BioJava In Anger蹇熸寚鍗?/span>浠嬬粛錛?/span>BioJava 鐨勮璁℃兜鐩栦簡鐢熺墿淇℃伅瀛︾殑寰堝鏂歸潰錛屾湰韜氨姣旇緝澶嶆潅鍜屽簽澶э紝鏈夋椂鍊欑敋鑷充護浜虹敓鐣忋傚浜庨偅浜涙兂蹇熶簡瑙e茍涓斿埄鐢ㄨ繖涓己澶х殑宸ュ叿鐨勭敓鐗╀俊鎭瀹朵滑鏉ヨ錛屾湁鏃跺欓潰瀵硅繖涓澶у爢鐨勬帴鍙e父甯鎬細澶寸棝嬈茶銆傛湰鎸囧崡鑳藉甯姪浣犲埄鐢?span class="SpellE">BioJava寮鍙?span lang="EN-US">99錛呭父鐢ㄧ殑紼嬪簭錛岃屼笉蹇呬負姝ゆ帉鎻?span lang="EN-US">99錛呯殑BioJava鎺ュ彛銆?/span> 鏈寚鍗椾嬌鐢ㄥ鏁扮紪紼嬪揩閫熸寚鍗楃殑鏍煎紡錛岄噰鐢ㄢ滄垜濡備綍浣跨敤.....鈥濈殑涓婚褰㈠紡鏉ュ府鍔╁ぇ瀹朵嬌鐢?span class="SpellE">BioJava銆傛瘡涓富棰橀兘鎻愪緵浣犲彲鑳戒細鏈熸湜騫剁粡甯鎬嬌鐢ㄧ殑婧愪唬鐮併傝繖浜涗唬鐮佸熀鏈笂鍙互鐩存帴鍦ㄤ綘鐨勬満鍣ㄤ腑緙栬瘧榪愯銆傛垜灝介噺璇︾粏娉ㄩ噴榪欎簺浠g爜錛岃澶у鏇村鏄撶悊瑙g▼搴忎腑鍙兘鐨勪竴浜涙櫐娑╀唬鐮併?/span> 鈥?span class="SpellE">BioJava In Anger鈥濈敱Mark Schreiber緇存姢銆備換浣曞緩璁拰闂璇瘋仈緋?span lang="EN-US">biojava mailing list銆傜偣鍑?span lang="EN-US">榪欓噷璁㈤槄閭歡鍒楄〃銆?/span> 鏈寚鍗椾嬌鐢ㄧ殑渚嬪瓙緇忚繃BioJava1.3, Java1.4嫻嬭瘯銆?/span> 鏈寚鍗椾腑鏂囩増鐢?span lang="EN-US"> Wu Xin(Center of Bioinformatics,Peking University)緲昏瘧,浠諱綍緲昏瘧闂璇烽氳繃閭歡鍒楄〃鑱旂郴鎴栬呯櫥褰?span lang="EN-US">BBS銆?/span> 鎴戝浣曚嬌鐢?span lang="EN-US">.......?瀹夎> 瀹夎Java 鎴愬垎琛?span lang="EN-US">(alphabets)鍜屾爣璁?span lang="EN-US">(symbol)>鎴戝浣曠敤鑷畾涔夌殑鏍囪寤虹珛鑷畾涔夌殑鎴愬垎琛? >鎴戝浣曞緩绔嬫潅浜や駭鐗╂垚鍒嗚〃(cross product alphabet),渚嬪瀵嗙爜瀛楁垚鍒嗚〃(codon alphabet)? >鎴戝浣曚粠鏉備氦浜х墿鎴愬垎琛?cross product alphabet)涓垎瑙e嚭浠栦滑鐨勭粍鎴愭爣璁?component symbol)? >鎴戝浣曞垽鍒袱涓垚鍒嗚〃鎴栦袱涓爣璁版槸鍚︾浉鍚? >鎴戝浣曞緩绔嬩竴涓涔夋爣璁?ambiguous symbol),渚嬪Y鎴朢? 鍩烘湰搴忓垪鎿嶄綔>鎴戝浣曚粠瀛椾覆涓垱寤轟竴鏉″簭鍒楀璞′互鍙婂皢鍏跺啓鍥炰竴鏉″瓧涓? >搴忓垪鏄笉鍙彉鐨?immutable),鎴戝浣曟敼鍙樺畠鐨勫悕瀛? >鎴戝浣曠紪杈戜竴鏉″簭鍒楁垨鑰呮爣璁伴摼(symbollist)? 緲昏瘧(translation)>鎴戝浣曞皢涓鏉NA鎴朢NA鎴栨爣璁伴摼緲昏瘧鎴愯泲鐧借川? 搴忓垪杈撳叆杈撳嚭(sequence I/O)>鎴戝浣曡鍙朑enBank/EMBL/SwissProt鏍煎紡鐨勬枃浠?/span> >鎴戝浣曚粠GenBank/EMBL/SwissProt鏍煎紡涓娊鍙栧簭鍒楀茍涓斾互FASTA鏍煎紡杈撳嚭? 娉ㄩ噴(annotation)>鎴戝浣曠敤鐗╃榪欎釜鍙傛暟(鎴栧叾浠栨敞閲婂睘鎬?鏉ョ瓫閫夊簭鍒? 浣嶇疆鍜岀壒寰?span lang="EN-US">(location and feature)>鎴戝浣曟寚瀹氫竴涓偣浣嶇疆(point location)? >鎴戝浣曟寚瀹氫竴涓?span class="GramE">鍩熶綅緗?/span>(range location)? >鎴戝浣曚嬌鐢ㄧ幆鐘朵綅緗?circular location)? BLAST鍜?span lang="EN-US">FASTA璁℃暟鍜屽垎甯?span lang="EN-US">(count and distribution)>鎴戝浣曡綆楀簭鍒椾腑鏌愮鏍囪(symbol)鐨勯鐜? >鎴戝浣曡兘鎵懼埌涓縐嶇畝鍗曠殑鏂規硶鏉ュ垽鏂袱縐嶅垎甯冩槸鍚﹀叿鏈夌浉鍚岀殑鏉冮噸? >鎴戝浣曞涓涓嚜瀹氫箟鐨勬垚鍒嗚〃鍒涘緩涓涓狽闃跺垎甯?order N distribution)? 鏉冮噸鐭╅樀鍜屽姩鎬佽鍒?span lang="EN-US">(weight matrix and dynamic programming)>鎴戝浣曞埄鐢ㄤ竴涓潈閲嶇煩闃?span class="GramE">瀵繪壘妯′綋? >鎴戝浣曞垱寤?span class="GramE">涓涓殣椹ā鍨?/span>璋?profile HMM)? >鎴戝浣曞緩绔嬩竴涓嚜瀹氫箟鐨勯殣椹ā鍨?/span>(HMM)? 鐢ㄦ埛鐣岄潰(user interfaces)OBDA鍏嶈矗澹版槑:榪欎簺婧愪唬鐮佺敱鍚勪釜浣滆呰礎鐚?span lang="EN-US">,灝界緇忚繃鎴戜滑嫻嬭瘯,浣嗕粛鐒跺彲鑳芥湁閿欒鍙戠敓銆傛墍鏈変唬鐮佸彲浠ュ厤璐逛嬌鐢紝浣嗘垜浠茍涓嶄繚璇佸拰璐熻矗浠g爜鐨勬紜с傚湪浣跨敤鍓嶏紝璇瘋嚜鎴戞祴璇曘?/span> 鐗堟潈錛?/span>鏈珯鏂囨。灞炰簬鍏惰礎鐚呫傚鏋滃湪鍑虹増鐗╀腑浣跨敤錛岃鍏堝瀭璇?span lang="EN-US">biojava mailing list銆傛簮浠g爜鏄?span lang="EN-US">寮鏀捐祫婧?/span>,濡傛灉浣犲悓鎰忓叾澹版槑鍒欏彲浠ュ厤璐逛嬌鐢ㄣ?/span> |
Maintainted by Wu Xin, CBI, Peking University, China, 2003 |
Bioperl 鏈榪戝凡緇忓埌浜?.0鐗?鍏堣bioperl.org,璇ョ粍緇囨寮忔垚绔嬩簬1995騫?鍦ㄦ涔嬪墠宸茬粡浣滀負闈炴寮忕殑鍥綋瀛樺湪閭e緢澶氬勾,鐜板湪浠栧凡緇忓艦鎴愪簡涓涓浗闄? 鎬х殑寮鍙戣呯殑鍗忎細,榪欎簺寮鍙戣呭紑鍙戠敤浜庣敓鐗╀俊鎭,鍩哄洜緇勫,鍜岀敓鍛界瀛︾爺絀剁殑寮鏀炬簮鐮佺殑Perl 宸ュ叿.
璇ョ粍緇囩殑鏀寔鑰呭拰鎺ㄥ姩鑰呮槸Open Bioinformatics Foundation. 浠栦滑鐨勪紮浼磋繕鏈塨iojava.org, biopython.org, DAS, bioruby.org, biocorba.org, ENSEMBL 鍜?EMBOSS.
Bioperl鐨勬湇鍔″櫒鎻愪緵渚涗笅鍒楁湇鍔?鐢ㄤ簬鐢熷懡縐戝鐨勫熀浜巔erl鐨勬ā鍧?鑴氭湰,web鑱旀帴鐨勮蔣浠?
Bioperl鐜板湪宸插彂灞曟垚涓轟竴涓護浜虹灘鐩殑鍥介檯鎬х殑鑷敱杞歡寮鍙戣鍒掞紝bioperl鍦ㄧ敓鐗╀俊鎭鐨勪嬌鐢ㄥ姞閫熶簡鐢熺墿淇℃伅瀛︺佸熀鍥犵粍瀛︿互鍙婂叾浠栫敓鍛? 縐戝鐮旂┒鐨勫彂灞曘傛渶榪慴ioperl 1.0鐗堟湰姝e紡鍙戝竷錛岃繖鍏墮棿鍘嗘椂涓冨勾錛屾垚緇╂枑鐒躲侭ioperl 1.0 鍖呮嫭832涓枃浠訛紝93涓猄cript錛屽姛鑳戒赴瀵岋紝婧愮爜鍏ㄩ儴寮鏀俱傚畠鏄敓鐗╀俊鎭鐮旂┒鐨勫埄鍣ㄣ傝緇嗙殑鍐呭澶у鍙互璁塊棶www.bioperl.org銆?/p>
Bioperl浣滀負perl鐨勬墿鍏呯殑涓撻棬鐢ㄤ簬鐢熺墿淇℃伅鐨勫伐鍏蜂笌鍑芥暟闆?鑷劧涔熺戶鎵夸簡perl鐨勪紬澶氫紭鐐?
絎竴. Perl寮哄ぇ鐨勬鍒欒〃紺哄紡(regular expression)姣斿浠ュ強瀛楃涓叉搷浣滀嬌榪欎釜宸ヤ綔鍙樺緱綆鍗曡屾病鏈夊叾瀹冭璦鑳界浉姣斻侾erl 闈炲父鎿呴暱浜庡垏鍓詫紝鎵漿錛岀粸錛屽紕騫籌紝鎬葷粨錛屼互鍙婂叾瀹冪殑鎿嶄綔鏂囧瓧鏂囦歡銆傜敓鐗╄祫鏂欏ぇ閮ㄥ垎鏄枃瀛楁枃浠?鐗╃鍚嶇О,縐嶅睘鍏崇郴錛屽熀鍥犳垨搴忓垪鐨勬敞瑙o紝璇勪綇錛岀洰褰曟煡闃? 鐢氳嚦DNA搴忓垪涔熸槸綾繪枃瀛楃殑銆傜幇鍦ㄤ簰鐩鎬氦鎹互浠ユ枃瀛楁枃浠剁殑褰㈠紡瀛樺湪鐨勪絾鏄叿鏈変笉鍏煎鐨勮祫鏂欐牸寮忕敓鐗╀俊鎭祫鏂欐槸涓涓緢澶寸柤鐨勯棶棰?perl鐨勮繖涓柟闈㈢殑浼? 鐐?鍙互鍦ㄨ繖涓鏂歸潰瑙e喅涓嶅皯闂.
絎簩. Perl 鑳藉閿欍傜敓鐗╄祫鏂欓氬父鏄笉瀹屽叏鐨勶紝閿欒鎴栬呰璇樊浠庢暟鎹殑浜х敓鏃跺欏彲鑳藉氨浜х敓浜?鍙﹀鐢熺墿鏁版嵁鐨勬煇欏瑰兼爮浣嶅彲浠ヨ蹇界暐 ,鍙兘鏄┖鐫鐨勶紝鎴栨槸鏌愪釜鏍忎綅涔熷氨鏄煇涓?琚鏈熻鍑虹幇濂藉嚑嬈?涓句緥鏉ヨ錛屼竴涓疄楠屽彲鑳借閲嶅鐨勬搷浣?錛屾垨鏄祫鏂欎互鎵嬪姩杈撳叆鎵浠ユ湁閿欒銆侾erl騫朵笉浠? 鎰忔煇涓兼槸絀虹殑鎴栨槸鏈夊鎬殑瀛楃銆傛瑙勮〃紺哄紡鑳藉琚啓鎴愬彇鍑哄茍涓旀洿姝i敊璇殑涓鑸敊璇傚綋鐒惰繖縐嶅脊鎬т篃鍙兘鏄悇鍧忓銆?
榪樻湁,Perl 鏄粍浠跺鍚戠殑銆侾erl 榧撳姳浜轟滑灝嗕粬浠殑杞歡鍐欐垚灝忔ā緇勶紝涓嶈鏄敤 Perl 鍑藉紡搴撴ā緇勬垨鏄緇熺殑
Unix 宸ュ叿瀵煎悜鐨勬柟寮忋傚閮ㄧ▼搴忚兘澶熻交鏄撶殑琚暣鍚堣繘 Perl 紼嬪簭,闈犵潃綆¢亾(pipe),緋葷粺鍛煎彨,鎴栨槸鎻掑駭(socket)銆侾erl5
寮曡繘鐨勫姩鎬佽澆鍏ュ櫒鍏佽浜轟滑浣跨敤 C 鐨勫嚱寮忥紝鎴栬呰鏁翠釜緙栫▼榪囩殑鍑藉紡搴擄紝琚嬌鐢ㄥ湪 Perl
鐩磋瘧鍣ㄤ腑銆傛渶榪戠殑鎴愭灉鏄笘鐣屽悇鍦扮殑鏅鴻兘緇撴櫠閮戒細鏀跺綍鍦ㄤ竴緇勬ā緇勯噷闈紝縐頒負鈥漛ioPerl鈥濓紙璇峰弬鑰?Perl Journal錛?br>
Perl
寰堝鏄撳幓鍐欏茍涓旇兘寰堝揩寮鍙戝畬銆傜洿璇戝櫒璁╀綘涓嶉渶瑕佸鍛婁綘鎵鏈夌殑鍑芥暟鍨嬪紡浠ュ強璧勬枡鍨嬫侊紝褰撴湭瀹氫箟鐨勫嚱寮忚鍛煎彨鏃跺彧浼氬紩璧蜂竴涓敊璇紝闄ら敊鍣ㄤ篃鑳戒笌Emacs寰堝ソ
鐨勫悎浣滃茍涓旇浣犺兘鐢ㄤ護浜鴻垝鏈嶇殑浜よ皥寮忕殑寮鍙戞ā寮忋?br>
Perl 鏄壇濂界殑鍘熷瀷璇█銆傚洜涓哄畠蹇屼笖鑴?quick and dirty)錛岀敤 Perl
寤烘瀯鏂版紨綆楃殑鍘熷瀷姣旂洿鎺ュ啓鎴愪竴涓揩鐨勯渶瑕佺紪紼嬭繃鐨勮璦鏉ョ殑鏈夋剰涔夈傛湁鏃跺欏彂鐜扮粨鏋滄槸Perl宸茬粡澶熷揩浜嗭紝鎵浠ョ▼搴忓彉涓嶉渶瑕佺Щ妞?鏇村鎯呭艦鏄煇浜哄彲浠ョ敤C鍐?
涓涓皬鐨勬牳蹇冪▼搴忥紝緙栫▼鎴愬姩鎬佽澆鍏ョ殑妯$粍鎴栨槸澶栭儴鐨勫彲鎵ц紼嬪簭錛岀劧鍚庡叾瀹冪殑閮ㄥ垎鐢≒erl鏉ュ畬鎴愩傝繖閮ㄥ垎鐨勪緥瀛愬彲浠ュ弬鑰?http://waldo.wi.mit.edu/ftp/distribution/software/rhmapper/)銆?/a>
鏈変竴鐐硅寮鴻皟鐨勬槸, Perl 鍦ㄥ啓浣滅綉欏?CGI 鏂歸潰闈炲父浼樼錛岃屼笖閲嶈鎬ч殢鐫鍚勫疄楠屽皢璧勬枡鍙戣〃鍦ㄧ綉緇滀笂涔嬪悗鏇存槸澧炲姞銆傛垜鍦ㄥ熀鍥犱腑蹇冪幆澧冧笅浣跨敤 Perl 鐨勭粡楠屼粠澶村埌灝鵑兘鏄煎緱縐拌禐鐨勩傜劧鑰屾垜鍙戠幇 Perl 涔熸湁瀹冪殑闂銆傚畠鐨勬澗鏁g殑紼嬪簭椋庢牸瀵艱嚧璁稿閿欒錛岃繖浜涘湪鍏跺畠涓ユ牸鐨勮璦閮戒細琚姄鍒般備婦渚嬫潵璇達紝Perl 璁╀綘鍦ㄤ竴涓彉鏁板湪琚寚瀹氬間箣鍓嶅氨鑳戒嬌鐢紝榪欐槸涓緢鏈夌敤鐨勭壒鎬у綋浣犻渶瑕佺殑鏃跺欙紝浣嗘槸鍗存槸涓涓伨闅懼綋浣犲崟綰殑鎵撻敊浜嗚鯨璇嗗悕縐般傚悓鏍風殑錛屽緢瀹規槗蹇樿瑕佸鍛婁竴涓嚱 寮忛噷闈㈢殑鍖哄煙鍙樻暟錛屽鑷翠笉灝忓績鍦版敼鍒頒簡鍏ㄥ煙鍙樻暟銆?br> 鏈鍚庯紝Perl 鐨勪笉瓚充箣澶勫湪浜庡緩绔嬪浘褰㈠寲鐨勪嬌鐢ㄨ呮帴鍙c傝櫧鐒?Unix蹇犲疄淇″緬鎵鏈変簨鎯呴兘鑳藉湪鍛戒護妯″紡涓嬪畬鎴愶紝澶у鏁扮殑緇堢浣跨敤鑰呭嵈涓嶅悓鎰忋傝紿楋紝閫夊崟錛屽脊璺崇殑鍥炬宸茬粡鍙樻垚浜嗗繀瑕佺殑鏃跺皻銆?/p>
鐩村埌鏈榪戯紝鐩村埌鏈榪戯紝Perl 鐨勪嬌鐢ㄨ呯晫闈?GUI)鍙戝睍浠嶆槸涓嶆垚鐔熺殑銆傜劧鑰?Nick
Ing-Simmons鐨勫姫鍔涗嬌寰?perlTK(pTK) 鐨勬暣鍚堜嬌寰椾互 Perl 椹卞姩鐨勪嬌鐢ㄨ呮帴鍙e湪
X-window涓婇潰鎴愪負鍙兘銆傛垜鐨勪紮浼村拰鎴戞浘緇忓湪 MIT 鍩哄洜涓績鍐欒繃鍑犱釜 pTK
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