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MARC: Developing Bioinformatics ProgramsJuly 2009

Alex RopelewskiPSC-NRBSC

Bienvenido VélezUPR Mayaguez

Reference: How to Think Like a Computer Scientist: Learning with Python

Essential Computing for Bioinformatics

Lecture 2

High-level Programming with Python

Controlling the flow of your program

•The following material is the result of a curriculum development effort to provide a set of courses to support bioinformatics efforts involving students from the biological sciences, computer science, and mathematics departments. They have been developed as a part of the NIH funded project “Assisting Bioinformatics Efforts at Minority Schools” (2T36 GM008789). The people involved with the curriculum development effort include:

•Dr. Hugh B. Nicholas, Dr. Troy Wymore, Mr. Alexander Ropelewski and Dr. David Deerfield II, National Resource for Biomedical Supercomputing, Pittsburgh Supercomputing Center, Carnegie Mellon University.•Dr. Ricardo González Méndez, University of Puerto Rico Medical Sciences Campus.•Dr. Alade Tokuta, North Carolina Central University.•Dr. Jaime Seguel and Dr. Bienvenido Vélez, University of Puerto Rico at Mayagüez.•Dr. Satish Bhalla, Johnson C. Smith University.

•Unless otherwise specified, all the information contained within is Copyrighted © by Carnegie Mellon University. Permission is granted for use, modify, and reproduce these materials for teaching purposes. •Most recent versions of these presentations can be found at http://marc.psc.edu/

Essential Computing for Bioinformatics

These materials were developed with funding from the US National Institutes of Health grant #2T36 GM008789 to the Pittsburgh Supercomputing Center

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Basics of FunctionsDecision statementsRecursionIteration statements

Outline

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Basics of FunctionsDecision statementsRecursionIteration statements

Outline

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Some Inaccurate Yet Popular Perceptions of Computing• Computing = Computers• Computing = Programming• Computing = Software

Computing = Computers

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Computing is about solving problems using computers

A.K.A. The Computing Device View of Computing

Computing = Programming

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Computing is about writing programs for computers

A.K.A. The Programming Language view of Computing

Computing = Software

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Computing is not concerned withhardware design

A.K.A. The “Floppy Disk” view of Computing

Part I - Outline

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• What is Computing?• Computing Models and

Computability• Interpretation and Universal

Computers• Church’s Thesis

What is computing then?

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AlgorithmicComputation

Function

InputInformation

OutputInformation

Computing is the study of Computation:the process of transforming information

The Computation Process

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011011001010100101…

encode

011011001010100101…

compute

Problem

decode

SolutionInformation Information

Fundamental Questions Addressed by the Discipline of Computing

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• What is the nature of computation?• What can be computed?• What can be computed efficiently?• How can we build computing

devices?

The Computation Process

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011011001010100101…

encode

011011001010100101…

compute

Problem

decode

Solution

Integer IntegerIntegerFunction

Every Algorithm is in Essence an Integer Function

Computability

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All Integer Functions (IF)

ComputableInteger Functions

(CF)

IF ≟ CF

HaltingProblem

IF ≠ CF

ComputableInteger Functions

(CF)

The Halting Problem(Alan Turing 1936)

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Given a program and an input to the program, determine if the program will eventually stop

when it is given that input.Compute

Program P

Input IP Halts on I?Cannot Build This

Want to describethe set of computable

functions?

Mathematical Computers:The Turing Machine (1936)

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Alan Turing

0 1

0 1FSM

Infinite

I/OTAPE

0/{1,0,R}

1/{0,1,L}

TapeHead

NextState Write

Symbol

HeadMovement

Input Symbol

Mathematical Computers:The Turing Machine (1936)

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Alan Turing

0 1

0 1FSM

InfiniteTAPE

0/{1,0,R}

1/{0,1,L}

FSM

Infinite

I/OTAPE

TapeHead

Turing demonstrated how to solve several problems using his computing model

Ad-hoc Turing Machines

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FSM

Sorting TMFSM

Sorting TMFSM

Sorting TMFSM

Sorting TM FSM

Searching TM FSM

Integrating TM

Can we build a general purpose TM?

The Universal Turing Machine (UTM)The Paradigm for Modern General Purpose Computers

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Universal TM

Coded TM M Coded Tape for M

• Capable of Emulating Every other TM• Shown possible by Alan Turing (1936)• BIG IDEA: INTEPRETATION!!!

Software(flexible)

Hardware(fast)

Programming = Encoding Algorithms

Other Familiar Models of Computation

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• Combinational Circuits• Sequential Circuits (FSM’s)• Pentium Instruction Set Architectures• Lambda Calculus• Recursive Functions• C++

Can you tell which ones are Turing Universal? That is, which ones can emulate any other Turing Machine?

Computing in Perspective

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CMOSGateFSM

ISA

Assembler 1 Assembler 2 Assembler 3

C++Pascal Fortran

MatLab

BuildOne

BuildMany

Excel

Interpreter Design Demands Programming Language Design

PSpice

All have embedded PL’s

Why Abstraction Layers?

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• Resilience to change:– Each layer provides a level of indirection

• Divide and Conquer Approach:– Can work on one small semantic gap at a

time

• Building Block Approach:– Can build many higher layer on same lower

layer Because we know of no other way of

doing anything

Church’s Thesis

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Alonso Church

“All the models of computation yet developed, and all those that may be developed in the future, are equivalent in power.”

“Any realizable computing device can be simulated by a Turing machine”

Issues not considered: Size, Programmability, PerformanceBut they must be considered if one is to build …

The (John) Von Neumann Architecture(late 40’s)

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I/Odevices

CentralProcessingUnit (CPU)

Memory

Allow communication with outside world

Interprets instructions

Stores both programs and data

After 60 years … most processors still look like this!

Practical Universal Computers(John) Von Neumann Architecture

(1945)

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DataPaths

PCABR

ALU

AC Program

Data

Memory

Control Unit (FSM)

CPU

CPU is a universal TM An interpreter of some programming language (PL)

status control

This looks just like a TM Tape