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

Hi all,

This January in San Diego is the annual Plant and Animal Genomes (PAG)
meeting (http://www.intlpag.org).  As in previous PAGs, there will be
several opportunities to present content related to GMOD projects.  If you
are interested in attending PAG and giving a talk at the GMOD workshop on
Wednesday, January 17, please let me know.  Your talk can either be about
new developments/functionality in existing GMOD software, about how your
organization is using the suite of GMOD software to good effect, or about
technologies that you think the GMOD community would be interested in
hearing about.  Please email me directly with a title, an abstract or a
vague idea of what you'd like to talk about.

Also, if you'd really like to come but are having a hard time coming up
with travel funds, please let me know, I might be able to help you with
that too (up to a limit of one person anyway).

Cheers,
Scott


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

[GMOD-devel] GMOD hackathon before PAG San Diego in January

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

Hi all,

This January before PAG on the Wednesday and Thursday before PAG (January
10-11) in San Diego we are planning a GMOD hackathon.  We expect that
participants will be interested in solving problems/creating solutions
related to Tripal, JBrowse, Apollo, and Galaxy but if you're interested in
another GMOD project, by all means, let us know!  We expect this hackathon
to overlap with the Tripal hackathon that is on January 11 (I'm pretty
sure; right Stephen?)

If you are interested in attending this hackathon, please let me know so I
can be sure we have an appropriately sized space.  And if you're coming for
the pre-PAG hackathon, consider staying for PAG, since there is always a
lot of GMOD-related content at the meeting!

Thanks,
Scott


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

[GMOD-devel] Tripal Events with PAG in January

[Meg S. <me...@gm...>]

Interested in learning more about Tripal or already developing in Tripal?
Tripal will be having a number of exciting events at PAG this year that you
might want to check out.

1. PAG Tripal Session - Abstract submissions due Oct 27th
2. Hackathon and User Meeting on January 11th and 12th
3. Tripal install and demo short class - sign up to gauge interest!

More info here.  <http://tripal.info/node/395>

Hope to see you in San Diego!

Meg Staton
-- 
Margaret Staton
Assistant Professor
Department of Entomology and Plant Pathology
370 PBB, 2505 EJ Chapman Drive
Knoxville, TN 37996-4560

864-506-4515 Mobile
mst...@ut...

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

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

PS, if you can get the e-mail lists of subscribers from sourceforge admins,
along with mail archives, these lists can be reconstituited in any Gnu
Mailman setup (e.g. as bionet has, or as you/others can run).  It is my
guess they were forced to hide the subscriber lists by some mis-use and
then complaints from a subset of projects .. ask and you may be able to get
the subscriber lists for GMOD groups.

On Wed, Jul 19, 2017 at 7:04 AM, Don Gilbert <gil...@gm...>
wrote:

> I looked at sourceforge's changed mail list policy: this seems to have
> been implemented with no warning to project admins (removing list member
> addresses from your view) and then on top of that instituting this
> one-month de-subscribe of list members : a badly planned double effect on
> any sf projects.
>
> You should complain, loudly (IN CAPS) to those sf managers, at least ask
> for a delay in their de-subsribing list members, to allow you time to move
> your mailing lists elsewhere.
>
> As for moving list archives, they do appear to support your downloading
> all the archived mails, in mbox format, which is what Gnu Mailman software
> uses for archived messages.
>
> - Don
>
>
> On Tue, Jul 18, 2017 at 10:03 PM, Chris Mungall <cjm...@lb...> wrote:
>
>> 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.
>>>
>>
>>
>
>
> --
> don gilbert - www.bio.net - bioinformatics - indiana.u.
>



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

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

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

I looked at sourceforge's changed mail list policy: this seems to have been
implemented with no warning to project admins (removing list member
addresses from your view) and then on top of that instituting this
one-month de-subscribe of list members : a badly planned double effect on
any sf projects.

You should complain, loudly (IN CAPS) to those sf managers, at least ask
for a delay in their de-subsribing list members, to allow you time to move
your mailing lists elsewhere.

As for moving list archives, they do appear to support your downloading all
the archived mails, in mbox format, which is what Gnu Mailman software uses
for archived messages.

- Don


On Tue, Jul 18, 2017 at 10:03 PM, Chris Mungall <cjm...@lb...> wrote:

> 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.
>>
>
>


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

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

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

I'm running several mailing lists via google groups with subscribers in the 1000s. 

While mass migrating that many users is a pain, the benefits have been worth it. 

I have seen very rare occurrences of subscription problems from people using primarily .edu addresses like Dave mentioned. This is usually institutional and remedied by having the user subscribe via a non-institutional address. I don't know many institutes that block mail from Google these days. 

The added benefit is that there is no hardware or software to maintain, no security to tend to, no backups to worry about, easy administrative handovers as necessary, etc. I'm a fan, but I guess I can see why people may be hesitant. 

> On Jul 18, 2017, at 8:03 PM, Chris Mungall <cjm...@lb...> wrote:
> 
> 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
>>>>> 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
>>> 
>>> ------------------------------------------------------------------------------
>>> 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

[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/