Tips And Tricks For Bioinformatics Software Engineering
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Tips And Tricks For Bioinformatics Software Engineering

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This is a talk I've given twice at Stanford recently. It's essentially a brain dump of my thoughts on being a Bioinformatician with lots of links to useful tools.

This is a talk I've given twice at Stanford recently. It's essentially a brain dump of my thoughts on being a Bioinformatician with lots of links to useful tools.

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  • 1. Tips & Tricks for Software Engineering in Bioinformatics Presented by: Joel Dudley
  • 2. Who is this guy?
  • 3. 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)
  • 4. http://www.megasoftware.net
  • 5. Kumar S. and Dudley J. “Bioinformatics software for biologists in the genomics era.” Bioinformatics (2007) vol. 23 (14) pp. 1713-7
  • 6. Bioinformatics Philosophy
  • 7. Build Your Toolbox
  • 8. Learn UNIX!
  • 9. Be a jack of all trades, but master of one. http://oreilly.com/news/graphics/prog_lang_poster.pdf
  • 10. R C/C++ PHP VB PERL Python Ruby Java LISP
  • 11. Java is not just for Java http://jruby.codehaus.org http://www.jython.org
  • 12. Simplified Wrapper and Interface Generator (SWIG) Greasy-fast C library Doughy-soft scripting language http://www.swig.org/
  • 13. Frameworks are Friends BioBike
  • 14. Stand on the slumped, dandruff-covered shoulders of millions of computer nerds.
  • 15. Don’t trust yourself (or your hard disk).
  • 16. 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''$/=2048;while(<>){G=29;R=142;if((@a=unqT=quot;C*quot;,_)[20]&48){D=89;_=unqb24,qT,@ b=map{ord qB8,unqb8,qT,_^$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,quot;xbntdxbzx14dquot;)[_/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
  • 17. Object-Oriented Software Design Decisions shment compli Ac tecture Archi
  • 18. 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=>quot;GraphNode#{self.object_id}quot;, :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
  • 19. 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
  • 20. 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
  • 21. A little performance optimization goes a long way • General tools • DTrace • strace • gdb • Language specific • Ruby-prof • Psyco/Pyrex • JBoss Profiler/JIT
  • 22. Working with data
  • 23. # 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 //
  • 24. 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
  • 25. 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
  • 26. “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...”
  • 27. But seriously, don’t write any SQL (What?) Relational Database (MySQL, PostgreSQL, Oracle, etc) Object Relational Mapper (ORM) Model Instance
  • 28. Beyond the RDBMS http://strokedb.com/ http://incubator.apache.org/couchdb http://www.hypertable.org
  • 29. Thinking in Parallel
  • 30. 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
  • 31. Use your idle CPU cores!
  • 32. Start thinking in terms of MapReduce (old hat for Lisp programmers!) Image source: http://code.google.com/edu/parallel/mapreduce-tutorial.html
  • 33. map(String key, String value): // key: document name // value: document contents for each word w in value: EmitIntermediate(w, quot;1quot;); 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]
  • 34. 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]
  • 35. http://sourceforge.net/projects/cloudburst-bio/
  • 36. MapReduce Implementations http://hadoop.apache.org/core/ http://skynet.rubyforge.org/ http://discoproject.org/ http://labs.trolltech.com/page/Projects/Threads/QtConcurrent
  • 37. Embracing Hardware
  • 38. Single Instruction, Multiple Data (SIMD)
  • 39. Graphics Processing Unit (GPU): Not just fun and games
  • 40. GPU Programming is Getting Easier Compute Unified OpenCL Device Architecture http://www.nvidia.com/cuda http://s08.idav.ucdavis.edu/munshi-opencl.pdf
  • 41. Field Programmable Gate Arrays (FPGA)
  • 42. Field Programmable Gate Arrays (FPGA)
  • 43. Playing nice with others
  • 44. Data Interchange Formats • JSON • YAML • XML • Microformats • RDF
  • 45. person = { quot;namequot;: quot;Joel Dudleyquot;, quot;agequot;: 32, quot;heightquot;: 1.83, quot;urlsquot;: [ quot;http://www.joeldudley.com/quot;, quot;http://www.linkedin.com/in/joeldudleyquot; ] } 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>
  • 46. Web Services • Remote Procedure Call (RPC) • Representational State Transfer (ReST) • SOAP • ActiveResource Pattern
  • 47. class Video < ActiveYouTube self.site = quot;http://gdata.youtube.com/feeds/apiquot; ## 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| quot;-quot;+keyword}.join(quot;/quot;) else from_urls << quot;-quot;+excludes[:exclude] end end from_urls << options.find_all{|keyword| keyword =~ /^[a-z]/}.join(quot;/quot;) from_urls << options.find_all{|category| category =~ /^[A-Z]/}.join(quot;%7Cquot;) from_urls.delete_if {|x| x.empty?} self.find(:all,:from=>quot;/feeds/api/videos/-/quot;+from_urls.reverse.join(quot;/quot;)) end end class User < ActiveYouTube self.site = quot;http://gdata.youtube.com/feeds/apiquot; end class Standardfeed < ActiveYouTube self.site = quot;http://gdata.youtube.com/feeds/apiquot; end class Playlist < ActiveYouTube self.site = quot;http://gdata.youtube.com/feeds/apiquot; end
  • 48. search = Video.find(:first, :params => {:vq => 'ruby', :quot;max-resultsquot; => '5'}) puts search.entry.length ## video information of id = ZTUVgYoeN_o vid = Video.find(quot;ZTUVgYoeN_oquot;) puts vid.group.content[0].url ## video comments comments = Video.find_custom(quot;ZTUVgYoeN_oquot;).get(:comments) puts comments.entry[0].link[2].href ## searching with category/tags results = Video.search_by_tags(quot;Comedyquot;) puts results[0].entry[0].title # more examples: # Video.search_by_tags(quot;Comedyquot;, quot;dogquot;) # Video.search_by_tags(quot;Newsquot;,quot;Sportsquot;,quot;footballquot;, :exclude=>quot;soccerquot;)
  • 49. Teamwork
  • 50. 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/
  • 51. Be Agile As a [role], I want to [goal], so I can [reason]. Storyboard Iterate! Feedback Acceptance Unit Testing Testing
  • 52. Automate Development http://nant.sourceforge.net/ http://www.scons.org/ http://www.capify.org/ http://nant.sourceforge.net/
  • 53. Lightweight Tools for Project Management
  • 54. 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!