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/encodeUvaDnaRepSuper.html src/hg/makeDb/trackDb/human/encodeUvaDnaRepSuper.html
index 036a0a85ea4..2db59e6a7b2 100644
--- src/hg/makeDb/trackDb/human/encodeUvaDnaRepSuper.html
+++ src/hg/makeDb/trackDb/human/encodeUvaDnaRepSuper.html
@@ -1,43 +1,43 @@
 <H2>Overview</H2>
 <P>
 This super-track combines related tracks of DNA
 replication data from the University of Virginia.
 DNA replication is carefully coordinated, both across the genome and with
 respect to development. Earlier replication in S-phase is broadly correlated
 with gene density and transcriptional activity. </P>
 <P>
 These tracks contain temporal profiling of DNA replication and
 origin of DNA replication in multiple cell lines, such as
 <A HREF= "https://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CCL-2&Template=cellBiology"
 TARGET=_blank>HeLa</A> cells (cervix carcinoma). Replication timing was measured by
 analyzing Brd-U-labeled fractions from synchronized cells on tiling arrays.</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>
 Giacca M, Pelizon C, Falaschi A.
 <A HREF="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=9441856&query_hl=7"
 TARGET=_blank>Mapping replication origins by quantifying relative abundance
 of nascent DNA strands using competitive polymerase chain reaction</A>.
 <em>Methods</em>. 1997 Nov;13(3):301-12.</P>
 <P>
 Mesner LD, Crawford EL, Hamlin JL.
 <A HREF="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16507369&query_hl=4"
 TARGET=_blank>Isolating apparently pure libraries of replication origins
 from complex genomes</A>. <em>Mol Cell</em>. 2006 Mar 3;21(5):719-26.</P>
 <P>
 Jeon Y, Bekiranov S, Karnani N, Kapranov P, Ghosh S, MacAlpine D, Lee C,
 Hwang DS, Gingeras TR, 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>. 2005 May 3;102(18):6419-24. </P>