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New page: * Home * Contact Prototype HSP filtering algorithm Whom to contact with comments, suggestions, bug reports, etc? Eric Lyons: elyons (@) nature.berkeley.edu Or, visit o...
 
 
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== Who do I contact with comments, suggestions, bug reports, general questions, etc? ==
CoGe Support: coge.genome (@) gmail.com


We will respond within 24 hrs. (usually)  [mailto:coge.genome@gmail.com Contact us!]


    * Home
== CoGe Team:  Many thanks to many good people ==


=== [[User:Elyons|Eric Lyons]] ===
*'''CoGe's Project Manager'''
* Assistant Professor
* [http://cals.arizona.edu/spls/ School of Plant Sciences]
* [http://www.iplantcollaborative.org iPlant Collaborative Member]
* [http://bio5.org/ Bio5 Institute at the University of Arizona, Tucson]
** For CoGe related inquires:  elyons.uoa (@) gmail.com


=== Matt Bomhoff ===
* '''Lead CoGe Software Engineer'''
* Developer of
** [[EPIC-CoGe Browser]]
** [[User-Data Management System]]
** RNA-seq Pipelines


    * Contact
=== Haibao Tang ===
*'''Senior Bioinformatics Engineer @ JCVI'''
*Developer of
** BaoTools: https://github.com/tanghaibao
** [[SynMap]]
** [[SynFind]]
** Quota Align algorithm in [[SynMap]]
** Synteny finding algorithm used in [[SynFind]]


=== Blake Joyce ===
* Postdoctoral Researcher at [http://cals.arizona.edu/spls/content/blake University of Arizona School of Plant Sciences]
** bjoyce3 (@) email.arizona.edu
* Adjunct Professor at [https://www.pima.edu/directory/employee/detail?uid=jblake Pima Community College]
** jblake@pima.edu


=== Asher Baltzell ===
* PhD Student in the [http://www.genetics.arizona.edu/ Genetics GIDP]
** ahaug (@) email.arizona.edu


Prototype HSP filtering algorithm


Whom to contact with comments, suggestions, bug reports, etc?
== How to cite CoGe? ==


{{main|References}}
* '''CoGe in General''': [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2007.03326.x/full Eric Lyons, Michael Freeling (2008) How to usefully compare homologous plant genes and chromosomes as DNA sequences The Plant Journal 53 (4) , 661-673]


Eric Lyons: elyons (@) nature.berkeley.edu
* '''[[CoGeBlast]]''': [http://www.plantphysiol.org/content/148/4/1772.full Eric Lyons*, Brent Pedersen, Josh Kane, Maqsudul Alam, Ray Ming, Haibao Tang, Xiyin Wang, John Bowers, Andrew Paterson, Damon Lisch and Michael Freeling (2008) Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids Plant Physiology 2008 vol. 148 no. 4 1772-1781]


Or, visit our online bug and feature request system.
* '''[[SynMap2]] and [[SynMap3D]]''': [https://academic.oup.com/bioinformatics/article/33/14/2197/3072872 Asher Haug-Baltzell, Sean A. Stephens, Sean Davey, Carlos E. Scheidegger, Eric Lyons; SynMap2 and SynMap3D: web-based whole-genome synteny browsers, Bioinformatics, Volume 33, Issue 14, 15 July 2017, Pages 2197–2198, https://doi.org/10.1093/bioinformatics/btx144]


Who is responsible for CoGe?
** '''[[SynMap]]''': [http://www.springerlink.com/content/x8295245274t240l/ Lyons E, Pedersen B, Kane J, Freeling M (2008) The value of nonmodel genomes and an example using SynMap within CoGe to dissect the hexaploidy that predates rosids. Tropical Plant Biol 1 (3-4) , 181-190]


Eric Lyons:
* '''[[Syntenic Path Assembly]]''': [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0016717 Lyons E, Freeling M, Kustu S, Inwood W (2011) Using Genomic Sequencing for Classical Genetics in E. coli K12. PLoS ONE 6(2): e16717. doi:10.1371/journal.pone.0016717 ]


elyons (@) nature.berkeley.edu
* '''[[FractBias]]''': [http://bioinformatics.oxfordjournals.org/content/early/2016/10/26/bioinformatics.btw666.abstract Blake L. Joyce, Asher Haug-Baltzell, Sean Davey, Matthew Bomhoff, James C. Schnable, and Eric Lyons FractBias: a graphical tool for assessing fractionation bias following polyploidy Bioinformatics first published online October 29, 2016 doi:10.1093/bioinformatics/btw666]


Michael Freeling:
* '''[[LoadExp+]]''': [http://onlinelibrary.wiley.com/doi/10.1002/pld3.8/full Grover JW, Bomhoff M, Davey S, Gregory BD, Mosher RA, Lyons E. CoGe LoadExp+: A web-based suite that integrates next-generation sequencing data analysis workflows and visualization. Plant Direct. 2017;00:1–7. https://doi.org/10.1002/pld3.8]


freeling (@) nature.berkeley.edu
==How to acknowledge CoGe?==


Brian C. Thomas:
If you have an acknowledgement for CoGe, please reference one (or more) of the following grant numbers:


bcthomas (@) berkeley.edu
''NSF'':
* '''IOS-1339156'''  Years: 2014-2017
* '''IOS-1444490'''  Years: 2015-2019
''USDA'':
* '''2013-00984'''  Years: 2013-2016
''Gordon and Betty Moore Foundation'':
* '''3833'''  Years: 2012-2014


Josh Kane:
==Former Team Members==


Project Manager, Lead Developer, Head Programmer, etc.
=== Alex Frank ===
* Undergraduate student worker
* Developer of the Admin Dashboard


Department of Plant and Microbial Biology
=== Shabari Subramaniam ===
* Scientific Analyst


University of California, Berkeley
===Evan Briones===
* CoGe Developer
* Developer for CoGe's [[Job Execution Framework]] ([[JEX]])


PI and application critic
===Roey Chasman===
* CoGe Developer
* Developer for CoGe's internal usage monitoring
* Developer for [[EPIC-CoGe Browser]]


Professor
=== [[User:Jschnable| James Schnable]] ===
* [http://pmb.berkeley.edu Department of Plant and Microbial Biology]
* [http://www.berkeley.edu University of California, Berkeley]
**jschnable (@) berkeley.edu


Department of Plant and Microbial Biology
=== Brent Pedersen ===
*Developer of [[Gobe]] (visualization system used [[GEvo]]
*Developer of [http://code.google.com/p/genome-browser/ OpenGenes] (navigation system used in visualization system for [[GenomeView]])
*Much code work behind the scenes to get algorithms working quickly


University of California, Berkeley
=== Joshua Kane ===
* Graduate Student
* Tetrad Department
* [http://www.ucsf.edu/ University of California, San Francisco]


Lead developer of SeqView and CoGeBlast.
=== Brian Thomas ===


Interface developer extraordinaire
=== Sara Castelletti ===


Undergraduate Researcher
=== Dan Hembry ===


University of California, Berkeley


OpenGenes tiler application and image caching system, Gobe Flash Viewer


Programmer Analysist
== CoGe Development Testers ==


Department of Plant and Microbial Biology
=== Michael Freeling ===
* Professor, PI of the CoGe Project
* [http://pmb.berkeley.edu Department of Plant and Microbial Biology]
* [http://www.berkeley.edu University of California, Berkeley]
* freeling (@) berkeley.edu


University of California, Berkeley
=== Damon Lisch ===
 
* Principal Investigator
Brent Pedersen:
* [http://pmb.berkeley.edu/ Department of Plant and Microbial Biology]
 
* [http://www.berkeley.edu University of California, Berkeley]
Transposon and Maize expert scientist
* dlisch (@) berkeley.edu
 
Application beta tester and vociferous critic
 
Department of Plant and Microbial Biology
 
University of California, Berkeley
 
Damon Lisch:
 
dlisch (@) nature.berkeley.edu
 
Eric Lyons, Michael Freeling (2008) How to usefully compare homologous plant genes and chromosomes as DNA sequences The Plant Journal 53 (4) , 661–673
 
How to cite CoGe?

Latest revision as of 21:05, 23 February 2018

Who do I contact with comments, suggestions, bug reports, general questions, etc?

CoGe Support: coge.genome (@) gmail.com

We will respond within 24 hrs. (usually) Contact us!

CoGe Team: Many thanks to many good people

Eric Lyons

Matt Bomhoff

Haibao Tang

Blake Joyce

Asher Baltzell


How to cite CoGe?

Main article: References

How to acknowledge CoGe?

If you have an acknowledgement for CoGe, please reference one (or more) of the following grant numbers:

NSF:

  • IOS-1339156 Years: 2014-2017
  • IOS-1444490 Years: 2015-2019

USDA:

  • 2013-00984 Years: 2013-2016

Gordon and Betty Moore Foundation:

  • 3833 Years: 2012-2014

Former Team Members

Alex Frank

  • Undergraduate student worker
  • Developer of the Admin Dashboard

Shabari Subramaniam

  • Scientific Analyst

Evan Briones

Roey Chasman

  • CoGe Developer
  • Developer for CoGe's internal usage monitoring
  • Developer for EPIC-CoGe Browser

James Schnable

Brent Pedersen

  • Developer of Gobe (visualization system used GEvo
  • Developer of OpenGenes (navigation system used in visualization system for GenomeView)
  • Much code work behind the scenes to get algorithms working quickly

Joshua Kane

Brian Thomas

Sara Castelletti

Dan Hembry

CoGe Development Testers

Michael Freeling

Damon Lisch

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