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Bioinformatic Harvester

Bioinformatic Harvester

The Bioinformatic-Harvester is a bioinformatic meta search engine for genes and protein associated information. Harvester currently works for human, mouse and rat proteins. Harvester crosslinks 16 popular bioinformatic resources and allows cross searches. A special ranking systems similar to Google pagerank sorts the search results and displays most relevant information.

How does Harvester work?

Harvester collects information from protein and gene databases along with information from so called "prediction servers". Prediction server e.g provide online sequence analysis for a single protein. Harvesters search index is based on the Uniprot protein information collection. The Uniprot collections consists of ~72.000 human (2005-08) ~48.000 mouse and ~15.000 rat protein information pages which are curated and updated on a regular basis. Harvester collects two types of information: A) text based information from the following databases:
- Uniprot, world largest protein database
- SOURCE, convenient gene information overview
- Simple Modular Architecture Research Tool (SMART),
- SOSUI, predicts transmembrane domains
- PSORT, predicts protein localisation
- Homologene, compares proteins from different species
- gfp-cdna, proteins localisation with fluorescence microscopy
- International Protein Index (IPI). B) Databases rich in graphical elements are not collected, but crosslinked via iframes. Iframes are transparent windows within a HTML pages. The iframe windows allows realtime view on the "iframed" = linked databases. Several such iframes are combined on a Harvester protein page. This mehtod allows convenient comparison of information from several databases. Currently Harvester crosslinks the following (graphical elements rich) servers via iframes:
- NCBI-BLAST, an algorithm for comparing biological sequences NCBI
- Genome Browser, working draft assemblies for genomes UCSC
- Ensembl, automatic gene annotation. EMBL-EBI and Sanger-Institute
- RZPD, German resources Center for genome research in Berlin/Heidelberg
- STRING, Search Tool for the Retrieval of Interacting Genes/Proteins EMBL
- iHOP, information hyperlinked over proteins via gene/protein synonyms

What can i find?

Harvester allows both combination of different search terms and single words. Search Examples:
- Gene-name: "golga3"
- Gene-alias: "ADAP-S ADAS ADHAPS ADPS" (one gen name is sufficient)
- Gene-Ontologies: "Enzyme linked receptor protein signaling pathway"
- Unigene-Cluster: "Hs.449360"
- Go-annotation: "intra-Golgi transport"
- Molecular function: "protein kinase binding"
- Protein: "Q9NPD3"
- Protein domain: "SH2 sar"
- Protein Localisation: "endoplasmic reticulum"
- Chromosome: "2q31"
- Disease relevant: use the word "diseaselink"
- Combinations: "golgi diseaselink" (finds all golgi proteins associated with a disease)
- mRNA: "AL136897"
- Word: "Cancer"
- Comment: "highly expressed in heart"
- Author: "Bush, Schroeder"
- Publication oder project: "cDNA sequencing project"

How to link your project or excel-sheet to the Bioinformatic Harvester

The following query string searches the human set of proteins. Simply replace the term "brain" with your search term. http://www-db.embl.de/jss/servlet/de.embl.bk.htmlfind.HarvesterOutputMysql?m=doSearch&fH=0&search=brain
- Use &fH=0 for searches within the human protein set
- Use &fH=1 for searches within the mouse protein set
- Use &fH=2 for searches within the rat protein set

External links

- http://harvester.embl.de Category:Bioinformatics

Ranking

Ranking is the process of positioning individuals, groups or businesses on a scale in relation to others. A list arranged in this way is said to be in rank order. Some examples:
- In many sports, individuals or teams are given rankings, generally by the sport's governing body
- In football (soccer), national teams are ranked in the FIFA World Rankings.
- In snooker, players are ranked using the Snooker world rankings
- In ice hockey, national teams are ranked in the IIHF World Ranking
- In golf, the top male golfers are ranked using the Official World Golf Rankings
- In relation to credit standing, the ranking of a security refers to where that particular security would stand in a wind up of the issuing company. For instance, capital notes are subordinated securities; they would rank behind senior debt in a wind up. In other words the holders of senior debt would be paid out before subordinated debt holders received any funds.
- Search engines rank web pages depending on their relevance to a user's query. See HITS algorithm, PageRank, TrustRank.
- In video gaming, players may be given a ranking. To "rank up" is to achieve a higher ranking relative to other players, especially with strategies that do not depend on the player's skill.
- A bibliogram ranks common noun phrases in a piece of text.

Google

:For the search engine produced by this company, see Google search; for the underlying technology, see Google platform; for other uses see Google (disambiguation). Google, Inc. () is a U.S. public corporation, initially established as a privately held corporation in 1998, which designed and currently manages the Internet Google search engine. Google's corporate headquarters is at the "Googleplex" in Mountain View, California and employs almost 5,000 workers. Dr. Eric Schmidt, former CEO of Novell, was named the Chief Executive Officer when co-founder Larry Page stepped down. The company's overview web page states that "Google's mission is to organize the world's information and make it universally accessible and useful."

History

Beginnings

Larry Page Google began as a research project in January 1996 ^{[http://www.google.com/intl/en/corporate/history.html]} by Larry Page and Sergey Brin, two Ph.D. students at Stanford. They developed the hypothesis that a search engine based on analysis of the relationships between Web sites would produce improved results over the basic techniques then in use. (At the time, other search engines ranked results essentially based on how many times the search term appeared on a page.) It was originally nicknamed BackRub because the system checked backlinks to estimate a site's importance. (A small search engine called RankDex was already exploring a similar strategy.) Convinced that the pages with the most links to them from other highly relevant Web pages must be the most relevant pages associated with the search, Page and Brin tested their thesis as part of their studies, and laid the foundation for their search engine. Originally the search engine used the Stanford website with the domain google.stanford.edu (see the [http://www.archive.org/web/web.php Internet Archive Wayback Machine] search for [http://web.archive.org/web/
- /http://google.stanford.edu http://google.stanford.edu]). The domain google.com was registered on September 15, 1997. They formally incorporated their company, Google Inc., on September 7, 1998 at a friend's garage in Menlo Park, California. In March 1999, the company moved into offices at 165 University Avenue in Palo Alto, home to a number of other noted Silicon Valley technology startups. Google received a big break in 1999 when one of the most popular search engines, AltaVista, relaunched itself as a user Web entry point, or portal. This unexpected change alienated part of AltaVista's user base. Google quickly outgrew its University Avenue home. After outgrowing two subsequent sites, the company settled into a complex of buildings (referred to by some as "The Googleplex") in Mountain View at 1600 Amphitheater Parkway, in 2003. The Google search engine attracted a loyal following among the growing number of Internet users. They were attracted to its simple, uncluttered, clean design — a competitive advantage to attract users who did not wish to enter searches on web pages filled with visual distractions. This appearance, while imitating the early AltaVista, had behind it Google's unique search capabilities. In 2000, Google began selling advertisements associated with the search keyword to produce enhanced search results for the user. This strategy was important for increasing advertising revenue, which is based upon the number of "hits" users make upon ads. The ads were text-based in order to maintain an uncluttered page design and to maximize page loading speed. It also only cost a very small amount per click to the websites that advertised this way. The model of selling keyword advertising was originally pioneered by Goto.com (renamed Overture, and now Yahoo! Search Marketing)[http://www.content.overture.com/d/USm/about/news/mile.jhtml]. While many of its dot-com rivals failed in the new Internet marketplace, Google quietly rose in stature while generating revenue. describing Google's ranking mechanism (PageRank) was granted on September 4 2001. The patent was officially assigned to Stanford University and lists Lawrence Page as the inventor. In February 2003, Google acquired Pyra Labs, owner of Blogger, a pioneering and leading weblog hosting Web site. Some analysts considered the acquisition inconsistent with Google's business model. However, the acquisition secured the company's competitive ability to use information gleaned from blog postings to improve the speed and relevance of articles contained in a companion product to the search engine, Google News. At its peak in early 2004, Google handled upwards of 84.7 percent of all search requests on the World Wide Web through its Web site and through its partnerships with other Internet clients like Yahoo!, AOL, and CNN.[http://www.onestat.com/html/aboutus_pressbox21.html] In February 2004 Yahoo! dropped its partnership with Google in order to provide users at its site independent search results and to maintain their loyalty. Google lost user share of the search market. Yet Yahoo!'s move highlighted Google's own distinctiveness and today the verb "to google" has entered a number of languages first as a slang verb and now as a standard word meaning, "to perform a web search". Google's declared code of conduct is "Don't Be Evil", a phrase which they went so far as to include in their prospectus (aka "red herring" or "S-1") for their IPO, noting "We believe strongly that in the long term, we will be better served — as shareholders and in all other ways — by a company that does good things for the world even if we forgo some short term gains." IPO The Google site includes humorous features such as cartoon modifications [http://www.google.com/holidaylogos.html] of the Google logo to recognize special occasions and anniversaries, known as "Google Doodles". Not only may decorative drawings be attached to the logo, but as well the font design may mimic a fictional or humorous language such as the Star Trek Klingon[http://www.google.com/intl/xx-klingon/] and Leet[http://www.google.com/intl/xx-hacker/]. The logo is notorious among web users for April Fool's Day tie-ins and jokes about the company. Analysts speculate that Google's response to Yahoo! will be to continue to make technical and visual enhancements to personalized searches, using the personal data that is gathering from Orkut, Gmail, and Froogle to produce unique results based on the user. Frequently, new Google enhancements or products appear in its inventory. Products and demos [http://labs.google.com/ Google Labs], the experimental section of Google.com help Google maximize its relationships with its users by including them in the beta development, design and testing stages of new products and enhancements of already existing ones.

Original Hardware

The [http://web.archive.org/web/19990209043945/google.stanford.edu/googlehardware.html original hardware] used by Google included:
- Sun Ultra II with dual 200MHz processors, and 256MB of RAM. This was the main machine for the original Backrub system.
- 2 x 300 MHz Dual Pentium II Servers donated by Intel, they included 512MB of RAM and 9 x 9GB hard drives between the two. It was on these that the main search ran.
- F50 IBM RS6000 donated by IBM, included 4 processors, 512MB of memory and 8 x 9GB hard drives.
- Two additional boxes included 3 x 9GB hard drives and 6 x 4GB hard drives respectively (the original storage for Backrub). These were attached to the Sun Ultra II.
- IBM disk expansion box with another 8 x 9GB hard drives donated by IBM.
- Homemade disk box which contained 10 x 9GB SCSI hard drives

Logo Evolutions

The [http://www.google.com/intl/en/stickers.html Google logo] has changed over the years. The following are the official Google logos. Image:googlelogo_5.jpg|Late 1996 Image:googlelogo_6.jpg|1998 - July 1999 Image:googlelogo_current.gif|July 1999 - Present Google is also known for its innovative holiday logos; [http://www.google.com/holidaylogos.html see their logo archive]. A website has been created that relives these imaginative logos by displaying them randomly on every page-load: [http://google.abrahamjoffe.com.au/ Holiday Google]. The site [http://www.logoogle.com/ logoogle] contains images users have made about google

Etymology

The name "Google" is a play on the word "Googol", which was coined by Milton Sirotta, nine-year-old nephew of U.S. mathematician Edward Kasner in 1938, to refer to the number represented by 1 followed by one hundred zeros. Google's use of the term reflects the company's mission to organize the immense amount of information available on the Web. As a further play on this, Google's headquarters are referred to as "the Googleplex" — a googolplex being 1 followed by a googol of zeros, and the HQ being a complex of buildings (cf. multiplex, cineplex, etc). The name has also been interpreted as a merging of the words "Go ogle", though this is widely accepted to be coincidental. The term appears in James Joyce's Finnegans Wake: "who thought him a Fonar all, feastking of shellies by googling Lovvey" [231.12]. To "throw a googly" means to ask a difficult or unanswerable question in British slang, a googly being a tricky ball in the game of cricket. Chambers Twentieth Century Dictionary (1972) allows the verb "to google" from this, and the phrase has come to be synonymous with "to search for on the Internet".

Financing and IPO

The first funding for Google as a company was secured in the form of a $100,000 check from Andy Bechtolsheim, co-founder of Sun Microsystems, made out to a corporation which didn't yet exist. After a frantic few weeks, this was topped up to give an initial investment of almost $1 million. Around six months later, a much larger round of funding was announced, with the major investors being rival venture capital firms Kleiner Perkins Caufield & Byers and Sequoia Capital. In October 2003, while discussing a possible IPO (Initial Public Offering of shares), Microsoft approached the company about a possible partnership or merger; no such deal ever materialized. In January 2004, Google announced the hiring of Morgan Stanley and Goldman Sachs Group to arrange an IPO. That IPO (one of the most anticipated in history) was projected to raise as much as $4 billion. According to a banker involved in the transaction, the deal would yield an estimated $12 billion market capitalization for Google. On April 29, 2004, Google made an S-1 form SEC filing for an IPO to raise as much as USD $2,718,281,828 (with a touch of mathematical humor as e = 2.718281828...). April 29th was the 120th day of 2004, and according to section 12(g) of the Securities Exchange Act of 1934, "a company must file financial and other information with the SEC 120 days after the close of the year in which the company reaches $10 million in assets and/or 500 shareholders, including people with stock options.[http://management.itmanagersjournal.com/article.pl?sid=04/05/21/1934249&tid=103&tid=4] Google has stated in its Annual filing for 2004 that every one of its 3,021 employees, "except temporary employees and contractors, are also equity holders, with significant collective employee ownership", so Google would have needed to make its financial information public by filing them with the SEC regardless of whether or not they intended to make a public offering. As Google stated in the filing, their "growth has reduced some of the advantages of private ownership. By law, certain private companies must report as if they were public companies. The deadline imposed by this requirement accelerated our decision." The SEC filing revealed that Google turned a profit every year since 2001 and earned a profit of $105.6 million on revenues of $961.8 million during 2003. In May 2004, Google officially cut Goldman Sachs from the IPO, leaving Morgan Stanley and Credit Suisse First Boston as the joint underwriters. They chose the unconventional way of allocating the initial offering through an auction (specifically, a "Dutch auction"), so that "anyone" would be able to participate in the offering. The smallest required account balances at most authorized online brokers that are allowed to participate in an IPO, however, are around $100,000. In the run-up to the IPO the company was forced to slash the price and size of the offering, but the process did not run into any technical difficulties or result in any significant legal challenges. The initial offering of shares was sold for $85 a piece. The public valued it at $100.34 at the close of the first day of trading which saw 22,351,900 shares change hands. Before Google initiated its initial public offering, Larry Page & Sergey Brin faced legal action for giving Playboy an interview about themselves and Google. The SEC (Security & Exchange Commission) forbids giving out information pertaining to a company's specifications before an IPO is launched. After some initial stumbles, Google's initial public offering took place on August 19, 2004. 19,605,052 shares were offered at a price of $85 per share. Of that, 14,142,135 (another mathematical reference as √2 = 1.4142135...) were floated by Google and 5,462,917 by selling stockholders. The sale raised $1.67 billion, of which approximately $1.2 billion went to Google. The vast majority of Google's 271 million shares remained under Google's control. The IPO gave Google a market capitalization of more than $23 billion. Many of Google's employees became instant paper millionaires. Yahoo!, a competitor of Google, also benefited from the IPO because it owns 2.7 million shares of Google. The company was listed on the NASDAQ stock exchange under the ticker symbol GOOG. On August 18 2005 (one year after the initial IPO), Google announced that it would sell 14,159,265 (a mathematical joke, see pi) more shares of its stock to raise money. The move would double Google's cash stockpile to $7 billion. Google said it would use the money for "acquisitions of complementary businesses, technologies or other assets". [http://informationweek.com/story/showArticle.jhtml?articleID=169400356]

Today

Since the IPO, Google's stock market capitalization has risen greatly and the stock price has more than quadrupled. On August 19, 2004 the number of shares outstanding was 172.85 million while the "free float" was 19.60 million (which makes 89% held by insiders). In January 2005 the shares outstanding was up 100 million to 273.42 million, 53% of that was held by insiders which made the float 127.70 million (up 110 million shares from the first trading day). The two founders are said to hold almost 30% of the outstanding shares. The actual voting power of the insiders is much higher, however, as Google has a dual class stock structure in which each Class B share gets ten votes compared to each Class A share getting one. Page says in the prospectus that Google has "a dual class structure that is biased toward stability and independence and that requires investors to bet on the team, especially Sergey and me." The company has not reported any treasury stock holdings as of the Q3 2004 report. On June 1, 2005, Google shares gained nearly 4 percent after Credit Suisse First Boston raised its price target on the stock to $350. On the same day, rumors circulated in the financial community that Google would soon be included in the S&P 500. (Source: ) When companies are first listed on the S&P 500 they typically experience a bump in share price. On June 7, 2005, Google was valued at nearly $52 billion, making it one of the world's biggest media companies by stock market value. With Google's increased size comes more competition from large mainstream technology companies. One such example is the rivalry between Microsoft and Google [http://www.pcmag.com/article2/0,1759,1706872,00.asp]. Microsoft has been touting its MSN Search engine to counter Google's competitive position. Furthermore, the two companies are increasingly offering overlapping services, such as webmail (Gmail vs. Hotmail), search (both online and local desktop searching), and other applications (for example, Microsoft's Virtual Earth competes with Google Earth). Some have even suggested that in addition to an Internet Explorer replacement Google is designing its own Linux based operating system called Google OS to directly compete with Microsoft Windows. Rumors of a Google browser are fueled by the fact that Google is the owner of the domain name "gbrowser.com". This corporate feud is most directly expressed in hiring offers and defections. Many Microsoft employees who worked on Internet Explorer have left to work for Google. This feud boiled over into the courts when Kai-Fu Lee, a former vice-president of Microsoft, quit Microsoft to work for Google. Microsoft sued to stop his move by citing Lee's non-compete contract (he had access to much sensitive information regarding Microsoft's plans in China). [http://today.reuters.com/news/newsArticle.aspx?type=internetNews&storyID=2005-09-02T215817Z_01_MCC278865_RTRIDST_0_NET-MICROSOFT-GOOGLE-DC.XML] The case is still in the courts. While Google is the #1 search engine, the company struggles to keep up with rivals such as the well known Yahoo. Although Google and Yahoo differ greatly in the services they offer, Google is trying to redefine itself from an Internet search company to an Internet media company, similar to Yahoo!. Google is trying to become a jack of all trades for the Internet. They are foraying into other businesses which other companies have recently dominated. On June 21 2005 Google announced it has plans to release a pay service and a classified ads service, to rival companies like eBay [http://www.iht.com/articles/2005/06/20/business/google.php]. During the third quarter 2005 Google Conference Call, Eric Schmidt said, "We don't do the same thing as everyone else does. And so if you try to predict our product strategy by simply saying well so and so has this and Google will do the same thing, it's almost always the wrong answer. We look at markets as they exist and we assume they are pretty well served by their existing players. We try to see new problems and new markets using the technology that others use and we build."

Salaries

2005 Prior to the IPO offering, typical salaries at Google were considered within the industry to be quite low. For instance, some system administrators earned no more than $33,000 — while $37,000 at that time was considered to be low by Bay Area employment market levels. Nevertheless, Google's excellent stock performance following the IPO has enabled these early employees to be competitively compensated by participation in the corporation's remarkable equity growth. In 2005 Google has implemented other employee incentives such as the [http://query.nytimes.com/gst/abstract.html?res=F40C1EFC395F0C728CDDAB0894DD404482 Founder's award], as well making higher salary offers to new employees. Beyond monetary compensation, Google's workplace amenities, culture, global popularity, stellar prospects (relative to most Bay Area companies), and strong brand recognition continues to attract far more applicants than there are positions available. (It is estimated that less than one job offer is made per thousand resumes submitted.) Google reportedly employs one in-house legal recruiter just to assist the legal department in evaluating the high volume of resumes from attorneys seeking to join the corporation.

Management

Position: name, age, compensation in USD (as of June 2005)
- CEO: Eric E. Schmidt, 50, $1 see [http://money.cnn.com/2005/04/08/technology/google_salary/index.htm]
- CFO: George Reyes, 51, $781K
- President of Technology: Sergey Brin, 31, $1 see [http://money.cnn.com/2005/04/08/technology/google_salary/index.htm]
- President of Products: Larry E. Page, 32, $1 see [http://money.cnn.com/2005/04/08/technology/google_salary/index.htm]
- Sr. VP of Worldwide Sales: Omid Kordestani, 41, $572K
- VP of Corp. Development, Secretary and Gen. Counsel: David C. Drummond, 42, $776K Founders Brin and Page reportedly earned $1 billion in 2004, but after the IPO in Aug 2004, their compensation is reported in SEC filings annually. Page, Brin, and Schmidt have all declined recent offers of bonuses and increases in compensation by Google's board of directors. Institutional Shareholder Services ranked Google's corporate governance dead last in the list of members of the Standard & Poor's 500. [http://sfgate.com/cgi-bin/article.cgi?file=/chronicle/archive/2004/08/24/BUGBU8D46M1.DTL&type=business] According to the Forbes 400 list (2005), the combined net worth of [http://www.forbes.com/lists/2005/54/XFXI.html Larry Page] and [http://www.forbes.com/lists/2005/54/D664.html Sergey Brin] is $22 billion US. But due to the recent surge in stock price (April 2005-June 2005), their net worth is significantly higher. When recorded on the Forbes 400, Google's stock was around $111. In late 2005 Google shares were valued at $400. Page and Brin, however, had sold $2 billion before some of the largest stock gains.

Analysts

Research analysts covering Google Inc. See also [http://finance.yahoo.com/q/sa?s=GOOG GOOG: Star Analysts for GOOGLE - Yahoo! Finance]
- Mark Mahaney (Citigroup Investment Research)
- John Tinker (Thinkequity Partners)
- Michael Gallant (CIBC World Markets)
- Steve Weinstein (Pacific Crest Securities)
- Imran Kahn (J.P. Morgan Chase)
- Heath Terry (Credit Suisse First Boston)
- Marianne Wolk (Susquehanna Financial Group)
- Nafi Bekteshi (SOS Group)

Technology

Google's services are run on several server farms, each consisting of many thousand low-cost commodity computers running customized versions of Linux. While the company does not provide detailed information about its hardware, it was estimated in 2004 that they were using over 60,000 Linux machines. See Google platform for the details.

Corporate culture

Philosophy

Google is known for its relaxed corporate culture, reminiscent of the Dot-com boom. Google's corporate philosophy is based on many casual principles including: "You can make money without doing evil", "You can be serious without a suit" and "Work should be challenging and the challenge should be fun." A complete list of corporate fundamentals is available on Google's Web site [http://www.google.com/corporate/tenthings.html]. The company encourages equality within corporate levels. Twice a week there is a roller hockey game in the company parking lot.

"Twenty percent" time

Every Google engineer is encouraged to spend 20 percent (20%) of their work time on projects that interest them. Some of these end up as Google services, notably Adsense/Adwords (which provide the majority of the company's revenue), as well as Gmail, Google News and Orkut.

Googleplex

Google's headquarters is called the Googleplex. The lobby is decorated with a piano, lava lamps, and a real-time projection of current search queries. The hallways are full of exercise balls and bicycles. Each employee has access to the corporate recreation center. Recreational amenities are scattered throughout the campus, and include a workout room with weights and rowing machines, locker rooms, washers and dryers, a massage room, assorted video games, Foosball, a baby grand piano, a pool table, and ping pong. In addition to the rec room, there are snack rooms stocked with various cereals, gummy bears, toffee, licorice, cashews, yogurt, carrots, fresh fruit, and dozens of different drinks including fresh juice, soda, and make-your-own cappuccino. After eating, people can relieve themselves on digital toilets similar to Japanese toilets.

IPO and culture

Many people have suggested that after Google's IPO the corporate culture will not be able to stay so "fun" and focused on the future.[http://www.wired.com/news/business/0,1367,63241,00.html?tw=wn_story_related] [http://www.ciol.com/content/news/2004/104043001.asp] The company may be required to answer to its new shareholders who may press the company to reduce employee benefits and to focus on short term advances. Also, it may be more challenging for the company to maintain a collegial atmosphere when approximately 1,000 (30%) of the employees are paper-millionaires. In a report given to potential investors, co-founders Sergey Brin and Larry Page promised that the IPO would not change the company's culture. Later Mr. Page said, "We think a lot about how to maintain our culture and the fun elements." In 2005, articles in The New York Times and other news sources [http://www.smh.com.au/news/technology/search-giant-may-outgrow-its-fans/2005/08/25/1124562975596.html] began suggesting that Google had lost its anti-corporate, no evil philosophy. The New York Times article was headlined, "Relax, Bill Gates; It's Google's Turn as the Villain" [http://www.nytimes.com/2005/08/24/technology/24valley.html].

Google partnerships

On Sept 28 Google announced a partnership with NASA which would involve Google building an R&D center at NASA's Ames Research Center. As reported by SearchEnginejournal.com, NASA and Google were said to be planning to work together on a variety of areas, including large-scale data management, massively distributed computing, bio-info-nano convergence, and encouragement of the entrepreneurial space industry. The new building would also include labs, offices, and housing for Google engineers. Google also has a partnership with Sun Microsystems to help share and distribute each other's technologies [http://www.vnunet.com/computing/news/2143242/sun-partners-google]. As part of the partnership Google will hire employees to help the open source office program OpenOffice.org. Google has an unknown partnership with the Mozilla Foundation. They are looking for software engineers to join them (Google) in collaborative development on the FireFox browser. This is confirmed by a [http://www.google.com/support/jobs/bin/answer.py?answer=29553 job listing] posted on Google. They also offer a download of Firefox with the Google Toolbar pre-installed.

Google's Acquisitions

2001

- Feb 2001: Deja (the Usenet archive, not the company) was acquired, and was incorporated to become part of the re-launched Google Groups [http://groups.google.com/googlegroups/deja_announcement.html].
- Sep 2001: Google acquired Outride Inc. [http://www.google.com/press/pressrel/outride.html].

2003

- Feb 2003: Google acquired Pyra Labs, a weblogging provider and owner of Blogger [http://www.google.com/corporate/timeline.html].
- Apr 2003: Neotonic Software was acquired as part of Google's plan to bring its CRM technology in house [http://www.searchenginejournal.com/index.php?p=621].
- Apr 2003: [http://www.appliedSemantics.com Applied Semantics] was acquired [http://www.appliedsemantics.com] for $102 Million [http://www.businessweek.com/magazine/content/05_49/b3962001.htm].
- Sep 2003: Kaltix was acquired to develop and launch Google Personal [http://www.clickz.com/news/article.php/3085921].
- Oct 2003: Sprinks was acquired to enhance Google's Adwords and AdSense program [http://www.searchnewz.com/searchnewz-12-20031105GoogleAcquiresSprinks.html].
- Oct 2003: Google acquired Genius Labs, another web logging provider [http://www.bizstone.com/archive/2003_10_01_archive.html#106553958799049227].

2004

- Apr 2004: Ignite Logic was acquired [http://battellemedia.com/archives/000653.php].
- Jun 2004: Google made a $10M investment into partial ownership of Baidu [http://english.people.com.cn/200406/16/eng20040616_146493.html].
- Jul 2004: [http://www.picasa.com Picasa] was acquired to provide picture management tools to Blogger [http://www.google.com/press/pressrel/picasa.html].
- Oct 2004: Keyhole was acquired to provide the core mapping capabilities in Google Maps and Google Earth [http://www.google.com/press/pressrel/keyhole.html].
- Sept-Dec 2004, Google revealed in its annual [http://www.sec.gov/Archives/edgar/data/1288776/000119312505065298/d10k.htm 10-K filing] that it had acquired 2 Silicon Valley start-up companies: [http://www.zipdash.com ZipDash] and Where2. The technology provided by ZipDash was used to develop and launch Google Ride Finder. Where2 was a mapping software provider.

2005

- Mar 2005: Web analytics tools provider Urchin Software Corporation was acquired [http://www.google.com/intl/en/press/pressrel/urchin.html].
- May 2005: DodgeBall [http://www.dodgeball.com], a social networking software provider for mobile devices, was acquired [http://www.dodgeball.com/aboutus_dball_google.php].
- Jul 2005: Google, in combination with Goldman Sachs, and the Hearst Corp., invests a total of $100 Million into [http://www.currentgroup.com Current Communications Group] [http://www.lightreading.com/document.asp?doc_id=76942&WT.svl=news1_5].
- Jul 2005: Google announced in its Q2 quarterly conference call that it had acquired [http://www.akwan.com.br/index_en.html Akwan Information Technologies] as a part of its plan to open an R&D office and expand its presence into Latin and South America. [http://blog.searchenginewatch.com/blog/050720-175228]
- Aug 2005: Google acquires [http://www.Android.com Android Inc.], a software provider for mobile devices [http://www.businessweek.com/technology/content/aug2005/tc20050817_0949_tc024.htm]
- September 28: both Google and Ames Research Center disclosed details to a long-term research partnership. In addition to pooling engineering talent, Google plans to build a 1-million square foot facility on the ARC campus.[http://www.nasa.gov/centers/ames/news/releases/2005/05_50AR.html]

Criticism and controversy

Copyright issues

A number of organizations have used the Digital Millennium Copyright Act to demand that Google remove references to allegedly copyrighted material on other sites. Google typically handles this by removing the link as requested and including a link to the complaint in the search results. There have also been complaints that Google's Web cache feature violates copyright. However, Google provides mechanisms for requesting that caching be disabled (which Google respects; it also honors the robots.txt file which is another mechanism that allows operators of a website to request that part or all of their site not be included in search engine results). On June 2005, Google Watch revealed the details of a contract between the University of Michigan and Google to create digitized copies of the copyrighted materials stored at the University's library. This contract is part of Google Print's effort to digitize millions of books and make the full text searchable. There are claims that it is a violation of copyright laws to use copyrighted material for profit by placing search ads beside the search results of these digitized books. Also, Google is setting a new precedent by making digital copies of copyrighted material on a wide scale without explicit permission from copyright holders. Meanwhile, Google claims that it is in compliance with all existing and historical applications of copyright laws regarding books. The contract between Google and the U. of Michigan does make it clear that Google will provide only excerpts of copyright text in a search. The contract says that it will comply with "fair use", an exemption in copyright law that allows people to reproduce portions of text of copyrighted material for research purposes.

Dispute with Agence France Presse

In March 2005, Agence France Presse (AFP) sued Google for $17.5 million, alleging that Google News infringed on its copyright because "Google includes AFP's photos, stories and news headlines on Google News without permission from Agence France Presse." [http://news.dcealumni.com/376/20305-googles-news-sued-for-infringing-agence-france-presse-copyrighted-work/] It was also alleged that Google ignored a cease and desist order, though Google counters that it has opt-out procedures which AFP could have followed but did not. It is possible that AFP will make additional arguments in court that it has not yet made in public, but currently, many pundits are confused by the decision to sue [http://weblog.physorg.com/news1362.html][http://www.bayoubuzz.com/articles.aspx?aid=3538][http://www.earthtimes.org/articles/show/2080.html] because Google does not display the full article on its site, provides a link to one of AFP's 600 online clients such as Singapore's Channel NewsAsia (which presumably benefits AFP because more people view the article and advertising), and because the articles are available via the providers' websites regardless of Google's actions. It was argued that had AFP wanted to prevent free use of its articles, it should have asked its providers to require subscriptions rather than suing Google. Additionally, "in 2002, a federal appeals court ruled that Web sites may reproduce and post 'thumbnail' or downsized versions of copyrighted photographs," so Google News' thumbnails are likely legal. [http://news.dcealumni.com/376/20305-googles-news-sued-for-infringing-agence-france-presse-copyrighted-work/] Still, AFP argues that the headline and first sentence of an article constitutes the "heart" of the work and that reproducing it is copyright infringement. According to the Canada Free Press, "Google Inc. is now attempting to remove all postings of Agence-France Presse material from its site, although AFP spokesmen say that even if this is done, the lawsuit will continue... It seems that the basis of the lawsuit is just the abstract notion of copyright without any real damages to justify the action." The article concluded "It would be a sad day for those who look to the Internet for news if AFP is successful in limiting what Google can display... AFP's lawsuit, if successful, is bound to have a major impact on how news is delivered on the Internet." The lawsuit's outcome will likely depend on whether Google can successfully argue that its use of AFP's material constitutes "fair use" under copyright law. Google could even argue that it "adds value" to AFP's news without harming the French news wholesaler.[http://www.michigandaily.com/vnews/display.v/ART/2005/03/29/424942b9271ad]

Lawsuit by Authors Guild

On September 20, 2005, the Authors Guild, a group that represents 8,000 U.S. authors, with a children's book author, and a former Poet Laureate of the United States, filed a class action suit in federal court in Manhattan against Google over its unauthorized scanning and copying of books through its Google Library program. The lawsuit seeks damages and an injunction that will prevent the company from continuing their very ambitious digitization project. Arguments in the case will hinge around the interpretation of the four factors of Fair Use. Many commentators in the world of copyright law and technology were not surprised by this development as The Authors Guild has also been involved in attempting to make online publishers pay royalties to writers whose stories appear in any number of online databases without their express consent. In a concession to general concerns about the nature of their project, Google had announced plans back in August that they would respect the wishes of copyright holders who contacted the company to inform them that they did not want their works included in this digitization project.
- [http://scout.wisc.edu/Reports/ScoutReport/2005/scout-050923-inthenews.php#1 Scout Report] "Authors’ group files lawsuit against Google" Sept, 2005
- [http://www.policybandwidth.com/doc/googleprint.pdf The Google Print Library Project: A Copyright Analysis - .pdf]
- [http://www.washingtonpost.com/wp-dyn/content/article/2005/09/20/AR2005092001416.html Washington Post] Sept. 20, 2005 "Google library push faces lawsuit by US authors"

Multinational corporation

Google is a multinational corporation, having offices in over a dozen countries [http://www.google.ie/intl/en/corporate/address.html]. In order to comply with the varying laws of these countries, several versions of Google restrict very specific keyword searches. According to American law, any copyright owner can require material to be removed via the Digital Millennium Copyright Act, whereas under French and German law, for example, hate speech and Holocaust denial are illegal. Google complies with these laws by banning keyword searches related to these terms. Google's Terms of Service allow it to comply with the laws of any one country, providing information that was originated (or that Google stores) in another country. Any data stored on Google is therefore subject to being turned over to any country, including China.

China's Censoring

The People's Republic of China, whose human rights record has been widely criticized by the international community, has in the past restricted citizen access to popular search engines such as Altavista, Yahoo!, and Google. The mirror search site elgooG has been used by Chinese citizens to get around blocked content. This complete ban is currently lifted. However, the government remains active in filtering Internet content. In the summer of 2005 Google's name became associated with commercial contracts between the Government of China, Microsoft and Cisco Systems which block access to websites using words like "democracy." Google has been involved with the removal of specific sites that are blocked in China from their Chinese news portal. The French news agency, AFP, reported that Microsoft, Yahoo! and Google have all agreed to cooperate in censoring the Internet from their China based sites by filtering out content objectionable to the Chinese government. The list of forbidden words includes "democracy," "freedom," "human rights," and "Taiwan independence." In October 2005, Blogger and access to the Google Cache were made available in China; however, in December 2005, some Chinese users of Blogger reported that their access to the site was once again restricted.

Legal issues

Google's efforts to refine its database has led to some legal controversy, notably a lawsuit in October 2002 from the company SearchKing which sought to sell advertisements on pages with inflated Google rankings. In its defense, Google stated that its rankings are its constitutionally protected opinions of the web sites that it indexes. A judge subsequently threw out SearchKing's lawsuit in mid-2003 on precisely these grounds. In late 2003 and early 2004, there were rumors that Google would be sued by the SCO Group over their use of the Linux operating system, in conjunction with SCO's lawsuit against IBM over the claimed ownership of intellectual property rights relating to Linux. In May 2004, the Baltimore Sun interviewed Peri Fleisher, a great-niece of Edward Kasner, the mathematician whose nephew coined the word googol, who said Kasner's descendants were "exploring" legal action against Google due to its name. Google recently settled a patent infringement lawsuit with Yahoo! by issuing 2.7 million shares. Yahoo! had earlier alleged that Google's AdSense program violated a patent held by Yahoo!'s Overture unit. The settlement cost Google around $275 million which resulted in the company posting a net loss in the third quarter of 2004.

Personnel issues

Former Google sales executive Christina Elwell, promoted to national sales director at Google in late 2003, accused her supervisor of discrimination against her after informing him of her pregnancy [http://news.com.com/Google+hit+with+job+discrimination+lawsuit/2100-1030_3-5807158.html?tag=nl]. After the loss of 3 of her quadruplets, which she claimed was due to the stressful circumstances created by Google, Elwell sued the company. She also refused an offer from Shona Brown, Google Vice President of Business Operations, to reinstate her to a "low-level operations position".

Partiality

In February 2003, Google banned the ads of Oceana, a two-and-a-half-year-old non-profit organization, which was protesting the environmental effects of a major cruise ship operation's sewage treatment practices. Google claimed that their editorial policy states, "that Google does not accept advertising if the ad or site advocates against other individuals, groups, or organizations."

Offensive search results

In April 2004, Google received complaints that a search for "Jew" on its site listed the anti-Semitic website Jew Watch at or near the top of the list. Google responded that this was due to the content-neutrality of the PageRank algorithm, and the fact that racists used the specific word "Jew" (as opposed to "Jewish" or "Judaism") more often than others. [http://www.google.com/explanation.html] As a reaction, some webloggers launched a Google bomb to put the corresponding Wikipedia article at the top of the search results. As of December 2005, Jew Watch remains the #1 link. There is also an option for google account users, who are logged in, to remove offensive search results.

Privacy

Main article: Google and privacy issues Some have pointed out the dangers and privacy implications of having a centrally located, widely popular data warehouse of millions of Internet users' searches, and how under controversial existing U.S. law, Google can be forced to hand over all such information to the U.S. government, or any other government of a country which Google serves. It has been claimed that Google infringes the privacy of visitors by uniquely identifying them using cookies which are used to track Web users' search history. The cookies possess notably distant expiration dates and it is claimed users' searches are recorded without permission for advertising purposes. In response Google claims cookies are necessary to maintain user preferences between sessions and offer other search features. The use of cookies with such distant expiration dates is not very uncommon. Some users believe the processing of email message content by Google's Gmail service goes beyond proper use. The point is often made that people without Gmail accounts, who have not agreed to the Gmail terms of service, but send email to Gmail users have their correspondence analyzed without permission. Google claims that mail sent to or from Gmail is never read by a human being beyond the account holder, and is only used to improve relevance of advertisements. Other popular email services such as Hotmail also scan incoming email to try to determine whether it is unsolicited spam email (which Gmail also does). Chris Hoofnagle, associate director of the Electronic Privacy Information Center in Washington, DC warned that "As courts become more frequent integrators of electronic records, there is a greater risk of Google ... becoming a serious privacy threat."

The PageRank system

Google's central PageRank system has been criticized. Some, such as Daniel Brandt, calling it "undemocratic". Common arguments are that the system is unfairly biased towards large web sites, and that the criteria for a page's importance are not subject to peer review. It must be stated in Google's defense that PageRank is a fully automated system which is impartial insofar as it knows no personal bias. However, it must also be stated that Google's system relies on human oversight, and use of company names on Adwords, or deletion of critical sites from Google results (for example, sites critical of Scientology), is decided by individual human beings according to company policy. It remains unclear whether any process could assert the importance of a page in a way that would draw less criticism than the current PageRank system. The system is also susceptible to manipulation and fraud through the use of dummy sites, an issue which does, however, plague all search engines. See Google bomb and Spamdexing.

Specific searches

Spamdexing See also List of Google services and tools For users searching for more specific results, at the top of Google pages are additional tabs to more narrowly define a user's search results.
- Images: Allows the user to limit a search to images on the Internet; the images are identified by Google by the image name saved on the webpage and context information about the page.
- Groups: Allows the user to create, search and browse groups for discussion.
- News: Brings the user directly to the Google News search page, formatted similar to news websites such as MSNBC or BBC News. The search page provides the option for twenty countries. Google.com.au allows selection criteria for Australia.
- Froogle: Allows the user to shop online searching websites within a user specified budget.
- Local: Searches for places (such as shops or other landmarks) in a geographical area, and displays maps and driving directions. Maps include road maps, medium-resolution satellite images, and "hybrid" maps combining both. See also Google Maps. Currently it provides full service only in the U.S., Canada, and the U.K.
- Earth: Allows the user to download a program to have a 3D version of satellite pictures.
- Desktop: Allows the user to search their computer for files, folders, and emails. See Google Desktop.
- Talk: Allows users with Gmail accounts to communicate with each other through instant messaging and have online conversations.
- Videos: Allows the user to limit a search to videos on the Internet; Use Google to find reviews and showtimes for movies playing somewhere near you.
- Blogs: Blog Search allows the user to only search blogs based on RSS feeds. Results can be sorted by relevance or by date. Although it allows you to search specific blogs, this feature is currently malfunctioning.
- Scholar: Allows users to search some peer-reviewed, scholarly journals. Non-peer reviewed material is also included in the index. Clicking on the "More" tab at the top directs the user to even more Google Services such as Blogger, University Searches, Google products in their Labs section, Help and Alerts.

April Fool's Day jokes

Main article: Google's hoaxes Google has a tradition of creating April Fool's Day jokes such as [http://www.google.com/mentalplex/ Google MentalPlex] which featured the use of mental power to search the Web. In 2002 they claimed that pigeons were the [http://www.google.com/technology/pigeonrank.html secret] behind their growing search engine. In 2004 it featured [http://www.google.com/jobs/lunar_job.html Google Lunar] which featured jobs on the moon and in 2005 a fictitious, brain-boosting drink termed [http://www.google.com/googlegulp/ Google Gulp] was announced. You can find other pranks hidden between google's pages. In the languages list you can find the [http://www.google.com/intl/xx-bork/ Bork! Bork! Bork!] version. Bork! is the mock Swedish of the Muppets Show's Swedish Chef. Some people thought the announcement of Gmail in 2004 around April Fools Day was actually a joke.

References

- Mahadevan, Jeremy (Nov. 16, 2005). "Googlicious". New Straits Times, p. L12–L13.
- "What's the catch?" (Nov. 16, 2005). New Straits Times, p. L13.

External links

Company websites

- [http://www.google.com Google]
- [http://base.google.com/ Google Base]
- [http://www.google.com/help/features.html Google Help: Search Features]
- [http://www.google.com/sms Google SMS Search]
- [http://www.google.com/ig Google Personalized Start Page]
- [http://video.google.com/ Google Video Search] - Also see: [http://video.google.com/videoplay?docid=3383042311441257769&q=google+factory+tour Google Factory Tour]
- [http://www.google.com/downloads/ Google Software Downloads]
- [http://www.google.com/corporate/ Google Corporate Information]
- [http://www.google.com/corporate/history.html Google's History]
- [http://gmail.google.com Gmail] — Google's e-mail service
- [http://www.ipogoogle.org/ Google's Initial Public Offering]
- [http://www.google.org Google.org] — The philanthropic arm of Google
- [http://googleblog.blogspot.com Google Blog] — Off

Protein

. This protein was the first to have its structure solved by X-ray crystallography by Max Perutz and Sir John Cowdery Kendrew in 1958, which led to them receiving a Nobel Prize in Chemistry.]] A protein (in Greek πρωτεϊνη = first thread) is a complex, high-molecular-weight organic compound that consists of amino acids joined by peptide bonds. Proteins are essential to the structure and function of all living cells and viruses. Many proteins are enzymes or subunits of enzymes. Other proteins play structural or mechanical roles, such as those that form the struts and joints of the cytoskeleton, serving as biological scaffolds for the mechanical integrity and tissue signalling functions. Still more functions filled by proteins include immune response and the storage and transport of various ligands. In nutrition, proteins serve as the source of amino acids for organisms that do not synthesize those amino acids natively. Proteins are one of the classes of bio-macromolecules, alongside polysaccharides, lipids, and nucleic acids, that make up the primary constituents of living things. They are among the most actively-studied molecules in biochemistry, and were discovered by Jöns Jakob Berzelius in 1838. Almost all natural proteins are encoded by DNA. DNA is transcribed to yield RNA, which serves as a template for translation by ribosomes.

Properties of Protein

Structure

ribosome Main article: Protein structure Proteins are amino acid chains that fold into unique 3-dimensional structures. The shape into which a protein naturally folds is known as its native state, which is determined by its sequence of amino acids. Thus, proteins are their own polymers, with amino acids being the monomers. Biochemists refer to four distinct aspects of a protein's structure:
- Primary structure: the amino acid sequence
- Secondary structure: highly patterned sub-structures—alpha helix and beta sheet—or segments of chain that assume no stable shape. Secondary structures are locally defined, meaning that there can be many different secondary motifs present in one single protein molecule.
- Tertiary structure: the overall shape of a single protein molecule; the spatial relationship of the secondary structural motifs to one another
- Quaternary structure: the shape or structure that results from the union of more than one protein molecule, usually called subunit proteins subunits in this context, which function as part of the larger assembly or protein complex. In addition to these levels of structure, proteins may shift between several similar structures in performing their biological function. In the context of these functional rearrangements, these tertiary or quaternary structures are usually referred to as "conformations," and transitions between them are called conformational changes. Proteins are separated into two groups: Complete and Incomplete. Incomplete proteins are from plants and do not include all 20 amino acids. Complete proteins come from an animal and include all 20 amino acids. You get protein from mostly everything you eat, but whether all the amino acids are in them depends on what the substance is. The primary structure is held together by covalent peptide bonds, which are made during the process of translation. The secondary structures are held together by hydrogen bonds. The tertiary structure is held together primarily by hydrophobic interactions but hydrogen bonds, ionic interactions, and disulfide bonds are usually involved too. The process by which the higher structures form is called protein folding and is a consequence of the primary structure. The mechanism of protein folding is not entirely understood. Although any unique polypeptide may have more than one stable folded conformation, each conformation has its own biological activity and only one conformation is considered to be the active, or native conformation. The two ends of the amino acid chain are referred to as the carboxy terminus (C-terminus) and the amino terminus (N-terminus) based on the nature of the free group on each extremity.

Working with proteins

Proteins are sensitive to their environment. They may only be active in their native state, over a small pH range, and under solution conditions with a minimum quantity of electrolytes. A protein in its native state is often described as folded. A protein that is not in its native state is said to be denatured. Denatured proteins generally have no well-defined secondary structure. Many proteins denature and will not remain in solution in distilled water. One of the more striking discoveries of the 20th century was that the native and denatured states in many proteins were interconvertible, that by careful control of solution conditions (by for example, dialyzing away a denaturing chemical), a denatured protein could be converted to native form. The issue of how proteins arrive at their native state is an important area of biochemical study, called the study of protein folding. Through genetic engineering, researchers can alter the sequence and hence the structure, "targeting", susceptibility to regulation and other properties of a protein. The genetic sequences of different proteins may be spliced together to create "chimeric" proteins that possess properties of both. This form of tinkering represents one of the chief tools of cell and molecular biologists to change and to probe the workings of cells. Another area of protein research attempts to engineer proteins with entirely new properties or functions, a field known as protein engineering. Protein-protein interactions can be screened for using two-hybrid screening.

Protein regulation

Various molecules and ions are able to bind to specific sites on proteins. These sites are called binding sites. They exhibit chemical specificity. The particle that binds is called a ligand. The strength of ligand-protein binding is a property of the binding site known as affinity. Since proteins are involved in practically every function performed by a cell, the mechanisms for controlling these functions therefore depend on controlling protein activity. Regulation can involve a protein's shape or concentration. Some forms of regulation include:
- Allosteric modulation: When the binding of a ligand at one site on a protein affects the binding of ligand at another site.
- Covalent modulation: When the covalent modification of a protein affects the binding of a ligand or some other aspect of the protein's function.

Diversity

Proteins are generally large molecules, having molecular masses of up to 3,000,000 (the muscle protein titin has a single amino acid chain 27,000 subunits long). Such long chains of amino acids are almost universally referred to as proteins, but shorter strings of amino acids are referred to as "polypeptides," "peptides" or rarely, "oligopeptides". The dividing line is undefined, though "polypeptide" usually refers to an amino acid chain lacking tertiary structure which may be more likely to act as a hormone (like insulin), rather than as an enzyme (which depends on its defined tertiary structure for functionality). Proteins are generally classified as soluble, filamentous or membrane-associated (see integral membrane protein). Nearly all the biological catalysts known as enzymes are soluble proteins (with a recent notable execption being the discovery of ribozymes, RNA molecules with the catalytic properties of enzymes.) Antibodies, the basis of the adaptive immune system, are another example of soluble proteins. Membrane-associated proteins include exchangers and ion channels, which move their substrates from place to place but do not change them; receptors, which do not modify their substrates but may simply shift shape upon binding them. Filamentous proteins make up the cytoskeleton of cells and much of the structure of animals: examples include tubulin, actin, collagen and keratin, all of which are important components of skin, hair, and cartilage. Another special class of proteins consists of motor proteins such as myosin, kinesin, and dynein. These proteins are "molecular motors," generating physical force which can move organelles, cells, and entire muscles. muscle

Role of Protein

Functions

Proteins are involved in practically every function performed by a cell, including regulation of cellular functions such as signal transduction and metabolism. For example, protein catabolism requires enzymes termed proteases and other enzymes such as glycosidases.

Within Nutrition

Protein is an important macronutrient to the human diet, supplying the body's needs for nitrogen and amino acids, the building blocks of proteins. The exact amount of dietary protein needed to satisfy these requirements may vary widely depending on age, sex, level of physical activity, and medical condition, as well as the RDA specified by the state. The recommended intake of protein differs from country to country, but it is marginalised between 0.8 and 1.2g / kg b.w (Per kilogram of bodyweight), however , in more serious athletes, requiring strength, the figure is somewhat between 1.0 and 2.0g per kilogram of Body weight, which is referred to as the maximum protein intake:benefits ratio. Although proteins are found in all foods, be it only in small amounts , protein is still well concentrated in foods such as legumes, nuts, and dairy products, the majority of which are protein choices for vegetarians. Protein is the major component in the regulation, growth and differentation of muscles, tendons, enzymes, skin, hair, eyes, as well as a tremendous variety of other organs and processes. The quality of protein intake is particularly important because different proteins supply essential amino acids in different proportions. Given an adequate intake of nitrogen, the human body can manufacture 10 of the 18 amino acids from glucose. The remaining 8 amino acids (threonine, valine, tryptophan, isoleucine, leucine, lysine, phenylalanine, and methionine) cannot be manufactured by the body and must be acquired through supplementation. Thus, they are termed essential amino acids. For use within the body, the majority of protein taken from food consumed is converted by protein catabolism into ammonia which, due to its toxicity, must be converted to either urea or uric acid,or in some animals is excreted in urine. Proteins possessing equal proportions of all essential amino acids in relatively abundant quantities are often termed "complete", or "High-Quality" Proteins, which are generally obtained from animal proteins, such as meat , and are rated using PDCAAS (Protein Digestibility Corrected Amino Acid Score). Despite what the name suggests, quality proteins are not essential for good supplementation or nutrition within the average person, however, the difference between amino acids in plant and animal proteins is discernable, particularly for athletes or bodybuilders as plant proteins lack two major amino acids found in animal proteins; lysine within grains, and methionine within legumes, major benefactors to a major athlete's dietary regime. Neverthelss, in terms of quality, amino acids found in plant and animal extracts are identical. Protein deficiency can lead to symptoms such as fatigue, insulin resistance, hair loss, loss of hair pigment, loss of muscle mass , low body temperature, hormonal irregularities, as well as loss of skin elsaticity . Severe protein deficiency, encountered only in times of famine, is fatal, due to the lack of material for the body to facilitate as energy. It has been known that in some "wild diets", in which people lose mass amounts of weight in a short period of time are attributed to deficiencies in protein, and thus loss in muscle mass, and not fat, which is widely known as a dangerous practice, particularly because of the benefits of muscle mass over fat. Excessive protein intake has also been linked to several problems;
- overreaction within the immune system
- liver dysfunction due to increased toxic residues
- loss of bone density, frailty of bones due to increased acidity in the blood and foundering (foot problems) in horses. It is assumed by reasearchers on the field, that excessive intake of protein forced increased calcium excretion. If there is to be excessive intake of protein, it is thought that a regular intake of calcium would be able to stablilise, or even increase the uptake of calcium by the small intestine, which would be more beneficial in older women . Proteins are often progenitors in allergies and allergic reactions to certain foods. This is because the structure of each form of protein is slightly different; some may trigger a response from the immune system while others remain perfectly safe. Many people are allergic to casein, the protein in milk; gluten, the protein in wheat and other grains; the particular proteins found in peanuts; or those in shellfish or other seafoods. It is extremely unusual for the same person to adversely react to more than two different types of proteins, due to the diversity between protein or amino acid types.

History

The first mention of the word protein, which means of first rank, were from a letter sent by Jöns Jakob "Jinglehimer Schmidt" Berzelius to Gerhardus Johannes Mulder on 10. July 1838, where he wrote: :«Le nom protéine que je vous propose pour l’oxyde organique de la fibrine et de l’albumine, je voulais le dériver de πρωτειοξ, parce qu’il paraît être la substance primitive ou principale de la nutrition animale.» Translated as: :"The name protein that I propose for the organic oxide of fibrin and albumin, I wanted to derive from [the Greek word] πρωτειοξ, because it appears to be the primitive or principal substance of animal nutrition." Investigation of proteins and their properties had been going on since about 1800 when scientists were finding the first signs of this, at the time, unknown class of organic compounds.

References

# Kerstetter, J. E., O'Brien, K. O., Insogna, K. L. (2003) "[http://www.ajcn.org/cgi/content/full/78/3/584S Dietary protein, calcium metabolism, and skeletal homeostasis revisited]" . J Clin Endocrinol Metab Vol 78, p584S-592S. # Kerstetter, J. E., O'Brien, K. O., Caseria, D.M, Wall, D. E. & Insogna, K. L (2005) "The impact of dietary protein on calcium absorption and kinetic measures of bone turnover in women" . J Clin Endocrinol Metab (2005) Vol 90, p26-31, . # Devine, A., Dick, I. M,, Islam I. M., Dhaliwal, S. S. & Prince, R. L. (2005) "Protein consumption is an important predictor of lower limb bone mass in elderly women" . Am J Clin Nutr (2005) volume 81 pages 423-428, . # Jeukendrup, A. & Gleeson, M. (2004) Sport Nutrition - An Introduction to Energy Production and Performance USA : Human Kinetics # Bean, A. (2004) Sport Nutrition for Serious Athletes London : Routledge

External links

- [http://www.expasy.uniprot.org UniProt the Universal Protein Resource]
- [http://www.proteinatlas.org Human Protein Atlas]
- [http://www.ihop-net.org/UniPub/iHOP/ iHOP - Information Hyperlinked over Proteins]
- [http://www.biochemweb.org/proteins.shtml Proteins: Biogenesis to Degradation - The Virtual Library of Biochemistry and Cell Biology]
- [http://web.mit.edu/lms/www/ MIT's Laboratory for Protein Molecular Self-Assembly]
- [http://www.puramatrix.com/pubs Numerous publications on synthetic biomimetic protein-based biomaterials]
- [http://www.westernblotting.org Protein Research: Western Blot Protocols, Troubleshooting and Theory]
- [http://www.rcsb.org The Protein Databank: The single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data.]
- [http://web.indstate.edu/thcme/mwking/amino-acid-metabolism.html Amino acid metabolism]
- [http://www.biochem.szote.u-szeged.hu/astrojan/protein2.htm Protein Images] Category:Molecular biology Category:Biochemistry Category:Nutrition zh-min-nan:Nn̄g-pe̍h-chit ko:단백질 ja:蛋白質 simple:Protein th:โปรตีน

UniProt

UniProt is the universal protein database, a central repository of protein data created by combining Swiss-Prot, TrEMBL and PIR. This makes it the world's most comprehensive resource on protein information. As the diverse worldwide genome projects advance, new data about proteins is added daily.

External references

- [http://www.expasy.uniprot.org/ expasy.uniprot.org] Category:Proteins

UniProt

External references

- [http://www.expasy.uniprot.org/ expasy.uniprot.org] Category:Proteins

Source

The word source has more than one meaning:

Information

- Journalism sourcing
- in research: a source of information referred to by citation (see primary source, secondary source, tertiary source)

Sciences

- Source (river or stream), the origin of a river or stream, usually a lake, a spring or headwaters
- an area of positive divergence, or more generally, including a negative source or sink, an area of non-zero divergence
- one of the terminals of a field-effect transistor (the others are the gate and drain terminals)
- in acoustics: the sound source, mostly as noise, but also as useful music of an orchestra.

Technology

- Source code for software, see also free software or open-source software
- The Source engine, a proprietary game engine developed by Valve Software for Half-Life 2
- Short name used by PC gamers for the version of Counter-Strike utilizing the Source engine
- A SCSI endpoint
- Communication source

Entertainment

- Source (singer), a singer from Japan

IFRAME

HTML element#Other_containers

HTML

In computing, HyperText Markup Language (HTML) is a markup language designed for the creation of web pages and other information viewable in a browser. HTML is used to structure information — denoting certain text as headings, paragraphs, lists and so on — and can be used to describe, to some degree, the appearance and semantics of a document. Originally defined by Tim Berners-Lee and further developed by the IETF with a simplified SGML syntax, HTML is now an international standard (ISO/IEC 15445:2000). Later HTML specifications are maintained by the World Wide Web Consortium (W3C). Early versions of HTML were defined with looser syntactic rules which helped its adoption by those unfamiliar with web publishing. Web browsers commonly made assumptions about intent and proceeded with rendering of the page. Over time, the trend in the official standards has been to create an increasingly strict language syntax; however, browsers still continue to render pages that are far from valid HTML. XHTML, which applies the stricter rules of XML to HTML to make it easier to process and maintain, is the W3C's successor to HTML. As such, many consider XHTML to be the "current version" of HTML, but it is a separate, parallel standard; the W3C continues to recommend the use of either XHTML 1.1, XHTML 1.0, or HTML 4.01 for web publishing.

Introduction

HTML is a form of markup that is oriented toward the construction of single-page text documents with specialized rendering software called HTML user agents, the most common example of which is a web browser. HTML provides a means by which the document's content can be annotated with various kinds of metadata and rendering hints. The rendering cues may range from minor text decorations, such as specifying that a certain word be underlined or that an image be inserted, to sophisticated imagemaps and form definitions. The metadata may include information about the document's title and author, structural information such as headings, paragraphs, lists, and information that allows the document to be linked to other documents to form a hypertext web. HTML is a text based format that is designed to be both readable and editable by humans using a text editor. However, writing and updating a large number of pages by hand in this way is time consuming, requires a good knowledge of HTML and can make consistency difficult to maintain. Visual HTML editors such as Macromedia Dreamweaver, Adobe GoLive or Microsoft FrontPage allow the creation of web pages to be treated much like word processor documents. The code generated by these programs can be of poor quality. However, the open-source visual HTML editor Nvu generates code of high quality. HTML can be generated on the fly using a server-side scripting system such as Perl, PHP, JSP, or ASP. Many web applications like content management systems, wikis and web forums generate HTML pages.

Version history of the standard

- [http://www.w3.org/MarkUp/draft-ietf-iiir-html-01.txt Hypertext Markup Language (First Version)], published June 1993 as an Internet Engineering Task Force (IETF) working draft (not standard).
- [http://www.ietf.org/rfc/rfc1866.txt HTML 2.0], published November 1995 as IETF RFC 1866, and declared obsolete/historic by RFC 2854 in June 2000.
- [http://www.w3.org/TR/REC-html32 HTML 3.2], published January 14, 1997 as a W3C Recommendation.
- [http://www.w3.org/TR/REC-html40-971218/ HTML 4.0], published December 18, 1997 as a W3C Recommendation.
- [http://www.w3.org/TR/html401 HTML 4.01], published December 24, 1999 as a W3C Recommendation.
- [http://www.purl.org/NET/ISO+IEC.15445/15445.html ISO/IEC 15445:2000] ("ISO HTML", based on HTML 4.01 Strict), published May 15, 2000 as an ISO/IEC international standard.
- [http://www.w3.org/TR/xhtml1/ XHTML 1.0], published January 26, 2000 as a W3C Recommendation, later revised and republished August 1, 2002. There is no official standard HTML 1.0 specification because there were multiple informal HTML standards at the time. However, some people consider the initial edition provided by Tim Berners-Lee to be the definitive HTML 1.0. That version did not include an IMG element type. Work on a successor for HTML, then called "HTML+", began in late 1993, designed originally to be "A superset of HTML…which will allow a gradual rollover from the previous format of HTML". The first formal specification was therefore given the version number 2.0 in order to distinguish it from these unofficial "standards". Work on HTML+ continued, but it never became a standard. The HTML 3.0 standard was proposed by the newly formed W3C in March 1995, and provided many new capabilities such as support for tables, text flow around figures, and the display of complex math elements. Even though it was designed to be compatible with HTML 2.0, it was too complex at the time to be implemented, and when the draft expired in September 1995 work in this direction was discontinued due to lack of browser support. HTML 3.1 was never officially proposed, and the next standard proposal was HTML 3.2 (code-named "Wilbur"), which dropped the majority of the new features in HTML 3.0 and instead adopted many browser-specific element types and attributes which had been created for the Netscape and Mosaic web browsers. Math support as proposed by HTML 3.0 finally came about years later with a different standard, MathML. HTML 4.0 likewise adopted many browser-specific element types and attributes, but at the same time began to try to "clean up" the standard by marking some of them as deprecated, and suggesting they not be used. Minor editorial revisions to the HTML 4.0 specification were published as HTML 4.01. The most common extension for files containing HTML is .html, however, older operating systems, such as DOS, limit file extensions to three letters, so a .htm extension is also used. Although perhaps less common now, the shorter form is still widely supported by current software.

Markup element types

Below are the kinds of markup element types in HTML.
- Structural markup. Describes the purpose of text. For example, ::Golf :directs the browser to render "Golf" as a second-level heading, similar to "Markup element types" at the start of this section. Structural markup does not denote any specific rendering, but most web browsers have standardised on how elements should be formatted. For example, by default, headings like these will appear in large, bold text. Further styling should be done with Cascading Style Sheets (CSS).
- Presentational markup. Describes the appearance of the text, regardless of its function. For example, ::boldface :will render "boldface" in bold text. In the majority of cases, using presentational markup is inappropriate, and presentation should be controlled by using CSS. In the case of both bold and italic there are elements which usually have an equivalent visual rendering but are more semantic in nature, namely strong emphasis and emphasis respectively. It is easier to see how an aural user agent should interpret the latter two elements.
- Hypertext markup. Links parts of the document to other documents. For example, ::Wikipedia :will render the word [http://wikipedia.org Wikipedia] as a hyperlink to the specified URL.

The Document Type Definition

In order to specify which version of the HTML standard they conform to, all HTML documents should start with a Document Type Declaration (informally, a "DOCTYPE"), which makes reference to a Document Type Definition (DTD). For example: This declaration asserts that the document conforms to the Strict DTD of HTML 4.01, which is purely structural, leaving formatting to Cascading Style Sheets. In some cases, the presence or absence of an appropriate DTD may influence how a web browser will display the page. In addition to the Strict DTD, HTML 4.01 provides Transitional and Frameset DTDs. The Transitional DTD was intended to gradually phase in the changes made in the Strict DTD, while the Frameset DTD was intended for those documents which contained frames.

Separation of style and content

Efforts of the web development community have led to a new thinking in the way a web document should be written; XHTML epitomizes this effort. Standards stress using markup which suggests the structure of the document, like headings, paragraphs, block quoted text, and tables, instead of using markup which is written for visual purposes only, like <font>, <b> (bold), and <i> (italics). Some of these elements are not permitted in certain varieties of HTML, like HTML 4.01 Strict. CSS provides a way to separate the HTML structure from the content's presentation, by keeping all code dealing with presentation defined in a CSS file. See separation of style and content.

Serving HTML

The World Wide Web primarily uses HTTP to serve HTML documents to users. In order to do this correctly, it is necessary for the document to be described correctly: the necessary metadata includes the MIME Type (typically "text/html", although other choices include "application/xhtml+xml") and the character encoding (see Character encodings in HTML).

HTML Email

HTML is also used in email messages. Many email clients include a GUI HTML editor for composing emails and a rendering engine for displaying them once received. Use of HTML in email is quite controversial due to a variety of issues. The main benefit is the ability to decorate an email with presentational attributes (bold headings etc). However, there are a number of disadvantages, which include:
- the recipient may not have an email client that can display HTML
- the email has larger size because lots of formatting will be much larger than the plain text equivalent. This issue is made slightly worse by the fact that, for compatibility, most clients send a plaintext version as well.
- overuse of formatting (there was at one stage a craze for making letterheads using HTML and sending them as part of every e-mail)
- potential security issues of deluding the recipient to accept an email as being from an authoriative source (such as a bank) when this is not the case; this is related to phishing scams.
- potential security issues of simply rendering a complex format like HTML. For these reasons many mailing lists deliberately block HTML email either stripping out the HTML part to just leave the plain text part or rejecting the entire message.

External links

W3C Specifications

- [http://www.w3.org/TR/html401/ HTML 4.01 Specification]
- [http://www.w3.org/TR/xhtml1/ XHTML 1.0 Specification]
- [http://www.w3.org/TR/xhtml-media-types/ XHTML Media Types]

Validators

- [http://validator.w3.org/ W3C's Markup Validator]
- [http://www.htmlhelp.com/tools/validator/ WDG HTML Validator]
- [http://uitest.com/en/analysis/ Validators and checkers] ([http://uitest.com/en/check/ Site Check])

Selected Tutorials/Guides

- [http://www.yourhtmlsource.com/ HTMLSource: HTML Tutorials]
- [http://htmldog.com/ HTML Dog] Category:Markup languages Category:Technical communication Category:W3C standards Category:ISO standards ko:HTML ja:Hypertext Markup Language simple:HTML th:HTML

Blast

Blast can be
- an initialism:
- An algorithm, used in bioinformatics, see BLAST.
- [http://www-cad.eecs.berkeley.edu/~rupak/blast/ BLAST] can also mean "Berkeley Lazy Abstraction Software Verification Tool".
- BLAST can also mean Balloon-borne Large Aperture Submillimeter Telescope
- The journal of the Vorticism movement, published in 1914 and 1915: see BLAST.
- A figure from Norse mythology, see Hrimthurs.
- In the sense of explosion, see explosion or explosive.
- In the sense of blasting or explosive excavation.
- In medicine, blasts generally refer to new, immature white blood cells.
- Irish concert organiser for alternative music groups. Blast
- A Broadway show, Blast!
- blast disease of cereal crops
- A single cylindered motorcycle manufactured By The Bell Motorcycle Co. BUELL BLAST

NCBI

The National Center for Biotechnology Information (NCBI) is part of the US National Library of Medicine (NLM), which is a branch of the US National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988. The NCBI houses genome sequencing data in GenBank and an index of biomedical research articles in PubMed Central and PubMed, as well as other information relevant to biotechnology. All these databases are available online through the Entrez search engine. The NCBI is directed by David Lipman, one of the original authors of the BLAST sequence alignment program and a widely respected figure in Bioinformatics. He also leads an intramural research program, including groups led by Stephen Altschul (another BLAST co-author), David Landsman, and Eugene Koonin (a prolific author on comparative genomics).

NCBI Bookshelf

The NCBI Bookshelf is a collection of freely available on-line versions of biomedical books provided by the NCBI. As of May 2005, the Bookshelf had [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books 38 titles] touching molecular biology, biochemistry, cell biology, genetics, microbiology, a couple of disease states from a molecular and cellular point of view, research methods, and virology. The Bookshelf is a complement to the Entrez PubMed repository of peer-reviewed publication abstracts in that Bookshelf contents provide established perspectives on evolving areas of study and a context in which many disparate individual pieces of reported research can be organized.

External links

- [http://www.ncbi.nlm.nih.gov/ Website for the National Center for Biotechnology Information]
- [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books NCBI Bookshelf titles list]
- [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed Entrez PubMed] Category:Bioinformatics Biotechnology Information ja:NCBI

UCSC

The University of California, Santa Cruz (UCSC or UC Santa Cruz) is a coeducational public university located in Santa Cruz, California, USA. It is one of the ten campuses of the University of California, and ranked by US News as the [http://www.usnews.com/usnews/edu/college/rankings/brief/natudoc/natudoc_pub_brief.php twenty-eighth best public university] in the nation. .

Academics

After UC Merced, UCSC has the second smallest student body of its sister UC campuses and is the second newest along with UC Irvine, which opened at about the same time. Majors and graduate degrees are offered in a broad range of academic fields. The undergraduate program is organized around a residential college system. Though similar to the undergraduate program framework at schools such as Oxford and Yale, UCSC's system is less formal, and is comparable to the college structure at UC San Diego. The colleges provide services such as housing, academic assistance and student activities. Each college has a distinct architectural style and student housing, along with at least one resident faculty provost. Each provides a mandatory "core course" for incoming freshmen based on a central topic, or "theme," that is unique to each college. College sizes vary, but roughly half of students live on campus within their college community. Upon enrollment, students select five colleges they want to join in order of preference and are assigned to a college based on a lottery system. Most students get into their first college choice, and nearly all are assigned to at least their second or third choice. Students choose their colleges based on a variety of factors, such as the college's physical setting, perceived social atmosphere and core course. Coursework, academic majors and general areas of study are not limited by college membership, though colleges "host" the offices of various departments and faculty. UCSC's ten colleges are: provosts]]
- Cowell College
- Stevenson College
- Crown College
- Merrill College
- Porter College
- Kresge College
- Oakes College
- College Eight
- College Nine
- College Ten McHenry Library houses UCSC's main collections, with most of the scientific reading at the newer Science and Engineering Library. McHenry's Special Collections include the archives of Robert A. Heinlein ("Dean of American science fiction writers"), the Hayden White collection of 16th century Italian printing and a photographic collection with nearly half a million items. [http://library.ucsc.edu/speccoll/collections/collections_intro.html] As of 2005, a renovation and expansion program is underway at McHenry, scheduled for completion in 2009. In addition to the two major libraries, many of the colleges host smaller libraries, which primarily serve as quiet places to study. Until 1997, most classes did not assign letter grades, using written evaluations instead. Letter grades are now given, as at other UC campuses, but in many courses grades are still supplemented with evaluations. Students may still take some of their courses on a pass-no pass basis, but each academic program has different policies regarding how this may be done, and a few majors do not permit pass-no pass grading. To graduate, students must "have no more than 25 percent of your UCSC credits graded on a Pass/No Pass basis." About 95% of seniors graduate, and most alumni proceed to graduate schools in law, business administration, engineering, medicine, and the arts, as well as to financial, administrative or scientific occupations. written evaluations As of 2004, UCSC's faculty includes two members of the Institute of Medicine, twenty members of the Academy of Arts and Sciences, eleven members of the National Academy of Sciences, and one MacArthur Fellow. The University spent $54 million on research for the 2002-2003 academic year, and holds claim to 79 active inventions and 18 patents (2002). The young Baskin School of Engineering, UCSC's first professional school, and the Center for Biomolecular Science and Engineering are garnering recognition, as has the work UCSC researchers have done on the Human Genome Project. UCSC has prestigious science departments in Astronomy/Astrophysics and Ocean Sciences, as UCSC administers Lick and Keck Observatories as well as the Long Marine Laboratory. Furthermore, according to a 2003 Thomson Institute for Scientific Information (ISI) report, UCSC ranked 1st in the nation for academic research impact in the field of space sciences. UCSC also ranked first in the nation for its academic research on physics and second in the world for most influential research institution in the physical sciences, according to two 2001 ISI reports. In September 2003, the NASA Ames Research Center took a bold step towards increasing the science output, safety, and effectiveness of NASA's missions through the infusion of new technologies and scientific techniques. A ten-year task order contract valued at more than $330 million was awarded to the University of California to establish and operate a University Affiliated Research System (UARC) [http://uarc.arc.nasa.gov]. UCSC manages the UARC for the University of California.

Setting

NASA Ames Research Center] The 2000 acre (8 km²) UCSC campus is located 75 miles (120 km) south of San Francisco and has an elevation change of about 900 feet (275 m) from the base of campus at 285 feet (87 m) to the upper boundary at 1,195 feet (364 m). The lower portion of the campus primarily consists of the Great Meadow, and most of the upper campus is within a redwood forest. The campus is bounded on the south by the city's upper-west-side neighborhoods, on the east by Harvey West Park [http://www.santacruzparksandrec.com/parks/harvey.html] and the Pogonip open space preserve [http://www.santacruzparksandrec.com/parks/pogo.html] [http://www.pogonip.org/future.htm], on the north by Henry Cowell Redwoods State Park [http://www.parks.ca.gov/default.asp?page_id=546] [http://www.mnn.net/cowell.htm] [http://www.openspacecouncil.org/Camp/Cowell.htm] in the town of Felton, and on the west by Gray Whale Ranch, a portion of Wilder Ranch State Park [http://www.parks.ca.gov/default.asp?page_id=549] [http://www2.ucsc.edu/ppc/lrdp/graphical/context/setting.html]. The northern half of the campus, while originally intended to house ten colleges in addition to the ten that currently exist, has remained in its undeveloped, forested state aside from hiking and bicycle trails. Some students live in tent communities and treehouses in the denser parts of the woods, despite restrictions against camping on campus and in the surrounding state parks. The heavily-forested area has allowed UC Santa Cruz to operate a recreational vehicle park as a form of "student housing" (see link below).

History

Although the original founders had outlined their plans for the University in the 1930s, the opportunity did not present itself to build such a unique educational experiment until the City of Santa Cruz made a bid to the University of California Regents in the mid-1950s to build a campus in the mountains outside town. The formal design of the Santa Cruz campus begun in the late 1950s and construction started in the early 1960s. The campus was originally intended to be a showcase for contemporary architecture as well as a place for learning. The first building on campus to be completed was Hahn Student Services Building. Not long after opening, Hahn Student Services Building was subject to a devastating fire that gutted the building. It was then rebuilt using the undamaged concrete structure. 1960s in the background]] Until recently, most of the buildings on campus have been named after people of great worth: educators, writers, philosophers, and alternative thinkers. This tradition has slowed recently in favor of selling naming rights to buildings and colleges (for example, Kresge College received its name from an endowment by K-Mart founder Sebastian S. Kresge's Kresge Foundation). The roads on campus are named after the UC Regents who voted in favor of building the campus. Clark Kerr Hall is named after the then-President of the University of California, who imagined building a university as several Swarthmores (i.e., small liberal arts colleges) in close proximity to each other. (As such, each college was originally intended to be primarily educationally self-sustaining.) When UCSC opened, student protests on college campuses across the United States were common. According to popular myth, the campus was designed on a decentralized plan, with no central quadrangle or central administrative buildings to serve as rallying points for protests. However, the architectural plans and layout for the campus were already completed by the early 1960's, so this legend is generally regarded as untrue. According to the founding chancellor, Dean McHenry, the purpose of the college system was to combine the benefits of a major research university with the intimacy of a smaller college. [http://www.ucsc.edu/oncampus/currents/97-98/03-23/release.htm] UCSC has a long history of student activism. Protracted demonstrations in the 1970s and 1980s, some of which culminated in the occupation of the Chancellor's Office, were organized in opposition to the expansion into formally neutral countries of American hostilities in Southeast Asia, the United States Supreme Court's Bakke decision, and apartheid. The substantial population of UCSC alumni in Santa Cruz has helped to change the electorate of the town from predominantly Republican [http://www.santacruzsentinel.com/archive/2004/June/06/local/stories/01local.htm] to markedly left-leaning, voting nearly three to one for Democrat John Kerry over Republican George W. Bush in the 2004 U.S. presidential election [http://www.ss.ca.gov/elections/sov/2004_general/sov_2004_entire.pdf]. Mike Rotkin, a UCSC alumnus, lecturer in Community Studies, and self-described 'socialist-feminist,' has been elected Mayor of Santa Cruz several times, and the City Council of Santa Cruz recently issued a proclamation opposing the USA Patriot Act.

Geology

USA Patriot Act The geology and history of the campus are closely tied. The campus is built on a portion of the Cowell Family ranch, which was given as a gift to the University of California. The original living quarters for ranch employees are mostly still standing at the base of campus, as is the stonehouse which served as the paymaster's house. The stonehouse was home to the campus newspaper, City on a Hill Press, from the 1970s to the mid-1990s. Many of the other original ranch buildings have been renovated to be comfortable modern offices despite their antiquated appearance. The Cowell Ranch was a part of the Henry Cowell Lime and Cement Company. The limestone that runs under most of campus was pulled from one of several quarries, the most notable being the Upper Quarry, which is popular with students that wish to smoke cannabis away from the patrolled colleges despite its central location. There is an amphitheater in this quarry that is used for most of the large gatherings on campus. Many visiting dignitaries have addressed crowds here, including George McGovern and César Chávez. It also was used for an outdoor introductory psychology course commonly called "Sunshine Psych". The original campus plan indicated a stadium in the Lower Quarry, but this plan never was realized. (Indeed, the Lower Quarry is now home to The Village, a student housing community, ending any forseeable possibility of a stadium there.) Once the limestone was quarried, lime was extracted by burning it in limekilns adjacent to the quarries. The fires were fueled by the redwood trees that were logged from adjacent land. Although most of these kilns are fenced off, they are still visible in several locations on and around campus and in Pogonip. Another interesting feature of UCSC are the creeks traversing the campus within several ravines. Footbridges span these ravines on pedestrian paths linking various areas of campus. These footbridges make it possible to walk to any part of campus within 20 minutes despite the campus being built on a mountainside with varying elevations. At night, fog shrouds the ends of these bridges, so that one can be in the center without being able to see either end or the bottom of the ravine below, with only the orange lights along the path twisting away into the woods providing any sense of place. There are a number of caves on the UCSC grounds, some of which have challenging passages. One unfortunate result of the combination of porous limestone bedrock with torrential coastal winter rains is sinkholes, and there are two large 'bottomless' pits right across from the Science Hill complex. The Jack Baskin Engineering Building, formerly known as the Applied Sciences Building, began inadvertently sinking shortly after being built, and in the late 1970's hundreds of tons of concrete were poured beneath its foundation to prevent it from sinking.

Athletics and student traditions

UCSC competes in Division III of the NCAA as a Independent member. They have 14 varsity sports (men's and women's basketball, soccer, water polo, volleyball, water polo, swimming & diving, women's golf & women's cross country). They nationally ranked in tennis, soccer, water polo and swimming. They have won five men's tennis team championships (most recently in 2004) and were runner-ups in men's soccer in 2004. UCSC is one of the largest NCAA Division III members. UCSC's mascot is the banana slug. In 1981, when the university began participating in NCAA intercollegiate sports, the then-chancellor and some student athletes changed the mascot to the "sea lions," which they considered more dignified and suitable for intercollegiate play. Most students disliked the new mascot and continued to root for the Banana Slugs. In 1986, students overwhelmingly voted to return to the Slugs as UCSC's sole mascot, a vote the chancellor refused to honor, on the grounds it was the athletes who should choose the mascot. When a poll of athletes showed that they also wanted to be "slugs", the chancellor relented (although, a painting of a sea lion remains on the gymnasium floor to this day, and a popular prank pulled by students involves painting a statue of several sea lions outside of Thimann Lecture Hall yellow to represent the university's current mascot, despite the statues being in honor of a former Marine Biology professor, and not the old mascot). [http://reg.ucsc.edu/catalog/html/student_life.htm] The Banana Slug mascot was celebrated in an unreleased 2003 song by the Austin Lounge Lizards. The Austin Lounge Lizards have often played Santa Cruz, and this is their tribute to their home away from home. This 52 second faux collegiate "Fight Song" creates an entirely new image of the Slugs "leaping toward a dunk...oozing lots of spunk," "zipping through the grass....gonna kick your ass," "...slather you with slime...we win another time." It even includes the requisite crowd participation cheer. This surreal blend of Texas rah-rah and Santa Cruz ironic detachment is now considered the unofficial UCSC fight song. A favorite trick played on new students is to claim that banana slugs actually smell like bananas (they do not). Another is to convince them to lick a slug (the slime contains a mild anesthetic). Although some students claim the slugs are hard to find, and even go their entire college career without seeing one, during the wet early spring they are hard to avoid just a little ways out in the surrounding woods. In the 1970s there was a huge wooden labyrinth in the area where College Nine is now, north of the Campus Health Center, an abandoned 'Senior Thesis' project. A popular tradition was to take new students to this maze in the dead of night when the moon was new and have them find the center of the maze in the dark. On the way, the initiated would tell a ghost story about a student who hanged himself center of the maze: "and now...his ghost sometimes appears on moonless nights." While not hazing exactly, some people panicked while trying to accomplish this task. The maze was torn down quietly by the administration because it was becoming a hazard after a student hurt himself, and upgrades to improve safety were not cost effective given its location. A noteworthy annual tradition on campus is "First Rain". Traditionally, during the first autumn rain, students strip down and run the span of the campus nude (nearly one mile), gathering more participants as they pass through each residential college. The run usually begins at Porter College and ends there once again with students congregating in a drum circle. Another campus tradition is the full moon drum circle. On the eve of every full moon, students congregate in the Upper Meadow to drum or simply relax.

Notable alumni

- William D. Adams - President of Colby College, Waterville, Maine
- Jello Biafra
- - Singer, activist
- John T. Doolittle, BA 1972 - Member, U.S. House of Representatives, California 4th Congressional District
- J. Doyne Farmer, PhD 1981 - Physics Researcher at Santa Fe Institute
- Laurie Garrett, BA 1975 - Newsday science reporter and author
- Ron Gonzales, BA - Mayor of San Jose, California
- Alexander Gonzalez, PhD 1979 - President of California State University, Sacramento
- Victor Davis Hanson, BA 1975 - Classicist and Senior Fellow at the Hoover Institution
- Steven Hawley, PhD 1977 - Astronaut
- bell hooks, PhD 1983 - Feminist social critic
- Miranda July
- - Filmmaker and writer
- Camryn Manheim, BA 1984 - actress
- Geoffrey Marcy, PhD 1982 - Professor of Astronomy at UC Berkeley and planet finder
- Kent Nagano, BA 1974 - Conductor of the Los Angeles Opera and the Montreal Symphony Orchestra
- Huey P. Newton, PhD 1980 - Founding Black Panther and activist, studied History of Consciousness
- Marti Noxon, BA - TV Producer
- Bradley Nowell
- , Singer and songwriter with Sublime
- Marc Okrand, BA 1972 - Linguist, creator of the Klingon language
- Julie Packard, BA 1974 - Executive Director, Monterey Bay Aquarium
- Joe Palca, PhD 1982 - National Public Radio science reporter
- Dana Priest, BA 1981 - Washington Post reporter and author
- Rebecca Romijn
- - Supermodel, actress
- Maya Rudolph, BA 1995 - Comedian, musician, SNL cast member
- Kathryn D. Sullivan, BS 1973 - Astronaut, first American woman to walk in space
- Ally Walker, BS - Actress
- Gillian Welch, BA 1990 - Singer and songwriter
- Attended but did not graduate.

Notable faculty

- Ralph Abraham - Professor Emeritus of Mathematics; notable for founding the Visual Mathematics Institute and for his pioneering work on Chaos Theory
- Norman O. Brown - late Professor Emeritus of Humanities
- David Cope - Professor of Music; notable for his experiments in A.I. and computer-created musical compositions
- Angela Davis - Professor of History of Consciousness; writer and activist
- Frank Drake - Professor Emeritus of Astronomy and Astrophysics. Proposed the Drake Equation.
- Sandra Faber - Professor of Astronomy. Instrumental in inventing Cold dark matter theory and fundamental work in the field of Galaxy formation and evolution.
- Gordon Mumma - Professor Emeritus of Music, composer
- Tom Lehrer - lecturer in American Studies and Mathematics. Also well known for his satire and songwriting.
- Joel Primack - Professor of Physics, noted cosmologist; renowned for Cold Dark Matter Theory proposed along with Sandra Faber (see above) and Sir Martin Rees.
- Geoffrey Pullum - Professor of Linguistics and Distinguished Professor of Humanities. Co-author of the Cambridge Grammar of the English Language ISBN 0521431468.
- Stan Woosley - Professor of Astronomy and AAAS member, noted for his work on supernova gamma ray bursts
- David A. Huffman - Founding faculty of the Computer Science Department. Developed the famous Huffman coding
- Ben Stein - Actor and commercial personality
- Elliot Aronson - Professor Emeritus of Psychology, Author of The Social Animal and Nobody Left to Hate: Teaching Compassion after Columbine, creator of the Jigsaw Classroom model only psychologists to win the American Psychological Association's highest honor in all three fields.
- Roland G. Tharp - Professor Emeritus of Education. Considered to be the most influential expert in modern social constructivist theories in education.

Points of interest

- University of California, Santa Cruz, Arboretum
- [http://www.housing.ucsc.edu/housing/rvcamperpark.html The UCSC trailer park] - a unique housing opportunity!
- [http://www2.ucsc.edu/kresge/commlife/food.shtml The Kresge Food Co-op] - student run natural foods store

External links

- [http://www.ucsc.edu Official website]
- [http://people.ucsc.edu/~rosewood/guidebook/text.html The Campus Guide: A Tour of the Natural Environment and Point of Historical Interest], written by Elizabeth Spedding Calciano and Ray Collett, 1973
- [http://www.santacruzpl.org/history/people/cowell5.shtml Henry Cowell history website]
- [http://www.cse.ucsc.edu/ Baskin School of Engineering website]
- [http://www.cbse.ucsc.edu/ Center for Biomolecular Science and Engineering website]
- [http://genome.ucsc.edu/ UCSC Genome Bioinformatics]
- [http://www.ucsc.edu/about/campus_mascot.asp Information on the UCSC Banana Slug] Santa Cruz
- Category:Universities and colleges in California

Sanger Institute

The Wellcome Trust Sanger Institute (formerly the Sanger Centre) is a genome research centre in Cambridgeshire, England. It was set up in 1992 by the Wellcome Trust and the Medical Research Council, the purpose of which is stated on their website (http://www.sanger.ac.uk) as "to further our knowledge of genomes, and in particular to play a substantial role in the sequencing and interpretation of the human genome. This information will underpin research on human biology and disease in this century and beyond." Besides its involvement in a large number of genome sequencing projects, the institute hosts many different (large-scale) research projects and is regarded as a key player in the international research community. The projects include: # [http://www.sanger.ac.uk/HGP Human Genome Project] # [http://www.sanger.ac.uk/genetics/CGP Cancer Genome Project] # [http://www.ensembl.org The EnsEMBL Genome Annotation] # [http://www.sanger.ac.uk/Projects/Pathogens Pathogen Sequencing] and others PhD students trained at the institute are registered at the University of Cambridge. The institute is named after the Nobel prize-winning biochemist Frederick Sanger. The history of the institute can be read [http://www.sanger.ac.uk/Info/Intro/history.shtml here]

External links

- [http://www.sanger.ac.uk/ The Sanger Institute]
- [http://www.sanger.ac.uk/Info/Intro/sanger.shtml About Fred Sanger, biography from the Sanger Institute] Category:Science and technology in the United Kingdom

String

Generally, string is a thin piece of fiber which is used to tie, bind, or hang other objects. String can be made from a variety of fibres. The term has more specific meanings within certain academic disciplines. __NOTOC__

Biology

In biology, a string is a chain of biochemicals.
- A string of nucleotides is called DNA or RNA.
- A string of amino acids is called a peptide or protein.

Mathematics and computer science

In various branches of mathematics and computer science, strings are sequences of various simple objects (symbols, tokens, characters, etc.), used in many contexts. See string (computer science) and string literal.

Music

A string is a vibrating cord of metal, nylon, gut or other substance such as wound hair that vibrates to produce a tone in a variety of musical instruments. Strings can also refer to the section of an orchestra or band consisting in stringed instruments. See string instrument. String is the name of Thai pop music.

Physics

In theoretical physics, a string is the basic object of study in string theory. In string theory, strings replace the notion of elementary particles in quantum field theory.

Community Radio

On Community Radio Station 3MDR, string is the basis of an entire radio program, called The Three Strings. Wow, string really is everywhere! See Community Radio, The Three Strings. See also strings.

Information Hyperlinked over Proteins

Information Hyperlinked over Proteins (or iHOP) is an online service that provides this gene-guided network as a natural way of accessing millions of PubMed abstracts and brings all the advantages of the internet to scientific literature research. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource. Navigating across interrelated sentences within this network is closer to human intuition than the use of conventional keyword searches and allows for stepwise and controlled acquisition of information. Moreover, this literature network can be superimposed upon experimental interaction data to facilitate the simultaneous analysis of novel and existing knowledge. The network presented in iHOP currently contains 5 million sentences and 40000 genes from Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Danio rerio, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli. The system was published in Nature Genetics 36, 664 (2004) as 'A gene network for navigating the literature'.

External links

- [http://www.ihop-net.org/UniPub/iHOP/ iHOP server]
- [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=15226743 Scientific article] Category:Biology Category:Genes Category:Proteins Category:Bioinformatics Category:Academic publishing Category:Search engines Category:Medical research Category:Health sciences

Excel

- Microsoft Excel, a spreadsheet application by Microsoft Corporation
- Excel, Alabama
- Hyundai Excel, a car also called Hyundai Pony in some markets (Europe), the name of the X3 version of Hyundai Accent in some markets (Australia), a car made by Hyundai Motor Company.
- A brand of chewing gum, produced by Wrigley's
- The name of the protagonist in the manga and anime series Excel Saga
- ExCeL Exhibition Centre in London, England
- Edexcel is an examination board based in London, England.
- Excel Corporation wholly owned subsidiary of Cargill. Major US meat processor.
- Excel was a crossover/thrash metal band from Venice, California which was related to Suicidal Tendencies.

Category:Bioinformatics

Bioinformatics is an interdisciplinary field applying computer science to biological questions, particularly questions in genomics. Category:Biology Category:Biotechnology Category:Genomics Category:Interdisciplinary fields Category:Statistics Category:Computational science

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Oscar Freire
Óscar Freire Gomez (born 1976) is a Spanish cyclist. He is known as a good sprinter, but he is also strong in hilly races. He became professional in 1998 at the Vitalicio Seguros team. That year he only won a stage in the Vuelta a Castilla y Léon. The next

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