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Index of /release1/dpulex_jgi060905

      Name                                Last modified       Size  Description

[DIR] Parent Directory 19-Jul-2007 17:33 - [DIR] gff/ 21-Feb-2014 21:32 - [DIR] genome-assembly/ 06-Feb-2014 14:57 - [DIR] gene-predictions/ 18-Jan-2013 13:04 - [DIR] supplement/ 06-Dec-2010 14:34 - [DIR] pasa/ 26-Jul-2010 11:45 - [TXT] release-files.html 09-Dec-2008 10:13 3k [DIR] repeats/ 09-Dec-2008 09:46 - [DIR] genepages/ 01-Aug-2008 16:57 - [DIR] gene-duplicates/ 13-Feb-2008 17:44 - [DIR] bacteria/ 24-Oct-2007 14:11 - [DIR] pseudogenes/ 17-Sep-2007 18:50 - [DIR] trna-ncrna/ 07-Aug-2007 10:07 - [DIR] fasta/ 27-Jul-2007 19:26 - [TXT] DGC_Data_Release_Policy.html 19-Jul-2007 22:32 4k [DIR] est/ 19-Jul-2007 17:46 - [DIR] genome-assembly-full-jazz_20060901/ 19-Jul-2007 17:00 - [TXT] brief-methods.txt 28-Sep-2006 12:51 3k [DIR] genetic-map/ 26-Sep-2006 10:44 -

Daphnia Genome Consortium
Data Release Policy

As a public service, the raw sequence data from the Daphnia pulex genome sequencing project is being made available by the Department of Energy Joint Genome Institute (JGI) before scientific publication. The purpose of this policy is to balance the directive of DOE and JGI that the data from its sequencing projects be made available to the scientific community as soon as possible with the reasonable expectation that the collaborators and the JGI will publish their results without concerns about potential preemption by other groups that did not participate in the effort.

These pre-publication data are preliminary and incomplete and may contain errors. The goal of our policy is that early release should enable the progress of science. By accessing these data, you agree not to publish any articles containing analyses of genes or genomic data on a whole genome or chromosome scale prior to publication by JGI and its collaborators of its comprehensive genome analysis. These restrictions will be lifted on the publication of the whole genome description or the expiration of a 12-month period after initial release of the data, whichever comes first. During this waiting period, the data will be available for any kind of publication that does not compete directly with planned publications (e.g. reserved analyses) of the JGI and collaborators. A principal collaborator or “champion” is listed on the Info page in the above menu and is the point of contact and arbiter regarding publication plans. Scientists are strongly encouraged to contact the JGI and/or its principal collaborator about their intentions and any potential collaboration. An ideal collaboration consists of scientists contributing to the open community-wide annotation project that is currently ongoing. Information on this opportunity to be involved in the analysis of the data can be found at the Daphnia Genomics Consortium (DGC) website .

On selected data sets, the current status of which is indicated in the Info and Download pages, the JGI reserves the exclusive right to publish, not more than 12 months following completion of the draft sequencing phase, the assembly and sequence along with an initial genome-scale analysis. Reserved analyses include the identification of complete (whole genome) sets of genomic features such as genes, gene families, regulatory elements, repeat structures, GC content, etc., and whole-genome comparisons of regions of evolutionary conservation or change. Manually annotated genes within the Genome Portal are also reserved. A list of research projects is available at the DGC webpages.

Otherwise, it is our expectation that papers dealing with specific genes, pathways, etc. will not be considered competitive and scientific users are free to use the draft sequencing data for such publications, subject only to agreement from the collaborators. Studies of any type on the reserved data sets that are not in direct competition with those planned by the JGI and its collaborators may also be undertaken following an agreement to that effect. Interested parties are encouraged to contact the JGI to discuss such possibilities.

If these data are used for publication, the following acknowledgment should be included: “These sequence data were produced by the US Department of Energy Joint Genome Institute http://www.jgi.doe.gov/ in collaboration with the Daphnia Genomics Consortium http://daphnia.cgb.indiana.edu” We request that you notify us upon publication so that this information can be included in the final annotation.

The data may be freely downloaded and used by all who respect the restrictions in the previous paragraphs. While still in waiting period status, the assembly and raw sequence reads should not be redistributed or repackaged without permission from the JGI. Any redistribution of the data during this period should carry this notice: “The Joint Genome Institute provides these data in good faith, but makes no warranty, expressed or implied, nor assumes any legal liability or responsibility for any purpose for which the data are used.” Once moved to unreserved status, the data are freely available for any subsequent use.