From clementsgalaxy at gmail.com  Mon Apr 11 11:57:48 2011
From: clementsgalaxy at gmail.com (Dave Clements)
Date: Mon, 11 Apr 2011 08:57:48 -0700
Subject: [Open-bio-l] Galaxy Community Conference, May 25-26, Lunteren,
	The Netherlands
In-Reply-To: <AANLkTin-5UobLgGRy_wSHzwtuKz4FYozLF-ecKHqmF1B@mail.gmail.com>
References: <AANLkTin-5UobLgGRy_wSHzwtuKz4FYozLF-ecKHqmF1B@mail.gmail.com>
Message-ID: <BANLkTik7enCcOA3tDokvWD6RcatPhLKDKQ@mail.gmail.com>

Hello all,

This is a reminder that early registration for the 2011 Galaxy Community
Conference ends in less than two weeks.  You can save 20% if you register on
or before 24 April.
  http://galaxy.psu.edu/gcc2011/Register.html

We've also added a partial list of confirmed speakers.  More will be added
in the coming weeks as the schedule firms up.
  http://galaxy.psu.edu/gcc2011/Programme.html

Please let me know if you have any questions, and hope to see you in May,

Dave C.

On Thu, Feb 3, 2011 at 5:01 PM, Dave Clements <clementsgalaxy at gmail.com>wrote:

> We are pleased to announce the *2011 Galaxy Community Conference*, being
> held *May 25-26 in Lunteren, The Netherlands*.  The meeting will feature
> two full days of presentations and discussion on extending Galaxy to use new
> tools and data sources, deploying Galaxy at your organization, and best
> practices for using Galaxy to further your own and your community's
> research.  See http://galaxy.psu.edu/gcc2011/* for complete details.
> *
> *About Galaxy:
> *Galaxy is an open, web-based platform for *accessible, reproducible, and
> transparent* computational biomedical research.
>
>    - *Accessibility:* Galaxy enables users without programming experience
>    to easily specify parameters and run tools and workflows.
>    - *Reproducibility:* Galaxy captures all information necessary so that
>    any user can repeat and understand a complete computational analysis.
>    - *Transparency:* Galaxy enables users to share and publish analyses
>    via the web and create Pages--interactive, web-based documents that describe
>    a complete analysis.
>
> Galaxy is open source for all organizations. The public Galaxy service (
> http://usegalaxy.org) makes analysis tools, genomic data,
> tutorial demonstrations, persistent workspaces, and publication services
> available to any scientist that has access to the Internet. Local
> Galaxy servers can be set up by downloading the Galaxy application and
> customizing it to meet particular needs.
>
> *Conference Overview:
> *
> This event aims to engage a broader community of developers, data
> producers, tool creators, and core facility and other research hub staff to
> become an active part of the Galaxy community.   We'll cover defining
> resources in the Galaxy framework, increasing their visibility and making
> them easier to use and integrate with other resources, how to extend Galaxy
> to use custom data sources and custom tools, and best practices for using
> Galaxy in your organization.
>
> Additional topics include, but are not limited to:
> * Talks submitted by the Galaxy community
> * Integration of tools (including NGS analysis tools) and distributed job
> management
> * Deployment of Galaxy instances on local resources and on the Cloud
> * Management of large datasets with the Galaxy Library System
> * Using the Galaxy LIMS functionality at NGS sequencing facilities
> * Visualizing Data without leaving Galaxy
> * Performing reproducible research
> * Performing and sharing complex analyses with Workflows
> * An "Introduction to Galaxy" session, offered on May 24, for Galaxy
> newcomers.
>
> *Registration:
> *
> The conference fee is ?100 on or before April 24, and ?120 after that.  The
> meeting is being held at the Conference Centre De Werelt in Lunteren, The
> Netherlands, which is also the conference hotel.  You are encouraged to
> register early, as space at the hotel (and at the "Intro to Galaxy" session)
> is limited and is likely to fill up before the conference itself does.  See
> http://galaxy.psu.edu/gcc2011/Register.html
> *
> Abstract Submission:
> *
> Abstracts are now being accepted for short oral presentations.  Proposals
> on any topic of interest to the Galaxy community are welcome and
> encouraged.   The abstract submission deadline is the end of February 28.
> See http://galaxy.psu.edu/gcc2011/Abstracts.html
> * *
> *Sponsors
> *
> The 2011 Galaxy Community Conference is co-sponsored by the US National
> Science Foundation (NSF, http://www.nsf.gov/), and the Netherlands
> Bioinformatics Centre (NBIC, http://www.nbic.nl/).  NBIC is a
> collaborative institute of the bioinformatics groups in the Netherlands.
> Together, these groups perform cutting-edge research, develop novel tools
> and support platforms, create an e-science infrastructure and educate the
> next generations of bioinformaticians.
>
> We are looking forward to a great conference and hope to see you in the
> Netherlands!
>
> The Galaxy and NBIC Teams
>
> --
> http://galaxy.psu.edu/gcc2011/
> http://getgalaxy.org
> http://usegalaxy.org/
>



-- 
http://galaxy.psu.edu/gcc2011/
http://getgalaxy.org
http://usegalaxy.org/


From chapmanb at 50mail.com  Tue Apr 12 08:34:59 2011
From: chapmanb at 50mail.com (Brad Chapman)
Date: Tue, 12 Apr 2011 08:34:59 -0400
Subject: [Open-bio-l] Bioinformatics Open Source Conference (BOSC
 2011)--Abstracts due April 18th!
Message-ID: <20110412123459.GC2105@kunkel>

Only one week left to submit an abstract to BOSC 2011! We have
two great keynote speakers lined up (Lawrence Hunter and Matt
Wood) and session topics that include parallel and cloud-based
approaches to bioinformatics, genome content management, and tools for
next-generation sequencing. We'd love to hear about your Open Source
bioinformatics project!

The 12th Annual Bioinformatics Open Source Conference (BOSC 2011)
An ISMB 2011 Special Interest Group (SIG)
July 15-16, 2011, in Vienna, Austria
http://www.open-bio.org/wiki/BOSC_2011

Important Dates:
April 18, 2011: Deadline for submitting abstracts to BOSC 2011
May 9, 2011: Notifications of accepted abstracts emailed to corresponding authors
July 13-14, 2011: Codefest 2011 programming session 
  (see http://www.open-bio.org/wiki/Codefest_2011 for details)
July 15-16, 2011: BOSC 2011
July 17-19, 2011: ISMB 2011

The Bioinformatics Open Source Conference (BOSC) is sponsored by the
Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated
to promoting the practice and philosophy of Open Source software
development within the biological research community. To be considered
for acceptance, software systems representing the central topic in a
presentation submitted to BOSC must be licensed with a recognized Open
Source License, and be freely available for download in source code
form.

We invite you to submit abstracts for talks and posters.  Sessions include:
- Approaches to parallel processing
- Cloud-based approaches to improving software and data accessibility
- The Semantic Web in open source bioinformatics
- Data visualization
- Tools for next-generation sequencing
- Other Open Source software

In addition to the above sessions, there will be a panel discussion
about "Meeting the challenges of inter-institutional collaboration".
We are also working to arrange a joint session with one of the other
ISMB SIGs.

Thanks to generous sponsorship from Eagle Genomics and an anonymous
donor, we are pleased to announce a competition for three Student
Travel Awards for BOSC 2011. Each winner will be awarded $250 to
defray the costs of travel to BOSC 2011. All students whose abstracts
are accepted for talks will be considered for this award.

For instructions on submitting your abstract, please visit
http://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information

BOSC 2011 Organizing Committee: Nomi Harris and Peter Rice (co-chairs);
 Brad Chapman, Peter Cock, Erwin Frise, Darin London, Ron Taylor

From dalloliogm at gmail.com  Thu Apr 14 11:14:30 2011
From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio)
Date: Thu, 14 Apr 2011 17:14:30 +0200
Subject: [Open-bio-l] provide examples of good and bad ML questions for a
 candidate 'Ten Simple Rules' article
Message-ID: <BANLkTinL95_FCDUg4f+D92JghFWrrQPmgg@mail.gmail.com>

Hello everybody,
I would like to invite you to an initiative that our group launched a
few weeks earlier this month.

We are writing a paper in the style of PLoS CompBiol 'Ten Simple
Rules' series, about 'How to get Help from Mailing Lists and Online
Scientific Communities'.
- http://www.wikigenes.org/e/pub/e/137.html

Mailing lists and forums/online communities can be an important
resource for researchers. The OpenBio.* mailing lists are an example
of this, as they are the medium where all the bio.* projects are
coordinated and where new users meet experts.
However, using mailing lists correctly is not easy, and there are some
rules that not everybody is aware of, but that must be respected in
order to obtain good answers. Taking inspiration from this last point,
we decided to launch the initiative of a candidate 'Ten Simple Rules'
article.

The article is open to contributions, which means that everybody is
free to edit the manuscript and that the authors of the most important
contributions will be invited to sign the paper.
More precisely, at this point of the writing, the main body of the
manuscript is almost complete. However, we need help for completing a
table with examples of good and bad mailing list questions. I bet that
the most experienced followers of this mailing list can easily provide
many examples of badly posed questions they have seen (and hopefully
some good ones); so, if you have the time to make your contribution,
please join the wiki and the mailing list and help us making this
manuscript more complete.

Please feel free to forward this message to who you believe interested.


-- 
Giovanni Dall'Olio, phd student
Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain)

My blog on bioinformatics: http://bioinfoblog.it

From clementsgalaxy at gmail.com  Mon Apr 11 15:57:48 2011
From: clementsgalaxy at gmail.com (Dave Clements)
Date: Mon, 11 Apr 2011 08:57:48 -0700
Subject: [Open-bio-l] Galaxy Community Conference, May 25-26, Lunteren,
	The Netherlands
In-Reply-To: <AANLkTin-5UobLgGRy_wSHzwtuKz4FYozLF-ecKHqmF1B@mail.gmail.com>
References: <AANLkTin-5UobLgGRy_wSHzwtuKz4FYozLF-ecKHqmF1B@mail.gmail.com>
Message-ID: <BANLkTik7enCcOA3tDokvWD6RcatPhLKDKQ@mail.gmail.com>

Hello all,

This is a reminder that early registration for the 2011 Galaxy Community
Conference ends in less than two weeks.  You can save 20% if you register on
or before 24 April.
  http://galaxy.psu.edu/gcc2011/Register.html

We've also added a partial list of confirmed speakers.  More will be added
in the coming weeks as the schedule firms up.
  http://galaxy.psu.edu/gcc2011/Programme.html

Please let me know if you have any questions, and hope to see you in May,

Dave C.

On Thu, Feb 3, 2011 at 5:01 PM, Dave Clements <clementsgalaxy at gmail.com>wrote:

> We are pleased to announce the *2011 Galaxy Community Conference*, being
> held *May 25-26 in Lunteren, The Netherlands*.  The meeting will feature
> two full days of presentations and discussion on extending Galaxy to use new
> tools and data sources, deploying Galaxy at your organization, and best
> practices for using Galaxy to further your own and your community's
> research.  See http://galaxy.psu.edu/gcc2011/* for complete details.
> *
> *About Galaxy:
> *Galaxy is an open, web-based platform for *accessible, reproducible, and
> transparent* computational biomedical research.
>
>    - *Accessibility:* Galaxy enables users without programming experience
>    to easily specify parameters and run tools and workflows.
>    - *Reproducibility:* Galaxy captures all information necessary so that
>    any user can repeat and understand a complete computational analysis.
>    - *Transparency:* Galaxy enables users to share and publish analyses
>    via the web and create Pages--interactive, web-based documents that describe
>    a complete analysis.
>
> Galaxy is open source for all organizations. The public Galaxy service (
> http://usegalaxy.org) makes analysis tools, genomic data,
> tutorial demonstrations, persistent workspaces, and publication services
> available to any scientist that has access to the Internet. Local
> Galaxy servers can be set up by downloading the Galaxy application and
> customizing it to meet particular needs.
>
> *Conference Overview:
> *
> This event aims to engage a broader community of developers, data
> producers, tool creators, and core facility and other research hub staff to
> become an active part of the Galaxy community.   We'll cover defining
> resources in the Galaxy framework, increasing their visibility and making
> them easier to use and integrate with other resources, how to extend Galaxy
> to use custom data sources and custom tools, and best practices for using
> Galaxy in your organization.
>
> Additional topics include, but are not limited to:
> * Talks submitted by the Galaxy community
> * Integration of tools (including NGS analysis tools) and distributed job
> management
> * Deployment of Galaxy instances on local resources and on the Cloud
> * Management of large datasets with the Galaxy Library System
> * Using the Galaxy LIMS functionality at NGS sequencing facilities
> * Visualizing Data without leaving Galaxy
> * Performing reproducible research
> * Performing and sharing complex analyses with Workflows
> * An "Introduction to Galaxy" session, offered on May 24, for Galaxy
> newcomers.
>
> *Registration:
> *
> The conference fee is ?100 on or before April 24, and ?120 after that.  The
> meeting is being held at the Conference Centre De Werelt in Lunteren, The
> Netherlands, which is also the conference hotel.  You are encouraged to
> register early, as space at the hotel (and at the "Intro to Galaxy" session)
> is limited and is likely to fill up before the conference itself does.  See
> http://galaxy.psu.edu/gcc2011/Register.html
> *
> Abstract Submission:
> *
> Abstracts are now being accepted for short oral presentations.  Proposals
> on any topic of interest to the Galaxy community are welcome and
> encouraged.   The abstract submission deadline is the end of February 28.
> See http://galaxy.psu.edu/gcc2011/Abstracts.html
> * *
> *Sponsors
> *
> The 2011 Galaxy Community Conference is co-sponsored by the US National
> Science Foundation (NSF, http://www.nsf.gov/), and the Netherlands
> Bioinformatics Centre (NBIC, http://www.nbic.nl/).  NBIC is a
> collaborative institute of the bioinformatics groups in the Netherlands.
> Together, these groups perform cutting-edge research, develop novel tools
> and support platforms, create an e-science infrastructure and educate the
> next generations of bioinformaticians.
>
> We are looking forward to a great conference and hope to see you in the
> Netherlands!
>
> The Galaxy and NBIC Teams
>
> --
> http://galaxy.psu.edu/gcc2011/
> http://getgalaxy.org
> http://usegalaxy.org/
>



-- 
http://galaxy.psu.edu/gcc2011/
http://getgalaxy.org
http://usegalaxy.org/



From chapmanb at 50mail.com  Tue Apr 12 12:34:59 2011
From: chapmanb at 50mail.com (Brad Chapman)
Date: Tue, 12 Apr 2011 08:34:59 -0400
Subject: [Open-bio-l] Bioinformatics Open Source Conference (BOSC
 2011)--Abstracts due April 18th!
Message-ID: <20110412123459.GC2105@kunkel>

Only one week left to submit an abstract to BOSC 2011! We have
two great keynote speakers lined up (Lawrence Hunter and Matt
Wood) and session topics that include parallel and cloud-based
approaches to bioinformatics, genome content management, and tools for
next-generation sequencing. We'd love to hear about your Open Source
bioinformatics project!

The 12th Annual Bioinformatics Open Source Conference (BOSC 2011)
An ISMB 2011 Special Interest Group (SIG)
July 15-16, 2011, in Vienna, Austria
http://www.open-bio.org/wiki/BOSC_2011

Important Dates:
April 18, 2011: Deadline for submitting abstracts to BOSC 2011
May 9, 2011: Notifications of accepted abstracts emailed to corresponding authors
July 13-14, 2011: Codefest 2011 programming session 
  (see http://www.open-bio.org/wiki/Codefest_2011 for details)
July 15-16, 2011: BOSC 2011
July 17-19, 2011: ISMB 2011

The Bioinformatics Open Source Conference (BOSC) is sponsored by the
Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated
to promoting the practice and philosophy of Open Source software
development within the biological research community. To be considered
for acceptance, software systems representing the central topic in a
presentation submitted to BOSC must be licensed with a recognized Open
Source License, and be freely available for download in source code
form.

We invite you to submit abstracts for talks and posters.  Sessions include:
- Approaches to parallel processing
- Cloud-based approaches to improving software and data accessibility
- The Semantic Web in open source bioinformatics
- Data visualization
- Tools for next-generation sequencing
- Other Open Source software

In addition to the above sessions, there will be a panel discussion
about "Meeting the challenges of inter-institutional collaboration".
We are also working to arrange a joint session with one of the other
ISMB SIGs.

Thanks to generous sponsorship from Eagle Genomics and an anonymous
donor, we are pleased to announce a competition for three Student
Travel Awards for BOSC 2011. Each winner will be awarded $250 to
defray the costs of travel to BOSC 2011. All students whose abstracts
are accepted for talks will be considered for this award.

For instructions on submitting your abstract, please visit
http://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information

BOSC 2011 Organizing Committee: Nomi Harris and Peter Rice (co-chairs);
 Brad Chapman, Peter Cock, Erwin Frise, Darin London, Ron Taylor


From dalloliogm at gmail.com  Thu Apr 14 15:14:30 2011
From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio)
Date: Thu, 14 Apr 2011 17:14:30 +0200
Subject: [Open-bio-l] provide examples of good and bad ML questions for a
 candidate 'Ten Simple Rules' article
Message-ID: <BANLkTinL95_FCDUg4f+D92JghFWrrQPmgg@mail.gmail.com>

Hello everybody,
I would like to invite you to an initiative that our group launched a
few weeks earlier this month.

We are writing a paper in the style of PLoS CompBiol 'Ten Simple
Rules' series, about 'How to get Help from Mailing Lists and Online
Scientific Communities'.
- http://www.wikigenes.org/e/pub/e/137.html

Mailing lists and forums/online communities can be an important
resource for researchers. The OpenBio.* mailing lists are an example
of this, as they are the medium where all the bio.* projects are
coordinated and where new users meet experts.
However, using mailing lists correctly is not easy, and there are some
rules that not everybody is aware of, but that must be respected in
order to obtain good answers. Taking inspiration from this last point,
we decided to launch the initiative of a candidate 'Ten Simple Rules'
article.

The article is open to contributions, which means that everybody is
free to edit the manuscript and that the authors of the most important
contributions will be invited to sign the paper.
More precisely, at this point of the writing, the main body of the
manuscript is almost complete. However, we need help for completing a
table with examples of good and bad mailing list questions. I bet that
the most experienced followers of this mailing list can easily provide
many examples of badly posed questions they have seen (and hopefully
some good ones); so, if you have the time to make your contribution,
please join the wiki and the mailing list and help us making this
manuscript more complete.

Please feel free to forward this message to who you believe interested.


-- 
Giovanni Dall'Olio, phd student
Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain)

My blog on bioinformatics: http://bioinfoblog.it