Lecture 2&3: Computing, SQL, and Perl Flashcards
What are some types of programming languages?
General Purpose - Perl, Python, C++
Markup - HTML, (La)TeX, XML
Specialized - Matlab, SQL, Octave
What are the different categories of programming languages?
Interpreted - Perl, BASH
Part-compiled - Java, Python
JIT - Python, Perl
Compiled - C++, FORTRAN
What are the different paradigms of programming languages?
Object-oriented - Python
Functional
Procedural - C, Perl
What is the difference between compiled and interpreted languages?
-An Interpreted language converts the source file to the processor language (hexadecimal code) every time it runs.
-A compiled language converts the source file that is able to directly interact with the processor every time is is run.
As a result, a compiled language is faster, and you do not need the compiler present each time.
However, it is slower to develop.
What is SQL?
Structured Query Language (SQL) is programming language that allows to design and manipulate relational databases.
What is an algorithm?
A complete and precise set of steps that will solve a problem and achieve an identical result whenever given the same set of data to a defined level of accuracy.
What are some key SQL commands?
SELECT - What we want to output
FROM - The table we will query
WHERE - conditional statement (e.g.. if we want to select data WHEN two things are true)
DISTINCT - Only select unique values
What are some advantages of Perl over Python?
You can read files without opening them.
Calling external programs are trivial
Variable declaration possible
Stable language - no changes to syntax
How are variables defines in Perl?
$variable_name
How are lists/arrays defined in Perl?
defining: @list_name
Referring to one item: $list_name
How are dictionaries defined in Perl?
defining: %dict_name
Referring to one item: $dict_name{‘key’} = value
What are the comparison strings in Perl?
less than: lt
less than or greater to: le
equal to: eq
greater than or equal to: ge
greater than: gt
not equal to: ne
What is the syntax to select lines in Perl?
while(<>)
Mention the computer types that specialize in different parts of biology.
Mac & PC: Zoology, DNA, Phylogeny
Mini/Mainframe: Crystallography, Protein Sequence and Structure
What is a Databank and Database?
A Databank is a collection of data without an associated query tool.
A Database is a structured collection of data with some tool enabling it to be queried.
What is data mining and how can it be applied to biology?
Data mining extracts patterns, relationships, and meanings from data.
It can be used to extract sequence patterns or riles characteristic of a protein family.
What are some examples of Machine Learning in Bioinformatics?
NNPRED
JNET
PHD
PSIPred
