8fb15b4d208ce2521a398a5dea0e547ec589f68e jnavarr5 Thu Jan 7 17:17:36 2021 -0800 Fixing the indentation for the div tags, refs #20314 diff --git src/hg/htdocs/goldenPath/history.html src/hg/htdocs/goldenPath/history.html index 0f8659d..185be21 100755 --- src/hg/htdocs/goldenPath/history.html +++ src/hg/htdocs/goldenPath/history.html @@ -193,139 +193,132 @@ At least partly in response to competition from Celera, the IHGP changed its focus from producing finished clones to producing draft clones. To sequence a clone, the IHGP adopted a shotgun approach in miniature. Bits of a clone were read at random, and the bits were stitched together by a computer program into pieces called "contigs." After the shotgun phase, a clone was typically in 5-50 contigs, but the relative order of the contigs was not known. This was the state of the genome when David Haussler first attempted to locate the genes computationally, and he quickly discovered that computational gene-finding was nearly impossible, because the average size of a contig was considerably smaller than the average size of a human gene.</p> <a name="push"></a> <h3>Push to the Finish Line</h3> <div class="row"> <div class="col-md-6"> <p> In May of 2000, motivated to prevent Celera and its clients from locking up significant portions -of the human genome in patents, Jim Kent dropped his other work 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> - + of the human genome in patents, Jim Kent dropped his other work 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> </div> - <div class="col-md-6" style="text-align:center"> <img class="text-center" alt="Copy of first draft of the human genome on a CD" src="/images/genome_cd.jpg" style="margin-botton:5px; width:400px"> <div style="text-align:center; line-height:1"> <font SIZE=-1> Copy of first draft of the human genome sequence presented to <a href="https://www.soe.ucsc.edu/news/article/1020" target="_blank">President Clinton</a> and deposited in the Smithsonian. </font> </div> </div> </div> <div class="row"> <div class="col-md-6"> <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="../" 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 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. -UCSC was designated as the official repository of the early human genome assembly -iterations. Eventually, the <a href="https://www.ncbi.nlm.nih.gov/" target="_blank">National -Center for Biotechnology Information (NCBI)</a> and then the <a href = -"https://www.ncbi.nlm.nih.gov/grc" target = _blank>Genome Reference Consortium (GRC)</a> -would take over the assembly and official release of improvements on the genome assembly.</p> - -<p> -The UCSC team was a key part of the Hard Core Analysis Group that published in the -Feb 15, 2001 issue of Nature. We linked the genome sequence to previous genetic, -cytogenetic, and radiation hybrid maps, and to the new physical clone map. We did -this both to refine and validate the sequence assembly, and to explore phenomena -such as positional and gender variation in recombination rate, regional isochore -structure and repeat structure at the single base resolution for the first time. -David Kulp performed the mapping of STS markers, messenger RNAs and ESTs, -Terry Furey mapped the chromosome band positions, cytogenetic markers (~8,000 gene -regions mapped by Fluorescence In-Situ Hybridization) and isochores, and integrated -these data with the radiation hybrid and genetic maps. -</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="../" 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 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. UCSC + was designated as the official repository of the early human genome assembly iterations. + Eventually, the <a href="https://www.ncbi.nlm.nih.gov/" target="_blank">National Center for + Biotechnology Information (NCBI)</a> and then the <a href="https://www.ncbi.nlm.nih.gov/grc" + target = _blank>Genome Reference Consortium (GRC)</a> would take over the assembly and official + release of improvements on the genome assembly.</p> </div> - <div class="col-md-6" style="text-align:center"> <img class="text-center" alt="David in front of Dell cluster" src="/images/david_cluster.jpg" style="margin-botton:5px; width:350px"> <div style="text-align:center; line-height:1"> <font SIZE=-1> David Haussler next to the original Dell computer cluster used for the assembly of the first human genome. </font> </div> </div> +</div> -<div class="col-md-12"> +<p> +The UCSC team was a key part of the Hard Core Analysis Group that published in the +Feb 15, 2001 issue of Nature. We linked the genome sequence to previous genetic, +cytogenetic, and radiation hybrid maps, and to the new physical clone map. We did +this both to refine and validate the sequence assembly, and to explore phenomena +such as positional and gender variation in recombination rate, regional isochore +structure and repeat structure at the single base resolution for the first time. +David Kulp performed the mapping of STS markers, messenger RNAs and ESTs, +Terry Furey mapped the chromosome band positions, cytogenetic markers (~8,000 gene +regions mapped by Fluorescence In-Situ Hybridization) and isochores, and integrated +these data with the radiation hybrid and genetic maps. +</p> <p> The genome sequence at the time of release, however, was simply a few billion characters of Gs, As, Ts and Cs, many of them assigned to chromsomes. As indicated above, however, without landmarks it is unintelligible. During this time, Kent was also working on a computer program that would allow him to view genes of <em>C. elegans</em> and show via a web interface which parts of the genes are ultimately used by the cell to encode proteins. The process of "splicing" removes sequence called introns and was visualizable using Jim's program, The Intronerator. </p> <p> The Intronerator evolved into Genome Browser and ultimately became a tool to provide information about the functional significance of many other parts of the genome sequence. The process of annotation, as it is called, identifies sequences that represent not only the genes and which parts of the genes encode proteins, but also the control sequences that tell cells when and where to activate genes, which regions of the genome are conserved through evolution and can be found in other animals, and many other significant regions. Essentially, in the Browser the genome became a coordinate system upon which to hang any functionally significant annotation. </p> - <p> Once the human genome sequence became available and the Browser built to visualize it, other genome browsers also came online, most notably those at NCBI 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> - </div> - </div> - <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 orchestrate. 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, the UCSC Genome Browser group participated as the Data Coordination Center for the @@ -339,45 +332,47 @@ material of humans and other mammals. Non-protein-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> <div class="row"> <div class="col-md-6"> <p> UC Santa Cruz developed and ran the Data Coordination Center for the ENCODE project from its -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 + 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 genomic 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. + 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 genomic + 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> </div> <div class="col-md-6" style="text-align:center"> <img class="text-center" alt="Picture of Kate Rosenbloom from 2003" src="/images/kate2003.jpg" style="margin-botton:5px; width:250px"> <div style="text-align:center; line-height:1"> <font SIZE=-1> <p class="gbsCaption text-center"> Kate Rosenbloom while working on the ENCODE Project (2003).</p> </font> </div> </div> </div> <p>