(Note that the issue we are trying to address and the standards we try
to bring to bear here are closely related to what we discussed at the
workshop and the conference session in Perth. If you are interested in
participating, I'd encourage you to apply! -hilmar)
NESCent Hackathon on Evolutionary Database Interoperability
OPEN CALL FOR PARTICIPATION
The National Evolutionary Synthesis Center (NESCent; http://
nescent.org) is sponsoring an "Evolutionary Database Interoperability"
hackathon aimed at enhancing the value (and raising the profile) of
important community resources for evolutionary and biodiversity data
by increasing their accessibility to users and software. We are
broadly soliciting applications for participation from the community.
More information about the event is available online at http://evoinfo.nescent.org/Database_Interop_Hackathon
.
A hackathon is an event at which a group of programmers who otherwise
do not have the opportunity to interact on a routine basis meet with
users and domain experts to collaboratively develop working code that
is of utility to the community as a whole. The Database
Interoperability Hackathon will bring together developers from a
number of emerging standards for evolutionary data exchange (NeXML; http://nexml.org
), data and metadata semantics (CDAO; http://www.evolutionaryontology.org
), and programmatic access of evolutionary data providers (PhyloWS; http://evoinfo.nescent.org/PhyloWS)
with database programmers and metadata experts from a variety of
evolutionary and biodiversity community resources. In addition, the
mix of people will include programmers of embeddable widgets, mash-up
and aggregation applications that can showcase the value of the effort
for research applications.
We also welcome comments and suggestions for issues in database
interoperability that could be addressed at the event but are not yet
on our radar. Please email the organizers at hackathon3(a)nescent.org
with any suggestions you have.
GOALS AND ACTIVITIES
The focus of the programming aspect of the meeting will be to promote
interoperability among online evolutionary databases through the
following core set of activities.
1) Mapping the data and operation semantics of the participating
online resources to an ontology, CDAO.
2) Implement a NeXML transformation for participating online resources
as a formally defined query input and data output.
3) Implementation of programmable web-service interfaces following the
emerging PhyloWS standard.
4) Showcase some of the possibilities that can arise from achieving
data provider interoperability through small integration and/or mash-
up oriented prototype applications.
Supporting activities will include discussing input from end-users,
discussing compliance with emerging reporting standards (MIAPA) and
documentation of solutions and open problems on the hackathon wiki.
ORGANIZATION
The event will be 5 days in duration and will take place at NESCent in
Durham, North Carolina, on March 9-13, 2009. Participant travel,
accommodation, expenses for meals, etc, will be paid by NESCent.
Logistical and travel details will be communicated to accepted and
confirmed participants.
The specific development targets will be selected by the participants
through a hackathon wiki, a mailing list, and one or more conference
calls. The exact agenda for the event will be developed similarly, but
will be largely devoted to coding time. At the event itself,
participants will self-organize into small subgroups (of 2-5) focused
on particular targets.
The NeXML, CDAO, and PhyloWS standards are products of the
Evolutionary Informatics working group (http://evoinfo.nescent.org),
under the auspices of whom this event is being organized.
CALL FOR PARTICIPATION
We invite all individuals interested in attending to apply by
responding to the questions below. We specifically encourage
applications from members of underrepresented groups, specifically
women and minorities, and from graduate students and postdocs.
1. Please indicate if you would be available for all or only for part
of the March 9-13 time period.
2. All code and documentation produced at the event is to be made
available immediately under an OSI-approved open-source license or a
Creative Commons license. Please indicate if this would pose any
difficulty for your participation.
3. Please briefly describe your qualifications (programming languages,
metadata standards, experience with data schemas, web-service
programming, mash-up programming, etc).
4. Please state what you would most like to accomplish at the
hackathon, given your current understanding. If you would not be
writing software at the event, please state how you would like to
contribute and how you would expect to benefit.
5. Please indicate if you are a member of an underrepresented group
(including women, persons with disabilities, and any of the following
minorities: African American, Hispanic, American Indian, Alaska
Native, Native Hawaiian, and Pacific Islander).
To apply, please enter your personal information and your responses by
February 5 into the online form at
http://spreadsheets.google.com/viewform?key=p6ikV0To6fXpJ369ozyNSSw&hl=en
In addition, if possible please email a CV to the organizers at hackathon3(a)nescent.org
by the same deadline. If you are interested in participating but
are unable to respond in full by that deadline, please let us know as
soon as possible. Please understand that the funds as well as the
space for this event are limited. We also need to balance a critical
mass of developers in certain areas of expertise with a broad
participation of different data providers, and so not all qualified
applicants can be guaranteed acceptance.
Yours,
The Organizing Committee
Arlin Stoltzfus, Rutger Vos (Evolutionary Informatics Working Group)
Hilmar Lapp, Todd Vision (NESCent)
Katja Schulz (Tree of Life)
Hi Everyone,
it's been a while since the TDWG Meeting and workshop in Perth. Many
of you on this list have participated in the workshop, and it was
great to meet you there. I found the workshop to be productive and
very encouraging towards forming this Interest Group in a way that has
unique value.
You may have noticed that we have our own TDWG wiki site at
http://wiki.tdwg.org/Phylogenetics/
You can navigate there easily manually by going to the TDWG home page (http://tdwg.org
), then click 'Wiki' in the left hand navigation bar, then
'Phylogenetics'.
I've put up already last year some minimal initial content about what
we are about, and I also put up information about and notes from our
Perth workshop:
http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/PhylogeneticsStandardsWor…
While there hasn't been much activity since on the charter and the
BioSynC proposal due to the I guess all too familiar year-end frenzy,
this will change over the next few months. Stay tuned, we'll keep you
in the loop. Also, this is meant to be a discussion much more than an
announcement forum, so if you have any suggestions, concerns, or
thoughts, please don't hesitate to voice them here.
Speaking of keeping in the loop, I'll shortly forward a call for
participation in a NESCent-organized event that is very closely
aligned with the phylogenetics standards and targeted at the
interoperability issues we were talking about in Perth.
As for Markus' email, I don't know to what extent you have been part
of the respective discussion but I wasn't. While I see the possible
benefits of better avoiding the reinventing the wheel, I find the
question of merging with another and much larger community when we
aren't one really yet a bit premature, and I am concerned that the
loss of focus might cause some to tune out or ignore the list (more
than they might otherwise), which I find the much bigger risk than
reinventing as the latter can be prevented by cross-talk and
subscribing to multiple lists (which I'm used to, but again maybe not
everyone is).
That's just my opinion though - please don't hesitate to voice yours,
especially if you feel differently.
Cheers,
-hilmar
--
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at duke dot edu :
===========================================================
Dear TDWG groups,
I would like to inform you about a new TDWG mailing list that was
created today for discussing any TDWG standard definitions on a non
technical level.
The new list was created to help cross pollination of ideas between
the different TDWG groups and avoid the frequent duplication of work
that we have encountered so often in the past years.
Every subgroup is free to decide whether they want to freeze their
existing mailing list and migrate discussions to the central tdwg-
content list. If you want to take this step, please let me know and I
will take the required actions. A frozen mailing list will disallow
any new posts or member subscriptions, but the existing archive will
continue to be publicly available. An autoresponder will also be
configured to inform future users of the new content list. By default
I will transfer all existing subscriptions to the new list, so people
don't have to subscribe again.
You can also subscribe manually to the new mailing list here:
http://lists.tdwg.org/mailman/listinfo/tdwg-content
In addition to that, the 3 existing mailing lists that deal with
technical issues have already decided to hold all discussions from now
on on the technical architecture group (TAG) list. The existing guid
and tapir mailing lists have been frozen today.
Best wishes,
Markus Döring
