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/allenBrainAli.html src/hg/makeDb/trackDb/allenBrainAli.html
index 23218d8e042..9e9dda28c9d 100644
--- src/hg/makeDb/trackDb/allenBrainAli.html
+++ src/hg/makeDb/trackDb/allenBrainAli.html
@@ -1,35 +1,35 @@
 <H2>Description</H2>
 <P>
 This track provides a link into the 
-<A HREF="http://portal.brain-map.org/" TARGET=_blank> Allen Brain Atlas</A> (ABA)
+<A HREF="https://brain-map.org/" TARGET=_blank> Allen Brain Atlas</A> (ABA)
 images for this probe.  The ABA is an extensive
 database of high resolution in-situ hybridization images of adult
 male mouse brains covering the majority of genes.</P>
 
 <H2>Methods</H2>
 <P>
 The ABA created a platform for high-throughput <em>in situ</em> hybridization 
 (ISH) that allows a highly systematic approach to analyzing gene expression in 
 the brain. ISH is a technique that allows the cellular localization of mRNA 
 transcripts for specific genes. Labeled antisense probes, specific to a 
 particular gene, are hybridized to cellular (sense) transcripts and subsequent 
 detection of the bound probe produces specific labeling in those cells 
 expressing the particular gene. This method involves tagged nucleotides 
 detected by colorimetric methods.</P>
 
 <P>The platform used for the ABA utilizes this non-isotopic approach, with 
 digoxigenin-labeled nucleotides incorporated into a riboprobe produced by <em>in
 vitro</em> transcription. This method produces a label that fills the cell body,
 in contrast to autoradiography that produces scattered silver grains surrounding
 each labeled cell. To enhance the ability to detect low level expression, the 
 ABA has incorporated a tyramide signal amplification step into the protocol that
 greatly increases sensitivity. The specific methodology is described in detail 
 within the <A HREF="https://community.brain-map.org/c/how-to/mouse-atlas/22"
 TARGET=_blank>ABA Data Production Processes document</A>.</P>
 
 <H2>Credits</H2>
 <P>
 Thanks to the <A HREF="https://alleninstitute.org/" TARGET=_blank>Allen 
 Institute for Brain Science</A> in general, and Susan 
 Sunkin in particular, for coordinating with UCSC on this annotation.</P>