Bioinformatics, 協議, DNA 核糖核酸蛋白質Proteomics
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家庭 > bioinformatics > 常見問題解答 > index.php
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我認為科學享受非常成功因為它有聚焦其工作成績的這樣一個有限和狹窄的領土。即, 實際宇宙。~Ken Jenkins
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大致, bioinformatics 描述 對電腦的任一個用途處理生物資訊。
實踐上, 定義由多數人員使用是更加狹窄的; bioinformatics 對他們是一個同義詞為"計算分子生物學" - - -對電腦的用途描繪生存事分子要素。
多數生物學家談論"做bioinformatics" 當他們使用 電腦 存儲, 比較, 檢索, 分析 或 預言 構成 或原生質 結構。因為電腦變得更加強有力您能大概補充說 模擬 對bioinformatics 動詞這個列表。"原生質" 包括您基因物料核酸酸和您的基因產品: 蛋白質。這些是"古典" bioinformatics 關心, 應付主要 順序分析。
Khairuddin Itam 得出了我的對bioinformatics 的這個酥脆定義的注意建於到1987 年, 從P. Hogeweg:"[Bioinformatics 是] 資訊科學的進程的研究在生物系統"
Fredj Tekaia 在 Institut Pasteur 提供bioinformatics 的這個定義:
"打算解決生物問題使用DNA 和氨基酸順序和相關資訊的數學, 統計和計算的方法。"
這是多數大生物分子一個數學上興趣的屬性, 他們是 聚合物; 更加簡單的分子模塊被定□的鏈子叫 單體。認為單體作為, 儘管有不同的顏色和形狀, 所有有同樣厚度和同樣方式連接到互相的小珠或構件。
可能結合在鏈子的單體是同樣常規組, 但各种單體選件類有其自己明確定義的套特性。
許多單體分子可能一起被連接形成唯一, 更大, 大分子。大分子可能有精妙地特定與資訊有關的美滿並且/或者化工屬性。
根據這份計劃, 單體在DNA 一個指定的大分子或蛋白質可能計算上被對待作為 字母表的信函, 被彙集在被預編程式的安排傳播消息或工作在電池。
bioinformatics 方法的最巨大的成績, 人的染色體項目, 當前被完成。因此bioinformatics 研究本質和優先級和申請更改。預兆經常居於談話我們的生活在" 過帳genomic" 時代。我的私有意圖是, 這將影響bioinformatics 用幾個方式:
分子生物學 增長出於英國的生物物理學的 社團定義生物物理學 和的生物物理學The:
"申請技術從物理學嚮瞭解生物結構和功能" 的一個學科域關於學科的各種各樣的小平面的更多資訊 可能被查找在 社團的站點 被主持在 Birkbeck 學�&, 倫敦。
麥克·Goodrich 寫問什麼生物物理學的狀況被給了計算生物的定義由保□·Schulte 提交(下面) 。一個 最近條款 在 科學家 [ 自由註冊被要求] 處理了這問題感謝對Jo Wixon (比較和功能 Genomics 的管理的編輯) 作為參考。
計算生物學家也許反對(請), 但, 我發現人們使用"計算生物" 當討論那個子集bioinformatics (在廣義) 最緊密對古典常規生物的域。
計算生物學家感興趣自己更以演變, 填寫和理論生物而不是電池和分子生物醫學。它是不可避免的, 分子生物學是深刻地重要在計算生物, 但它一定不是 什麼計算生物是所有關於(參見下段) 。在計算生物這些面積看起來計算生物學家傾向於更喜歡統計設計為生物現象物理化學那些。這經常是明智的...
一名計算生物學家(保□J Schulte) 反對了在上面和做這個定義從對術語的一個普遍的用途派生的整個地有效點, 而不是一正確一個。在水的保□工作流在工廠電池裡。他指出, 生物可變的動力學是計算生物的域本質上。他爭辯說, 這, 和計算的任一個申請對生物, 作為"計算生物" 可能被描述(參見也bioinformatics 的 "寬鬆" 定義 如下) 。那裡我們不同意, 或許, 是在他得出這我充分再生產的結論:
"計算生物不是" 域", 但是" 途�&"介入對電腦的用途學習生物進程和因此這是面積一樣不同像生物。"
理查·Durbin, 資訊學頭在 Wellcome 信任Sanger 學�&, 用面試表達了關於這分別的一個有趣的 觀點:
"我不認為所有生物計算是bioinformatics, 即。 數學塑造不是bioinformatics, 既使當連接用與生物相關的問題。以我所見, bioinformatics 必須處理管理和對生物資訊, 特殊基因資訊的隨後用途。"
醫療資訊學常見問題解答 (沒有關係) 提供以下定義:
"生物醫學的資訊學是被定義作為結構和算法研究、發明, 和實施改進通信、體格檢查資訊的瞭解和管理的一個湧現的學科。"
那常見問題解答並且指向得 這裡
Aamir Zakaria, 常見問題解答的作者, 強調, 醫療資訊學與結構和算法更有關為醫療資料的操作, 而不是以資料。
這建議, 一差額在bioinformatics 和醫療資訊學之間作為學科說謊以他們的途�&對資料; 有bioinformaticians 感興趣對理論在那的操作之後資料 並且 有bioinformatics 科學家擔憂資料和其生物涵義。(我相信一位好bioinformatics 研究員應該是對這兩個域感興趣的方面。)
醫療資訊學, 為實用原因, 是可能應付資料被獲得在"更總" 生物級別是資訊從超級蜂窩電話系統, 直到填寫級別當多數bioinformatics 與關於蜂窩電話和biomolecular 結構和系統的資訊有關。
在這兩點我�&是愉快使所有醫療資訊學專家 更正我。
萬維網廣告為劍橋Healthtech 學�&的第六個每年Cheminformatics �&議描述域因而:
"化工綜合、生物審查, 和資料開採途�&的組合□去□常引導藥物發現和發展"
但這, 再, 聽起來更多像域由包括被辨認由一些其最普遍(和最賺錢的) 活動, 而不是受到其常規標題的所有不同的研究。
故事 所有時刻最成功的藥物, 青黴素的當中一個, 似乎異常, 但我們發現和開發藥物現在甚而有相似性的方式, 是機�&的結果, 觀察和很多緩慢, 密集的化學。近來, 藥物設計總似乎注定繼續是勞力密集的, 試算和錯誤進程。使用資訊技術的可能性, 智能計劃和自動化進程與可能的治療化合物有關化工綜合是非常扣人心弦為化學家和生化學家。帶來藥物的獎勵銷售更加迅速地是巨大的, 這那麼自然地是什麼很多cheminformatics 工作是關於。
這頁 以與關於術語鏈接"cheminformatics 的" 一些有趣的討論的商業偏鋒, 什麼它意味, 是否它存在作為一個分明學科, 並且甚而是否它應該由"chemoinformatics" 替換。
學術cheminformatics 間距是寬的和由cheminiformatics 組的利息�&例證明在 分子和Biomolecular 資訊學的中心 在奈梅亨 大學 在荷蘭。這些利息有:
三位一體大學' s Cheminformatics 網頁, 為其它實例, 與cheminformatics 有關自己作為對網際網路的用途在化學。
Genomics 是存在在染色體順序完成之前的一個域, 但在最粗暴表單, 例如經常re 參考的估計100 000 個基因在人的染色體從a(n) ("後面信包" genomics in)famous 片斷被派生, 猜測重量染色體和密度基因他們負擔。Genomics 是任一企圖分析或比較種類或種類的整個基因補全(複數) 。它是, 當然可能比較染色體由比較更多或代表性子集基因在染色體之內。
數理生物學比計算生物是容易與bioinformatics 區別。它使用應付他們的數理生物學並且應付生物問題, 但方法不需要是數字的和不需要被實施在軟體或硬體裡。的確, 這樣方法不需要"解決" 任何東西; 在數理生物學它�&被認為合理發布僅僅設立的結果一個生物問題屬於特殊常規選件類。
分別在bioinformatics 和數理生物學之間由我接受從亞歷克斯·Kasman 在 查爾斯頓 學�& 的電子郵件闡明了。根據他運作的定義, 他區別了 的bioinformatics (在 緊的定義之下 至少)...
"... 似乎幾乎完全集中於可能嚮大分子生物資料集被運用..." 的特定算法
... 從 數理生物學 ...
"... 包括不一定是算法的, 不一定分子在本質裡, 和不一定是有用的在分析被收集的資料的事理論利益。"
最近覆核在proteomics 在日記帳本質定義了域這樣:
"術語proteome 第一次鑄造 描述套蛋白質由genome1 輸入。proteome 的研究, 叫做proteomics, 現在召喚不僅所有蛋白質在任一個指定的電池裡, 而且套所有蛋白質isoforms 和修改, 交往在他們之間, 蛋白質和他們的高次複雜的結構說明, 和就此而言幾乎一切' 過帳genomic ' 。"
邁克爾J.Dunn, Proteomics 的編輯在�&長 定義"proteome" 和:
"染色體的蛋白質補全"
並且proteomics 有關與:
"基因表達的定性和定量研究在功能蛋白質的級別"
那是:
"一個界面在蛋白質生化和分子生物學之間"
描繪許多成千上萬蛋白質用一個指定的電池類型被表達在被給時間是否評定他們的分子量或等電位點, 辨認他們ligands 或確定他們結構介入資料的浩大的編號存貯和比較。這不可避免地要求bioinformatics 。這 建設性地懷疑覆核 由 盧克斯·Huber。
Pharmacogenomics 是genomic 途�&和技術的申請對藥物目標的確定。實例包括拖網的整個染色體為潛在感受器官通過bioinformatics 平均值, 或由調查基因表達的模式在病原生物和主機裡在傳染期間, 或由審查典型表達式模式被查找在腫瘤或患者範例為診斷目的(可能在對潛在癌症療法目標的追求中) 。
術語"pharmacogenomics" 被使用為更多"trivial" 但可爭論bioinformatics 途�&的更多有用申請對編目和處理資訊與藥理相關和遺傳學的, 例如累計資訊在資料庫像 這一個。(由於Ivanovi 。)
所有單個不同地回應藥物處理; 一些正, 其他人與一點明顯的變化在他們的情況上仍然其他人以副作用或過敏反應。這差異為人所知有一個基因基本類型。藥物遺傳學是使用genomic/bioinformatic 方法辨認genomic correlates, 例如SNPs 的一個子集pharmacogenomics (Single Nucleotide Polymorphisms), 典型特殊耐心回應配置文件和使用那些標記通知管理和發展療法。醒目, 這樣途�&被使用了"復活" 藥物早先認為是無效的, 但隨後被查找對工作以在子集患者。他們可能並且被使用為優選化療劑量為特殊患者。
每天bioinformatics 做以順序搜索程式像 疾風, 順序分析程式, 像 裝飾 和 Staden 程式包、結構預言程式像 THREADER 或 PHD 或分子imaging/modelling 程式像 RasMol 和 WHATIF。
當前, 很多bioinformatics 工作與資料庫有關(感謝 技術再對Ivanovi 。) 這些資料庫包括基因資料兩個"公共" 程式庫像 GenBank 或 蛋白質資料庫 (PDB), 和專用資料庫, 像那些由研究小組使用介入基因映射項目或那些由biotech 公司暫掛。使這樣資料庫容易接近通過開放標準非常重要。bioinformatics 資料的消費者使用電腦平臺的範圍: 從更加強有力和禁止的UNIX 配件箱由開發員和館長傾向對更加友好的橡皮防水布經常查找了填寫電腦機警的生物學家實驗室。
現有的程式化的資料資料庫可能被使用 辨認 被放大了和程式化在實驗室裡新建分子的同源染色體。共享一個公用祖先屬性, 同源, 可能是非常強有力的指示符在bioinformatics (參見下面) 。
Bioinformatics 工具可能被使用獲得基因或蛋白質順序利益, 或從物料由各自的researchers/groups 獲得, 標記, 準備和審查在電場或從順序程式庫從早先被調查的物料。
兩類型順序可能然後被分析用許多方式與bioinformatics 工具。
他們可能 裝配。注意這是場合的當中一個當一個生物術語的含義與一計算一個明顯不同(參見可笑的 混亂 在問題在基於網際網路的怪傑論壇 Slashdot) 。電腦學家, 驅逐從您的頭腦彙編語言所有想法。程式化可能只進行為相對地原生質的短的舒展並且被完成的順序由安排準備因此重�&"讀" 單體 (唯一小珠在一個分子鏈子) 入"編碼" 一個唯一持續段落。 這 是裝配件bioinformatic 感覺。
他們可能 被映射是, 他們的順序可能被解析查找所謂的"限制酵素" 將剪切他們的站點。
他們可能 由排列對應的細分市場和尋找比較, 通常符合的和配錯的信函在他們的順序。充足地相似可能被關係的基因或蛋白質並且說因此是"同源的" 對各其他這整體真相比這相當複雜的。這樣表兄弟告訴"同源染色體" 。
如果同源染色體(一個相關分子) 存在, 新建被發現的蛋白質也許然後是塑造是基因產品的三維結構可能被預言沒有做實驗室實驗。
Bioinformatics 被使用在 更加雷管的設計。底漆依照被使用是短的順序必要做許多複製(放大) DNA 片斷在PCR ( Polymerase 鏈式反應) 。
Bioinformatics 使用嘗試 預言實際基因 產品的功能。
關於相似性的資訊, 和, 含蓄地, 蛋白質的relatedness 使用 跟蹤"系族樹" 不同的分子通過演變時間。
有電腦分析的各種各樣的申請程式化資料, 但, 與非常原始資料由人的染色體項目和其它主動性被生成在生物, 電腦目前是重要為許多生物學家管理他們的每日結果
分子塑造/結構生物是可能被認為一部分的bioinformatics 的一個增長的域。有, 例如, 允許您的工具(經常通過淨額) 做相當好 預言 蛋白質附屬結構升起由一個指定的氨基酸順序, 經常根據知道的"被解決的" 結構和其他程式化的分子由結構生物學家獲取。
結構生物學家使用"bioinformatics" 處理浩大和複雜資料從X-射線結晶學、核磁共振(核磁共振) 並且電子顯微鏡術調查和創建似乎是到處在媒體分子的3-D 設計。
詞"映射"不幸地被使用在幾個不同的方式在biology/genetics/bioinformatics 。定義被給以上是那個最頻繁地被使用在這個環境, 但基因可能說"被映射" 當其父項染色體被辨認了, 當其從其它基因的實際或基因距離被設立和頻繁當其各種各樣的編制程式要素(其"exons 的" 結構和地點) 被設立。
有其他域為也許被認為一部分的bioinformatics 的實例醫療想像/圖像分析。有並且整體生物被_發的計算其它學科; 基因算法, AI, 神經網路。經常這些面積互動用奇怪的方式。神經網路, 由作用的粗暴設計_發神經細胞在腦子, 被使用在程式稱PHD, 驚奇準確地, 預言蛋白質附屬結構從他們的主要順序。
什麼幾乎所有bioinformatics 有共同興趣是處理很多生物被派生的資訊, 是否DNA 程式化或乳房X-射線。
"多麼老的是bioinformatics?" 答復到這一個取決於哪個來源您選擇讀。
從T K Attwood 和D J Parry 史密斯的"介紹Bioinformatics", Prentice 霍爾1999 年[ Longman 高等教�&; 國際標準書號0582327881]:
"術語bioinformatics 使用包含幾乎所有電腦應用在生物科學, 但原始鑄造了在80 年代中期為對生物順序資料的分析。"
從標記S. Boguski 的條款在"趨勢指南對於Bioinformatics" Elsevier, 趨勢補充1998 p1:
"術語" bioinformatics "是一個相對地最近發明, 沒出現在文件直到1991 年和然後只就誕生的狀況電子出版業...
"... 然而, 一些我的榜樣當我是畢業生student (Margaret O. Dayhoff, Russell F. Doolittle, Walter M. Fitch and Andrew D. McLachlan) had been building databases, developing algorithms and making biological discoveries by sequence analysis since the 1960s---long before anyone thought to label this activity with a special term (if anything it was called `molecular evolution'). Even a relatively new kid on the block, the National Center for Biotechnology Information (NCBI), is celebrating its 10th anniversary this year, having been written into existence by US Congressman Claude Pepper and President Ronald Reagan in 1988. So bioinformatics has, in fact, been in existence for more than 30 years and is now middle-aged."
It's notoriously difficult to find any books on bioinformatics itself that cater well for all of those coming from computing, from mathematics and from biology backgrounds. The few textbooks available in the field tend to be eyewateringly expensive as well. I've divided suggested reading into books of general interest, those best suited to people coming from a computational/mathematical background and books for biologists interested in bioinformatics. Where a book is also listed in Bioinformatics.Org's books section I have linked the title to the relevant entry there. Links to other lists of bioinformatics books follow this section of suggested reading.
Many people are curious about the Human Genome (Project). The completion of the first draft probably represents bioinformatics' coming of age as a discipline. The first couple of books are aimed at the intelligent layperson.
A gossipy and insightful account of the race to sequence the genome can be found in "The Sequence" by Kevin Davies [Weidenfeld; ISBN 0297646982]. Matt Ridley's "Genome" [Fourth Estate; ISBN 185702835X] is both an interesting layperson's introduction to the issues raised by the bioinformatic revolution and an overview of its biology and enormous scope. If I remember rightly, Ridley's book received a slightly snooty review from Walter Bodmer. This is understandable, since his and Robin McKie's excellent "pre-genomic" guide to the Human Genome Mapping Project, "The Book of Life" [Oxford Paperbacks; ISBN 0195114876] was undeservedly in a remainders bin when I bought my copy a couple of years ago.
If you are a non-biological scientist (or a non-scientist) and are hooked by these, why not go back to the "real beginning" of the race and read James Watson's entertaining and indiscreet memoir of his and Francis Crick's determination of the structure of DNA, "The Double Helix" [Penguin; ISBN 0140268774]---now updated with an introduction by media don Steve Jones.
Nigel Barber at Peterborough Regional College in the UK recommends Gary Zweiger's "Transducing the Genome" [McGraw-Hill Professional Publishing: ISBN 0071369805]. The summary at Amazon makes it sound a tad pretentious, but all the reviews seem pretty positive so it might be worth a read.
If you are a quantitative scientist and would like a deeper knowledge of contemporary (molecular) biology, but you want to acquire it as painlessly as possible you could try the following:
There are two classic competing texts in cell and molecular biology which Maximilian Haeussler reminds me to include: Alberts et al's Molecular Biology of the Cell [Garland Science: ISBN 0815340729] and Molecular Biology of the Gene [Benjamin Cummings: ISBN 0321248643].
If you are a hardcore maths/computing person Michael Waterman's "Introduction to Computational Biology" [Chapman & Hall/CRC Statistics and Mathematics; ISBN 0412993910] and Pavel Pevzner's "Computational Molecular Biology - An Algorithmic Approach" [The MIT Press (A Bradford Book); ISBN 0262161974] will give you all the discrete maths you can shake a stick at, but perfunctory introductions to the biology.
Bioinformatics.Org's very own Jeff Bizzaro recommends Dan Gusfield's "Algorithms on Strings, Trees and Sequences" [Cambridge, 1997 ISBN 0-52158-519-8], Richard Durbin, S. Eddy, A. Krogh, G. Mitchison "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids" [Cambridge, 1997 ISBN 0-52162-971-3] (which I think is one of the clearest and most comprehensive guides to alignment algorithms) and---for that full "computers-to-biology conversion"--- Geoffrey M. Cooper "The Cell: A Molecular Approach" [ASM Press, 1996 ISBN 0-87893-119-8]. Jeff Ames writes that a second edition of this book is now available [Sinauer Associates, Incorporated, 2000 ISBN 0-87893-106-6] and that this version---if you can find it in the shops---comes with a CD.
One outstanding general text for the biologist is David W. Mount's "Bioinformatics" [Cold Spring Harbor Press; ISBN 0879696087]. It's not cheap, but it's the best I've seen if you are studying bioinformatics itself.
Bioinformatics has been dismissed by some as "the science of BLAST searches". The best collection of advice so far on doing BLAST searches is O'Reilly's BLAST book by Ian Korf, Mark Yandell and Joseph Bedell [O'Reilly ISBN 0-596-00299-8]. I reviewed it enthusiastically, but not uncritically, for the UK UNIX Users' Group magazine. I'd go as far as to say that all biologists thinking of using BLAST in their research should read the relevant sections before they even go near a computer.
If you wish to use general bioinformatics tools, especially if you are a little wary of computers, my new "best" book is "Bioinformatics for Dummies" [John Wiley and Sons ISBN 0764516965]. It is (obviously) aimed at people who are beginners, who are happier using the Web rather than typing commands, and who are more interested in learning than in impressing people---the writing is friendly clear and unpretentious. However, like several of my other tips (below) it concentrates on Web-based resources so it will, inevitably, date. (This is partially compensated for by there being a companion Website.)
Also, if you're coming to the subject as a computer user with a biological background, looking to exploit the many tools available, you might want to try Terry Attwood and David Parry-Smith's "Introduction to Bioinformatics" [Longman Higher Education; ISBN 0582327881], or Des Higgins and Willie Taylor's "Bioinformatics: Sequence Structure and Databanks" [Oxford University Press; ISBN 0199637903]. Another excellent practical introduction is Andreas Baxevanis and Francis Oulette's "Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins" [Wiley-Interscience; ISBN 0471383910], now in its new and improved second edition. Bax teaches bioinformatics all over Canada and the experience shows. Arthur Lesk has also produced an excellent teaching book particularly for protein bioinformatics in his Introduction to Bioinformatics
Bioinformatics.Org also recommends Cynthia Gibas and Per Jambeck's "Developing Bioinformatics Skills" [O'Reilly, 2001 ISBN 1-56592-664-1].
Stuart Brown recommends his own book "Bioinformatics: A Biologist's Guide to Biocomputing and the Internet" [Eaton Pub Co; ISBN: 188129918X]. If he sends me a review copy I might recommend it too ;-) .
"Darwin's Radio" by Greg Bear [Ballantine Books, ISBN: 0345435249] is a wonderful hard SF thriller which stretches ideas derived from genome discoveries to their breaking point. It's gripping and humane.
Leonard Crane, the author of Ninth Day of Creation kindly sent me a copy for review. So far it's an excellent read. I haven't finished it yet, not because it isn't a rattling good story, but because, like "Darwin's Radio", it is very long and because I am very busy. If you'd like to read a well-researched, but speculative, novel containing actual scenes of practising bioinformatics then try it.
Ken Allen contributed the following reviews:
"Frameshift [Tor Books, ISBN: 0812571088] by Robert J. Sawyer---based around the HGP---reasonable read, but poor / confused ending."
Calculating God [Tor Books, ISBN: 0812580354]by the same author---has a subtler bio connection and is a much better read. Near the start an alien spacecraft lands, the alien emerges and says 'take me to your paleontologist'
Further suggestions for this section are welcome.
See also compbiology.org's list, Steve Brenner's list, and Aik Choon Tan's collection of books.
The biggest and best source of bioinformatics links I have encountered is the Genome Web at the Rosalind Franklin Centre for Genomics Research at the Genome Campus near Cambridge, UK. Most of the links below come from that resource. My list is necessarily limited by comparison.
[XXXX INSERT DETAILS OF MORE SEQUENCING CENTRES HERE]
[XXXX INSERT DETAILS OF STANDARDS CENTRES HERE]
[XXXX INSERT MORE DETAILS OF VIRTUAL BIOINFORMATICS CENTRES HERE]
A great place to start, whether you come from a biological, physical or computational background is at Martin Vingron's superb online bioinformatics tutorial. (Begin by choosing a section from the left-hand-side menu bar.)
Tom Smith and Don Emmeluth have produced a nice little exploration of bioinformatics using NCBI resources and tools.
I recently stumbled upon a promising set of online lecture notes currently under construction by B. Steipe at the Genzentrum (Gene Center) at the Ludwig-Maximilians-Universität München (University of Munich).
A defiantly frames-free chemistry tutorial site.
First of all, an almost completely painless introduction to the horrors of the quadratic equation by Peter Whalen, James Walker, and Drew Marticorena.
C. J. Schwarz of the Department of Statistics and Acturial Science, Simon Fraser University has produced a course in statistics which is accompanied by set of sound, online PDF handouts.
Here is a great guide to a whole array of statistical learning/teaching resources prepared by Juha Puranen of the University of Helsinki (English).
Estrella Mountain Community College in the States offers this excellent short introduction to biology (actually "The Nature of Science and Biology". It's a great place for keyboard jockeys to start their journey to enlightenment. Thanks to Alex O'Neill for pointing out the broken link.
The Dolan DNA Learning Center at Cold Spring Harbor has an outstanding interactive tutorial introducing genetics. To take full advantage of the multimedia elements you should download the Flash and Real players.
The Institute of Arable Crop Research Beginner's Guide to Molecular Biology
Unilever Education Advanced Series tutorial on proteins.
The University of Arizona has made available a high-quality tutorial in cell biology. Not only does it cover the facts, but it also attempts to introduce some of the philosophy of the field---recommended. Even better, it's also available en Español and in Italiano.
Once you've worked your way through that you might like to see some scanning electron microscope images of some of the structures you've read about taken by members of John Heuser's lab.
Bob Patterson maintains his "Darwiniana" with amazing diligence.
jump straight to introduction to education section
This section is not complete, but contributions to broaden its coverage are welcome. Please do not direct questions about eligibility, course quality or admissions policy to me, but to ask the individual institutions directly. Use the links to obtain contact details. If an institution doesn't provide telephone numbers/email addresses or snailmail details on its Web site it doesn't deserve your patronage.
This resource focuses on complete, full-time degree programmes rather than on individual study modules. Curating a list of the latter would be a full-time job. You can go to other places, however, if you are looking for short courses. Thanks to various contributors, including Wentian Li who pointed me to this list at Rockefeller which is mirrored at various other sites. And to Humberto Ortiz Zuazaga for mailing me a link to the ICSB, where you can find this list.
If you are interested in U.S. programmes, here's a list from Curtin and here's a list from Stanford. Thanks to Amelie Stein who also supplied some of the individual entries in this section.
Those wanting to find programmes in the Asia Pacific region could have a look at this resource maintained by the Asia Pacific Bioinformatics Network APBioNet. Thanks to Sentausa.
In the UK The Bioinformatics Resource (part of the BBSRC's CCP11 project) project maintains (among many other resources) lists of (mainly) British Masters and PhDs in bioinformatics. If you have any suggestions or updates please contact me with them. You can publicize your course and offer a public service at the same time.
Rhodes University, Grahamstown, South Africa offers an MSc. in Bioinformatics and Computational Molecular Biology. Thanks to Natalie Twine.
Cathal Seoighe wrote a while back about the South African National Bioinformatics Institute (SANBI). Ruediger Braeuning has since written to point out that bioinformatics training in South Africa has been radically reorganized. He says:
"A new institute, the National Bioinformatics Nework (NBN), has been created. We have nodes at Universities all over the country (UWC, UCT, SUN, RU, UKZN, UP, WITS). Our main tasks are to:
- develop capacity in Bioinformatics
- perform world-class research
- support local Biotechnology initiatives
"We do offer courses on various topics in Bioinformatics ranging in length from 3 days to several weeks. We also train Bioinformaticists on MSc, PhD and post doc level. Undergraduate programs are currently being developed. Bursaries are available. For more information visit our Website."
South African National Bioinformatics Institute (SANBI) Honours Bioinformatics Course at the University of the Western Cape. Next year the same institute will be offering a Master's in bioinformatics---thanks to Cathal Seoighe.
If you know of any other bioinformatics courses on the African continent please feel free to mail me about them.
According to Pablo Nehab-Hess the Laboratório Nacional de Computação Científica (LNCC), Brazil and the Universidade Federal do Rio de Janeiro (UFRJ) recently created a joint Bioinformatics MSc programme, through the Genetics Department of UFRJ and the Department of Applied Computational Mathematics of LNCC.
Thanks to Jordan Patterson for the information that the University of Alberta offers four-year Biology or Computer Science degrees with a specialization in bioinformatics. The Faculty of Computer Science there offers Master's and PhD training in bioinformatics.
Benjamin Horsman wrote to tell me that Simon Fraser University and the University of British Columbia are collaborating on a new Bioinformatics training program with the British Columbia Cancer Agency. The program offers post-graduate diploma, Master's, and PhD training in Bioinformatics. Now Simon Fraser University also offers a joint major programme in Molecular Biology and Biochemistry (MBB) and Computer Science in Bioinformatics. Thanks to Brittany Nielsen for the info.
Thanks to Olga Likhodi for the information that Seneca College, Toronto offers a post-graduate diploma in Bioinformatics.
Peter Kublik informs me that from 2003/2004 the University of Calgary will offer a bioinformatics programme. He's part of the first intake.
The University of Waterloo, Department of Computer Science offers undergraduate and graduate courses in bioinformatics. More information is here.
The Keck Graduate Institute claims that computational biology is a core element of the curriculum in its Master of Bioscience degree.
Stanford University offers academic and professional (distance-learning) MSs in Biomedical Bioinformatics as well as its PhD programme. Thanks to Betty Cheng.
Thanks to Momchil Georgiev for the information that the University of California at San Diego offers a Bioinformatics graduate programme and to Dana Brehm that there is now a new bachelor's program, to quote her:
"[This is an] undergraduate, interdisciplinary program for undergraduates leading to a B.S. degree. The new Bioinformatics major is offered by the Division of Biology, and the departments of Chemistry/Biochemistry, Computer Science and Engineering, and Bioengineering. A student may choose to major in Bioinformatics in any one of the four departments or division. The Division of Biology currently offers two Bioinformatics courses, and with the advent of the cross-disicplinary major, even more courses are going to be taught 2002-03 and 2003-04."
University of California, Irvine Informatics in Biology and Medicine
David Delong wrote to me to point out that the College of Natural and Agricultural Sciences at the University of California, Riverside is developing a "Center in Genomics and Bioinformatics" which will offer a PhD curriculum in genomics and bioinformatics from academic year 2001-2002 onwards.
Catherine Velazquez says that The University of California, Santa Cruz offers a new undergraduate BS course in bioinformatics. They have a Frequently Asked Questions. Now they also offer an MS/PhD in Bioinformatics. Thanks to Kevin Karplus for the update.
Javier Rojas Balderrama emailed me to point out thatYale University offers a Bioinformatics and Computational Biology track as part of its combined Biological and Biomedical Sciences graduate programme.
Georgia Institute of Technology Masters of Science in Bioinformatics
According to Eric VanWieren Georgia State University offers a Master's and PhD in Computer Science with a focus on bioinformatics. The university's Bachelor of Science in Computer Science also offers a "Fundamentals of Bioinformatics" course.
The University of Illinois at Chicago offers graduate programmes covering Bioengineering Bioinformatics through its Bioengineering department as well as an undergraduate course track. Thanks to Amit Sabnis.
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