b40a7e5ae9e72257e0c76bbe8124171b7dd97a35 kuhn Mon Aug 16 15:38:25 2010 -0700 removed older items diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html old mode 100755 new mode 100644 index c14c4d1..ae1b80f --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,172 +1,76 @@ <!--News Section-----------------------------------------------> <TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1"> <TR><TD> <TABLE BGCOLOR="#fffee8" WIDTH="100%" BORDER="0" CELLSPACING="0" CELLPADDING="0"> <TR><TD> <TABLE BGCOLOR="#D9E4F8" BACKGROUND="images/hr.gif" WIDTH="100%" BORDER=0> <TR><TD> <!--cheap trick to get background on row to be continuous--> <TABLE CELLPADDING=0 CELLSPACING=0 WIDTH="100%"> <TR><TD ALIGN="left"> <FONT SIZE="4"><A NAME="TOC"></A><B> News</B></FONT></TD> <TD ALIGN="right"><A HREF="goldenPath/newsarch.html"><IMG SRC="images/news.jpg" ALT="" ALIGN="right" BORDER=0></A> </TD></TR></TABLE> </TD></TR></TABLE> <TABLE BGCOLOR="#fffee8" WIDTH="100%" CELLPADDING=0> <TR><TH HEIGHT=3></TH></TR> <TR><TD WIDTH=10></TD> <TD> <P> To receive announcements of new genome assembly releases, new software features, updates and training seminars by email, subscribe to the <A HREF="https://lists.soe.ucsc.edu/mailman/listinfo/genome-announce" TARGET=_blank>genome-announce</A> mailing list.</P> <!-- start news --> <P> <FONT FACE="courier" SIZE="3"><B>23 July 2010 - BigBed/BigWig Paper Published</B></FONT> </P> <P>Last summer, we announced the release of new data formats for very large data sets: BigBed and BigWig. Read more about these data formats <A HREF="https://lists.soe.ucsc.edu/pipermail/genome-announce/2009-July/000165.html" TARGET=_blank>here</A>. As a follow up, we are pleased to announce that we have published a paper on these new file formats. <BLOCKQUOTE> Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. <A HREF="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq351" TARGET=_blank>BigWig and BigBed: enabling browsing of large distributed data sets.</A> <EM>Bioinformatics</EM>. 2010 July 17. Published online in advance of print. </BLOCKQUOTE> <P>From the abstract:<BR> BigWig and BigBed files are compressed binary indexed files containing data at several resolutions that allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser. The visualization is implemented using a multi-layered software approach that takes advantage of specific capabilities of web-based protocols and Linux and UNIX operating systems files, R trees, and various indexing and compression tricks. As a result, only the data needed to support the current browser view is transmitted rather than the entire file, enabling fast remote access to large distributed data sets.</P> <P>The supplemental materials (available online) contain the technical details about the implementation. </P><HR> <P> - <FONT FACE="courier" SIZE="3"><B>21 July 2010 - Free Genome Browser - workshops available </B></FONT> - </P> - <P>In the years since its introduction, the UCSC Genome Browser has - become an important tool for research and teaching. As it has grown - in capacity and therefore complexity, however, even experienced users - sometimes have - difficulty leaning how to make the most of it. - </P> - - <P>We plan to - provide a limited number of free browser training workshops at selected - institutions during the coming year. - We invite you to apply. - Please indicate your - interest by completing our survey: - <A HREF = "http://www.surveymonkey.com/s/XJF93F5" - TARGET = _BLANK><B>Apply for free workshop</B></A> - - </P><HR> - - <P> <FONT FACE="courier" SIZE="3"><B>15 July 2010 - Conservation track available for zebrafish (danRer6): </b></FONT> We are pleased to announce the release of a new Conservation track based on the zebrafish (danRer6) assembly. <A HREF="goldenPath/newsarch.html#071510">Read more</A>. - </P><hr> - - <P> - <FONT FACE="courier" SIZE="3"><B>7 July 2010 - Happy - 10th Birthday, Human Genome!</B></FONT> - <P><TABLE ALIGN = RIGHT><TR><TD ALIGN = RIGHT WIDTH = 519 - HEIGHT = 344> - <IMG SRC = "../../images/10yrGraph4.gif" - WIDTH = 504 HEIGHT = 329 ALIGN = RIGHT> - - </TD></TR> - <TR><TD ALIGN=RIGHT> - <FONT SIZE=-1> Top graph: total traffic on the UCSC - domain during June-July, 2000. Bottom graph: page hit <BR> - statistics on genome.ucsc.edu in the - ensuing years since the Genome Browser was released. - <BR> - </FONT> - </TD></TR></TABLE> - <P> - UCSC is pleased to celebrate the 10-year anniversary of the - debut of the first assembled human genome sequence and its - then-fledgling visualization tool, the UCSC Genome Browser. - Released on July 7, 2000, the genome sequence instantly - created unprecedented web traffic on the - ucsc.edu domain as researchers around the world - scrambled to download the data: 0.5 terabytes per day, a - record that stood for many years. - <P> - David Haussler recounts that day: - "Seeing the waterfall of As, Gs, Cs, and Ts pouring - off our server was an emotional moment. We were witnessing - the product of more than three billion years of evolution, - sequences passed down from the beginning of life to - present-day humans." <sup>1</sup> - <P> - The UCSC Genome Bioinformatics group is proud of the role - we have played in bringing the - human genome, as well as the genomes of many other species, - to the world. We'd like to thank NHGRI, HHMI, and our other - funding agencies for making this service possible, and - also our many users and collaborators for their suggestions, - contributions, and support throughout the years. We look - forward to serving as a reliable - source of bioinformatics tools and genomic annotations in - the years to come while facing the exciting challenges - presented by rapidly advancing technology. - <P> - To read more about UCSC's role in the race to assemble the - first working draft of the human genome, including Jim - Kent's remarkable programming feat that pulled it all - together in the final weeks, see the - <A HREF="http://www.cbse.ucsc.edu/research/hgp_race" - TARGET=_blank>Center for Biomolecular Science and - Engineering</A> (CBSE) website. - </P><P> - <FONT SIZE=-1> - (1) Sansom C, Morrison McKay BJ (2008) ISCB Honors David Haussler and Aviv -Regev. PLoS Comput Biol 4(7): e1000101 - </FONT> </P> + <HR> <FONT FACE="courier" SIZE="3"><B>4 June 2010 - dbSNP 131 Available for hg19: </B></FONT> We are pleased to announce the release of dbSNP build 131, available from on the human assembly (GRCh37/hg19). <A HREF="goldenPath/newsarch.html#060410">Read more</A>. - </p><p> - <FONT FACE="courier" SIZE="3"><B>6 May 2010 - UCSC -Hosts Portal for Neandertal Sequence, Alignments, and Analyses: </B></FONT> - In conjunction with the publication of the paper Green - <em>et al.</em> <A HREF="http://www.sciencemag.org/cgi/content/full/328/5979/710" - TARGET=_blank>A Draft Sequence of the Neandertal Genome</A> - in the May 7 issue of <em>Science</em>, the UCSC - Genome Browser project has released a public - <A HREF="Neandertal">Neandertal portal</A> that may be - used to access the Neandertal sequence, alignments to - the UCSC hg18 (NCBI Build 36) human reference assembly and - the UCSC panTro2 (Chimpanzee Sequencing and Analysis - Consortium v2.1) chimpanzee reference assembly, and - several associated analyses. - <A HREF="goldenPath/newsarch.html#050610">Read more</A>. - </P> + </p> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>