Scope and Purposes
This page provides a concise summary of the outputs and interactions of the evoinfo working group, to be used for purposes of reporting outcomes to funding agencies, and for related purposes.
The products or outputs listed below should be information products that can be disseminated for the good of the evolutionary analysis community. It should not include intangible outcomes or products that will not be of use to anyone.
The categories of products are those used by NESCent for generating its internal reports to NSF.
Recommended Format: Use reference format for The American Naturalist (http://www.journals.uchicago.edu/AN/instruct.html#tprep)
- Prosdocimi, F., B. Chisham, E. Pontelli, J.D. Thompson, and A. Stoltzfus, Initial Implementation of a Comparative Data Analysis Ontology. (in review, BMC Evolutionary Biology)
- Chisham, B., E. Pontelli, F. Prosdocimi, A. Stoltzfus, J.D. Thompson, Framework for a comparative data analysis ontology. Evolution 2008, University of Minnesota, June 20-24.
- Prosdocimi, F., B. Chisham, E. Pontelli, J.D. Thompson, and A. Stoltzfus, CDAO: an evolutionary framework for comparative data analysis. Data Integration in the Life Sciences 2008, Paris, France, June 25-27.
- Prosdocimi, F. Framework for a comparative data analysis ontology (CDAO). 12th Evolutionary Biology Meeting Marseille 2008, France, September 24-26.
Proposals & Grants
Recommended Format: PI names. Year. Institution. Proposal title. Funding Agency. Duration. Award amount.
- revision of 2007 proposal to be submitted Nov 5: Stolzfus, A., E. Pontelli and G. Gupta. Workflow Environment for Evolutionary Comparative Analysis. NIH. 2009 to 2013. $1M direct.
Software and Data Sets
Recommended Format: Author names. Year. Title. Web url.
- Lapp, H., Vos R. 2008. PhyloWS: A standard web service-interface for phylogenetic data and service providers. http://evoinfo.nescent.org/PhyloWS
- Vos, R. 2007. nexml: an XML data exchange format for phylogenetic analysis. http://www.nexml.org
- Prosdocimi, F., B. Chisham, E. Pontelli, J.D. Thompson, and A. Stoltzfus. 2008. Comparative Data Analysis Ontology (CDAO), an OWL-DL ontology for evolutionary comparative analysis. (www.evolutionaryontology.org/cdao)
- Stoltzfus, A. 2008. MIAPA annotation tool (proof-of-concept software). (https://www.nescent.org/wg_evoinfo/Supporting_MIAPA#Proof-of-concept_.28annotation_software.29)
- Qiu, WG. 2007. A collection of data sets for phylogenetic analysis. (https://www.nescent.org/wg_phyloinformatics/Public:UseCases#Sample_Data_Sets)
- Qiu, WG. 2008. A new BioPerl module for reading nexml file. Bio::TreeIO:nexml (including new test files).
Recommended Format: Collaborator names. Year. Title. Web url.
Recommended Format: Author names. Date. Title. News organization.
For our wiki documents below, Arlin suggests to look at the document history, then list all the authors in order of effort (as estimated by the number of revisions)
- Stoltzfus, A., R. Vos, E. Pontelli, J. Thompson, M. Holder, P. Midford, B. De Vries, J. Felsenstein, Concept Glossary for Evolutionary Comparative Analysis. (https://www.nescent.org/wg_evoinfo/ConceptGlossary)
- Stoltzfus, A. 2008. MIAPA: Developing a Minimal Reporting Standard for Phylogenetics. A white paper developed for NESCent (https://www.nescent.org/wg_evoinfo/MIAPA_WhitePaper)
- Stoltzfus, A., R. Vos, M. Holder, H. Lapp, S. Kosakovsky Pond, and C. Zmasek. 2007. Supporting NEXUS. A guide for developers to implement and to improve support for the NEXUS file format. (https://www.nescent.org/wg_phyloinformatics/Supporting_NEXUS)