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/encodeUvaDnaRepTr50.html src/hg/makeDb/trackDb/human/encodeUvaDnaRepTr50.html
index e9c6a48525a..328b9c7961a 100644
--- src/hg/makeDb/trackDb/human/encodeUvaDnaRepTr50.html
+++ src/hg/makeDb/trackDb/human/encodeUvaDnaRepTr50.html
@@ -35,30 +35,30 @@
 was also classified as temporally specific or non-specific based on
 whether at least 50% of the accumulated signal appeared in a single
 time point or not.</P>
 <P>
 The TR<SUB>50</SUB> data for all specific probes were then lowess-smoothed within
 a 60 kb window to provide the profile displayed in the annotation.</P>
 
 <H2>Verification</H2>
 <P>
 The replication experiments were completed for two biological sets
 in the HeLa adherent cell line.</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/"
+DNA replication group in the <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).