Tips & Tricks for Software Engineering in

Bioinformatics

Presented by:Joel Dudley

Who is this guy?

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http://www.megasoftware.net

Kumar S. and Dudley J. “Bioinformatics software for biologists in the genomics era.” Bioinformatics (2007) vol. 23 (14) pp. 1713-7

Bioinformatics Philosophy

Build Your Toolbox

Learn UNIX!

Be a jack of all trades, but master of one.

http://oreilly.com/news/graphics/prog_lang_poster.pdf

C/C++ PHP R PERL

Python

Ruby

Java

LISP

VB

Java is not just for Java

http://www.jython.org http://jruby.codehaus.org

Simplified Wrapper and Interface Generator (SWIG)

http://www.swig.org/

Greasy-fast C library

Doughy-soft scripting language

Frameworks are Friends

BioBike

Stand on the slumped, dandruff-covered shoulders of millions of computer nerds.

Don’t trust yourself (or your hard disk).

#!/usr/bin/perl# 472-byte qrpff, Keith Winstein and Marc Horowitz <sipb-iap-dvd@mit.edu># MPEG 2 PS VOB file -> descrambled output on stdout.# usage: perl -I <k1>:<k2>:<k3>:<k4>:<k5> qrpff# where k1..k5 are the title key bytes in least to most-significant order

s''$/=\2048;while(<>){G=29;R=142;if((@a=unqT="C*",_)[20]&48){D=89;_=unqb24,qT,@b=map{ord qB8,unqb8,qT,_^$a[--D]}@INC;s/...$/1$&/;Q=unqV,qb25,_;H=73;O=$b[4]<<9|256|$b[3];Q=Q>>8^(P=(E=255)&(Q>>12^Q>>4^Q/8^Q))<<17,O=O>>8^(E&(F=(S=O>>14&7^O)^S*8^S<<6))<<9,_=(map{U=_%16orE^=R^=110&(S=(unqT,"\xb\ntd\xbz\x14d")[_/16%8]);E^=(72,@z=(64,72,G^=12*(U-2?0:S&17)),H^=_%64?12:0,@z)[_%8]}(16..271))[_]^((D>>=8)+=P+(~F&E))for@a[128..$#a]}print+qT,@a}';s/[D-HO-U_]/\$$&/g;s/q/pack+/g;eval

Don’t be afraid to use more than three letters to define a variable!

ArchitectureAccomplishment

Object-Oriented Software Design Decisions

module GraphBuilder LINE_TYPES = [:solid,:dashed,:dotted] module Nodes SHAPE_TYPES = [:rectangle,:roundrectangle,:ellipse,:parallelogram,:hexagon,:octagon,:diamond,:triangle,:trapezoid,:trapezoid2,:rectangle3d] class BaseNode attr_accessor :label,:geometry,:fill_colors,:outline,:degree,:data def initialize(opts={}) @opts = { :form=>:ellipse, :height=>50.0, :width=>50.0, :label=>"GraphNode#{self.object_id}", :line_type=>:solid, :fill_color => {:R=>255,:G=>204,:B=>0,:A=>255}, :fill_color2 => nil, :data => {}, :outline_color=>{:R=>0,:G=>0,:B=>0,:A=>255}, # Set to nil or {:R=>0,:G=>0,:B=>0,:A=>0} for no outline }.merge(opts) @data = @opts[:data] # for storing application-specific data @label = Labels::NodeLabel.new(@opts[:label]) @geometry = {:pos_x=>0.0,:pos_y=>0.0,:width=>1.0,:height=>1.0} @fill_colors = [@opts[:fill_color],nil] @outline = {:line_type=>@opts[:line_type],:color=>@opts[:outline_color]} @degree = {:in=>0,:out=>0} end def clone_params { :label=>text, :fill_color=>@fill_colors.first, :form=>@form, :height=>@geometry[:height], :width=>@geometry[:width] } end end

class ShapeNode < BaseNode attr_accessor :form def initialize(opts={}) super @form = @opts[:form] @geometry[:height] = @opts[:height] @geometry[:width] = @opts[:width] end

To Subclass or not to subclass? Use mixins!class Array def arithmetic_mean self.inject(0.0) { |sum,x| x = x.real if x.is_a?(Complex); sum + x.to_f } / self.length.to_f end def geometric_mean begin Math.exp(self.select { |x| x > 0.0 }.collect { |x| Math.log(x) }.arithmetic_mean) rescue Errno::ERANGE Math.exp(self.select { |x| x > 0.0 }.collect { |x| BigMath.log(x,50) }.arithmetic_mean) end end def median if self.length.odd? self[self.length / 2] else upper_median = self[self.length / 2] lower_median = self[(self.length / 2) - 1] [upper_median,lower_median].arithmetic_mean end end def standard_deviation mean = self.arithmetic_mean deviations = self.map { |x| x - mean } sqr_deviations = deviations.map { |x| x**2 } sum_sqr_deviations = sqr_deviations.inject(0.0) { |sum,x| sum + x } Math.sqrt(sum_sqr_deviations/(self.length - 1).to_f) end alias_method :sd, :standard_deviation def shuffle sort_by { rand } end

def shuffle! self.replace shuffle endend

• Come up with a convention for your “headers”

• Use automated documentation generation tools

• JavaDoc

• Rdoc

• Pydoc / Epydoc

• Save code snippets in a searchable repository

Documenting code sucks! Automate it.

• General tools

• DTrace

• strace

• gdb

• Language specific

• Ruby-prof

• Psyco/Pyrex

• JBoss Profiler/JIT

A little performance optimization goes a long way

Working with data

# Copyright © 1996-2007 SRI International, Marine Biological Laboratory, DoubleTwist Inc., # The Institute for Genomic Research, J. Craig Venter Institute, University of California at San Diego, and UNAM. All Rights Reserved.### Please see the license agreement regarding the use of and distribution of this file.# The format of this file is defined at http://bioinformatics.ai.sri.com/ptools/flatfile-format.html .## Species: E. coli K-12# Database: EcoCyc# Version: 11.5# File Name: dnabindsites.dat# Date and time generated: August 6, 2007, 17:32:33## Attributes:# UNIQUE-ID# TYPES# COMMON-NAME# ABS-CENTER-POS# APPEARS-IN-BINDING-REACTIONS# CITATIONS# COMMENT# COMPONENT-OF# COMPONENTS# CREDITS# DATA-SOURCE# DBLINKS# INSTANCE-NAME-TEMPLATE# INVOLVED-IN-REGULATION# LEFT-END-POSITION# REGULATED-PROMOTER# RELATIVE-CENTER-DISTANCE# RIGHT-END-POSITION# SYNONYMS#UNIQUE-ID - BS86TYPES - DNA-Binding-SitesABS-CENTER-POS - 4098761CITATIONS - 94018613CITATIONS - 94018613:EV-EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS:3310246267:martinCITATIONS - 14711822:EV-COMP-AINF-SIMILAR-TO-CONSENSUS:3310246267:martinCOMPONENT-OF - TU00064INVOLVED-IN-REGULATION - REG0-5521TYPE-OF-EVIDENCE - :BINDING-OF-CELLULAR-EXTRACTS//

http://www.oracle.com/technology/products/berkeley-db/index.html

If you can represent most of your data as key/value pairs, then at the very least use a BerkeleyDB

In most cases a relational database is an appropriate choice for bioinformatics data

•Clean and consolidated (vs. a rats nest of files and folders)

• Improved performance (memory usage and File I/O)

•Data consistency through constraints and transactions

• Easily portable (SQL92 standard)

•Querying (asking questions about data) vs. Parsing (reading and loading data)

•Commonly used data processing functions can be implemented as stored procedures

“But I’m a scientist, not a DBA! Harrumph!”

“...SQLite is a software library that implements a self-contained, serverless, zero-configuration, transactional SQL database engine...”

http://www.sqlite.org

But seriously, don’t write any SQL (What?)

Object Relational Mapper (ORM)

Relational Database(MySQL, PostgreSQL, Oracle, etc)

Model

Instance

Beyond the RDBMS

http://strokedb.com/

http://www.hypertable.org

http://incubator.apache.org/couchdb

Thinking in Parallel

• Each task is independent

• No synchronous inter-task communication

• Example: Computing a Maximum Likelihood Phylogeny for every gene family in the Panther Database

• Software: OpenPBS, SGE, Xgrid, PlatformLSF

• Tasks are interdependent

• Synchronous inter-task communication via messaging interface

• Example: Monte Carlo simulation of 3D protein interactions in cytoplasm

• Software: OpenMPI, MPICH, PVM

Loosely Coupled Tightly Coupled

Use your idle CPU cores!

Start thinking in terms of MapReduce (old hat for Lisp programmers!)

Image source: http://code.google.com/edu/parallel/mapreduce-tutorial.html

map(String key, String value): // key: document name // value: document contents for each word w in value: EmitIntermediate(w, "1");

reduce(String key, Iterator values):// key: a word// values: a list of countsint result = 0;for each v in values: result += ParseInt(v);Emit(AsString(result)); [1]

map(String key, String value): // key: Sequence alignment file name // value: multiple alignment for each exon w in value: EmitIntermediate(w, CpGIndex);

reduce(String key, Iterator values):// key: an exon// values: a list of CpG Index Valuesint result = 0;for each i in values: result += ParseInt(v);Emit(AsString(result/length(values)); [1]

http://sourceforge.net/projects/cloudburst-bio/

MapReduce Implementations

http://hadoop.apache.org/core/ http://skynet.rubyforge.org/

http://discoproject.org/

http://labs.trolltech.com/page/Projects/Threads/QtConcurrent

Embracing Hardware

Single Instruction, Multiple Data (SIMD)

Graphics Processing Unit (GPU): Not just fun and games

GPU Programming is Getting Easier

OpenCLCompute Unified

Device Architecture

http://www.nvidia.com/cuda http://s08.idav.ucdavis.edu/munshi-opencl.pdf

Field Programmable Gate Arrays (FPGA)

Field Programmable Gate Arrays (FPGA)

Playing nice with others

• JSON

• YAML

• XML

• Microformats

• RDF

Data Interchange Formats

person = { "name": "Joel Dudley", "age": 32, "height": 1.83, "urls": [ "http://www.joeldudley.com/", "http://www.linkedin.com/in/joeldudley" ]}

<person> <name>Joel Dudley</name> <age>32</age> <height>1.83</height> <urls> <url>http://www.joeldudley.com/</url> <url> http://www.linkedin.com/in/joeldudley </url> </urls></person>

VS.

• Remote Procedure Call (RPC)

• Representational State Transfer (ReST)

• SOAP

• ActiveResource Pattern

Web Services

class Video < ActiveYouTube self.site = "http://gdata.youtube.com/feeds/api"

## To search by categories and tags def self.search_by_tags (*options) from_urls = [] if options.last.is_a? Hash excludes = options.slice!(options.length-1) if excludes[:exclude].kind_of? Array from_urls << excludes[:exclude].map{|keyword| "-"+keyword}.join("/") else from_urls << "-"+excludes[:exclude] end end from_urls << options.find_all{|keyword| keyword =~ /^[a-z]/}.join("/") from_urls << options.find_all{|category| category =~ /^[A-Z]/}.join("%7C") from_urls.delete_if {|x| x.empty?} self.find(:all,:from=>"/feeds/api/videos/-/"+from_urls.reverse.join("/")) endend

class User < ActiveYouTube self.site = "http://gdata.youtube.com/feeds/api"end

class Standardfeed < ActiveYouTube self.site = "http://gdata.youtube.com/feeds/api"end

class Playlist < ActiveYouTube self.site = "http://gdata.youtube.com/feeds/api"end

search = Video.find(:first, :params => {:vq => 'ruby', :"max-results" => '5'}) puts search.entry.length

## video information of id = ZTUVgYoeN_o vid = Video.find("ZTUVgYoeN_o") puts vid.group.content[0].url

## video comments comments = Video.find_custom("ZTUVgYoeN_o").get(:comments) puts comments.entry[0].link[2].href

## searching with category/tags results = Video.search_by_tags("Comedy") puts results[0].entry[0].title # more examples: # Video.search_by_tags("Comedy", "dog") # Video.search_by_tags("News","Sports","football", :exclude=>"soccer")

Teamwork

Be Agile

Manifesto for Agile Software Development

We are uncovering better ways of developing software by doing it and helping others do it. Through this work we have come to value:

• Individuals and interactions over processes and tools• Working software over comprehensive documentation • Customer collaboration over contract negotiation • Responding to change over following a plan

That is, while there is value in the items on the right, we value the items on the left more.

http://agilemanifesto.org/

Be Agile

As a [role], I want to [goal], so I can [reason].

Storyboard

Feedback

Iterate!

Unit TestingAcceptance

Testing

Automate Development

http://nant.sourceforge.net/

http://nant.sourceforge.net/http://www.capify.org/

http://www.scons.org/

Lightweight Tools for Project Management

• Focus on the goal (Biology/Medicine)

• Don’t be clever (you’ll trick yourself)

• Value your time

• Outsource everything but genius

• Use the tools available to you

• Have fun!

Closing Remarks