d5932e4051a4885f0036831cdfc5fbf1eb08a499 lrnassar Tue Oct 10 17:16:27 2023 -0700 Fixing broken blog links, refs #32439 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 13e2a51..ca13f9c 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -894,31 +894,31 @@ <a href="../contacts.html" target="_blank">Genome Browser support emails</a>.</p> <a name="013023"></a> <h2>Jan. 30, 2023 Addition of GRCh38 patch 14 sequences to hg38</h2> <p> We are pleased to announce the addition of GRCh38 patch release 14 to the <a href="/cgi-bin/hgGateway?db=hg38">hg38</a> assembly. hg38 has been updated with patches since its release in 2013. The GRC patch releases do not change any previously existing sequences; they simply add new sequences for fix patches or alternate haplotypes that correspond to specific regions of the main chromosome sequences. For most users, the patches are unlikely to make a difference and may complicate the analysis as they introduce more duplication.</p> <p> More information on how patch sequences are incorporated can be found on the -<a href="http://genome.ucsc.edu/blog/patches/" target="_blank">Patching up the Genome</a> blog post. +<a href="https://genome-blog.gi.ucsc.edu/blog/patches/" target="_blank">Patching up the Genome</a> blog post. The blog post contains details about the new <a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/latest/" target="_blank">/latest</a>, <a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/initial/" target="_blank">/initial</a>, and <a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/p14/" target="_blank">/p14</a> download directories on the downloads server. With the addition of new sequences to hg38, we can expect to see BLAT return more matches to the genome.</p> <ul> <li> The <b>initial/</b> subdirectory contains files for the initial release of GRCh38, which has 455 sequences, 261 alternate sequences, and no fix sequences. It is the same as the parent download directory. This is probably the best genome file for aligners and most analysis tasks, a version called "analysisSet" for the human genome. @@ -2703,31 +2703,31 @@ can be found on the <a href="/cgi-bin/hgTrackUi?db=wuhCor1&g=variantMuts"> Variants of Concern (VOC) track description page</a>.</p> <a name="101221"></a> <h2>Oct. 18, 2021 Addition of GRCh38 patch 13 sequences to hg38</h2> <p> We are pleased to announce the addition of GRCh38 patch release 13 to the <a href="../../cgi-bin/hgGateway?db=hg38">hg38</a> assembly. hg38 has been updated with patches since its release in 2013. The GRC patch releases do not change any previously existing sequences; they simply add new sequences for fix patches or alternate haplotypes that correspond to specific regions of the main chromosome sequences. For most users, the patches are unlikely to make a difference and may complicate the analysis as they introduce more duplication.</p> <p> More information on how patch sequences are incorporated can be found on the -<a href="http://genome.ucsc.edu/blog/patches/" target="_blank">Patching up the Genome</a> blog post. +<a href="https://genome-blog.gi.ucsc.edu/blog/patches/" target="_blank">Patching up the Genome</a> blog post. The blog post contains details about the new <a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/latest/" target="_blank">/latest</a>, <a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/initial/" target="_blank">/initial</a>, and <a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/p13/" target="_blank">/p13</a> download directories on the downloads server. With the addition of new sequences to hg38, we can expect to see BLAT return more matches to the genome.</p> <ul> <li> The <b>initial/</b> subdirectory contains files for the initial release of GRCh38, which has 455 sequences, 261 alternate sequences, and no fix sequences. It is the same as the parent download directory. This is probably the best genome file for aligners and most analysis tasks, a version called "analysisSet" for the human genome. @@ -2821,31 +2821,31 @@ Mark Diekhans, and Jairo Navarro for the creation and release of this track. </p> <a name="080421"></a> <h2>Aug. 04, 2021 Addition of GRCm38 patch 6 sequences to mm10</h2> <p> We are pleased to announce the addition of GRCm38 patch release 6 to the mm10 assembly. mm10 has been updated with patches since its release in 2012. The GRC patch releases do not change any previously existing sequences; they simply add new sequences for fix patches or alternate haplotypes that correspond to specific regions of the main chromosome sequences. For most users, the patches are unlikely to make a difference and may complicate the analysis as they introduce more duplication.</p> <p> More information on how patch sequences are incorporated can be found on the -<a href="http://genome.ucsc.edu/blog/patches/" target="_blank">Patching up the Genome</a> blog post. +<a href="https://genome-blog.gi.ucsc.edu/blog/patches/" target="_blank">Patching up the Genome</a> blog post. The blog post contains details about the new <a href="https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/latest/" target="_blank">/latest</a>, <a href="https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/initial/" target="_blank">/initial</a>, and <a href="https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/p6/" target="_blank">/p6</a> download directories on the downloads server. With the addition of new sequences to mm10, we can expect to see BLAT return more matches to the genome.</p> <ul> <li> The <b>initial/</b> subdirectory contains files for the initial release of GRCm38, which has 66 sequences, no original alternate sequences, and no fix sequences. It is the same as the parent download directory. This is probably the best genome file for aligners and most analysis tasks, a version called "analysisSet" for the human genome. @@ -3012,31 +3012,31 @@ defining hub settings has been updated from version two to version three. This document primarily serves as a library of settings that users can refer to when they are setting up and configuring their own track hubs. The update in the version is to account for two new sections that highlight the new <a href="help/bigLolly.html">bigLolly</a> type specialized for variant data and the new <a href="help/vcf.html#trio" >vcfPhasedTrio</a> type specialized for phased VCF data.</p> <p> The new specifications for these types are included in their relevant sections such as <code>vcfChildSample</code> and <code>vcfUseAltSampleNames</code> for the new <a href="help/trackDb/trackDbHub.html#vcfPhasedTrio" target="_blank">vcfPhasedTrio settings</a>, or <code>lollySizeField</code> and <code>lollyField</code> for the new <a href="help/trackDb/trackDbHub.html#bigLolly" target="_blank">bigLolly settings</a> with full descriptions in the document.</p> <p> The Track Database Definition Document also serves a second function beyond defining settings as providing a versioned specification for those sites that support and display data from track hubs -such as Ensembl and NCBI. See this <a href="http://genome.ucsc.edu/blog/how-portable-is-your-track-hub-use-hubcheck-to-find-out/" +such as Ensembl and NCBI. See this <a href="https://genome-blog.gi.ucsc.edu/blog/how-portable-is-your-track-hub-use-hubcheck-to-find-out/" target="_blank">blog post</a> to learn more about this second element of the document and using the hubCheck utility to gain an idea of how your hub's settings might work on different sites.</p> <a name="062421"></a> <h2>June 24, 2021 New REVEL missense scores track for hg38 and hg19</h2> <p> The UCSC Genome Browser has just added the REVEL tracks to the hg38 and hg19 reference genomes. This much requested clinical dataset is now visualized and interactive on the Genome Browser. REVEL scores predict the pathogenicity of missense variants for every possible basepair change across the entire genome's coding sequences. This dataset bases its scores on 13 individual tools to produce high predictive performance of common and rare mutations. To learn more about the REVEL dataset, please visit their site below:</p> <ul> <li><a href="https://sites.google.com/site/revelgenomics/" target="_blank"> @@ -6570,31 +6570,31 @@ <a name="031720"></a> <h2>Mar. 17, 2020 New mitochondrial sequence for human (hg19)</h2> <p> We are pleased to announce the release of a patch to the hg19 assembly that will introduce a new mitochondrial sequence, <a href="../../cgi-bin/hgTracks?db=hg19&position=chrMT:4277-5648" target="_blank">chrMT</a>, to the assembly. We used GenBank sequence NC_001807 for chrM in hg19 and earlier, but the sequence preferred by the community is the revised Cambridge Reference Sequence (rCRS), <a href="https://www.ncbi.nlm.nih.gov/nuccore/251831106" target="_blank">NC_012920</a>. The new chrMT is the rCRS, NC_012920. <a href="https://www.ncbi.nlm.nih.gov/grc/help/patches/" target="_blank">Patch sequences</a> from <a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_000001405.14" target="_blank">GRCh37.p13</a> have also been added to hg19.</p> <p> More information on how patch sequences are incorporated can be found on the -<a href="http://genome.ucsc.edu/blog/patches/" target="_blank">Patching up the Genome</a> blog post. +<a href="https://genome-blog.gi.ucsc.edu/blog/patches/" target="_blank">Patching up the Genome</a> blog post. The blog post contains details about the new <a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/latest/" target="_blank">/latest</a> download directory on the downloads server. With the addition of new sequences to hg19, we can expect to see BLAT return more matches to the genome.</p> <p> Also, with these patches, the hg19 genome is not optimal anymore for aligners. So we added an "<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/analysisSet/" target="_blank">analysis set</a>" version of the hg19 genome fasta file to our <a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/" target="_blank">bigZips</a> directory, and indexes for BWA, Bowtie2, and Hisat2.</p> <p> We would like to thank the Genome Reference Consortium for creating the patches to hg19. We would also like to thank Angie Hinrichs and Jairo Navarro at UCSC for implementing and testing the latest patch to hg19.</a> @@ -7767,33 +7767,33 @@ <h2> Mar. 11, 2019 Addition of GRCh38 patch sequences to hg38 </h2> <p> We are pleased to announce the addition of GRCh38 patches to the GRCh38/hg38 database. <a href="https://www.ncbi.nlm.nih.gov/grc/human" target="_blank">Without a release date</a> for the next coordinate-changing assembly, incorporating these sequences is an important step towards providing the most up to date human assembly.</p> <p> This release includes new tracks visualizing patch sequences; the <a href="../cgi-bin/hgTrackUi?db=hg38&g=fixSeqLiftOverPsl" target="_blank">Fix Patches</a> track represents error corrections, and the <a href="../cgi-bin/hgTrackUi?db=hg38&g=altSeqLiftOverPsl" target="_blank">Alt Haplotypes</a> track represents novel patches (alt loci).</p> <p> -Additional information can be found on our <a href="http://genome.ucsc.edu/blog/patches/" +Additional information can be found on our <a href="https://genome-blog.gi.ucsc.edu/blog/patches/" target="_blank">Genome Browser blog</a> including a specific section detailing <a -href="http://genome.ucsc.edu/blog/patches/#changes" target="_blank">what changes to expect</a>.</p> +href="https://genome-blog.gi.ucsc.edu/blog/patches/#changes" target="_blank">what changes to expect</a>.</p> <p class="text-center"> <img class='text-center' src="../images/patches.jpg" alt="Patches increase"> <p class="gbsCaption text-center">The number of human assembly patch sequences is quickly growing. This is primarily due to alternative haplotypes (_alt) sequences, though fix sequences (_fix) are also being introduced. The fix patches reset from GRCh37.p13 to GRCh38 as they were integrated into the assembly.</p> <p> We would like to thank Angie Hinrichs and Lou Nassar for their work on this release.</p> <a name="030519"></a> <h2> Mar. 05, 2019 Single cell data from Tabula Muris available for mouse (mm10) </h2> <p> @@ -8162,31 +8162,31 @@ We would like to thank the <a href="https://www.gencodegenes.org/" target="_blank">GENCODE Project</a> for providing the data. The creation of this track was made possible thanks to Brian Raney, Mark Diekhans, and Jairo Navarro.</p> <a name="111318"></a> <h2>Nov. 13, 2018 New video: Saving and Sharing Sessions </h2> <p> We are pleased to announce the release of another video tutorial, <a href = "https://www.youtube.com/watch?v=d5rHBLXwraM&feature=youtu.be&feature=player_detailpage&v=8ATcoDTOc0g&list=UUQnUJepyNOw0p8s2otX4RYQ" target = _blank>Saving and sharing sessions</a>. The Saved Sessions feature of the Browser has been around for quite some time, but many of our users have not made full use of it. It offers a great way to keep track of your thinking on a particular topic and -has also been discussed in our <a href = "http://genome.ucsc.edu/blog/2015/08/" +has also been discussed in our <a href = "https://genome-blog.gi.ucsc.edu/blog/2015/08/" target = blank>blog</a>. </p> <p> This <a href = "https://www.youtube.com/watch?v=d5rHBLXwraM&feature=youtu.be&feature=player_detailpage&v=8ATcoDTOc0g&list=UUQnUJepyNOw0p8s2otX4RYQ" target = _ blank>video</a> shows how to create an account, how to save sessions for easy future access, how to share sessions with colleagues and how to make a public session that you can share with all Genome Browser users. The video comes with a full <a href = "../training/vids/transcript16.pdf" target = blank>transcript</a> </p> @@ -8612,31 +8612,31 @@ <li>RefSeq All – all annotations from the curated and predicted sets <li>RefSeq Curated – curated annotations beginning with NM, NR, or NP <li>RefSeq Predicted – predicted annotations beginning with XM or XR <li>RefSeq Other – all other RefSeq annotations not included in RefSeq All <li>RefSeq Alignments – alignments of transcripts to the genome provided by RefSeq </ul> <p> The new composite track also includes a "UCSC RefSeq" track that is based on our original "RefSeq Genes" track. As with before, this UCSC track is a result of our realignments of RefSeq RNAs to the genome, which means that there may be some cases where the annotations differ from those in the new NCBI RefSeq tracks. Also note that the <em>Predictions</em> subtrack is unavailable for the following assemblies: hg19, dm6, ce11, and sacCer3.</p> <p> More details about these tracks, their construction, and how to access their underlying data can be found on -<a href="http://genome.ucsc.edu/blog/the-new-ncbi-refseq-tracks-and-you/" +<a href="https://genome-blog.gi.ucsc.edu/blog/the-new-ncbi-refseq-tracks-and-you/" target="_blank">this blog post</a>.</p> <p> A huge thank you to Terence Murphy from the RefSeq group and to Hiram Clawson, Angie Hinrichs, Christopher Lee and many others from the UCSC Genome Browser staff for bringing this track to life.</p> <a name="040318"></a> <h2>Apr. 03, 2018 New genome browser tool: Track Collection Builder</h2> <p> We are pleased to announce a new tool in the UCSC Genome Browser:</p> <p> The <a href="../cgi-bin/hgCollection" target="_blank">Track Collection Builder</a> (My Data > Track Collection Builder) is a tool that allows multiple tracks to be copied and grouped together into one composite track or "collection". A <a href="../goldenPath/help/trackDb/trackDbHub.html#compositeTrack" target="_blank"> @@ -9246,31 +9246,31 @@ <ul> <li>RefSeq All – all annotations from the curated and predicted sets <li>RefSeq Curated – curated annotations beginning with NM, NR, or NP <li>RefSeq Predicted – predicted annotations beginning with XM or XR <li>RefSeq Other – all other RefSeq annotations not included in RefSeq All <li>RefSeq Alignments – alignments of transcripts to the genome provided by RefSeq </ul> <p> The new composite track also includes a "UCSC RefSeq" track that is based on our original "RefSeq Genes" track. As with before, this UCSC track is a result of our realignments of RefSeq RNAs to the genome, which means that there may be some cases where the annotations differ from those in the new NCBI RefSeq tracks.</p> <p> More details about these tracks, their construction, and how to access their underlying data can be found on -<a href="http://genome.ucsc.edu/blog/the-new-ncbi-refseq-tracks-and-you/" +<a href="https://genome-blog.gi.ucsc.edu/blog/the-new-ncbi-refseq-tracks-and-you/" target="_blank">this blog</a> or the <a href="../../cgi-bin/hgTrackUi?db=mm10&g=refSeqComposite">track description page</a>.</p> <p> A huge thank you to Terence Murphy from the RefSeq group and to Hiram Clawson, Brian Raney, Mark Diekhans, Angie Hinrichs, Jairo Navarro and many others from the UCSC Genome Browser staff for bringing this track to life.</p> <a name="111517"></a> <h2>Nov. 15, 2017 New genome browser: African clawed frog, xenLae2 <em> (Xenopus laevis)</em> </h2> <p>Please welcome <a href="../cgi-bin/hgGateway?db=xenLae2" target="_blank" >xenLae2</a>, the 192nd genome assembly in the UCSC Genome Browser. This is the first assembly for the African clawed frog <em>(Xenopus laevis)</em>.</p> <h3>About the assembly:</h3> <ul> @@ -9793,31 +9793,31 @@ Thanks to Kate Rosenbloom, Christopher Eisenhart and Christopher Lee for the development and testing of this new track format. </p> <a name="060817"></a> <h2>Jun. 8, 2017 New command line tool for annotating variants, vai.pl</h2> <p> We are pleased to announce the release of a new command-line tool for annotating variants, <code>vai.pl</code>. This program is similar to our web-based <a href="../../cgi-bin/hgVai">Variant Annotation Integrator (VAI)</a>, except it allows for bypassing the variant limit imposed by web-based VAI, and does not require connections to UCSC, allowing annotation of private clinical data.</p> <p> Along with the release of this program, we have published a -<a href="http://genome.ucsc.edu/blog/annotating-millions-of-private-variants-with-vai-pl/"> +<a href="https://genome-blog.gi.ucsc.edu/blog/annotating-millions-of-private-variants-with-vai-pl/"> new blog post</a> with some background on both web-based and command-line VAI, as well as some example usage to serve users. <code>vai.pl</code> is available for download from the <a href="https://genome-store.ucsc.edu">genome-browser store</a>, via purchase of the GBiB, GBiC, or full source. </p> <p> Thanks to Angie Hinrichs and Christopher Lee for the development and testing of the program.</p> <a name="060617"></a> <h2>Jun. 6, 2017 New genome browser available for ciona intestinalis</h2> <p> A genome browser is now available for the ciona intestinalis(<em>vase tunicate</em>) assembly released in April 2011 by The Graduate School of Science, Kyoto University. For more information and statistics @@ -9828,31 +9828,31 @@ 115,227,500 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/ci3/">FTP server</a> or the <a href="http://hgdownload.soe.ucsc.edu/downloads.html#ciona">Downloads</a> page. Please observe the <a href="credits.html#ciona">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#ciona_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="060217"></a> <h2>Jun. 2, 2017 New default tracks for human and mouse assemblies</h2> <p> We have made several changes to the sets of default tracks for some of our human and mouse assemblies. The -<a href="http://genome.ucsc.edu/blog/gtex-resources-in-the-browser/" target="_blank">GTEx +<a href="https://genome-blog.gi.ucsc.edu/blog/gtex-resources-in-the-browser/" target="_blank">GTEx Gene Expression</a> track is now part of the set of default tracks for both human genome assemblies hg38 and hg19. In addition, we have added the <a href="../../cgi-bin/hgTrackUi?db=hg19&g=dgvPlus">DGV Struct Var</a> track, which displays large structural variant such as CNVs, inversions and in/dels, to the default track set for the human genome assembly hg19. Lastly, for the mouse genome assembly mm10, we have added the <a href="../../cgi-bin/hgTrackUi?db=mm10&g=cons60way">60-way Vertebrate Conservation</a> track to its set of default tracks.</p> <a name="051617"></a> <h2>May 16, 2017 New genome browser available for golden eagle</h2> <p> A genome browser is now available for the golden eagle (<em>Aquila chrysaetos canadensis</em>) assembly released in October 2014 by Washington University. For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_000766835.1/" target="_blank">Aquila_chrysaetos-1.0.2</a>. @@ -10031,31 +10031,31 @@ <p> We're happy to announce the recent release of Version 2 of our <a href="help/trackDb/trackDbHub.html">Track Database Definition Document</a>. This document includes all of the currently supported track configuration options (trackDb) for track and assembly hubs in the UCSC Genome Browser.</p> <p> This latest version includes settings for our latest "big" track types: bigMaf, bigChain, bigPsl, and bigGenePred, as well as the "CRAM" track type. This newest version also marks the movement of some trackDb settings (html, priority, colorByStrand, autoScale, spectrum) from the "full" to the "base" support level to indicate that they are supported by other genome browsers. At this time, it is primarily Ensembl that supports the use of these new "base" settings in track hubs on their site.</p> <p> Additionally, we have published a -<a href="http://genome.ucsc.edu/blog/how-portable-is-your-track-hub-use-hubcheck-to-find-out/">new +<a href="https://genome-blog.gi.ucsc.edu/blog/how-portable-is-your-track-hub-use-hubcheck-to-find-out/">new blog post</a> that discusses the versioning of these trackDb settings and how you can use hubCheck to see if your hubs are compatible with other genome browsers. We have also added examples to our <a href="help/hgTrackHubHelp.html#Compatibility">help documentation</a> that show how to use hubCheck to test track hub compatibility.</p> <a name="031517a"></a> <h2>Mar. 15, 2017 New Genome Browsers available for Golden Snub-Nosed Monkey, Proboscis Monkey, and Turkey</h2> <p> A Genome Browser is now available for the Golden Snub-Nosed Monkey (<em>Rhinopithecus roxellana</em>) assembly released in October 2014 by Novogene. For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_000769185.1/" target="_blank">Rrox_v1</a>. There are 196,797 contigs and 135,512 scaffolds in this assembly with a total size of 2,899,552,139 bases.</p> @@ -10113,31 +10113,31 @@ <ul> <li>RefSeq All – all annotations from the curated and predicted sets <li>RefSeq Curated – curated annotations beginning with NM, NR, or YP <li>RefSeq Predicted – predicted annotations beginning with XM or XR <li>RefSeq Other – all other RefSeq annotations not included in RefSeq All <li>RefSeq Alignments – alignments of transcripts to the genome provided by RefSeq </ul> <p> The new composite track also includes a "UCSC RefSeq" track that is based on our original "RefSeq Genes" track. As with before, this UCSC track is a result of our realignments of RefSeq RNAs to the genome, which means that there may be some cases where the annotations differ from those in the new NCBI RefSeq tracks.</p> <p> More details about these tracks, their construction, and how to access their underlying data can be found in -<a href="http://genome.ucsc.edu/blog/the-new-ncbi-refseq-tracks-and-you/" +<a href="https://genome-blog.gi.ucsc.edu/blog/the-new-ncbi-refseq-tracks-and-you/" target="_blank">this blog</a> or on the <a href="../../cgi-bin/hgTrackUi?db=hg38&g=refSeqComposite">track description page</a>. </p> <p> A huge thank you to Terence Murphy from the RefSeq group and to Hiram Clawson, Brian Raney, Mark Diekhans, Matthew Speir and many others from the UCSC Genome Browser staff for bringing this track to life.</p> <a name="021617"></a> <h2>Feb. 13, 2017 New keyboard shortcuts for browser zoom views</h2> <p> Please welcome the newest additions to the UCSC Genome Browser keyboard shortcuts menu, now providing over 40 shortcuts. To view a menu of shortcuts, simply press the "?" key on your keyboard while on an assembly's browser display page (e.g., <a href="../cgi-bin/hgTracks?db=hg38" target="_blank">GRCh38/hg38 assembly display</a>). @@ -10526,31 +10526,31 @@ <p> The Genome Browser <a href="../cgi-bin/hgSession">session management</a> page has also received an update with the release of the new Public Sessions page. Sessions are now arranged in a table, where varying numbers of sessions can be displayed on a page of this table. Sessions can now be filtered and ordered based on session name, primary assembly, and creation date. Clicking on the session name now displays that session in the Genome Browser. Session details, such as the name or the description, can be changed using the "details" button in the new table layout.</p> <p> The release of the new Public Sessions page also marks a change in our session expiration policy. We no longer expire sessions and associated custom tracks four months after their last use. Please note, however, that the UCSC Genome Browser is not a data storage service and that we encourage you to keep local copies of your session contents and custom track data.</p> <p> For more information about using sessions to share snapshots of the UCSC Genome Browser, please see the <a href="help/hgSessionHelp.html">User Guide</a> or our blog post, -<a href="http://genome.ucsc.edu/blog/how-to-share-your-ucsc-screenthoughts/" +<a href="https://genome-blog.gi.ucsc.edu/blog/how-to-share-your-ucsc-screenthoughts/" target="_blank">How to share your UCSC screenthoughts</a>.</p> <p> Thanks to Jonathan Casper and Matthew Speir for their work on this new tool.</p> <a name="061516"></a> <h2>Jun. 15, 2016 New supported Asian mirror site released</h2> <p> We are pleased to announce the introduction of a new supported Genome Browser mirror to serve our users in Asia. The genome-asia server <a href="http://genome-asia.ucsc.edu" target="_blank">(http://genome-asia.ucsc.edu)</a>, which is administered by UCSC, is physically located at the <a href="http://www.yokohama.riken.jp/english/" target="_blank">RIKEN Yokohama Campus</a> in Japan.</p> <p> Genome-asia is intended as an alternate, faster access point for those Browser users who are geographically closer to Asia than to the western United States. The mirror @@ -11189,31 +11189,31 @@ PHAST package for all species. The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. Conserved elements identified by phastCons are also displayed in this track. For more details, visit the <a href="../cgi-bin/hgTrackUi?db=hg38&g=cons100way">track description page</a>.</p> <p> We would like to thank Hiram Clawson and Jonathan Casper for their efforts in creating this track.</p> <a name="081215"></a> <h2>Aug. 12, 2015 How to share your UCSC screenthoughts</h2> <p> Do you want to save your UCSC Browser screenthoughts, or share them with a colleague, or make a slide for a talk, or publish them in a paper? Saving the state of your screen can take two forms: static or dynamic. You can snap and save a picture of the screen, or you can share a link to an active Genome Browser. We talk about both approaches -<a href="http://genome.ucsc.edu/blog/how-to-share-your-ucsc-screenthoughts/" +<a href="https://genome-blog.gi.ucsc.edu/blog/how-to-share-your-ucsc-screenthoughts/" target="_blank">here</a> and discuss some of the advantages and pitfalls of each.</p> <a name="062915"></a> <h2>Jun. 29, 2015 GENCODE Genes now the default gene set on the Human (GRCh38/hg38) assembly</h2> <p> In a move towards standardizing on a common gene set within the bioinformatics community, UCSC has made the decision to adopt the GENCODE set of gene models as our default gene set on the human genome assembly. Today we have released the GENCODE v22 comprehensive gene set as our default gene set on human genome assembly GRCh38 (hg38), replacing the previous default UCSC Genes set generated by UCSC. To facilitate this transition, the new gene set employs the same familiar UCSC Genes schema, using nearly all the same table names and fields that have appeared in earlier versions of the UCSC set. </p> <p> By default, the browser displays only the transcripts tagged as "basic" by the GENCODE @@ -11496,31 +11496,31 @@ UDR establishes connections on TCP/9000, then transmits the data stream over UDP/9000-9100. Your institution may need to modify its firewall rules to allow inbound and outbound ports TCP/9000 and UDP/9000-9100 from either of the two download machines.</p> <p> If you decide to install and use UDR, we hope that you experience greatly increased download speeds. If you have difficulties installing UDR on your system, please contact the Laboratory for Advanced Computing through their github page: <a href="https://github.com/LabAdvComp/UDR" target="_blank">https://github.com/LabAdvComp/UDR</a>.</p> <a name="022615"></a> <h2>Feb. 26, 2015 New training video</h2> <p> Ever wondered how to find the tables associated with your favorite Browser track? Find out how in our new training video. See our <a href="../training/index.html" target="_blank">training page</a>, our <a href="http://bit.ly/genomebrowserYoutube" target=_"blank">YouTube channel</a>, and our -<a href="http://genome.ucsc.edu/blog/introducing-the-genome-browser-youtube-channel/" +<a href="https://genome-blog.gi.ucsc.edu/blog/introducing-the-genome-browser-youtube-channel/" target="_blank">blog</a> for details.</p> <a name="021215"></a> <h2>Feb. 12, 2015 Blat your assembly hub</h2> <p> Assembly data hubs, track hubs that allow researchers to annotate genomes that are not in the UCSC Genome Browser, can now use blat to quickly find DNA and protein sequences in their unique assemblies.</p> <p> While running remote blat servers with the gfServer utility, you can now add lines to your assembly hub's genomes.txt file to inform the Browser where to send blat searches. Or by downloading and installing a virtual machine Genome Browser In a Box <a href="help/gbib.html" target="_blank">(GBiB)</a>, you can alternatively locally run gfServers, preinstalled on GBiB, all from your laptop. For more information see the <a href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs" target="_blank">Assembly Hub Wiki</a> @@ -11667,31 +11667,31 @@ genomics data that you would like to view securely on your own laptop in the context of the UCSC Genome Browser, GBiB is for you.</p> <p> GBiB is an easy-to-install personal copy of the Genome Browser that comes preloaded with the most popular annotation tracks for human. It is highly configurable — you can access or download other annotation tracks of interest, or view any of the other 90+ organisms featured in the public Genome Browser. GBiB runs inside of Oracle's free VirtualBox virtual machine. It has the same core functionality as the UCSC Genome Browser, but keeps your data private and local to your own computer.</p> <p> GBiB is free for non-profit academic research and for personal use. Commercial use requires purchase of a license with setup fee and annual payment. Download or purchase GBiB in our secure online <a href="https://genome-store.ucsc.edu/">store</a>.</p> <p> You can read more about GBiB on our -<a href="http://genome.ucsc.edu/blog/genome-browser-in-a-box-gbib-origins/">blog</a> or in +<a href="https://genome-blog.gi.ucsc.edu/blog/genome-browser-in-a-box-gbib-origins/">blog</a> or in our <a href="help/gbib.html">documentation</a>.</p> <a name="102014"></a> <h2>Oct. 20, 2014 dbSNP 141 available for hg19 and hg38</h2> <p> We are pleased to announce the release of four tracks derived from NCBI <a href="https://www.ncbi.nlm.nih.gov/SNP/" target="_blank">dbSNP</a> Build 141 data, available on the two most recent human assemblies GRCh37/hg19 and GRCh38/hg38. The new tracks contain additional annotation data not included in previous dbSNP tracks, with corresponding coloring and filtering options in the Genome Browser.</p> <p> There are three SNP tracks available for the GRCh37/hg19 assembly. One is a track containing all mappings of reference SNPs to the human assembly, labeled "All SNPs (141)". The other two tracks are subsets of this track and show interesting and easily defined subsets of dbSNP:</p> <ul> @@ -11718,31 +11718,31 @@ By default, only the Common SNPs (141) are visible; other tracks must be made visible using the track controls. You will find the other SNPs (141) tracks on both of GRCh37/hg19 and GRCh38/hg38 browsers in the Variation group.</p> <p> The tracks were produced at UCSC by Angie Hinrichs and Matthew Speir. We'd like to thank the dbSNP group at NCBI for providing access to these data.</p> <a name="100714"></a> <h2>Oct. 7, 2014 Introducing the UCSC Genome Browser blog</h2> <p> We're excited to introduce a new <a href="http://genome.ucsc.edu/blog" target="_blank">blog</a> that will feature posts by Genome Browser staff and guests. On the blog we'll be publishing in-depth information about UCSC Genome Browser features, tools, projects and related topics that we hope people will find both useful and interesting. We just published our inaugural post written by Jim Kent, the UCSC Genome Browser Architect and PI, on the -<a href="http://genome.ucsc.edu/blog/2014-ebola-epidemic/" target="_blank">2014 Ebola +<a href="https://genome-blog.gi.ucsc.edu/blog/2014-ebola-epidemic/" target="_blank">2014 Ebola Epidemic</a>.</p> <p> If you have a suggestion for a blog post topic, please let us know via our <a href="/cgi-bin/hgUserSuggestion">suggestion box</a>.</p> <a name="093014"></a> <h2>Sep. 30, 2014 Genome Browser and portal released for the Ebola Virus</h2> <p> We are excited to announce the release of a Genome Browser and information portal for the Jun. 2014 assembly of the Ebola virus (UCSC version eboVir3, GenBank accession <a href="https://www.ncbi.nlm.nih.gov/nuccore/KM034562" target="_blank">KM034562</a>) submitted by the Broad Institute. We have worked closely with the Pardis Sabeti lab at the Broad Institute and other Ebola experts throughout the world to incorporate annotations that will be useful to those studying Ebola. Annotation tracks included in this initial release include genes from <a href="https://www.ncbi.nlm.nih.gov/"