gmod-devel — GMOD developer's mailing list

[GMOD-devel] Fwd: Nominate software: machado

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

Hello,

I wanted to forward this to a few mailing lists where I think it might be
of interest.  Adhemar is proposing a new project that is a web front end to
Chado based on Django be a GMOD project.  Please feel free to reply to this
email with comments and questions.

Thanks,
Scott


---------- Forwarded message ---------
From: Adhemar <az...@gm...>
Date: Thu, Mar 14, 2019 at 10:09 AM
Subject: Nominate software: machado
To: <he...@gm...>


Nominate software: machado
https://github.com/lmb-embrapa/machado

machado is a Django2-based application that contains tools to interact with
Chado databases. It provides users with a framework to store, search and
visualize biological data.

   - Data loaders for the major bioinformatics formats: fasta, gff, obo,
   bibtex, blast, interproscan, orthomcl
   - The machado API delivers data directly to the JBrowse genome browser
   - The Haystack framework provides a very fast query interface using the
   Elasticsearch engine


*Requirements for the nomination process*

The development of machado was triggered by an undergoing research project
at EMBRAPA, the largest public research institute on agriculture in Brazil.
In this project we'll analyze over 50 genomes of plants by integrating
diverse data, such as, RNA-Seq, orthology and functional annotation (blast,
diamond, interproscan). As an initial approach, the project leaders chose
to store data in an well-established ontology-based database (chado) using
Python3 and started to develop machado with some objectives in mind: i) to
have it integrated to JBrowse via API, and ii) to implement generic data
loading tools to store data from some of the main bioinformatics data
formats (fasta, gff, obo, bibtex, blast, interproscan, orthomcl). Future
demands include the implementation of databases for mammalians species and
the development of tools for additional data files such as vcf.

The software is in early stage of development and there are many
functionalities still remaining to be concluded, most of them related to
visualization and interfaces. It is open source under the GPL license.
Comprehensive documentation related to software installation/configuration
and the data loading/visualization is available at
http://machado.readthedocs.io

We put extra efforts to make sure it's an inviting open environment in urge
for new developers. It is hosted by Github and has a few quality control
features, such as, continuous integration, and unit tests. The code
contains type annotations and follow the coding styles specified at PEP8
(Style Guide for Python Code) and PEP20 (The Zen of Python). The Github's
'Issues' is the main communication method to inform bugs, request new
functionalities and discuss code contributions.

We intend to massively use it in further research projects and will be
happy to support users and collaborators for the next few years. EMBRAPA is
hosting a demo of machado containing only 4 genomes at
http://www.machado.cnptia.embrapa.br






-- 
------------------------------------------------------------------------
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] [GSoC 2019] [Open Genome Informatics] Google Summer of Code 2019 Participation

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

Dear All,
Our application to GSoC has been submitted. If you are interested in participating, please submit your project ideas here<http://gmod.org/wiki/GSOC_Project_Ideas_2019> or using this online form<https://docs.google.com/forms/d/1uQlpsbPCnhNwO5OFKAB-IiY9DLWlmaHZATnaeP6KHhw>.
Thanks,
Robin



On Jan 23, 2019, at 1:20 PM, Robin Haw <Rob...@oi...<mailto:Rob...@oi...>> wrote:

Dear All,

The Open Genome Informatics team serves as an “umbrella" organization to support the efforts of many open access open-source bioinformatics projects for Google Summer of Code (GSoC)<https://summerofcode.withgoogle.com/>. Among this list of projects are GMOD and its software projects -- GBrowse, JBrowse; Galaxy; Reactome; WormBase; DockStore; Bioconda; and others.

Call for 2019 Project Ideas and Mentors:  We are seeking project ideas to post and attract talented students to this year’s Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact Robin Haw, Marc Gillespie, Dave Clements, Dannon Baker, and Scott Cain (emails above). You can also submit your ideas here<http://gmod.org/wiki/GSOC_Project_Ideas_2019> or this online form<https://docs.google.com/forms/d/1uQlpsbPCnhNwO5OFKAB-IiY9DLWlmaHZATnaeP6KHhw>.

For more information please refer to the Open Genome Informatics page<http://gmod.org/wiki/GSoC>.

The mentoring organization application deadline with GSoC is February 6th, 2019 at 3 pm EST. So, if you are interested in taking part with the team please let us know as soon as possible.

Please forward this to others who might be interested in taking part.

If you have any questions please let us know.

Thanks,
Robin, Marc, Dave, Dannon, and Scott.

Re: [GMOD-devel] [Gmod-ajax] Nomination for new GMOD project

[Cook, M. <ME...@st...>]

Pro – I have used it and deployed it and integrated it with JBrowse and agree with all points Yannick raises – and it deserves more/better exposure and funding for further dev as needed.

Malcolm Cook - Database Application Manager
Computation Biology Group
Stowers Institute for Medical Research
1000 E 50th Street
Kansas City, Missouri 64110



From: Scott Cain <sc...@sc...>
Sent: Monday, January 28, 2019 5:58 PM
To: gmod-announce <gmo...@li...>; gmod-devel <gmo...@li...>; gmod-ajax <gmo...@li...>; gmod tripal devel <gmo...@li...>; Apollo Developers <apo...@li...>; Yannick Wurm <y....@qm...>; Anurag Priyam <anu...@gm...>
Subject: [Gmod-ajax] Nomination for new GMOD project

**CAUTION: Non-Stowers email**
Hello GMOD,

Last week, Yannick Wurm of SequenceServer fame approached me about adding SequenceServer as a GMOD project.  It seems like a great fit to me as a general and widely used tool.  Please take a moment to read a little about it if you aren't already familiar and if you have any thoughts (pro or con), please let me know. I included email groups of projects that I thought might be interested in SequenceServer.  If you know of somebody else involved with GMOD who isn't covered by one of these lists, please feel free to forward it to them.

In case you weren't aware, GMOD has guidelines for adding new projects:

http://gmod.org/wiki/GMOD_Membership

Here is what Yannick wrote in support of his nomination:
-----------------------------------------------------------

Dear all,

I would like to nominate SequenceServer as a GMOD tool.

Background:
A major hurdle I stumbled upon a few years ago as  collaborators and I began to obtain transcriptome and genome assemblies from new species, was the lack of a simple manner of BLASTing unpublished data. Using  a perl/cgi blast script was horrible - and it had a counterintuitive user interface. Same with the tool for custom databases that NCBI supplied at the time.
To overcome this, Anurag Priyam (an undergraduate at the time) and I began developing  SequenceServer. Its had 3 main aims:
 - provide an intuitive user interface and elegant user experience that increases researchers productivity
 - make it easy for individual users to run it autonomously on unpublished or custom data
 - make it easy to share a BLAST interface with others - in a lab or on a community database   (including the - now deprecated antgenomes.org<http://antgenomes.org> which I ran)

It was open source from the start, and has decent success:
 - 60,000 downloads
 - >50 citations.
 - >70 github forks and 130 stars
 - >190 members on mailing list

It is used on dozens of GMOD-esque community sites - often in combination with jBrowse, including:
reefgenomics.org<http://reefgenomics.org>  http://www.daphnia-stressordb.uni-hamburg.de, hymenopterabase, http://spottedwingflybase.org , bovine genome database, Lepbase, http://www.wheat-tilling.com,  PHIbase, GenomeHubs,http://pristionchus.org/about.html, http://planmine.mpi-cbg.de/planmine/begin.do,  and many more.

Allow me to provide specific comments regarding the GMOD membership criteria below.

Please do not hesitate if you have any questions.

Kind regards,

Yannick
-----

Meets a Common Need
Growing citations & userbase demonstrate this.

Useful Over Time
Usage has steadily increased since 2012. The tool wraps BLAST (we are seeking funding to hopefully also wrap DIAMOND). We are implementing novel visualisations to increase analysis power/researchers productivity (including thanks to a recent GSoC).

Configurable and Extensible
All source code is open. Key configurable things are separated out.
 - e.g. can use built-tin "sinatra" web server - or go via apache or nginx (as we do on antgenomes.org<http://antgenomes.org>)
 - the most common customization is to add links from BLAST hits to specific databases (e.g. genome browser or other cross-ref) - this is done in a modular manner, using custom "links.rb" plugins that remain stable even when the rest of sequenceserver is upgraded. E.g. see  http://gmod.org/wiki/JBrowse_FAQ#How_can_I_link_BLAST_results_to_JBrowse

Open Source License for All Users
GNU AGPL v3

Interoperable With Other GMOD Components
All it needs is a directory of one or more FASTA files.
There is no internal database (the directory is scanned on launch) - thus we don't connect to Chado. We do nothing with annotations and thus don't support GFF.
(the jbrowse page actually has a decent section on linking things up - http://gmod.org/wiki/JBrowse_FAQ#How_can_I_link_BLAST_results_to_JBrowse )

Commitment of Support
We've been supporting this without specfic funds since 2012 and hope to be able to continue doing so. Being part of GMOD will hopefully also help attract funding. Mailing list is here:
 https://groups.google.com/forum/?fromgroups#!forum/sequenceserver
The code is well documented, the site and doc page are decent - http://www.sequenceserver.com and http://www.sequenceserver.com/doc/
Issue tracker is here: https://github.com/wurmlab/sequenceserver/issues
We are happy to commit to continuing these efforts.
We have encouraged (and attracted) code contributions in the past and will continue to do so.

Users and Support Mailing List(s)
 https://groups.google.com/forum/?fromgroups#!forum/sequenceserver
 Issue tracker is here: https://github.com/wurmlab/sequenceserver/issues

Public repository
https://github.com/wurmlab/sequenceserver

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

[GMOD-devel] Nomination for new GMOD project

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

Hello GMOD,

Last week, Yannick Wurm of SequenceServer fame approached me about adding
SequenceServer as a GMOD project.  It seems like a great fit to me as a
general and widely used tool.  Please take a moment to read a little about
it if you aren't already familiar and if you have any thoughts (pro or
con), please let me know. I included email groups of projects that I
thought might be interested in SequenceServer.  If you know of somebody
else involved with GMOD who isn't covered by one of these lists, please
feel free to forward it to them.

In case you weren't aware, GMOD has guidelines for adding new projects:

http://gmod.org/wiki/GMOD_Membership

Here is what Yannick wrote in support of his nomination:
-----------------------------------------------------------

Dear all,

I would like to nominate SequenceServer as a GMOD tool.

Background:
A major hurdle I stumbled upon a few years ago as  collaborators and I
began to obtain transcriptome and genome assemblies from new species, was
the lack of a simple manner of BLASTing unpublished data. Using  a perl/cgi
blast script was horrible - and it had a counterintuitive user interface.
Same with the tool for custom databases that NCBI supplied at the time.
To overcome this, Anurag Priyam (an undergraduate at the time) and I began
developing  SequenceServer. Its had 3 main aims:
 - provide an intuitive user interface and elegant user experience that
increases researchers productivity
 - make it easy for individual users to run it autonomously on unpublished
or custom data
 - make it easy to share a BLAST interface with others - in a lab or on a
community database   (including the - now deprecated antgenomes.org which I
ran)

It was open source from the start, and has decent success:
 - 60,000 downloads
 - >50 citations.
 - >70 github forks and 130 stars
 - >190 members on mailing list

It is used on dozens of GMOD-esque community sites - often in combination
with jBrowse, including:
reefgenomics.org  http://www.daphnia-stressordb.uni-hamburg.de,
hymenopterabase, http://spottedwingflybase.org , bovine genome database,
Lepbase, http://www.wheat-tilling.com,  PHIbase, GenomeHubs,
http://pristionchus.org/about.html,
http://planmine.mpi-cbg.de/planmine/begin.do,  and many more.

Allow me to provide specific comments regarding the GMOD membership
criteria below.

Please do not hesitate if you have any questions.

Kind regards,

Yannick
-----

Meets a Common Need
Growing citations & userbase demonstrate this.

Useful Over Time
Usage has steadily increased since 2012. The tool wraps BLAST (we are
seeking funding to hopefully also wrap DIAMOND). We are implementing novel
visualisations to increase analysis power/researchers productivity
(including thanks to a recent GSoC).

Configurable and Extensible
All source code is open. Key configurable things are separated out.
 - e.g. can use built-tin "sinatra" web server - or go via apache or nginx
(as we do on antgenomes.org)
 - the most common customization is to add links from BLAST hits to
specific databases (e.g. genome browser or other cross-ref) - this is done
in a modular manner, using custom "links.rb" plugins that remain stable
even when the rest of sequenceserver is upgraded. E.g. see
http://gmod.org/wiki/JBrowse_FAQ#How_can_I_link_BLAST_results_to_JBrowse

Open Source License for All Users
GNU AGPL v3

Interoperable With Other GMOD Components
All it needs is a directory of one or more FASTA files.
There is no internal database (the directory is scanned on launch) - thus
we don't connect to Chado. We do nothing with annotations and thus don't
support GFF.
(the jbrowse page actually has a decent section on linking things up -
http://gmod.org/wiki/JBrowse_FAQ#How_can_I_link_BLAST_results_to_JBrowse )

Commitment of Support
We've been supporting this without specfic funds since 2012 and hope to be
able to continue doing so. Being part of GMOD will hopefully also help
attract funding. Mailing list is here:
 https://groups.google.com/forum/?fromgroups#!forum/sequenceserver
The code is well documented, the site and doc page are decent -
http://www.sequenceserver.com and http://www.sequenceserver.com/doc/
Issue tracker is here: https://github.com/wurmlab/sequenceserver/issues
We are happy to commit to continuing these efforts.
We have encouraged (and attracted) code contributions in the past and will
continue to do so.

Users and Support Mailing List(s)
 https://groups.google.com/forum/?fromgroups#!forum/sequenceserver
 Issue tracker is here: https://github.com/wurmlab/sequenceserver/issues

Public repository
https://github.com/wurmlab/sequenceserver

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

[GMOD-devel] [GSoC 2019] [Open Genome Informatics] Google Summer of Code 2019 Participation

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

Dear All,

The Open Genome Informatics team serves as an “umbrella" organization to support the efforts of many open access open-source bioinformatics projects for Google Summer of Code (GSoC)<https://summerofcode.withgoogle.com/>. Among this list of projects are GMOD and its software projects -- GBrowse, JBrowse; Galaxy; Reactome; WormBase; DockStore; Bioconda; and others.

Call for 2019 Project Ideas and Mentors:  We are seeking project ideas to post and attract talented students to this year’s Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact Robin Haw, Marc Gillespie, Dave Clements, Dannon Baker, and Scott Cain (emails above). You can also submit your ideas here<http://gmod.org/wiki/GSOC_Project_Ideas_2019> or this online form<https://docs.google.com/forms/d/1uQlpsbPCnhNwO5OFKAB-IiY9DLWlmaHZATnaeP6KHhw>.

For more information please refer to the Open Genome Informatics page<http://gmod.org/wiki/GSoC>.

The mentoring organization application deadline with GSoC is February 6th, 2019 at 3 pm EST. So, if you are interested in taking part with the team please let us know as soon as possible.

Please forward this to others who might be interested in taking part.

If you have any questions please let us know.

Thanks,
Robin, Marc, Dave, Dannon, and Scott.

[GMOD-devel] Galaxy Administrator Training, Jan 28 - Feb 1, Penn State University

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

Hello all,

*The 2019 Galaxy Admin Training
<https://galaxyproject.org/events/2019-admin-training/> will be offered
January 28 through February 1 at Penn State University*. The workshop
offers a 2 day introductory session
<https://github.com/galaxyproject/dagobah-training#basic-sessions> followed
by a 3 day advanced topics session
<https://github.com/galaxyproject/dagobah-training#advanced-sessions>.
Participants can register for one or both sessions.

*Galaxy <https://galaxyproject.org/> is a widely deployed platform for data
integration and analysis in the life sciences.*  It is open source and be
deployed on lab servers, institutional computing resources, and public and
private clouds.  Having your own Galaxy server enables your researchers to
have a customized and collaborative analysis environment that enables then
to learn, perform, and share their own bioinformatics analysis.

This workshop will cover what you need to know to set up your own
high-performance and multi-user production Galaxy instance. Sessions will
be *intensive and hands-on*, and taught by experienced instructors from the
Galaxy Community. 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.

Registration
<https://galaxyproject.org/events/2019-admin-training/#registration> is now
open and starts at $65 / day for participants from non-profits and
academia. Advance registration ends December 31. The 2016 and 2018 admin
training workshops were both full, so you are strongly encouraged to *register
now*.
Thanks,
Dave C.


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

[GMOD-devel] Call for GMOD/PAG abstracts

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

Hi All,

It's that time of year again: if you would be interested in presenting in
the GMOD workshop at PAG in San Diego this January, please let me know.
You don't have to have a full blown abstract yet; a general idea of what
you'd like to talk about is fine.  If you know anybody who might be
interested but isn't on one of these lists, please feel free to forward
this to them.

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] 2019 Galaxy Administrator Training, Jan 28 - Feb 1, Penn State University

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

Hello all,

We are pleased to announce that* the 2019 Galaxy Admin Training
<https://galaxyproject.org/events/2019-admin-training/> will be offered
January 28 through February 1 at Penn State University*. The workshop
offers a 2 day introductory session
<https://github.com/galaxyproject/dagobah-training#basic-sessions> followed
by a 3 day advanced topics session
<https://github.com/galaxyproject/dagobah-training#advanced-sessions>.
Participants can register for one or both sessions.

This workshop will cover what you need to know to set up your own
high-performance and multi-user production Galaxy instance. Sessions will
be *intensive and hands-on*, and taught by experienced instructors from the
Galaxy Community. 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.

Registration
<https://galaxyproject.org/events/2019-admin-training/#registration> is now
open and starts at $40 / day for participants from non-profits and
academia. Early registration ends October 31. However, the 2016 and 2018
admin training were both full, so you are strongly encouraged to *register
now*.

*The workshop does have prerequisites
<https://galaxyproject.org/events/2019-admin-training/#prerequisites>.
Please read them before you register.*
Cheers,
Dave C.


*About Galaxy *
Galaxy <https://galaxyproject.org/> is an open web based platform for
biomedical data integration and analysis. It is deployed at large and small
organizations around the world and used in a broad range of biomedical
research domains, and across the tree of life.  Galaxy has been an active
member of GMOD for over 10 years.

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

[GMOD-devel] Fwd: [isb-biocuration] Function @ISMB 2018: Abstract Deadline this week

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

---------- Forwarded message ----------
From: Iddo Friedberg <id...@gm...>
Date: Mon, Apr 2, 2018 at 10:19 AM
Subject: [isb-biocuration] Function @ISMB 2018: Abstract Deadline this week
To: isb...@go...


Call for Abstracts: Function Special Interest Group at ISMB 2018

We call upon all researchers involved in the computational study of
macromolecular function to submit an abstract to the Function-SIG meeting.
Authors of selected abstracts will be invited to give a talk and/or present
a poster.
Travel fellowships will be available for qualifying graduate students and
postdoctoral trainees.

Time and place: Chicago, IL, USA  July 6, 2018
ISMB 2018 home page: https://www.iscb.org/ismb2018


Key Dates:

*Thursday April 5, 2018* Abstract Submission Deadline
*April 26, 2018*: Notification of Acceptance
*July 7, 2018*: Function SIG at ISMB/ECCB 2018


Abstract submission:

http://biofunctionprediction.org/content/submit-abstract



Sequence and structure genomics have generated a wealth of data, but
extracting meaningful information from genomic data is challenging. Both
the number and the diversity of discovered sequences are increasing. In
addition, there is a need for standardized annotation that could be
incorporated into functional annotation on a large scale. Finally, there is
a need to assess the quality of the function prediction algorithms and
software.

For these reasons and many more, automated protein function prediction is
of interest to computational biologists in academia and industry. The
Function-SIG meetings offer researchers and students in the field to meet
with like-minded colleagues, learn about the latest developments in the
field, and forge new collaborations. More on the Function SIG: http://biofu
nctionprediction.org/

We will also present the more results from the third round of the Critical
Assessment of Functional Annotation (CAFA3) and from the additional
CAFA3.14 (CAF-Pi). CAFA is an international computational challenge funded
by the NSF and BBSRC which aims to asses the accuracy of protein
function prediction
methods which is drawing dozens of participating groups worldwide. More on
CAFA: http://biofunctionprediction.org/cafa/



-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html
++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.>
++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.
.>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>>
>>----.<--.>++++++.<<<<------------------------------------.

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

[GMOD-devel] Call for Abstracts: GCCBOSC 2018

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

*GCCBOSC 2018: A Bioinformatics Community Conference*
*Call for Abstracts *



* Dates*: June 25-30, 2018
* Location*: Reed College, Portland, OR
* GCCBOSC website*: https://gccbosc2018.sched.com/
* BOSC website: *https://www.open-bio.org/wiki/BOSC_2018
* Email BOSC organizers*: b <bo...@op...>os...@op...
* BOSC announcements mailing list*: http://lists.open-bio.
org/mailman/listinfo/bosc-announce
* Twitter*: @OBF_BOSC <https://twitter.com/OBF_BOSC>, #GCCBOSC


*Important Dates*

   - *Abstract submission
   <https://www.open-bio.org/wiki/BOSC_Abstract_Submission> deadline: March
   16, 2018*
   - Authors notified: April 10, 2018
   - Travel fellowship
   <https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md>
application
   deadline: April 15, 2017
   - GCCBOSC 2018 Training: June 25-26, 2018
   - GCCBOSC 2018 Talks: June 27-28
   - GCCBOSC CollaborationFest: June 29-30

*About BOSC*
Since 2000, the yearly Bioinformatics Open Source Conference (BOSC) has
provided a forum for developers and users to interact and share research
results and ideas in open source bioinformatics. BOSC’s broad spectrum of
topics includes practical techniques for solving bioinformatics problems;
software development practices; standards and ontologies; approaches that
promote open science and sharing of data, results and software; and ways to
grow open source communities while promoting diversity within them.

*Why is BOSC partnering with GCC in 2018?*
In past years, BOSC has been part of the ISMB conference. Because of our
continuing focus on broadening and deepening the BOSC community, we've been
exploring ways to reach those in the bioinformatics community who aren’t
already part of the audience attracted by ISMB. As part of that
exploration, we have looked at other organizations and conferences that
have been successful at establishing a strong and growing community of
participants, such as the Galaxy Community Conference (GCC).

After much discussion and planning, we decided to hold BOSC in conjunction
with GCC in 2018. We hope that this will be an enjoyable and productive
experience for all participants, and we welcome your feedback before,
during and after the event.

As always, BOSC 2018 will include two days of talks and posters, two keynote
speakers <https://galaxyproject.org/events/gccbosc2018/keynotes/>, a panel
discussion, Birds of a Feather, and more. BOSC sessions will run in
parallel with GCC 2018 sessions, with some sessions shared. The two days of
talks will be preceded by two days of training
<https://galaxyproject.org/events/gccbosc2018/training/> on topics
nominated by the community, and will be followed by a two-day
CollaborationFest that merges BOSC's Codefest and Galaxy's Developer and
User Hackathon Days.

*Abstract submission*
We encourage you to submit one-page abstracts (due March 16) on any topic
relevant to open source bioinformatics or open science. After review, some
abstracts will be selected for lightning talks, longer talks, demos and/or
posters. Abstract submission instructions and a link to the EasyChair
submission portal can be found on https://www.open-bio.org/
wiki/BOSC_Abstract_Submission

*BOSC session topics include* (but are not limited to):

   - Open Science and Reproducible Research
   - Open Biomedical Data
   - Citizen/Participatory Science
   - Standards and Interoperability
   - Data Science
   - Workflows
   - Visualization
   - Medical and Translational Bioinformatics
   - Developer Tools and Libraries
   - Bioinformatics Open Source Project Progress Reports

We look forward to receiving your abstract and meeting you at GCCBOSC 2018!

Sincerely,
      BOSC 2018 Organizing Committee: Nomi Harris (chair), Heather Wiencko
(co-chair), Brad Chapman (co-chair), Peter Cock, Christopher Fields,
Bastian Greshake, Karsten Hokamp, Hilmar Lapp, Monica Munoz-Torres


P.S. Don't forget to submit your BOSC abstract by March 16 at
https://www.open-bio.org/wiki/BOSC_Abstract_Submission! Please share this
announcement with your colleagues!


-- 
------------------------------------------------------------------------
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] [GSoC 2018] [Open Genome Informatics] Google Summer of Code 2018 Participation

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

Hi Folks,

Please send project ideas ASAP!

Marc

> On Jan 7, 2018, at 5:32 PM, Robin Haw <rob...@gm...> wrote:
> 
> Dear All,
> 
> The Open Genome Informatics team serves as an "umbrella organization" to a variety of open bioinformatics projects, including GMOD and its software projects -- GBrowse, JBrowse, etc.; Galaxy; Reactome; SeqWare; WormBase; DockStore and others. I’ll update the Open Genome Informatics page: http://gmod.org/wiki/GSoC <http://gmod.org/wiki/GSoC>, in preparation for applying for this year’s Google Summer of Code.
> 
> Call for 2018 Project Ideas and Mentors:  We are seeking project ideas to post and attract talented students to this year’s Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact Marc Gillespie, Robin Haw and Scott Cain (emails above).
> 
> Mentoring organization application deadline: 23rd January 2018.
> 
> Please forward this to others who might be interested in taking part.
> 
> If you have any questions please let Marc, Scott and I know.
> 
> Thanks,
> Robin Haw
> 

[GMOD-devel] GCCBOSC 2018 Training Topic Voting is now open

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

Hello all,

Voting is now open <http://bit.ly/gccbosc2018-vote> on what training topics
<https://galaxyproject.org/events/gccbosc2018/training/> will be
offered at GCCBOSC
2018 <https://gccbosc2018.sched.com/>.

Your vote <http://bit.ly/gccbosc2018-vote> will determine the topics that
are offered, which topics should be offered more than once, and which ones
should not be scheduled at the same time. Your vote matters.

*Topic voting closes January 31.* The Training schedule, including
instructors, will be published before early registration opens.

GCCBOSC2018 <https://gccbosc2018.sched.com/> will be held 25-30 June in
Portland, Oregon, United States. It will feature two days of training: the
second of which is multi-track and will feature content for both the BOSC
and Galaxy communities. Workshops will be hands-on and participants will be
strongly encouraged to bring a laptop and follow along. If you work in
data-intensive biomedical research, there is no better place than GCCBOSC
2018 to present your work and to learn from others.

Thanks, and see you in Portland!

The GCCBOSC 2018 Organizers
<https://galaxyproject.org/events/gccbosc2018/organizers>

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

Re: [GMOD-devel] [GSoC 2018] [Open Genome Informatics] Google Summer of Code 2018 Participation

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

Hi All,

With the approaching date we will nEed to hear from you shortly.

Please let me know what your plans for participation are.

I look forward to hearing from you!

Marc

Marc E. Gillespie
Reactome biocurator
reactome.org

> On Jan 7, 2018, at 5:32 PM, Robin Haw <rob...@gm...> wrote:
> 
> Dear All,
> 
> The Open Genome Informatics team serves as an "umbrella organization" to a variety of open bioinformatics projects, including GMOD and its software projects -- GBrowse, JBrowse, etc.; Galaxy; Reactome; SeqWare; WormBase; DockStore and others. I’ll update the Open Genome Informatics page: http://gmod.org/wiki/GSoC, in preparation for applying for this year’s Google Summer of Code.
> 
> Call for 2018 Project Ideas and Mentors:  We are seeking project ideas to post and attract talented students to this year’s Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact Marc Gillespie, Robin Haw and Scott Cain (emails above).
> 
> Mentoring organization application deadline: 23rd January 2018.
> 
> Please forward this to others who might be interested in taking part.
> 
> If you have any questions please let Marc, Scott and I know.
> 
> Thanks,
> Robin Haw
> 

[GMOD-devel] SRA2Genes pipeline of EvidentialGene for Accurate Plant and Animal gene reconstruction

[<gil...@bi...>]

Dear animal and plant genome information engineers,

Accurate gene set reconstruction is now a solvable information-engineering
problem, one of collecting gene evidence and piecing it together, with
validations, rather than the uncertain gene predictions of twenty years
back.  Yet these are not fully solved for many animal and plant gene sets
now in use, including models with extensive effort.

This is the usual result I and others get for coding genes pieced together
from RNA evidence, then validated with reference/related species proteins.

SRA2Genes pipeline collects several EvidentialGene methods into a complete,
automated gene set reconstruction pipeline.  It fetches public RNA-seq from
NCBI SRA, over-assembles that into many millions of gene models, by varying
assembly methods and data slices, then reduces this over-assembly  to its
most accurate, non-redundant coding gene loci and alternates, followed by
annotation with reference species genes. Included are checks for
contaminants, and formatting of gene sequences for public database
submission.

The Evigene software package including omnibus evgpipe_sra2genes.pl is at
  http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/
   evigene18jan01.tar  (draft2 of evgpipe_sra2genes)
  
This early draft of SRA2Genes is one you should not expect to work fully
yet for you.  If you have interests in testing it, and some experience
in RNA assembly, I am looking for feedback on how to generalize this for
others.

A preliminary Zebrafish gene set from this evigene sra2genes is at
  http://eugenes.org/EvidentialGene/vertebrates/zebrafish/
  
The resulting gene set is more accurate and complete than NCBI and Ensembl
gene sets for zebrafish, at recovering gene evidence of homology to related
fish and vertebrate conserved proteins, and in recovering expressed introns.

Another SRA2Genes result, for green sea urchin, is at
  http://eugenes.org/EvidentialGene/inverts/sea_urchin/
  
Likewise, recent EvidentialGene reconstructions of plant and animal genes
for Arabidopsis, Zea mays, white fly and water flea do recover gene
evidence more accurately than popular methods including MAKER, AUGUSTUS and
related genome-gene modeling, Trinity gene assemblies, PacBio "no-assembly"
gene assemblies, as well as NCBI EGAP and Ensembl/Gramene gene set
reconstructions.

Evigene SRA2Genes is built from components that work well on cluster
systems that I use, courtesy of NSF-XSEDE cyberinfrasturcture.  It
should work for others, once needed software components are linked (RNA
assemblers velvet/oases, idba_tran, soap, trinity, NCBI blast, vecscreen,
exonerate fastanrdb, etc.). This pipleline writes cluster shell scripts to
be run asynchonously.  
 
Who should consider EvidentialGene for gene reconstruction?
* genomicists who want accurate, complete and objectively reconstructed genes,  
  including those of you who may not believe these results, but are
  interested enough to check my claims.
  
* model and well-supported genome projects, where curators can use these 
  to improve precision of high value gene information.
  
* new species genomes, use as a primary gene set, including alternate transcripts,
  and/or use to assess gene predictions and chromosome assemblies for accuracy.

* population-level gene set comparisons within a species
  
* gene/genome improvement projects, to add alternate transcripts, 
  un-discovered and fragmented gene models.
  
* transcriptome and expression projects for more accurate genes.

Reconstruction from RNA only provides independent gene evidence, free of
errors and biases from chromosome assemblies and other species gene sets.
The well known ortholog genes are reconstructed well, but also harder gene
problems of alternate transcripts, paralogs, and complex structured genes
are usually more complete from Evigene methods.

This methodology is highly automatable, and can deal with BIG DATA, but
needs improvements.  Genes built with Evigene by independent authors
include a range of plants and animals, and several of these papers provide
independent reviews of Evigene versus other methods.

-- Don Gilbert
gilbertd at indiana.edu or gilbert.bionet at gmail.com

[GMOD-devel] [GSoC 2018] [Open Genome Informatics] Google Summer of Code 2018 Participation

[Robin H. <rob...@gm...>]

Dear All,

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

Call for 2018 Project Ideas and Mentors:  We are seeking project ideas to post and attract talented students to this year’s Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact Marc Gillespie, Robin Haw and Scott Cain (emails above).

Mentoring organization application deadline: 23rd January 2018.

Please forward this to others who might be interested in taking part.

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

Thanks,
Robin Haw

[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.
>