[BiO BB] Evolutionary Database Interoperability Hackathon

Hilmar Lapp hlapp at gmx.net
Mon Jan 26 22:52:59 EST 2009

   NESCent Hackathon on Evolutionary Database Interoperability


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 at nescent.org  
with any suggestions you have.


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.


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.


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

In addition, if possible please email a CV to the organizers at hackathon3 at 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.


The Organizing Committee
Arlin Stoltzfus, Rutger Vos (Evolutionary Informatics Working Group)
Hilmar Lapp, Todd Vision (NESCent)
Katja Schulz (Tree of Life)

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