Jim Kent
Encyclopedia
William James Kent (born February 10, 1960) is an American
research scientist and computer programmer. He has been a contributor to genome
database projects and the 2003 winner of the Benjamin Franklin Award (Bioinformatics)
.
and grew up in San Francisco, California
, United States
.
home computer. This program combined polygon tweening in 3D with simple 2D cel-based animation. In 1985 he founded and ran a software company, Dancing Flame, which adapted the Aegis Animator to the Atari ST, and created Cyber Paint for that machine. Cyber Paint was a 2D animation program that brought together a wide variety of animation and paint functionality and the delta-compressed animation format developed for CAD-3D. The user could move freely between animation frames and paint arbitrarily, or utilize various animation tools for automatic tweening movement across frames. Cyber Paint was one of the first, if not the first, consumer program that enabled the user to paint across time in a compressed digital video format. Later he developed a similar program, the Autodesk Animator for PC compatibles, where the image compression improved to the point it could play off of hard disk, and one could paint using "inks" that performed algorithmic transformations such as smoothing, transparency, and tiled patterns. The Autodesk Animator was used to create artwork for a wide variety of video games.
at the University of California, Santa Cruz
, Kent in May 2000, wrote a program, GigAssembler, that allowed the publicly funded Human Genome Project
to assemble and publish the human genome sequence. His efforts were motivated by the research needs of himself and his colleagues, but also out of concern that the data might be made proprietary via patents by Celera Genomics
. In his close race with Celera, Kent and the UCSC Professor David Haussler
quickly built a modest cluster of 50 commodity Personal Computer
s running the Linux
operating system
to run the software. In contrast Celera was using what was thought of then as one of the most powerful civilian supercomputers in the world. His first assembly on the human genome was released on June 22. Celera finished its assembly on June 25, and the dual results were announced at the White House on June 26. On July 7, the Santa Cruz data was made publicly available on the Web Wide Web. In 2002 Tim O'Reilly
described Kent's work as "the most significant work of open source development in the past year". While all of Kent's genomics software is open source in the sense that the source code can be downloaded and read for free, and all of the software can be freely used for academic, nonprofit, and personal use, some of it requires a license, either from UCSC or from Kent Informatics Inc., for commercial use.
After GigAssembler, Kent went on to write BLAT
(BLAST-like alignment tool) and the UCSC Genome Browser to help analyze important genome data, receiving his PhD in biology in 2002. Today at UCSC he works primarily on web tools to help understand the human genome. He helps maintain and upgrade the browser, and has worked on comparative genomics, Parasol, a job control management software for the UCSC kilocluster, and the ENCODE
Project.
United States
The United States of America is a federal constitutional republic comprising fifty states and a federal district...
research scientist and computer programmer. He has been a contributor to genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
database projects and the 2003 winner of the Benjamin Franklin Award (Bioinformatics)
Benjamin Franklin Award (Bioinformatics)
The Benjamin Franklin Award is an award for Open Access in the Life Sciences presented by the Bioinformatics Organization-Laureates:*2002 - Michael B. Eisen*2003 - Jim Kent*2004 - Lincoln D. Stein*2005 - Ewan Birney*2006 - Michael Ashburner...
.
Early life
Kent was born in HawaiiHawaii
Hawaii is the newest of the 50 U.S. states , and is the only U.S. state made up entirely of islands. It is the northernmost island group in Polynesia, occupying most of an archipelago in the central Pacific Ocean, southwest of the continental United States, southeast of Japan, and northeast of...
and grew up in San Francisco, California
San Francisco, California
San Francisco , officially the City and County of San Francisco, is the financial, cultural, and transportation center of the San Francisco Bay Area, a region of 7.15 million people which includes San Jose and Oakland...
, United States
United States
The United States of America is a federal constitutional republic comprising fifty states and a federal district...
.
Computer Animation
Kent began his programming career in 1983 with Island Graphics Inc. where he wrote the Aegis Animator program for the AmigaAmiga
The Amiga is a family of personal computers that was sold by Commodore in the 1980s and 1990s. The first model was launched in 1985 as a high-end home computer and became popular for its graphical, audio and multi-tasking abilities...
home computer. This program combined polygon tweening in 3D with simple 2D cel-based animation. In 1985 he founded and ran a software company, Dancing Flame, which adapted the Aegis Animator to the Atari ST, and created Cyber Paint for that machine. Cyber Paint was a 2D animation program that brought together a wide variety of animation and paint functionality and the delta-compressed animation format developed for CAD-3D. The user could move freely between animation frames and paint arbitrarily, or utilize various animation tools for automatic tweening movement across frames. Cyber Paint was one of the first, if not the first, consumer program that enabled the user to paint across time in a compressed digital video format. Later he developed a similar program, the Autodesk Animator for PC compatibles, where the image compression improved to the point it could play off of hard disk, and one could paint using "inks" that performed algorithmic transformations such as smoothing, transparency, and tiled patterns. The Autodesk Animator was used to create artwork for a wide variety of video games.
Involvement with the Human Genome Project
While working on his PhD in BiologyBiology
Biology is a natural science concerned with the study of life and living organisms, including their structure, function, growth, origin, evolution, distribution, and taxonomy. Biology is a vast subject containing many subdivisions, topics, and disciplines...
at the University of California, Santa Cruz
University of California, Santa Cruz
The University of California, Santa Cruz, also known as UC Santa Cruz or UCSC, is a public, collegiate university; one of ten campuses in the University of California...
, Kent in May 2000, wrote a program, GigAssembler, that allowed the publicly funded Human Genome Project
Human Genome Project
The Human Genome Project is an international scientific research project with a primary goal of determining the sequence of chemical base pairs which make up DNA, and of identifying and mapping the approximately 20,000–25,000 genes of the human genome from both a physical and functional...
to assemble and publish the human genome sequence. His efforts were motivated by the research needs of himself and his colleagues, but also out of concern that the data might be made proprietary via patents by Celera Genomics
Celera Genomics
Celera Corporation was a business unit of the Applera Corporation, but was spun off in July 2008 to become an independent publicly traded company. In May 2011 Quest Diagnostics Incorporated completed the acquisition of Celera, which thus became a wholly owned subsidiary...
. In his close race with Celera, Kent and the UCSC Professor David Haussler
David Haussler
David Haussler is a Howard Hughes Medical Institute Investigator. He is also Professor of Biomolecular Engineering and Director of the Center for Biomolecular Science and Engineering at the University of California, Santa Cruz; director of the California Institute for Quantitative Biosciences on...
quickly built a modest cluster of 50 commodity Personal Computer
Personal computer
A personal computer is any general-purpose computer whose size, capabilities, and original sales price make it useful for individuals, and which is intended to be operated directly by an end-user with no intervening computer operator...
s running the Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...
operating system
Operating system
An operating system is a set of programs that manage computer hardware resources and provide common services for application software. The operating system is the most important type of system software in a computer system...
to run the software. In contrast Celera was using what was thought of then as one of the most powerful civilian supercomputers in the world. His first assembly on the human genome was released on June 22. Celera finished its assembly on June 25, and the dual results were announced at the White House on June 26. On July 7, the Santa Cruz data was made publicly available on the Web Wide Web. In 2002 Tim O'Reilly
Tim O'Reilly
Tim O'Reilly is the founder of O'Reilly Media and a supporter of the free software and open source movements.-Life and career:...
described Kent's work as "the most significant work of open source development in the past year". While all of Kent's genomics software is open source in the sense that the source code can be downloaded and read for free, and all of the software can be freely used for academic, nonprofit, and personal use, some of it requires a license, either from UCSC or from Kent Informatics Inc., for commercial use.
After GigAssembler, Kent went on to write BLAT
BLAT (bioinformatics)
Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species protein alignments.BLAT is a software program developed by Jim Kent at UCSC to identify similarities between DNA sequences and protein sequences. It was developed to assist in the annotation of the human genome sequence...
(BLAST-like alignment tool) and the UCSC Genome Browser to help analyze important genome data, receiving his PhD in biology in 2002. Today at UCSC he works primarily on web tools to help understand the human genome. He helps maintain and upgrade the browser, and has worked on comparative genomics, Parasol, a job control management software for the UCSC kilocluster, and the ENCODE
ENCODE
ENCODE is a public research consortium launched by the US National Human Genome Research Institute in September 2003. The goal is to find all functional elements in the human genome, one of the most critical projects by NHGRI after it completed the successful Human Genome Project...
Project.