089c09e98db52e92da694ab1a0c8891c1a7fd3e8
gperez2
  Thu Apr 2 15:50:07 2026 -0700
Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run).

Updated 261 trackDb HTML and .ra files:
- Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs,
chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations;
removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download,
oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs).
- Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com,
drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains
(blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix);
removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com).
- Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org,
cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org,
hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path).

No RM.

diff --git src/hg/makeDb/trackDb/human/encodeUvaDnaRep.html src/hg/makeDb/trackDb/human/encodeUvaDnaRep.html
index f947685f152..6c336854eab 100644
--- src/hg/makeDb/trackDb/human/encodeUvaDnaRep.html
+++ src/hg/makeDb/trackDb/human/encodeUvaDnaRep.html
@@ -1,60 +1,60 @@
 <H2> Description </H2>
 <P>
 The five subtracks in this annotation correspond to five different time points
 relative to the start of the DNA synthesis phase (S-phase) of the cell cycle.  
 </P>
 
 <H2>Display Conventions and Configuration</H2>
 <P>
 Regions that are replicated during the given time interval are shown in green.  
 Varying shades of green are used to distinguish one subtrack from another.
 To display only selected subtracks, uncheck the boxes next to the tracks you 
 wish to hide.</P>
 
 <H2> Methods </H2>
 <P>
 The experimental strategy adopted to map this profile involved isolation of 
 replication products from HeLa cells synchronized at the G1-S boundary by 
 thymidine-aphidicolin double block. Cells released from the block were
 labeled with BrdU at every two-hour interval of the 10 hours of S-phase and
 DNA was isolated from them. The heavy-light(H/L) DNA representing the pool of 
 DNA replicated during each two-hour labeling period was separated from the
 unlabeled DNA by double cesium chloride density gradient centrifugation.
 The purified heavy-light DNA was then hybridized to a high-density 
 genome-tiling Affymetrix array comprised of all unique probes within the 
 ENCODE regions.</P>
 <P>
 The raw data generated by the microarray experiments was 
 processed by computing the enrichment of signal in a particular 
 part of the S-phase relative to the entirety of the S-phase (10 hours).
 High confidence regions (P-value = 1E-04) of 
 replication were mapped by applying the Wilcoxon Rank Sum test in a sliding
 window of size 10 kb using the standard Affymetrix data analysis tools
 and the April 2003 (hg15) version of the human genome assembly. 
 These coordinates were then mapped to the July 2003 (hg17) assembly by UCSC
 using the liftOver tool.</P>
 
 <H2> Verification </H2>
 <P>
 The submitted data are from two biological experimental sets.  Regions of
 significant enrichment were included from both of the biological replicates.
 </P>
    
 <H2> Credits </H2>
 <P>
 Data generation and analysis for this track were performed by the 
 DNA replication group in the 
-<A HREF= "http://genome.bioch.virginia.edu/" TARGET=_blank>Dutta Lab</A>
+<A HREF= "https://app05.bioinformatics.virginia.edu/" TARGET=_blank>Dutta Lab</A>
 at the University of Virginia: Neerja Karnani, Christopher Taylor, 
 Hakkyun Kim, Louis Lim, Ankit Malhotra, Gabe Robins and Anindya Dutta.</P>
 <P>
 Neerja Karnani and Christopher Taylor prepared the data for presentation in 
 the UCSC Genome Browser.</P>
 
 <H2>References</H2>
 <P>
 Jeon, Y., Bekiranov, S., Karnani, N., Kapranov, P., Ghosh, S., MacAlpine, D., 
 Lee, C., Hwang, D.S., Gingeras, T.R. and Dutta, A.
 <A HREF="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15845769&query_hl=1"
 TARGET=_blank>Temporal profile of replication of human chromosomes</A>.
 <em>Proc Natl Acad Sci U S A</em> <B>102</B>(18), 6419-24 (2005).</P>