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WikiSysop: Reverted edits by MediaWiki default (talk) to last revision by Hilmar

2016-04-13T15:47:38Z

Reverted edits by MediaWiki default (talk) to last revision by Hilmar

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-<strong>MediaWiki has been successfully installed.</strong>
+== Who we are ==
-Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
+The EvoIO collaboration emerged in 2009 from several NESCent-sponsored activities that focused on software and data interoperability for evolutionary analysis, including the Evolutionary Informatics working group (2006-2009), and the Evolutionary Database Interoperability hackathon (2009).  EvoIO aims to be a nucleating center for developing, applying and  disseminating interoperability technology that connects and coordinates between stakeholders, developers, and standards bodies.
-== Getting started ==
+Members of the EvoIO group, which include biologists and computer scientists, have over the past 3  years harnessed a variety of collaborative events to successfully build an initial stack of interoperability  technologies that is owned by the community and open to participation:
-* [//www.mediawiki.org/wiki/Special:MyLanguage/Manual:Configuration_settings Configuration settings list]
+* [http://nexml.org NeXML], a NEXUS-inspired XML format that is validatable yet extensible
-* [//www.mediawiki.org/wiki/Special:MyLanguage/Manual:FAQ MediaWiki FAQ]
+* [http://www.evolutionaryontology.org CDAO], an ontology of comparative data analysis formalizing the semantics of evolutionary data and metadata; and
-* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
+* [http://evoinfo.nescent.org/PhyloWS PhyloWS], a web-services interface standard for querying, retrieving, and referencing phylogenetic data on the web.
-* [//www.mediawiki.org/wiki/Special:MyLanguage/Localisation#Translation_resources Localise MediaWiki for your language]

MediaWiki default at 10:18, 13 April 2016

2016-04-13T10:18:56Z

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-== Who we are ==
+<strong>MediaWiki has been successfully installed.</strong>
-The EvoIO collaboration emerged in 2009 from several NESCent-sponsored activities that focused on software and data interoperability for evolutionary analysis, including the Evolutionary Informatics working group (2006-2009), and the Evolutionary Database Interoperability hackathon (2009).  EvoIO aims to be a nucleating center for developing, applying and  disseminating interoperability technology that connects and coordinates between stakeholders, developers, and standards bodies.
+Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
-Members of the EvoIO group, which include biologists and computer scientists, have over the past 3  years harnessed a variety of collaborative events to successfully build an initial stack of interoperability  technologies that is owned by the community and open to participation:
+== Getting started ==
-* [http://nexml.org NeXML], a NEXUS-inspired XML format that is validatable yet extensible
+* [//www.mediawiki.org/wiki/Special:MyLanguage/Manual:Configuration_settings Configuration settings list]
-* [http://www.evolutionaryontology.org CDAO], an ontology of comparative data analysis formalizing the semantics of evolutionary data and metadata; and
+* [//www.mediawiki.org/wiki/Special:MyLanguage/Manual:FAQ MediaWiki FAQ]
-* [http://evoinfo.nescent.org/PhyloWS PhyloWS], a web-services interface standard for querying, retrieving, and referencing phylogenetic data on the web.
+* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
+* [//www.mediawiki.org/wiki/Special:MyLanguage/Localisation#Translation_resources Localise MediaWiki for your language]

Hilmar: /* What's happening */

2015-05-03T17:49:30Z

What's happening

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	== What's happening ==		== What's happening ==
	* A grant proposal to NSF's Advances in Biological Informatics (ABI) program titled "An Ontology-Based System for Querying Life in a Post-Taxonomic Age" (PIs: Cellinese and Lapp) has now been funded. The proposal and public abstract] are available on Figshare ([http://dx.doi.org/10.6084/m9.figshare.1401984 doi:10.6084/m9.figshare.1401984]). The project picks up some ideas from the [[Phyloreferencing subgroup]] of the [[VoCamp1\|Phyloinformatics VoCamp]].		* A grant proposal to NSF's Advances in Biological Informatics (ABI) program titled "An Ontology-Based System for Querying Life in a Post-Taxonomic Age" (PIs: Cellinese and Lapp) has now been funded. The proposal and public abstract are available on Figshare ([http://dx.doi.org/10.6084/m9.figshare.1401984 doi:10.6084/m9.figshare.1401984]). The project picks up some ideas from the [[Phyloreferencing subgroup]] of the [[VoCamp1\|Phyloinformatics VoCamp]].

	* Many of us are PIs or Leadership Team members of a NESCent working group called [http://www.evoio.org/wiki/HIP Hackathons, Interoperability, Phylogenies (HIP)]. HIP is the current locus of most of our activity . So far we have had two '''[[Phylotastic]]''' hackathons focused on a web-services implementation of the pruning, grafting, name-reconciliation and other functionalities necessary for researchers to take advantage of emerging megatrees. HIP is planning a third hackathon to develop a socially networked phyloinformatics community of practice.		* Many of us are PIs or Leadership Team members of a NESCent working group called [http://www.evoio.org/wiki/HIP Hackathons, Interoperability, Phylogenies (HIP)]. HIP is the current locus of most of our activity . So far we have had two '''[[Phylotastic]]''' hackathons focused on a web-services implementation of the pruning, grafting, name-reconciliation and other functionalities necessary for researchers to take advantage of emerging megatrees. HIP is planning a third hackathon to develop a socially networked phyloinformatics community of practice.

Hilmar: /* What's happening */

2015-05-03T17:49:04Z

What's happening

← Older revision		Revision as of 17:49, 3 May 2015
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	== What's happening ==		== What's happening ==
	* A grant proposal to NSF's Advances in Biological Informatics (ABI) program titled "An Ontology-Based System for Querying Life in a Post-Taxonomic Age" (PIs: Cellinese and Lapp) has now been funded. The proposal and public abstract] are available on Figshare ([http://dx.doi.org/10.6084/m9.figshare.1401984 doi:10.6084/m9.figshare.1401984].		* A grant proposal to NSF's Advances in Biological Informatics (ABI) program titled "An Ontology-Based System for Querying Life in a Post-Taxonomic Age" (PIs: Cellinese and Lapp) has now been funded. The proposal and public abstract] are available on Figshare ([http://dx.doi.org/10.6084/m9.figshare.1401984 doi:10.6084/m9.figshare.1401984]). The project picks up some ideas from the [[Phyloreferencing subgroup]] of the [[VoCamp1\|Phyloinformatics VoCamp]].

	* Many of us are PIs or Leadership Team members of a NESCent working group called [http://www.evoio.org/wiki/HIP Hackathons, Interoperability, Phylogenies (HIP)]. HIP is the current locus of most of our activity . So far we have had two '''[[Phylotastic]]''' hackathons focused on a web-services implementation of the pruning, grafting, name-reconciliation and other functionalities necessary for researchers to take advantage of emerging megatrees. HIP is planning a third hackathon to develop a socially networked phyloinformatics community of practice.		* Many of us are PIs or Leadership Team members of a NESCent working group called [http://www.evoio.org/wiki/HIP Hackathons, Interoperability, Phylogenies (HIP)]. HIP is the current locus of most of our activity . So far we have had two '''[[Phylotastic]]''' hackathons focused on a web-services implementation of the pruning, grafting, name-reconciliation and other functionalities necessary for researchers to take advantage of emerging megatrees. HIP is planning a third hackathon to develop a socially networked phyloinformatics community of practice.

Hilmar: /* What's happening */

2015-05-03T17:47:01Z

What's happening

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	== What's happening ==		== What's happening ==
			* A grant proposal to NSF's Advances in Biological Informatics (ABI) program titled "An Ontology-Based System for Querying Life in a Post-Taxonomic Age" (PIs: Cellinese and Lapp) has now been funded. The proposal and public abstract] are available on Figshare ([http://dx.doi.org/10.6084/m9.figshare.1401984 doi:10.6084/m9.figshare.1401984].

	* Many of us are PIs or Leadership Team members of a NESCent working group called [http://www.evoio.org/wiki/HIP Hackathons, Interoperability, Phylogenies (HIP)]. HIP is the current locus of most of our activity . So far we have had two '''[[Phylotastic]]''' hackathons focused on a web-services implementation of the pruning, grafting, name-reconciliation and other functionalities necessary for researchers to take advantage of emerging megatrees. HIP is planning a third hackathon to develop a socially networked phyloinformatics community of practice.		* Many of us are PIs or Leadership Team members of a NESCent working group called [http://www.evoio.org/wiki/HIP Hackathons, Interoperability, Phylogenies (HIP)]. HIP is the current locus of most of our activity . So far we have had two '''[[Phylotastic]]''' hackathons focused on a web-services implementation of the pruning, grafting, name-reconciliation and other functionalities necessary for researchers to take advantage of emerging megatrees. HIP is planning a third hackathon to develop a socially networked phyloinformatics community of practice.

Hilmar: /* What's happening */

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Hilmar: /* What's happening */

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Hilmar: /* What's happening */

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	* In December 2010, EvoIO participants submitted a proposal to NESCent for a working group entitled [[HIP\| HIP: Hackathons, Interoperability, Phylogenies]] (Vos, Stoltzfus). The proposal is for a series of hackathons partly supported by outside partners. NESCent recently announced that this proposal will be funded. Woo hoo!		* In December 2010, EvoIO participants submitted a proposal to NESCent for a working group entitled [[HIP\| HIP: Hackathons, Interoperability, Phylogenies]] (Vos, Stoltzfus). The proposal is for a series of hackathons partly supported by outside partners. NESCent recently announced that this proposal will be funded. Woo hoo!

	* ~~EvoIO participants (Stoltzfus, Vos, Cranston, Lapp) recently received notice of an award of funding from NESCent~~ for a new course titled "Phyloinformatics: linking with online data and services"~~. The course~~ was ~~anticipated to be held~~ in ~~summer 2011 at NESCent~~, but had to be canceled ~~meanwhile~~ due to conflicting obligations of the PIs.		* A proposal for a new NESCent course titled "Phyloinformatics: linking with online data and services" was submitted by EvoIO participants (Stoltzfus, Vos, Cranston, Lapp) in July 2010 and subsequently selected for funding, but had since to be canceled due to conflicting obligations of the PIs. Instead, Vos and Piel co-taught a [http://academy.nescent.org/wiki/Computational_phyloinformatics Computational Phyloinformatics course] modeled after previous instances of this course, but supplemented with programming exercises using PhyloWS wrappers for ToLWeb and uBio. The course was held in Kyoto in August 2011, and supported by the Bioinformatics Center of Kyoto University and DBCLS/JST, with co-sponsorship by NESCent.

	* EvoIO participants in various ways participated in the [http://ievobio.org iEvoBio satellite conference] at Evolution 2010 in Portland, OR:		* EvoIO participants in various ways participated in the [http://ievobio.org iEvoBio satellite conference] at Evolution 2010 in Portland, OR:

Hilmar: /* What's happening */

2011-09-05T22:35:25Z

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Hilmar: /* What's happening */

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== Who we are ==

The EvoIO collaboration emerged in 2009 from several NESCent-sponsored activities that focused on software and data interoperability for evolutionary analysis, including the Evolutionary Informatics working group (2006-2009), and the Evolutionary Database Interoperability hackathon (2009). EvoIO aims to be a nucleating center for developing, applying and disseminating interoperability technology that connects and coordinates between stakeholders, developers, and standards bodies.

Members of the EvoIO group, which include biologists and computer scientists, have over the past 3 years harnessed a variety of collaborative events to successfully build an initial stack of interoperability technologies that is owned by the community and open to participation:
* [http://nexml.org NeXML], a NEXUS-inspired XML format that is validatable yet extensible
* [http://www.evolutionaryontology.org CDAO], an ontology of comparative data analysis formalizing the semantics of evolutionary data and metadata; and
* [http://evoinfo.nescent.org/PhyloWS PhyloWS], a web-services interface standard for querying, retrieving, and referencing phylogenetic data on the web.

For more information about how to get involved, read on.

== What's happening ==

* In December 2010, EvoIO participants submitted a proposal to NESCent for a working group entitled [[HIP| HIP: Hackathons, Interoperability, Phylogenies]] (Vos, Stoltzfus). The proposal is for a series of hackathons partly supported by outside partners. NESCent recently announced that this proposal will be funded. Woo hoo!

* EvoIO participants (Stoltzfus, Vos, Cranston, Lapp) recently received notice of an award of funding from NESCent for a new course titled "Phyloinformatics: linking with online data and services". The course was anticipated to be held in summer 2011 at NESCent, but had to be canceled meanwhile due to conflicting obligations of the PIs.

* EvoIO participants in various ways participated in the [http://ievobio.org iEvoBio satellite conference] at Evolution 2010 in Portland, OR:
** Rutger Vos gave a talk on "TreeBase2: Rise of the machines" (Rutger Vos, Hilmar Lapp, Bill Piel, Val Tannen)
** Brandon Chisham presented "CDAO-Store: A New Vision for Data Integration" (Brandon Chisham, Trung Le, Enrico Pontelli, Tran Son, Ben Wright)
** Arlin Stoltzfus presented "EvoIO: Community-driven standards for sustainable interoperability" (Arlin Stoltzfus, Nico Cellinese, Karen Cranston, Hilmar Lapp, Sheldon McKay, Enrico Pontelli, Rutger Vos)

* The EvoIO group staged a successful [[VoCamp1|Phyloinformatics VoCamp]] November 7-11, 2009 in Montpellier, France, co-located with the annual meeting of the <span class="plainlinks">[http://www.tdwg.org/ International Biodiversity Information Standards Organization (TDWG)]</span>. A VoCamp is a hands-on meeting for investigators to create and develop ontologies and lightweight vocabularies in support of data integration and re-use-- in this case, the integration and re-use of phylogenetic trees and associated data and metadata. More information at [[VoCamp1]].

== How to get involved ==

How to get involved? Each stack component has an open community of developers and a mailing list. Click on the links below to find out more. You can sign up for the mailing list and start to contribute.
* [http://nexml.org NeXML]'s mailing list is nexml-discuss@lists.sourceforge.net (contact Rutger Vos, <firstname>aldo@gmail.com)
* [http://evoinfo.nescent.org/PhyloWS PhyloWS]'s group is phylows@googlegroups.com (contact Hilmar Lapp, <firstinitial>lapp@nescent.org)
* [http://www.evolutionaryontology.org CDAO]'s mailing list is cdao-discuss@lists.sourceforge.net (contact Arlin Stoltzfus, <firstname>@umd.edu)
Also EvoIO folks are looking for interoperability “targets”, which can be either single projects that want to make resources more interoperable, or pairs of resources that want to integrate. Contact any of us if you have an idea.

== TolWeb2 ? ==

Based on some meetings in the winter, we developed a whitepaper calling for a meeting of ToLWeb stakeholders (contributors, research users, educational users, linked data providers) to develop a vision for ToLWeb2. This meeting would be followed by a process to develop a concrete plan and a proposal for funding. Stay tuned for further updates.

== The EvoIO INTEROP project ==

=== Background ===

Over several years a variety of people, including [http://informatics.nescent.org NESCent's informatics staff], NESCent's [http://evoinfo.nescent.org Evolutionary Informatics working group], and the participants in the recent [http://evoinfo.nescent.org/DB_Interop_Hackathon Evolutionary Database Interoperability hackathon] laid the foundation that put us in a position to apply to the [http://www.nsf.gov/pubs/2007/nsf07565/nsf07565.htm NSF INTEROP] program. This program provides up to 250 K per year to support a ''data interoperability network''. The network should be multidisciplinary; and the network proposal should have a community aspect and a technology aspect. The deadline for this program in 2009 was July 23.

What makes us competitive:
* our past success in developing interop technologies nexml, CDAO and PhyloWS
* the 3-part interop formula of data syntax (nexml), semantics (CDAO) and services (phyloWS)
* our past success in actual demonstration projects that show off interop technology
* our demonstrated commitment to including diverse projects
* our connections with a network of researchers, programmers, and data providers

In light of this, we developed a proposal for a data interoperability network focused on trees and associated data and metadata. Two key features of the proposal are the use of hackathons, and the use of the "EvoIO Stack" (<span class="plainlinks">[http://nexml.org NeXML], [http://www.evolutionaryontology.org CDAO], [http://evoinfo.nescent.org/PhyloWS PhyloWS]) as a technological nucleus for growing an Interop network. The proposal, the project summary and description of which are given below, was declined from funding in March 2010.

=== The EvoIO NSF Interop Proposal ===

==== Project Summary ====

'''INTEROP: A network for enabling community-driven standards to link evolution into the global web of data (EvoIO)'''

PI: '''Arlin Stoltzfus''', Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute (CDAO, Bio::NEXUS, Nexplorer). Co-PIs: '''Karen Cranston''', EOL and Field Museum of Natural History; '''Enrico Pontelli''', New Mexico State University, Computer Science (CDAO); '''Sheldon McKay''', Cold Spring Harbor Laboratory (GMOD, modENCODE, iPlant), '''Hilmar Lapp''', NESCent (PhyloWS, BioSQL); '''Nico Cellinese''', University of Florida, Florida Museum of Natural History (TOLKIN, RegNum).

[[Image:EvoIO Network.png|thumb|right|384px|Components of the proposed EvoIO interoperability network and their interactions]] '''Intellectual Merit'''. Evolutionary trees (“phylogenies”) organize knowledge of biodiversity and provide a framework for rigorous methods of comparative analysis used throughout the biosciences. In the past, the scope of a tree-based analysis was limited to the researcher’s “own” small data set. The great mass of currently available data makes possible far-reaching and systematic analyses, but only if trees (and associated data and metadata) can be accessed, searched, retrieved, and repurposed— that is, only if the data are interoperable. An integrated solution to this problem requires attention to the syntax and semantics of data, metadata, and services. Over the past 3 years, an “Evolutionary Informatics” working group funded by NESCent (an NSF Center) developed an interoperability “stack” consisting of NeXML (a file format for comparative data), the Comparative Data Analysis Ontology (CDAO) and PhyloWS (a web services standard). Recently, the group staged a “hackathon” that engaged a fresh group of researcher-programmers (chosen to represent community data resources) to learn, apply, and extend the EvoIO Stack, with results that show the remarkable promise of this approach to train early-career scientists, disseminate standards, and improve interoperability. The investigators will build on this approach and on their unique technology and experience to engage a larger community in improving interoperability of trees with associated data and metadata (e.g., taxonomic affiliations, sources, character data, etc). The EvoIO Network will organize hackathons, hold training workshops, host working groups, and implement infrastructure for community-building around emerging standards. Network staff will provide technical expertise in knowledge representation and bioinformatics, working to support standards and to build reference implementations. The resulting EvoIO community will extend broadly into systematics-biodiversity, comparative genomics, and phylogenetics, and will penetrate into key areas of community ecology, phylogenetic epidemiology and paleobiology.

'''Broader impacts'''. The research areas affected by this proposal— all those areas in which
phylogenetic trees are used routinely— are diverse and currently are not unified by professional organizations, software platforms, or standards. By bringing together scientists from
various disciplines, we will develop awareness of the need for standards, cohesion around
preferred approaches to interoperability, and ultimately a broad consensus on specific standards. This will be accomplished by building on the momentum of work done under prior NSF
funding via NESCent. The key to developing a cohesive community in the absence of pre-
existing cohesion is the hackathon mechanism, which generates success stories and arms
young researcher-programmers with the know-how to create further successes. Through this
mechanism, user requirements will be translated into standards and specifications, and implemented in community software tools. Reference Implementations (developed concurrently
with standards and specifications) will be used to aid in standards development and training.
Hackathons will take place in eastern, western, and central locations to maximize diversity in
impact, and will include strategically selected participants as well as a large fraction of participants chosen in response to a broad solicitation in the biodiversity, systematics, genomics,
and phylogenetics communities. Standards and specifications developed by the Network will
be disseminated via the relevant international standards group (the TDWG Phylogenetics
Standard Interest Group). Efforts will be made to integrate ideas from this project into existing
educational and outreach programs, with particular focus on involving students from NMSU (a
minority-serving institution).

==== Project Description ====

The [[Media:EvoIO ProjectDescription_opt.pdf|Project Description]] is available as a PDF.

== MediaWiki Help if you need it ==

* [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide User's Guide]
* [http://www.mediawiki.org/wiki/Help:FAQ MediaWiki FAQ]