Tips & Tricks for
Software Engineering in
Bioinformatics
Presented by:
Joel Dudley

Who is this guy?

Avg. time spent programming (hours)
10.0
7.5
5.0
2.5
0
5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 25 25 26 27 28 29 30 31 32
Age (years)

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

R
C/C++ PHP
VB PERL
Python
Ruby
Java
LISP

Java is not just for Java
http://jruby.codehaus.org
http://www.jython.org

Simplified Wrapper and Interface Generator (SWIG)
Greasy-fast C library
Doughy-soft
scripting language
http://www.swig.org/

Frameworks are Friends
BioBike

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

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

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

Object-Oriented Software Design Decisions
shment
compli
Ac
tecture
Archi

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
end
end

Documenting code sucks! Automate it.
• Come up with a convention for your
“headers”
• Use automated documentation generation
tools
• JavaDoc
• Rdoc
• Pydoc / Epydoc
• Save code snippets in a searchable
repository

A little performance optimization goes a long way
• General tools
• DTrace
• strace
• gdb
• Language specific
• Ruby-prof
• Psyco/Pyrex
• JBoss Profiler/JIT

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 - BS86
TYPES - DNA-Binding-Sites
ABS-CENTER-POS - 4098761
CITATIONS - 94018613
CITATIONS - 94018613:EV-EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS:3310246267:martin
CITATIONS - 14711822:EV-COMP-AINF-SIMILAR-TO-CONSENSUS:3310246267:martin
COMPONENT-OF - TU00064
INVOLVED-IN-REGULATION - REG0-5521
TYPE-OF-EVIDENCE - :BINDING-OF-CELLULAR-EXTRACTS
//

If you can represent most of your data as key/value
pairs, then at the very least use a BerkeleyDB
http://www.oracle.com/technology/products/berkeley-db/index.html

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!”
http://www.sqlite.org
“...SQLite is a software library that implements a self-contained, serverless,
zero-configuration, transactional SQL database engine...”

But seriously, don’t write any SQL (What?)
Relational Database
(MySQL, PostgreSQL, Oracle, etc)
Object Relational Mapper (ORM)
Model
Instance

Beyond the RDBMS
http://strokedb.com/ http://incubator.apache.org/couchdb
http://www.hypertable.org

Thinking in Parallel

Loosely Coupled Tightly Coupled
• •
Each task is independent Tasks are interdependent
• •
No synchronous inter- Synchronous inter-task
task communication communication via
messaging interface
• Example: Computing a
•
Maximum Likelihood Example: Monte Carlo
Phylogeny for every gene simulation of 3D protein
family in the Panther interactions in cytoplasm
Database
• Software: OpenMPI,
• Software: OpenPBS, MPICH, PVM
SGE, Xgrid, PlatformLSF

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 counts
int 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 Values
int 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
Compute Unified
OpenCL
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

Data Interchange Formats
• JSON
• YAML
• XML
• Microformats
• RDF

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

Web Services
• Remote Procedure Call (RPC)
• Representational State Transfer (ReST)
• SOAP
• ActiveResource Pattern

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(\"/\"))
end
end
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
Iterate!
Feedback
Acceptance
Unit Testing
Testing

Automate Development
http://nant.sourceforge.net/ http://www.scons.org/
http://www.capify.org/ http://nant.sourceforge.net/

Lightweight Tools for Project Management

Closing Remarks
• 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!