System Support
CoGe System Support, 2011, University of California, Berkeley and The iPlant Collaborative
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 [Dr. Freeling] 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