Uploads by Hiram

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This special page shows all uploaded files.

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Date Name Thumbnail Size Description Versions
18:56, 4 November 2022 BME-18.2022-11-04.pptx (file) 8.59 MB   1
00:11, 15 October 2022 Mac background Catalina.png (file) 6.2 MB test upload function and thumbnail 1
18:46, 15 September 2022 Hg38.grcIncidentDb.bb (file) 282 KB gwUploadFile upload 359
16:33, 28 June 2022 DanRer11.grcIncidentDb.bb (file) 202 KB gwUploadFile upload 17
16:33, 28 June 2022 DanRer10.grcIncidentDb.bb (file) 126 KB gwUploadFile upload 127
16:33, 28 June 2022 Mm9.grcIncidentDb.bb (file) 74 KB gwUploadFile upload 282
16:33, 28 June 2022 DanRer7.grcIncidentDb.bb (file) 111 KB gwUploadFile upload 336
16:33, 28 June 2022 Mm10.grcIncidentDb.bb (file) 101 KB gwUploadFile upload 289
16:33, 28 June 2022 Hg19.grcIncidentDb.bb (file) 106 KB gwUploadFile upload 867
22:32, 20 May 2021 VGP 2021-05-21.pptx (file) 1.24 MB VGP meeting 2021-05-21 presentation, VGP assembly resources in the UCSC genome browser 1
17:24, 3 September 2019 GalGal6.grcIncidentDb.bb (file) 19 KB gwUploadFile upload 1
00:56, 19 May 2019 NationalYoYoMuseum ChicoCA 50.jpg (file) 553 KB National YO YO Museum, Chico CA 1
17:33, 30 January 2019 GalGal5.grcIncidentDb.bb (file) 27 KB gwUploadFile upload 7
21:54, 1 October 2018 AwsAttachVolume.sh.txt (file) 4 KB Script for AWS instance initialization to attach a data volume to a running instance. Used in the startParaHub.sh script upon starting the machine. 1
17:35, 26 September 2018 OpenStackParaHubSetup.sh.txt (file) 8 KB reorganize NFS setups, parameterize the installation directory 5
17:10, 26 September 2018 InitParasol.sh.txt (file) 3 KB less restrictive subnet specification and separate hub/node logs in ./logs/ directory 3
20:32, 25 September 2018 NodeReport.sh.txt (file) 1 KB add usage message and directory argument for result file 4
17:42, 11 July 2018 OpenStackParaNodeSetup.sh.template.txt (file) 4 KB correctly fixup /mnt filesystem for broken openstack installation, and mount /mnt/data from the hub 2
17:09, 28 April 2018 LastzProcessingTimeHistogram.png (file) 53 KB lastz cluster compute time histogram 1,635 measurements from alignments performed at UCSC 459 measurements are less than 0.05 days (less than 1 hour) due to very small genome sizes 59 measurements are longer than 5 days processing time due to high c... 1
23:13, 27 April 2018 SizeVsTime.png (file) 156 KB lastz cluster run processing time vs. genome size blue points plot times 2 days or less processing time, left axis scale 0 - 2 days red points plot times over 2 days processing time, right axis scale 0 - 70 days 1
02:53, 6 April 2018 ParasolInstall.sh.txt (file) 1 KB adding git fetch of automation scripts into /data/scripts/ 3
22:10, 28 September 2017 GenbankPrimates.jpg (file) 113 KB primate phylogenetic tree from genbank taxIds Given a set of taxon IDs, utilizing [http://phylot.biobyte.de/ phylot.biobyte.de] to derive this phylogenetic tree. NOTE: not necessarily completely accurate. Image drawn by [http://itol.embl.de/ itol.embl. 1
18:17, 2 June 2017 Btrfs filesystem readWrite performance.png (file) 120 KB read/write performance test results for 'btrfs' filesystem 1
22:48, 31 May 2017 Xfs filesystem readWrite performance.png (file) 97 KB testing read/write performance on xfs filesystem in a directory overloaded with up to 7 million files 1
22:47, 31 May 2017 Tmpfs filesystem readWrite performance.png (file) 101 KB testing read/write performance into a /dev/shm directory overloaded with up to 7 million files 1
22:45, 31 May 2017 Ext4 fs readWrite performance.png (file) 106 KB writing over 7 million files into one directory to see how performance degrades. 1
18:26, 26 January 2017 BME230 Winter 2017.ppt (file) 12.98 MB (Hiram's presentation to BME230 Winter 2016 12 January - brief browser usage introduction, assembly hub demonstration, table browser intersection, plus information on source code but not part of the discussion) 1
05:39, 9 June 2016 BejeranoLab 2016-06-09.pptx (file) 2.92 MB   2
18:22, 12 January 2016 BME230 Winter 2016.ppt (file) 13.8 MB (Hiram's presentation to BME230 Winter 2016 12 January - brief browser usage introduction, assembly hub demonstration, table browser intersection, plus information on source code but not part of the discussion)) 1
17:43, 19 March 2015 MatrixSummary pl.txt (file) 6 KB used in lastz tuning procedure, examines output of the four lastz_D outputs to survey the differences 1
17:17, 19 March 2015 Create scores file control.txt (file) 653 bytes Parameters from Bob Harris for lastz tuning procedure 1
17:14, 19 March 2015 Expand scores file py.txt (file) 4 KB Script created by Bob Harris for lastz tuning operations 1
17:10, 19 March 2015 AdjustSizes pl.txt (file) 3 KB chrom.sizes files are now expected to exist as created by selectedFasta.sh 2
17:09, 19 March 2015 SelectedFasta sh.txt (file) 2 KB generalize the chrom.size creation and noMask option on fasta creation 2
23:34, 18 March 2015 TopAll sh.txt (file) 2 KB script used in lastz tuning procedure to run lastz_D on different sets of DNA sequences from query and target 1
23:18, 18 March 2015 MafScoreSizeScan pl.txt (file) 2 KB script used to scan a MAF file to extract scores, sizes, and coverage statistics of each alignment block. Used in lastz tuning procedures. 1
20:59, 4 February 2014 BME230 Winter 2014.ppt (file) 13.79 MB Hiram's presentation to BME230 Winter 2014 11 February - brief browser usage introduction, assembly hub demonstration, table browser intersection, plus information on source code but not part of the discussion) 1
22:36, 6 June 2013 AssemblyHubs BoG 2013.pptx (file) 2.72 MB Assembly Hubs, Biology of Genomes meeting 2013 CSHL 1
22:35, 6 June 2013 AssemblyHubs BoG 2013.pdf (file) 3.06 MB Assembly Hubs, Biology of Genomes meeting 2013 CSHL 1
05:43, 13 March 2013 SameSpeciesChainNet.sh.txt (file) 5 KB Same species lift over, step 2 of 2, chain/net the blat psl results together into the result file 1
05:04, 13 March 2013 BlatJob.csh.txt (file) 2 KB script to use for the same species lift over procedure run.blat/ step 1 1
04:57, 13 March 2013 SameSpeciesBlatSetup.sh.txt (file) 6 KB First step in the same species lift over procedure, set up for blat run, adding 11.ooc file construction for blat 2
02:56, 29 June 2012 FireCracker10KElevationProfile.png (file) 6 KB Elevation profile for the Santa Cruz FireCracker 10K run, July 4th. Corrected the GPS readings with Google Earth information and known ground truth. 2
16:44, 27 April 2012 DanRer7.ncbiIncidentDb.bb (file) 168 KB gwUploadFile upload 27
16:43, 27 April 2012 Mm9.ncbiIncidentDb.bb (file) 136 KB gwUploadFile upload 80
16:43, 27 April 2012 Hg19.ncbiIncidentDb.bb (file) 179 KB gwUploadFile upload 67
21:27, 25 January 2012 BME230 Winter 2012.ppt (file) 7.31 MB Hiram's presentation to BME230 Winter 2012 26 January 2012 - brief browser usage introduction, table browser intersection, plus information on source code but not part of the discussion 1
21:51, 5 October 2011 XLDB 2011.pptx (file) 1.23 MB bigBed/bigWig 5 minute presentation at XLDB conference, Stanford, 18 October 2011. 2
18:48, 24 August 2011 Sol GCBias GeneCats 2011-08-24.pdf (file) 1.4 MB Sol Katzman presentation, genecats 24 Aug 2011 1
16:43, 24 June 2011 ExtractRepeats.txt (file) 2 KB Small perl script used to extract lineage specific repeats from RepeatMasker .out files 1
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