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biotelerock made 1 file-release changes.
2009-10-30 19:29:02 UTC in USeq
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biotelerock made 1 file-release changes.
2009-10-26 18:38:01 UTC in USeq
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Allow the deselection of autoloaded resources. Hiding the track does not prevent it from loading and consuming memory. Hiding does not persist between IGB sessions. Ideally, no resources load without the user selecting them. But once selected, these are set in the users preferences and loaded every time. Having things autoload and not be able to deselect them is a real bother.
2009-10-15 16:31:56 UTC in GenoViz
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There appears to be a problem loading refseq annotations from the Affy DAS2 server. The Affy Quickload refseq retrieval is uneffected. I can reproduce this on H_sapiens_Mar_2006 for all chromosomes.
2009-10-15 15:24:35 UTC in GenoViz
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biotelerock made 1 file-release changes.
2009-10-14 16:59:01 UTC in USeq
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OK, this is driving me nuts. STEVE and ED, can you look into this and fix it ASAP! Otherwise I'm going to recommend reverting to IGB 5.5. These extra tracks are loaded even when you hide them. It's killing memory and making IGB really slow down.
I'm going to give a demo of IGB and DAS/2 to a group at NIH this weekend so please fix it before then.
John, can you detail exactly what they...
2009-10-13 22:40:31 UTC in GenoViz
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Ah, it's working again. But only because the Affy Quickload is providing the files. All of the DAS/2 servers failed. Here's the log from the IGB console:
trying to load residues via DAS/2
request URI: http://bioserver.hci.utah.edu:8080/DAS2DB/genome/H_sapiens_Mar_2006/chr1?format=bnib&range=0:247249719
response content-type: null
Improper response from DAS/2; aborting DAS/2...
2009-10-12 19:57:17 UTC in GenoViz
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Seems like the failure to load sequence from DAS/2 sources has returned. Try loading sequence for H_sapiens_Mar_2006. Throws an error saying it cannot be found. Don't know if this is actually true and the Affy folks deleted their files or if it's an IGB bug. Other genome builds may be effected. This did work with 5.5.
2009-10-09 14:08:25 UTC in GenoViz
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Note, the spec for gff is 1 based encoding. IGB follows interbase coordinates (1st base zero, last base excluded) so you should see a 1 off error if your gff file is correct.
2009-10-09 14:05:24 UTC in GenoViz
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Far too many resources are being autoloaded from the Affy DAS2 server upon IGB selection, see H_sapiens_Mar_2006.
Affy folks can you follow John's advice and modify the configuration file specifying what to load ASAP!!!! At most there should be refseq and cytobands.
Also, even more anoying, there isn't a way to deselect these tracks?.
2009-10-06 17:41:10 UTC in GenoViz
