Many thanks for alerting us to this- we're looking into it and I will email you as soon as we have it resolved. All the best, Sawsan
------------------------------- Sawsan Khuri, Ph.D. Bioinformatics Senior Scientist, Center for Computational Science & Assistant Professor, The Dr. John T. Macdonald Foundation Department of Human Genetics http://www.ccs.miami.edu http://medgen.med.miami.edu ________________________________________ From: Brooke Rhead [[email protected]] Sent: Monday, October 04, 2010 9:00 PM To: Bennett, Bill Cc: [email protected]; Khuri, Sawsan Subject: Re: [Genome] Unable to display Nucleosome Exclusion Prediction data sets on UCSC genome browser Hi Bill, The med.miami.edu site that hosts the data appears to be unavailable. I have also sent an email to Sawsan Khuri (before I saw that your email went there, too) to see if we need to change our pointers to the data, or if the website is temporarily down. I'll let you know what I hear. -- Brooke Rhead UCSC Genome Bioinformatics Group Bennett, Bill wrote on 10/3/10 6:30 PM: > Dear UCSC, > > I tried and failed to load Nucleosome Exclusion Prediction data from the > public data tracks section of the genome browser. I tried to load the > tracks for Chromosomes 17-19 on 2 and 3 October. One error message > appeared consistently, and it is shown below. A description of the > Nucleosome Exclusion Prediction data set is also shown below. > > Please look into this problem when you can. > > Thank you. > > Bill Bennett > > City of Hope > > [email protected] <mailto:[email protected]> > > > > ERROR MESSAGE > > Error(s): > > Connection refused > > Couldn't connect to umsis.miami.edu 80 > > Couldn't open http://umsis.miami.edu/~aradwan/nx/nxregions/chr17.gff > > Nucleosome Exclusion Prediction data sets (hg18) accompanying the paper > Radwan A et al. Prediction and analysis of nucleosome exclusion regions > in the human genome <http://www.biomedcentral.com/1471-2164/9/186> . BMC > Genomics. 2008 Apr 22;9(1):186. View the Nucleosome Regions tracks to > see the whole genome annotation for nucleosome exclusion regions. View > the Nucleosome Scores tracks to see the nucleosome exclusion scores > which were calculated individually for each nucleotide. This annotation > was contributed by Ahmed Radwan, Akmal Younis, Peter Luykx, and Sawsan > Khuri, at the University of Miami, Miami, FL, USA. Contact Sawsan Khuri > at [email protected]. Click on the chromosome you wish to display. > Nucleosome Regions: 1 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1 > :25000000-26000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nxr > egions/chr1.gff> 2 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr2 > :99000000-100000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nx > regions/chr2.gff> 3 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr3 > :50000000-51000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nxr > egions/chr3.gff> 4 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr4 > :100000000-101000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/n > xregions/chr4.gff> 5 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr5 > :50000000-51000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nxr > egions/chr5.gff> 6 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr6 > :30000000-31000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nxr > egions/chr6.gff> 7 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr7 > :150000000-151000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/n > xregions/chr7.gff> 8 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr8 > :22000000-23000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nxr > egions/chr8.gff> 9 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr9 > :130000000-131000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/n > xregions/chr9.gff> 10 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1 > 0:72000000-73000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nx > regions/chr10.gff> 11 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1 > 1:65000000-66000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nx > regions/chr11.gff> 12 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1 > 2:120000000-121000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/ > nxregions/chr12.gff> 13 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1 > 3:19000000-20000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nx > regions/chr13.gff> 14 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1 > 4:49000000-50000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nx > regions/chr14.gff> 15 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1 > 5:20000000-21000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nx > regions/chr15.gff> 16 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1 > 6:65000000-66000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nx > regions/chr16.gff> 17 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1 > 7:40000000-41000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nx > regions/chr17.gff> 18 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1 > 8:9000000-10000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nxr > egions/chr18.gff> 19 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1 > 9:2000000-3000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nxre > gions/chr19.gff> 20 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr2 > 0:30000000-31000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nx > regions/chr20.gff> 21 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr2 > 1:46000000-47000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nx > regions/chr21.gff> 22 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr2 > 2:37000000-38000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nx > regions/chr22.gff> X > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chrX > :47000000-48000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nxr > egions/chrX.gff> Y > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chrY > :1000000-2000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nxreg > ions/chrY.gff> M > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg19&position=chrM > :1-16571&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nxregions/chr > M.gff> . Nucleosome Scores: 1 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1 > :25000000-26000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nxs > cores/chr1.wig> 2 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr2 > :99000000-100000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nx > scores/chr2.wig> 3 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr3 > :50000000-51000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nxs > cores/chr3.wig> 4 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr4 > :100000000-101000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/n > xscores/chr4.wig> 5 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr5 > :50000000-51000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nxs > cores/chr5.wig> 6 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr6 > :30000000-31000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nxs > cores/chr6.wig> 7 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr7 > :150000000-151000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/n > xscores/chr7.wig> 8 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr8 > :22000000-23000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nxs > cores/chr8.wig> 9 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr9 > :130000000-131000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/n > xscores/chr9.wig> 10 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1 > 0:72000000-73000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nx > scores/chr10.wig> 11 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1 > 1:65000000-66000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nx > scores/chr11.wig> 12 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1 > 2:120000000-121000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/ > nxscores/chr12.wig> 13 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1 > 3:19000000-20000000hgt.customText=http://umsis.miami.edu/~aradwan/nx/nxs > cores/chr13.wig> 14 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1 > 4:49000000-50000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nx > scores/chr14.wig> 15 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1 > 5:20000000-21000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nx > scores/chr15.wig> 16 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1 > 6:65000000-66000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nx > scores/chr16.wig> 17 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1 > 7:40000000-41000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nx > scores/chr17.wig> 18 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1 > 8:9000000-10000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nxs > cores/chr18.wig> 19 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1 > 9:2000000-3000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nxsc > ores/chr19.wig> 20 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr2 > 0:30000000-31000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nx > scores/chr20.wig> 21 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr2 > 1:46000000-47000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nx > scores/chr21.wig> 22 > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr2 > 2:37000000-38000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nx > scores/chr22.wig> X > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chrX > :47000000-48000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nxs > cores/chrX.wig> Y > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chrY > :1000000-2000000&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nxsco > res/chrY.wig> M > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chrM > :1-16571&hgt.customText=http://umsis.miami.edu/~aradwan/nx/nxscores/chrM > .wig> . > > > > > > --------------------------------------------------------------------- > SECURITY/CONFIDENTIALITY WARNING: > This message and any attachments are intended solely for the individual or > entity to which they are addressed. This communication may contain > information that is privileged, confidential, or exempt from disclosure under > applicable law (e.g., personal health information, research data, financial > information). Because this e-mail has been sent without encryption, > individuals other than the intended recipient may be able to view the > information, forward it to others or tamper with the information without the > knowledge or consent of the sender. If you are not the intended recipient, or > the employee or person responsible for delivering the message to the intended > recipient, any dissemination, distribution or copying of the communication is > strictly prohibited. If you received the communication in error, please > notify the sender immediately by replying to this message and deleting the > message and any accompanying files from your system. If, due to the security > risks, you do not w i! > sh to receive further communications via e-mail, please reply to this > message and inform the sender that you do not wish to receive further e-mail > from the sender. > > --------------------------------------------------------------------- > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
