Bioinformatics course - lesson 2
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Transcript of Bioinformatics course - lesson 2
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organizace dat
archive / origbin / programsdata / storageresultspic / figures / graphsdocws / tmp / working
oldhelpperl
project (electronic) notebook / notes
to-do / changes
README
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bezpečnost dat
přístupnost vs bezpečnostpoužitelnost ochrana
heslahttpssshpgp (gpg)
(šifrovaný souborový systém)
zálohy, verzechecklistformáty souborůtištěné kopie
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typy souborů
● obrázky:vektorové
svg (standart vector graphics)coreldraw, adobe illustrator
bitmapy (barevná hloubka - color depth)tiff, png, gif (komprese bez ztráty kvality)jpg (komprese se ztrátou kvality)
● dokumenty:txt, html, rtf (rich text format), pdf (portable document format)
● data:xml (extended markup language)
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síťová komunikace
high level protocol
low level protocol
tcp/ipnetbui
httpftpssh
ports802023
ports802023
client / serverp2p
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WWW
● URL: Unique Resource Locator● HTML: Hyper Text Markup Language● XML: eXtensible Markup Language
http://www.w3.org/XML
protocol://computer:port/dir/document#position
http://bio.img.cas.cz/index.html#prfuk
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social bookmarking
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social bookmarking
výhody:● oproti “web spiderům” (google,
yahoo) jsou stránky anotovány lidmi, kteří rozumějí jejich obsahu
● automatický ranking systém● tagy nejsou stanoveny rigidně
zvnějšku● seskupování uživatelů s podobnými
zájmy
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social bookmarking
nevýhody:● z hlediska vyhledávání tag systém
neobsahuje definovaný slovník● tagy nemají hierarchické uspořádání● absence systematičnosti a někdy i
logiky
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co se hodí jednomu,nemusí vyhovovat druhému
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del.icio.us
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del.icio.us
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del.icio.us
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organizace odborné literatury
● http://www.citeulike.org● http://www.conotea.org
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každý problém vyžadujespecifické nástroje
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citeulike
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citeulike
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citeulike
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citeulike
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databáze
SQL: Structured Query Language
● MySQL http://www.mysql.org● Postgres http://www.postgresql.org
● Access● Oracle http://www.oracle.com
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databáze - princip
databáze
tabulka
záznam
datový typ
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datové typy
● integer(M)● float(M,D)● char(M), varchar(M)● date, time● text, blob● set, enum● boolean
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datové typy
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problémy se záznamem dat
jména autorů:● John B. Smith● J. B. Smith● JB Smith● Smith, John B● Smith, JB● Smith JB● Smith J B
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problémy se záznamem dat
jména autorů:● John B. Smith● J. B. Smith● JB Smith● Smith, John B● Smith, JB● Smith JB● Smith J B
řešení● striktní datové
typy● definovaný
slovník
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relační databáze
databáze článků:
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hledejte efektní a elegantní řešení
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relační databáze
● časopis (VARCHAR)● název článku (TEXT)● rok vydání (DATE)● …
● autor (?)● keyword (?)
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relační databáze
id journal title year rest
INTEGER VARCHAR(20) TEXT DATE TEXT
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relační databáze
id journal title year rest
INTEGER VARCHAR(20) TEXT DATE TEXT
aid id name
INTEGER INTEGER VARCHAR(20)
kid id keyword
INTEGER INTEGER VARCHAR(20)
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relační databáze
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relační databáze
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relační databáze
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online help
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