Bioinformatics Data Management

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1 Οκτ 2013 (πριν από 3 χρόνια και 10 μήνες)

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Essential Computing for BioInformatics


Mathematical Computing: computing models, fundamental limits of computation.
Physical computing: binary i
nformation
encodings: integer numbers, floating
-
point
numbers, symbols;
essential computer architecture,

from
logic gates to processors,
machine instr
uctions and assembly language.
Algorithm and Data Structures: big O
notation, algorithm design, recursion, divide and conquer, dynamic programming.
Programming languages
and paradigms: object oriented, scripting. S
oftware engineering
conce
pts: software development cycle,

design, API’s
,
SDK’s, debugging
,

testing,
performance tuning.


Suggested
Readings:



The Practice of Programming, Kernigham & Pike



Introduction to Computing Systems: Form Bits and Gates to C and Beyon
d.
Yale Patt.


NOTE: The following two courses are graduate or advanced undergraduate courses for
computer science majors who have had at least undergraduate courses in data structures
and algorithms.


Bioinformatics Data Management


Fundamental Data Base

Management and Information Retrieval concepts

commonly
arising in Bionformatics systems
. The R
elational Data Model. Essentials of Data Base
Design
: E/R Models, normalization
. Data manipulation languages: relational algebra,
SQL.
Database API’s: embedded

SQL’s, JDBC. Information Retrieval

(IR)
: query
models, feature extraction, document ranking, clustering
, IR data structures
. Case studies
of popular Bioinformatics systems.


Computational Molecular Biology


Study of important molecular biology

problems
which are defined primarily on
computational terms such as strings, trees and grammars.

D
esign and use of classical
computer sc
ience methods in bioinformatics:
string
matching
, database searches,
determination of patterns and secondary structures.

Applic
ation

of computer science
concepts and skills such as correctness of proofs,
algorithm analysis, bounded
approximation results, randomized algorithms, among others
, to

the search
of

effective
solutions for molecular biology problems.