System Support: Difference between revisions

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'''Summary:''' There are now fees for some database uploads and a CoGe consultation/training charge of $200/hr plus expenses. The CoGe team includes 4 programmers, two PIs and a few researchers comfortable with using the various CoGe applications.
'''Summary:'''  


CoGe is a comparative genomics system funded by NSF and is provided as a public research toolbox. '''Use is without charge.''' CoGe is a collaboration with the Freeling lab at UC Berkeley and Eric Lyons at the iPlant Collaborative.  Thus far, all direct NSF support for CoGe is for research aims lead by Mike Freeling.  Additional tools and data are provided by volunteer contributors.


CoGe is a comparative genomics system funded by NSF and is provided as a public research toolbox. '''Use is without charge.''' The CoGe team in the Freeling lab, UC-Berkeley, will continue to provide on-line research support in comparative genomics. However, Eric Lyons, lead developer, and the rest of the CoGe team -- and also the two PIs in the Freeling lab, Damon Lisch and Michael Freeling -- need to limit time and computational resources spent in "service." Our funding is for research. CoGe's modest success brings with it this need to set limits.
We greatly value our users' experience with CoGe. Through user feedback, CoGe continues to improve. The ongoing communication between CoGe staff and users constitutes collaboration, not consultation. Bugs are fixed and tools that are easy to enable are added without charge.




We greatly value our experienced users. Through user feedback, CoGe continues to improve. The ongoing communication between CoGe staff and users constitutes collaboration, not consultation. Bugs are fixed and tools that are easy to enable are added without charge.
1) '''Public Data''': We will continue to upload and maintain any genome database that is available to the public free of charge. We consider this part of our public service and are happy to accommodate.  Please see [[FAQs#Can_you_add_a_genome.3F | this page]] for information we need to add a genome to CoGe. While the actual processing of data takes a few minutes to an hour, sometimes customization is needed in order to transform GFF3 or other gene model/annotation files for input into CoGe. Also, these activities usually take place after regular work hours. Thus, it may take a couple of days for your genome to be added.  However, we will let you know that we have received your request and our progress.




1) We will continue to upload and maintain any genome database that is available to the public free of charge. However, starting in 2009, we will charge for publicly funded genome uploads while they are protected from public use by the Ft Lauderdale convention ($3,000/upload) and charge more for each proprietary database upload (quote based on level of security). Charges stop when the public is granted access.
2) '''Private Data''': Please contact [mailto:elyons.uoa@gmail.com Eric Lyons] for requests regarding proprietary genomes.  Such data are supported by CoGe and are kept private from the general public. Unfortunately, such accommodations require an additional level of complexity as CoGe does not currently have an open user management system (CoGe was originally developed as a research tool for public data).  The CoGe team understands the necessity of keeping genomes private until publication, and are willing to participate in collaborations in order to leverage the thousands of genomes and dozens of comparative genomics tools available in CoGe.


3) Professional consulting from the Freeling Lab at UC Berkeley is $200/hr.  Please contact [[mailto:freeling@berkeley.edu]] for details.


2) Our consulting rate is $200/hr plus expenses for 2009, and everyone in the Freeling lab MUST charge this rate.


For all other inquires, please begin your discussions with [mailto:elyons.uoa@gmail.com?Subject=CoGe%20Support Eric Lyons].


Please begin your discussions with [mailto:elyons@berkeley.edu?Subject=CoGe%20Support Eric Lyons]. However, all transactions involving money to CoGe are administered through UC-Berkeley, and will comply with all applicable rules and regulations. All funds collected will support CoGe.


CoGe website: http://genomevolution.org/


CoGe website: http://synteny.cnr.berkeley.edu/CoGe /
Freeling lab websites: http://plantbio.berkeley.edu/~freeling/labweb/welcome.html


 
The iPlant Collaborative: http://iplantcollaborative.org
Freeling lab websites: http://plantbio.berkeley.edu/~freeling/labweb/welcome.html

Revision as of 00:21, 20 February 2011

CoGe System Support, 2009, University of California, Berkeley


Summary:

CoGe is a comparative genomics system funded by NSF and is provided as a public research toolbox. Use is without charge. CoGe is a collaboration with the Freeling lab at UC Berkeley and Eric Lyons at the iPlant Collaborative. Thus far, all direct NSF support for CoGe is for research aims lead by Mike Freeling. Additional tools and data are provided by volunteer contributors.

We greatly value our users' experience with CoGe. Through user feedback, CoGe continues to improve. The ongoing communication between CoGe staff and users constitutes collaboration, not consultation. Bugs are fixed and tools that are easy to enable are added without charge.


1) Public Data: We will continue to upload and maintain any genome database that is available to the public free of charge. We consider this part of our public service and are happy to accommodate. Please see this page for information we need to add a genome to CoGe. While the actual processing of data takes a few minutes to an hour, sometimes customization is needed in order to transform GFF3 or other gene model/annotation files for input into CoGe. Also, these activities usually take place after regular work hours. Thus, it may take a couple of days for your genome to be added. However, we will let you know that we have received your request and our progress.


2) Private Data: Please contact Eric Lyons for requests regarding proprietary genomes. Such data are supported by CoGe and are kept private from the general public. Unfortunately, such accommodations require an additional level of complexity as CoGe does not currently have an open user management system (CoGe was originally developed as a research tool for public data). The CoGe team understands the necessity of keeping genomes private until publication, and are willing to participate in collaborations in order to leverage the thousands of genomes and dozens of comparative genomics tools available in CoGe.

3) Professional consulting from the Freeling Lab at UC Berkeley is $200/hr. Please contact [[1]] for details.


For all other inquires, please begin your discussions with Eric Lyons.


CoGe website: http://genomevolution.org/

Freeling lab websites: http://plantbio.berkeley.edu/~freeling/labweb/welcome.html

The iPlant Collaborative: http://iplantcollaborative.org

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