Phylotastic/Participants: Difference between revisions

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To add your photo, [http://www.evoio.org/wiki/Special:Upload upload] an image and give it the "destination" file name of "firstname_lastname_face.jpg"-- if you keep this file name, your image will appear automatically in the gallery below.  If you have a personal web page, click the "edit" button above this section, then find the fake URL that has your name (it will be firstname_lastname.com) and replace this with the real URL. You can also create a user page on this wiki (see Karen and Hilmar for examples). To see participant's skills (declared in applications) refer to [[Skills_table|this page]].
To add your photo, [http://www.evoio.org/wiki/Special:Upload upload] an image and give it the "destination" file name of "firstname_lastname_face.jpg"-- if you keep this file name, your image will appear automatically in the gallery below.  If you have a personal web page, click the "edit" button above this section, then find the fake URL that has your name (it will be firstname_lastname.com) and replace this with the real URL. You can also create a user page on this wiki (see [[User:Kcranston|Karen]] and [[User:Hilmar|Hilmar]] for examples). To see participant's skills (declared in applications) refer to the [[#Skills_table|skills table]] below.


== Participant gallery ==
== Participant gallery ==
Line 52: Line 52:
Image:Enrico.jpg|[http://www.cs.nmsu.edu/~epontell Enrico Pontelli], NMSU (Leadership Team), [https://github.com/epontell epontell@github]
Image:Enrico.jpg|[http://www.cs.nmsu.edu/~epontell Enrico Pontelli], NMSU (Leadership Team), [https://github.com/epontell epontell@github]
</gallery>
</gallery>
== Skills table ==
For column descriptions hover over them (or see end of the page). For more info about participants, refer to [[PhylotasticParticipants|this page]].
{|
| align="center" style="background:#f0f0f0;"|'''Participant'''
| align="center" style="background:#f0f0f0;"|'''<span title="(back-end trees): you know where to get large trees (1K species or more) and make them available via some data store" >tree</span>'''
| align="center" style="background:#f0f0f0;"|'''<span title="(provenance annotation): you can use metadata to keep track of where results came from">prov</span>'''
| align="center" style="background:#f0f0f0;"|'''<span title="(branch length): estimation: you can adapt tools that estimate missing branch lengths on species trees">scale</span>'''
| align="center" style="background:#f0f0f0;"|'''<span title="(visualization): you can adapt an existing phylogeny visualization tool for new inputs and capabilities">viz</span>'''
| align="center" style="background:#f0f0f0;"|'''<span title="(workflows): you can assemble web services (or other resources) into an executable workflow">flow</span>'''
| align="center" style="background:#f0f0f0;"|'''<span title="(documentation): you can make screencasts and write clear how-to documents">doc</span>'''
| align="center" style="background:#f0f0f0;"|'''<span title="(grafting & pruning): you can implement algorithms for grafting and pruning input trees to create a synthetic tree">grft</span>'''
| align="center" style="background:#f0f0f0;"|'''<span title="(NeXML spec): you can help expand the NeXML spec to cover the Phylotastic use-case">NeX</span>'''
| align="center" style="background:#f0f0f0;"|'''<span title="(semantic integration, mashups): you can write tools to discover, collect and integrate online data">mash</span>'''
| align="center" style="background:#f0f0f0;"|'''<span title="(taxonomic name resolution): you can use and adapt tools to map one set of names to another">tnrs</span>'''
| align="center" style="background:#f0f0f0;"|'''<span title="(use-case expert): you know a real pruning-grafting-integration problem that can be used to test Phylotastic">use</span>'''
| align="center" style="background:#f0f0f0;"|'''<span title="(web service interfaces): you can design and implement interfaces to wrap existing tools">WS</span>'''
| align="center" style="background:#f0f0f0;"|'''<span title="(something else): you can contribute to this project in ways we haven't imagined yet">other</span>'''
| align="center" style="background:#f0f0f0;"|'''<span title="Please describe what those other skills are here.">Describe Other</span>'''
|-
| | [[jim_balhoff|Jim Balhoff]]||||prov||||||flow||||||NeX||mash||||||WS||||
|-
| | [[Image:jim_balhoff_face.jpg|50px|Jim Balhoff]]|| ! scope=row colspan=14 style="background:#f0f0f0"| '''Comments:'''
|-
| scope=row colspan=15 style="border-bottom:2px solid gray;"|
|-
| | [[christopher_baron|Chris Baron]]||||||||viz||flow||||grft||NeX||mash||||||WS||||
|-
| | [[Image:chris_baron_face.jpg|50px|Christopher Baron]]|| ! scope=row colspan=14 style="background:#f0f0f0"| '''Comments:''' I'm a web developer with little background in evolutionary biology, I can do front end and back end.  Currently, I've developing a web application that allows users to upload source trees, as well as prune, replace, and graft together larger trees from these source trees using a graphical interface rather than sophisticated algorithms.
|-
| scope=row colspan=15 style="border-bottom:2px solid gray;"|
|-
| | [[holly_bik|Holly Bik]]||||||||viz||flow||doc||graft||||||||use||||other||
|-
| | [[Image:holly_bik_face.jpg|50px|Holly Bik]]|| ! scope=row colspan=14 style="background:#f0f0f0"| '''Comments:'''
|-
| scope=row colspan=15 style="border-bottom:2px solid gray;"|
|-
| | [[Helena_deus|Helena Deus]]||||prov||||viz||flow||doc||||||mash||tnrs||||WS||other||
|-
| | [[Image:Helena_deus.jpg|50px|Helena Deus]]|| ! scope=row colspan=14 style="background:#f0f0f0"| '''Comments:'''
|-
| scope=row colspan=15 style="border-bottom:2px solid gray;"|
|-
| | [[James_estill|Jamie Estill]]||tree||||||||||||graft||NeX||||||||||||
|-
| | [[Image:James_estill_face.jpg|50px|Jamie Estill]]|| ! scope=row colspan=14 style="background:#f0f0f0"| '''Comments:'''
|-
| scope=row colspan=15 style="border-bottom:2px solid gray;"|
|-
| | [[tracy_heath|Tracy Heath]]||||||scale||||||doc||graft||||||tnrs||||||||
|-
| | [[Image:tracy_heath_face.jpg|50px|Tracy Heath]]|| ! scope=row colspan=14 style="background:#f0f0f0"| '''Comments:'''
|-
| scope=row colspan=15 style="border-bottom:2px solid gray;"|
|-
| | [[mark_holder|Mark Holder]]||||||||||flow||||graft||NeX||||||||WS||||
|-
| | [[Image:mark_holder_face.jpg|50px|Mark Holder]]|| ! scope=row colspan=14 style="background:#f0f0f0"| '''Comments:'''
|-
| scope=row colspan=15 style="border-bottom:2px solid gray;"|
|-
| | [[User:Hilmar|Hilmar Lapp]]|| tree ||  ||  || viz || flow ||  ||  || NeX || mash ||  ||  || WS ||  ||
|-
| | [[Image:Hilmar.jpg|50px|Participant Picture]]|| ! scope=row colspan=14 style="background:#f0f0f0"| '''Comments:''' I am interested in interoperability and reuse of software and data, and have considerable experience in data and metadata modeling, software architecture, and API design for reuse.
|-
| scope=row colspan=15 style="border-bottom:2px solid gray;"|
|-
| | [[naim_matasci|Naim Matasci]]||tree||||||viz||flow||doc||graft||||||tnrs||||||||
|-
| | [[Image:naim_matasci_face.jpg|50px|Naim Matasci]]|| ! scope=row colspan=14 style="background:#f0f0f0"| '''Comments:'''
|-
| scope=row colspan=15 style="border-bottom:2px solid gray;"|
|-
| | [[emily_jane_mctavish|Emily Jane McTavish]]||tree||prov||scale||||||doc||graft||||||tnrs||use||||other||
|-
| | [[Image:emily_jane_mctavish_face.jpg|50px|Emily Jane McTavish]]|| ! scope=row colspan=14 style="background:#f0f0f0"| '''Comments:''' My background is phylogenetics, and some bioinformatics. I'm most comfortable with python, fine with SQL, knew C++ and could probably remember if pressed. I'm particularly interested in how to incorporate uncertainty from source trees into phylotastic output, and make it handy without being dangerously blackboxy.
|-
| scope=row colspan=15 style="border-bottom:2px solid gray;"|
|-
| | [[peter_midford|Peter Midford]]||||||||||||||graft||NeX||||tnrs||||||other||
|-
| | [[Image:peter_midford_face.jpg|50px|Peter Midford]]|| ! scope=row colspan=14 style="background:#f0f0f0"| '''Comments:'''
|-
| scope=row colspan=15 style="border-bottom:2px solid gray;"|
|-
| | [[siavash_mirarab|Siavash Mirarab]]||||||scale||||flow||||graft||||||tnrs||||WS||||
|-
| | [[Image:siavash_mirarab_face.jpg|50px|Siavash Mirarab]]|| ! scope=row colspan=14 style="background:#f0f0f0"| '''Comments:''' I am interested in TNRS, but have little experience with it. I am familiar with gene duplication concepts, so I can help with the reconciliation use case (if included). I work on meta-genomics, so I can help with a meta-genomic use case.
|-
| scope=row colspan=15 style="border-bottom:2px solid gray;"|
|-
| | [[megan_pirrung|Megan Pirrung]]||||||||viz||flow||||||||||||||WS||other||
|-
| | [[Image:megan_pirrung_face.jpg|50px|Megan Pirrung]]|| ! scope=row colspan=14 style="background:#f0f0f0"| '''Comments:'''
|-
| scope=row colspan=15 style="border-bottom:2px solid gray;"|
|-
| | [[rick_ree|Rick Ree]]||tree||prov||scale||viz||flow||doc||graft||||||tnrs||use||WS||||
|-
| | [[Image:rick_ree_face.jpg|50px|Rick Ree]]|| ! scope=row colspan=14 style="background:#f0f0f0"| '''Comments:'''
|-
| scope=row colspan=15 style="border-bottom:2px solid gray;"|
|-
| | [[aaron_steele|Aaron Steele]]||tree||prov||||viz||flow||doc||||||mash||tnrs||||WS||||
|-
| | [[Image:aaron_steele_face.jpg|50px|Aaron Steele]]|| ! scope=row colspan=14 style="background:#f0f0f0"| '''Comments:'''
|-
| scope=row colspan=15 style="border-bottom:2px solid gray;"|
|-
| | [http://www.molevol.org Arlin Stoltzfus]|| tree|| prov||||viz|| flow||doc |||| NeX||||||use||||other||
|-
| | [[Image:arlin_stoltzfus_face.jpg|50px|Arlin Stoltzfus]]|| ! scope=row colspan=14 style="background:#f0f0f0"| '''Comments:''' I have experience (as a developer or project manager or scientist) with viz (Nexplorer); a toolbox with tree operations (Bio::NEXUS);  fossil-based calibrations (Norris & Stoltzfus, in review); automated workflow for gene-family trees (De Kee, et al. 2007); documentation (NeXML; Bio::NEXUS; Nexplorer); an ontology (CDAO).  I am familiar with a variety of phylotastic-relevant use-cases (Stoltzfus, et al., in review).
|-
| scope=row colspan=15 style="border-bottom:2px solid gray;"|
|-
| | [[jeet_sukumaran|Jeet Sukumaran]]||tree||prov||scale||||flow||||||NeX||mash||||||||||
|-
| | [[Image:jeet_sukumaran_face.jpg|50px|Jeet Sukumaran]]|| ! scope=row colspan=14 style="background:#f0f0f0"| '''Comments:'''
|-
| scope=row colspan=15 style="border-bottom:2px solid gray;"|
|-
| | [[User:Gaurav|Gaurav Vaidya]]||||||||||flow||||||||mash||tnrs||||WS||other||
|-
| | [[Image:gaurav_vaidya_face.jpg|50px|Gaurav Vaidya]]|| ! scope=row colspan=14 style="background:#f0f0f0"| '''Comments:'''
|-
| scope=row colspan=15 style="border-bottom:2px solid gray;"|
|-
| | [[ben_vandervalk|Ben Vandervalk]]||||||||||flow||||||||mash||||||WS||||
|-
| | [[Image:ben_vandervalk_face.jpg|50px|Ben Vandervalk]]|| ! scope=row colspan=14 style="background:#f0f0f0"| '''Comments:'''
|-
| scope=row colspan=15 style="border-bottom:2px solid gray;"|
|-
| | [[cam_webb|Cam Webb]]||tree||||scale||viz||flow||doc||graft||NeX||mash||tnrs||use||WS||||
|-
| | [[Image:cam_webb_face.jpg|50px|Cam Webb]]|| ! scope=row colspan=14 style="background:#f0f0f0"| '''Comments:'''
|-
| scope=row colspan=15 style="border-bottom:2px solid gray;"|
|-
| | [http://www.cmzmasek.net Christian Zmasek]||tree||||||viz||flow||||graft||||mash||tnrs||||||||
|-
| | [[Image:christian_m_zmasek_face.jpg|50px|Christian Zmasek]]|| ! scope=row colspan=14 style="background:#f0f0f0"| '''Comments:''' I am using phylogenetic trees (gene trees) as tools for comparative and functional genomics.
|-
| scope=row colspan=15 style="border-bottom:2px solid gray;"|
|-
| | [http://rutgervos.blogspot.com Rutger A. Vos]||tree||prov||scale||viz||flow||doc||graft||NeX||mash||tnrs||||WS||||
|-
| | [[Image:rutger_vos_face.jpg|50px|Rutger A. Vos]]|| ! scope=row colspan=14 style="background:#f0f0f0"| '''Comments:''' I am guilty of developing NeXML, which might become one of the output formats because it allows for semantic annotation of trees, nodes, taxa, etc. I've also implemented PhyloWS services for TreeBASE, and wrapper PhyloWS services for ToLWeb, uBio, TimeTree.
|-
| scope=row colspan=15 style="border-bottom:2px solid gray;"|
|-
| | [[participant_page|Participant Name]]|| || || || || ||doc || || NeX|| || || ||WS||other||
|-
| | [[Image:Enrico.jpg|50px|Participant Picture]]|| ! scope=row colspan=14 style="background:#f0f0f0"| '''Comments:''' 
|-
| scope=row colspan=15 style="border-bottom:2px solid gray;"|
|-
|
|}


[[Category:Phylotastic]]
[[Category:Phylotastic]]

Revision as of 16:49, 10 June 2012

To add your photo, upload an image and give it the "destination" file name of "firstname_lastname_face.jpg"-- if you keep this file name, your image will appear automatically in the gallery below. If you have a personal web page, click the "edit" button above this section, then find the fake URL that has your name (it will be firstname_lastname.com) and replace this with the real URL. You can also create a user page on this wiki (see Karen and Hilmar for examples). To see participant's skills (declared in applications) refer to the skills table below.

Participant gallery


Event photos

Skills table

For column descriptions hover over them (or see end of the page). For more info about participants, refer to this page.

Participant tree prov scale viz flow doc grft NeX mash tnrs use WS other Describe Other
Jim Balhoff prov flow NeX mash WS
Jim Balhoff Comments:
Chris Baron viz flow grft NeX mash WS
Christopher Baron Comments: I'm a web developer with little background in evolutionary biology, I can do front end and back end. Currently, I've developing a web application that allows users to upload source trees, as well as prune, replace, and graft together larger trees from these source trees using a graphical interface rather than sophisticated algorithms.
Holly Bik viz flow doc graft use other
Holly Bik Comments:
Helena Deus prov viz flow doc mash tnrs WS other
Helena Deus Comments:
Jamie Estill tree graft NeX
Jamie Estill Comments:
Tracy Heath scale doc graft tnrs
Tracy Heath Comments:
Mark Holder flow graft NeX WS
Mark Holder Comments:
Hilmar Lapp tree viz flow NeX mash WS
Participant Picture Comments: I am interested in interoperability and reuse of software and data, and have considerable experience in data and metadata modeling, software architecture, and API design for reuse.
Naim Matasci tree viz flow doc graft tnrs
Naim Matasci Comments:
Emily Jane McTavish tree prov scale doc graft tnrs use other
Emily Jane McTavish Comments: My background is phylogenetics, and some bioinformatics. I'm most comfortable with python, fine with SQL, knew C++ and could probably remember if pressed. I'm particularly interested in how to incorporate uncertainty from source trees into phylotastic output, and make it handy without being dangerously blackboxy.
Peter Midford graft NeX tnrs other
Peter Midford Comments:
Siavash Mirarab scale flow graft tnrs WS
Siavash Mirarab Comments: I am interested in TNRS, but have little experience with it. I am familiar with gene duplication concepts, so I can help with the reconciliation use case (if included). I work on meta-genomics, so I can help with a meta-genomic use case.
Megan Pirrung viz flow WS other
Megan Pirrung Comments:
Rick Ree tree prov scale viz flow doc graft tnrs use WS
Rick Ree Comments:
Aaron Steele tree prov viz flow doc mash tnrs WS
Aaron Steele Comments:
Arlin Stoltzfus tree prov viz flow doc NeX use other
Arlin Stoltzfus Comments: I have experience (as a developer or project manager or scientist) with viz (Nexplorer); a toolbox with tree operations (Bio::NEXUS); fossil-based calibrations (Norris & Stoltzfus, in review); automated workflow for gene-family trees (De Kee, et al. 2007); documentation (NeXML; Bio::NEXUS; Nexplorer); an ontology (CDAO). I am familiar with a variety of phylotastic-relevant use-cases (Stoltzfus, et al., in review).
Jeet Sukumaran tree prov scale flow NeX mash
Jeet Sukumaran Comments:
Gaurav Vaidya flow mash tnrs WS other
Gaurav Vaidya Comments:
Ben Vandervalk flow mash WS
Ben Vandervalk Comments:
Cam Webb tree scale viz flow doc graft NeX mash tnrs use WS
Cam Webb Comments:
Christian Zmasek tree viz flow graft mash tnrs
Christian Zmasek Comments: I am using phylogenetic trees (gene trees) as tools for comparative and functional genomics.
Rutger A. Vos tree prov scale viz flow doc graft NeX mash tnrs WS
Rutger A. Vos Comments: I am guilty of developing NeXML, which might become one of the output formats because it allows for semantic annotation of trees, nodes, taxa, etc. I've also implemented PhyloWS services for TreeBASE, and wrapper PhyloWS services for ToLWeb, uBio, TimeTree.
Participant Name doc NeX WS other
Participant Picture Comments:
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