a91282409ef8b3ef8fb6fe7932e5910a94714a9a jnavarr5 Wed Sep 4 16:45:15 2019 -0700 Updating hard-coded links to UCSC to be relative links. Fixing a misspelled 'target' HTML attribute for EBI. CR #24083 diff --git src/hg/htdocs/goldenPath/history.html src/hg/htdocs/goldenPath/history.html index 319875d..d6186c7 100755 --- src/hg/htdocs/goldenPath/history.html +++ src/hg/htdocs/goldenPath/history.html @@ -83,33 +83,33 @@ aggregate/overlay graphing view options to compare results. By merging experimental results from multiple sources, this powerful tool allows researchers to better understand how genes function.</p> <p> Today, the UCSC Genome Browser group continues to make genome sequences even more useful for science and medicine by facilitating the visualization of aggregate data so that it is easily accessible to researchers. This process of discovery and categorization is a critical step toward fully understanding the workings of the human genome, a project that will occupy science and medicine for many years. The browser platform has multiple potential uses that can aid in disease prevention, diagnostics, and the search for cures. The usefulness of the UCSC Genome Browser lead to spin-offs, or genome browser mirrors, such as the following:</p> <ul> <li><a href="https://news.ucsc.edu/2008/05/2242.html" target="_blank">The HIV Data Browser</a></li> <li><a href="https://xena.ucsc.edu/welcome-to-ucsc-xena/" target="_blank">The UCSC Cancer Genomics Browser</a></li> - <li><a href="https://genome.ucsc.edu/encode/" + <li><a href="../ENCODE/" target="_blank">The data collection center for the international ENCODE project</a></li> - <li><a href="http://genome.ucsc.edu/ebolaPortal/" + <li><a href="../ebolaPortal/" target="_blank">The UCSC Ebola Virus Genome Browser</a></li> </ul> <a name="race"></a> <h2>Human Genome Project — The Race</h2> <p> In December 1999, the <a href="https://www.genome.gov/human-genome-project" target="_blank">International Human Genome Project (IHGP)</a> came to UC Santa Cruz when Eric Lander, the director of the Whitehead sequencing center (Whitehead Institute/MIT Center for Genome Research), invited David Haussler to help annotate the human genome. In particular, Lander wanted help in discovering the locations of the genes, which make up only approximately 1.5% of the sequence. Haussler had previously applied a mathematical technique known as hidden Markov models (HMMs) to the task of computer gene-finding. This application of HMMs had quickly become the dominant gene-finding methodology and was used successfully on the <i>Drosophila melanogaster</i> (fruit fly) genome.</p> @@ -165,50 +165,50 @@ <p> Motivated to prevent Celera and its clients from locking up significant portions of the human genome in patents, Jim Kent dropped his other work in May of 2000 to focus on the assembly problem. In a remarkable display of energy and talent, Kent developed within four weeks a 10,000-line computer program that assembled the working draft of the human genome. The program, called GigAssembler, constructed the first working draft of the human genome on June 22, 2000, just days before Celera completed its first assembly. The IHGP working draft combined anonymous genomic information from human volunteers of diverse backgrounds, accepted on a first-come, first-taken basis. The Celera sequence was of a single individual. Since the public consortium finished the genome ahead of the private company, the genome and the information it contains are available free to researchers worldwide. Kent's assembly was celebrated at a White House ceremony on June 26, 2000, announcing the completion of the first drafts of the human genome by the IHGP and Celera.</p> <p> On July 7, 2000, after further examination by the principal scientists of the public genome project, and to facilitate the annotation process, the UCSC Genome Browser group released this first working -draft on the web at <a href="https://genome.ucsc.edu" target="_blank">https://genome.ucsc.edu</a>. +draft on the web at <a href="../" target="_blank">https://genome.ucsc.edu</a>. In the first 24 hours of free and unrestricted access to the human genome, the scientific community downloaded one-half trillion bytes of information from the assembled blueprint of our human species. The initial assembled human genome sequence was referred to as a working draft because there remained gaps where DNA sequence was missing, due either to a lack of raw sequence data or ambiguities in the positions of the fragments. With the gene assembly 90% complete, the assembled genome was published along with the findings of hundreds of researchers worldwide in the <a href="https://www.nature.com/nature/volumes/409/issues/6822" target="_blank">February 15, 2001 issue of <i>Nature</i></a>, which was largely devoted to the human genome. In the months following the release of the working draft, the UCSC team worked with other researchers worldwide to fill in the gaps. The resulting sequence made its debut in April of 2003. It encompasses 99% of the gene-containing regions of the human genome and is 99.99% accurate.</p> <p> The UCSC Genome Browser was designated as the official repository of the early human genome assembly iterations. Once the human genome sequence became available, other genome browsers also came online, most notably those at the <a href="https://www.ncbi.nlm.nih.gov/" target="_blank">National Center -for Biotechnology Information (NCBI)</a> and at the <a href="https://www.ebi.ac.uk/" taget="_blank"> -European Bioinformatics Institute (EBI)</a>. Reciprocal links provided on each of the three browsers -allow researchers to jump from any place in the human genome to the same region on either of the -other two browsers.</p> +for Biotechnology Information (NCBI)</a> and at the <a href="https://www.ebi.ac.uk/" +target="_blank">European Bioinformatics Institute (EBI)</a>. Reciprocal links provided on each of +the three browsers allow researchers to jump from any place in the human genome to the same region +on either of the other two browsers.</p> <a name="ENCODE"></a> <h2>The ENCODE Project</h2> <p> The human genome contains vast amounts of information, and all of the functions of a human cell are implicitly coded in the human genome. With the molecular sequence known, researchers have been mining it for clues as to how the body works in health and in disease, ultimately laying out the plan for the complex pathways of molecular interactions that the sequence orchestrates. The UCSC Genome Browser aids the worldwide scientific community in its challenge to understand the genome, to probe it with new experimental and informatics methodologies, and to decode the genetic program of the cell.</p> <p> After the sequence of the genome was first available, a researcher's ability to decode that sequence and tap into the wealth of information it holds was still quite limited. The next step beyond viewing the genome is gaining an understanding of the instructions encoded in it. Toward this end, @@ -220,31 +220,31 @@ ENCODE is a scientific reconnaissance mission aimed at discovering all regions of the human genome crucial to biological function. Before ENCODE, scientists focused on finding the genes, or protein-coding regions, in DNA sequences; but these account for only about 1.5% of the genetic material of humans and other mammals. Non-coding regions of the genome have important functions serving as the instruction set for when and in which tissues genes are turned on and off. The ENCODE project is developing a comprehensive "parts list" by identifying and precisely locating all functional elements in the human genome. This project, sponsored by the <a href="https://www.genome.gov/" target="_blank">National Human Genome Research Institute (NHGRI)</a>, involves an international consortium of scientists from government, industry, and academia.</p> <a name="ucsc"></a> <h3>UC Santa Cruz's Role</h3> <p> UC Santa Cruz developed and ran the data coordination center for the ENCODE project from its -inception in 2003 through the <a href="https://genome.ucsc.edu/ENCODE/" target="_blank">end of the +inception in 2003 through the <a href="../ENCODE/" target="_blank">end of the first production phase in 2012</a>. During that time, the UCSC Genome Browser group, directed by Jim Kent with technical management by Kate Rosenbloom, provided the database and web interface for all sequence-related data to the ENCODE project. This included integrating the data into the UCSC Human Genome Browser (where it continues to reside) on specialized tracks, and providing further in-depth information on detail pages. UC Santa Cruz also developed, performed, and presented computational and comparative analyses to glean further genomic and functional information from the collective data.</p> <p> UC Santa Cruz worked closely with labs producing data for the ENCODE project and with data analysis groups to define data and metadata reporting standards for a broad range of genomics assays. They implemented data submission and validation pipelines, created and maintained the <a href="https://www.encodeproject.org/" target="_blank">encodeproject.org</a> website, developed user access tools for ENCODE data, exported all ENCODE data to repositories at the National Center for Biotechnology Information (NCBI), and provided outreach and tutorial support for the project. </p>