Your SlideShare is downloading. ×
0
Ruby Conference Taiwan 2014
Ruby on
Bioinformatics
Tse-Ching Ho !
何澤清!
@tsechingho!
2014 / 4 / 26
Horse + Stripe = Zebra
Biology+Informatics=Bioinformatics
Age of Big Data
Age of Data Science
High Through Put Data
❖ Big Data!
❖ file size is small but there are many files!
❖ file size is large but there are just few ...
The Storage Demand is Increasing
from Dr. Yu-Tai Wang
Data Size of Sequencing After 5 Years
https://www.nanoporetech.com
70,000 New Born Baby X 500 GB = 35 TB
30,000 patients X...
Computing Power is Required
❖ HPC!
❖ Infiniband cluster!
❖ Amazon EC2 cluster!
❖ Hadoop cluster!
❖ Many cores of CPU!
❖ Lar...
http://arstechnica.com/business/2012/04/4829-per-hour-supercomputer-built-on-amazon-cloud-to-fuel-cancer-research/
$4,828....
http://www.hpcwire.com/2013/07/08/infiniband_snaps_up_strong_super_share/
Is 10 GB network
enough for I/O?
embarrassingly p...
http://glennklockwood.blogspot.tw/2013/12/high-performance-virtualization-sr-iov_14.html
Infiniband is good at
I/O efficie...
Data science is about DATA!
Data Scientist Concerns
❖ Data quality!
❖ Factors of filter!
❖ Statistics!
❖ Visualization!
❖ Interpretation
Programmer also Concerns
❖ High through put data (Big Data) handling!
❖ Data format / File format!
❖ Data parsing!
❖ Stati...
Biology
http://businessintelligence.com/bi-insights/the-personalized-medicine-revolution-is-almost-here/
A Dream of Personalized Medicine
from Dr. Yen-Hua Huang
Genomic Disease
http://www1.imperial.ac.uk/computationalsystemsmedicine/biomolecularmedicine/personalised/
Cure by Medicines
http://scienceroll.com/2008/04/25/personalized-medicine-real-clinical-examples/
Personalized Medicine
http://www.genomicslawreport.com/index.php/tag/personalized-medicine/
Personal Genomic Analysis
http://www.thecureisnow.org/index.php/our-strategy/philosophy-of-tcin/personalized-medicine
http://www.genengnews.com/insight-and-intelligence/personalized-medicine-not-quite-there-yet/77899649/
DNA
http://cisncancer.org/research/what_we_know/omics/personalized_medicine_02.html
DNA Sequencing
http://www.scq.ubc.ca/genome-projects-uncovering-the-blueprints-of-biology/
http://www.scq.ubc.ca/genome-pr...
No Teach for Reading DNA
http://intellimedix.com
Do The Right Things
http://www.dnadirect.com
http://biodbnet.abcc.ncifcrf.gov/dbInfo/netGraph.php
ID mapping of
Databases
Each node is a database.!
Each database has i...
Bioinformatics Sites for Rubists
NCBI
http://www.ncbi.nlm.nih.gov
Ensembl
http://www.ensembl.org
Nature Biotechnology
http://www.nature.com/nbt
PLOS Computational Biology
http://www.ploscompbiol.org
Biostarts
https://www.biostars.org
SEQanswers
http://seqanswers.com
Ruby Sites for Bioinformatists
GitHub
https://github.com/
RubyGems.org
https://rubygems.org
The Ruby Toolbox
https://www.ruby-toolbox.com
Biogems.info
http://www.biogems.info
BioRuby
http://bioruby.org
SciRuby
http://sciruby.com
What programming language is
best for a bioinformatics beginner?
Mapping Sequence Data
from Jui-Tse Hsu
Simple Mapping Sequence Data
Convert to SAM
Compress
to BAM
Index, Sort,
Remove duplicate
PCR (Rmdup)
1. .seq -> fastq
2. ...
C/C++
❖ Key Algorithms!
❖ Written by C/C++!
❖ Foundation Tools!
❖ BWA!
❖ Bowtie / Bowtie2!
❖ samtools / bamtools!
❖ GMAP /...
http://genomebiology.com/2010/11/12/220
Analysis Pipeline
Overview of the RNA-seq analysis
pipeline for detecting differen...
Perl
❖ First language!
❖ Bioperl!
❖ Ensembl
http://millionchimpanzees.blogspot.tw/2011/09/book-review-learning-perl-sixth-...
Java
❖ good part of java!
❖ GATK!
❖ Taverna!
❖ Hadoop
http://shop.oreilly.com/product/9780596803742.do
R
❖ Statistic tools!
❖ Bioconductor!
❖ EdgeR!
❖ Data Mining and Analysis
Books
http://exploringdata.github.io/data-visuali...
Python
❖ young people!
❖ Galaxy
http://news.oreilly.com/2008/08/python-for-unix-and-linux-syst.html
The Ruby Way in Bioinformatics
What kinds of libraries
would you think it is important?
Foundation gems
❖ activerecord!
❖ nokogiri!
❖ ffi!
❖ parallel!
!
!
❖ bioruby!
❖ sciruby!
!
!
!
C binding & wrapper
❖ bio-samtools!
❖ bio-bwa!
❖ bio-affy!
❖ bio-faster!
❖ mpi-ruby!
❖ bio-grid!
❖ gsl!
❖ rb-gsl!
❖ nmatri...
Data parser / analyser
❖ bio-genomic-interval!
❖ bio-blastxmlparser!
❖ bio-assembly!
❖ bio-gff3!
❖ bio-gff3-pltools!
❖ bio...
Data parser / analyser
❖ bio-phyloxml!
❖ bio-jplace!
❖ bio-gex!
❖ bio-ipcress!
❖ bio-stockholm!
❖ bio-synreport!
❖ bio-cig...
Data parser / analyser - protein
❖ protk!
❖ mascot-dat!
❖ bio-protparam!
❖ bio-plasmoap!
❖ bio-signalp!
❖ bio-exportpred!
...
Database / Web API
❖ ruby-ensembl-api!
❖ bio-ucsc-api!
❖ bio-liftover!
❖ intermine!
❖ bio-eupathdb!
❖ bio-krona!
❖ bio-sra...
Statistics
❖ statsample!
❖ statsample-sem!
❖ statsample-optimization!
❖ statsample-timeseries!
❖ distribution!
❖ rinruby
h...
SVG & Graph
❖ rubyvis!
❖ plotrb!
❖ bio-svgenes!
❖ bio-vis!
❖ gnuplot
http://rubyvis.rubyforge.org
Tools
❖ minimization!
❖ integration!
❖ quorum - rails engine
I am Not Analyst,

I am Programmer.
What can I get involved?
Pipeline / Workflow
Galaxy - python!
Taverna - java!
??? - Ruby
Web System
❖ Data warehouse!
❖ Pipeline management!
❖ Coordination center!
❖ Visualisation
Cloud / Distributed / Parallel
http://www.mynamesnotmommy.com/yes-there-are-dumb-questions/question-mark/
What We Are Doing By Ruby?
Ensembl Virtual Machine
❖ Powered by VeeWee, Vagrant and Chef!
❖ Automatic build versioned Ensembl system (perl)!
❖ Includ...
Ensembl Virtual Machine
Use existed
vagrant box
Prepare SOP for
Chef recipes
Provision VM
with Chef recipes
Write Chef rec...
Ensembl Virtual Machine
Web view of Ensembl
from Tse-Ching Ho
DR. RAW
❖ Derived from DRAW and SneakPeek!
❖ Composed of C/C++, bash, perl, java, ruby!
❖ Have both DNA and RNA re-sequenc...
DR. RAW
Analysis
Tools
Analysis
Pipeline
Quality
Control
Resource
Manager
System
DNA QC

Forward : Reverse
RNA QC!
Forward...
DR. RAW
Web view by Rails
from Hannah Lin
Neo4j - JRuby Data Parser
❖ Graph database for data integration of discrete clinical
research documents!
❖ Origin data are...
Neo4j - JRuby Data Parser
from Wei-Ming Wu, Chia-Hsuan Lee
Neo4j - JRuby Data Parser
from Wei-Ming Wu, Chia-Hsuan Lee
Collision Rate of Input Data: 1.3 %
API Server for Third Party Firm
❖ API server based on Rails, run by JRuby!
❖ ActiveRecord models for Oracle database!
❖ ac...
API Server for Third Party Firm
TCHC server
API server

(rails, jruby)
CSIS
(java, oracle)
Send data by XML
Write into dat...
Daily Checking Rule
❖ Based on Rails, run by JRuby!
❖ ActiveRecord models for Oracle database!
❖ activerecord-oracle_enhan...
Daily Checking Rule
from Wei-Ming Wu, Sean Wang
Daily Checking Rule
from Wei-Ming Wu, Sean Wang
Daily Checking Rule
from Wei-Ming Wu, Sean Wang
Daily Checking Rule
from Wei-Ming Wu, Sean Wang
Patient Randomization
❖ Based on Rails, run by JRuby!
❖ ActiveRecord models for Oracle database!
❖ activerecord-oracle_enh...
Patient Randomization
from Wei-Ming Wu, Sean Wang
Patient Randomization
from Wei-Ming Wu, Sean Wang
Patient Randomization
from Wei-Ming Wu, Sean Wang
Assign patients to treatment groups
Database Statistics Dashboard
❖ Based on Rails, run by JRuby!
❖ ActiveRecord models for Oracle database!
❖ activerecord-or...
Database Statistics Dashboard
from Wei-Ming Wu, Winnie Lui
Education
Learning Bioinformatics
❖ http://www.nature.com/nbt/journal/v31/n11/full/
nbt.2740.html!
❖ http://www.liacs.nl/~hoogeboo/m...
Books for Beginners
http://practicalcomputing.org
Python
Python Book for Bioinformatics
http://shop.oreilly.com/product/9780596154516.do
Python is very successful
in Teach than Ruby
Do we lack a killer application by Ruby?
http://www.witardroadbaptist.org/im-new/im-not-sure-im-ready-for-church-yet/
We Need Human !!
Are You Ready 

To Be A Data Scientist
Or A Binformactis?
Markets
http://www.genengnews.com/gen-articles/personalized-medicine-health-economic-aspects/4824/
http://www.bccresearch.com/market-research/biotechnology/bioinformatics-market-technology-bio051b.html
Under developing Do...
Topics to take in action
❖ data generation and data management!
❖ data analysis and software!
❖ data processing and storag...
Health Care in Cloud
❖ Health promotion cloud!
❖ Vaccination cloud!
❖ Exercise cloud!
❖ Workplace wellness!
❖ Physical che...
Code For Bioinformatics
Q & A
Upcoming SlideShare
Loading in...5
×

Ruby on bioinformatics

391

Published on

RubyConf Taiwan 2014

Published in: Science, Technology, Education
0 Comments
1 Like
Statistics
Notes
  • Be the first to comment

No Downloads
Views
Total Views
391
On Slideshare
0
From Embeds
0
Number of Embeds
2
Actions
Shares
0
Downloads
9
Comments
0
Likes
1
Embeds 0
No embeds

No notes for slide

Transcript of "Ruby on bioinformatics"

  1. 1. Ruby Conference Taiwan 2014 Ruby on Bioinformatics Tse-Ching Ho ! 何澤清! @tsechingho! 2014 / 4 / 26
  2. 2. Horse + Stripe = Zebra
  3. 3. Biology+Informatics=Bioinformatics
  4. 4. Age of Big Data
  5. 5. Age of Data Science
  6. 6. High Through Put Data ❖ Big Data! ❖ file size is small but there are many files! ❖ file size is large but there are just few files! ❖ Data size of bioinformatics! ❖ 1,000,000,000 records for a subject (person) is normal
  7. 7. The Storage Demand is Increasing from Dr. Yu-Tai Wang
  8. 8. Data Size of Sequencing After 5 Years https://www.nanoporetech.com 70,000 New Born Baby X 500 GB = 35 TB 30,000 patients X 10,000 cells X 500 GB = 1.5 X 1011 GB = 150 EB from Dr. Yu-Tai Wang 1. count by current NGS data! 2. not include civil medical institutes
  9. 9. Computing Power is Required ❖ HPC! ❖ Infiniband cluster! ❖ Amazon EC2 cluster! ❖ Hadoop cluster! ❖ Many cores of CPU! ❖ Large Memory! ❖ High IO efficiency http://arstechnica.com/business/2012/05/amazons-hpc-cloud-supercomputing-for-the-99/
  10. 10. http://arstechnica.com/business/2012/04/4829-per-hour-supercomputer-built-on-amazon-cloud-to-fuel-cancer-research/ $4,828.85 per hour 51,132 cores, 58.78TB RAM
 6,742 Amazon EC2 instances 2012! Protein simulation! Cycle Computing System! Ganglia HPC clusters! Deployed by Opscode Chef
  11. 11. http://www.hpcwire.com/2013/07/08/infiniband_snaps_up_strong_super_share/ Is 10 GB network enough for I/O? embarrassingly parallel:
 The calculations are independent of each other.
  12. 12. http://glennklockwood.blogspot.tw/2013/12/high-performance-virtualization-sr-iov_14.html Infiniband is good at I/O efficiency • Interconnect speed.! • I/O performance.! • Infiniband system is about 3.8GB/s of Bandwidth.! • 10 GB network is about 400MB/s of Bandwidth.
  13. 13. Data science is about DATA!
  14. 14. Data Scientist Concerns ❖ Data quality! ❖ Factors of filter! ❖ Statistics! ❖ Visualization! ❖ Interpretation
  15. 15. Programmer also Concerns ❖ High through put data (Big Data) handling! ❖ Data format / File format! ❖ Data parsing! ❖ Statistic tools! ❖ Visualization! ❖ Profit / Markets
  16. 16. Biology
  17. 17. http://businessintelligence.com/bi-insights/the-personalized-medicine-revolution-is-almost-here/
  18. 18. A Dream of Personalized Medicine from Dr. Yen-Hua Huang
  19. 19. Genomic Disease http://www1.imperial.ac.uk/computationalsystemsmedicine/biomolecularmedicine/personalised/
  20. 20. Cure by Medicines http://scienceroll.com/2008/04/25/personalized-medicine-real-clinical-examples/
  21. 21. Personalized Medicine http://www.genomicslawreport.com/index.php/tag/personalized-medicine/
  22. 22. Personal Genomic Analysis http://www.thecureisnow.org/index.php/our-strategy/philosophy-of-tcin/personalized-medicine
  23. 23. http://www.genengnews.com/insight-and-intelligence/personalized-medicine-not-quite-there-yet/77899649/
  24. 24. DNA http://cisncancer.org/research/what_we_know/omics/personalized_medicine_02.html
  25. 25. DNA Sequencing http://www.scq.ubc.ca/genome-projects-uncovering-the-blueprints-of-biology/ http://www.scq.ubc.ca/genome-projects-uncovering-the-blueprints-of-biology/ http://www.broadinstitute.org/blog/beyond-genome-new-uses-dna-sequencers
  26. 26. No Teach for Reading DNA http://intellimedix.com
  27. 27. Do The Right Things http://www.dnadirect.com
  28. 28. http://biodbnet.abcc.ncifcrf.gov/dbInfo/netGraph.php ID mapping of Databases Each node is a database.! Each database has it’s unique id.! These ids connected as a network.! 
 I think handling these complexity should be easy for the people seating here.
  29. 29. Bioinformatics Sites for Rubists
  30. 30. NCBI http://www.ncbi.nlm.nih.gov
  31. 31. Ensembl http://www.ensembl.org
  32. 32. Nature Biotechnology http://www.nature.com/nbt
  33. 33. PLOS Computational Biology http://www.ploscompbiol.org
  34. 34. Biostarts https://www.biostars.org
  35. 35. SEQanswers http://seqanswers.com
  36. 36. Ruby Sites for Bioinformatists
  37. 37. GitHub https://github.com/
  38. 38. RubyGems.org https://rubygems.org
  39. 39. The Ruby Toolbox https://www.ruby-toolbox.com
  40. 40. Biogems.info http://www.biogems.info
  41. 41. BioRuby http://bioruby.org
  42. 42. SciRuby http://sciruby.com
  43. 43. What programming language is best for a bioinformatics beginner?
  44. 44. Mapping Sequence Data from Jui-Tse Hsu
  45. 45. Simple Mapping Sequence Data Convert to SAM Compress to BAM Index, Sort, Remove duplicate PCR (Rmdup) 1. .seq -> fastq 2. Illumina score -> Phred score 1. cleaned bam file 2. quality control, get statistics, mapped, unmapped, etc. 1. SNVs in VCFs 2. structural variants 3. copy number changes, etc. Aligner (soap2, bwa, bowtie, etc.) from Jui-Tse Hsu Illumina Exome sequence reads Aligned reads Aligned reads! (sam file) Aligned reads! (bam file) Useful reads data Call variants Visualization 
 in browsers
  46. 46. C/C++ ❖ Key Algorithms! ❖ Written by C/C++! ❖ Foundation Tools! ❖ BWA! ❖ Bowtie / Bowtie2! ❖ samtools / bamtools! ❖ GMAP / GSNAP! ❖ BLAT! ❖ Tophat
  47. 47. http://genomebiology.com/2010/11/12/220 Analysis Pipeline Overview of the RNA-seq analysis pipeline for detecting differential expression
  48. 48. Perl ❖ First language! ❖ Bioperl! ❖ Ensembl http://millionchimpanzees.blogspot.tw/2011/09/book-review-learning-perl-sixth-edition.html
  49. 49. Java ❖ good part of java! ❖ GATK! ❖ Taverna! ❖ Hadoop http://shop.oreilly.com/product/9780596803742.do
  50. 50. R ❖ Statistic tools! ❖ Bioconductor! ❖ EdgeR! ❖ Data Mining and Analysis Books http://exploringdata.github.io/data-visualization-books/analysis/
  51. 51. Python ❖ young people! ❖ Galaxy http://news.oreilly.com/2008/08/python-for-unix-and-linux-syst.html
  52. 52. The Ruby Way in Bioinformatics
  53. 53. What kinds of libraries would you think it is important?
  54. 54. Foundation gems ❖ activerecord! ❖ nokogiri! ❖ ffi! ❖ parallel! ! ! ❖ bioruby! ❖ sciruby! ! ! !
  55. 55. C binding & wrapper ❖ bio-samtools! ❖ bio-bwa! ❖ bio-affy! ❖ bio-faster! ❖ mpi-ruby! ❖ bio-grid! ❖ gsl! ❖ rb-gsl! ❖ nmatrix! ❖ sambamba - D language! !
  56. 56. Data parser / analyser ❖ bio-genomic-interval! ❖ bio-blastxmlparser! ❖ bio-assembly! ❖ bio-gff3! ❖ bio-gff3-pltools! ❖ bio-alignment! ❖ bio-maf! ❖ bio-table! ❖ bio-rdf! ❖ bio-vcf! ❖ bio-velvet! ❖ bio-gngm! ❖ bio-gag! ❖ bio-dbsnp
  57. 57. Data parser / analyser ❖ bio-phyloxml! ❖ bio-jplace! ❖ bio-gex! ❖ bio-ipcress! ❖ bio-stockholm! ❖ bio-synreport! ❖ bio-cigar! ❖ bio-wolf_psort_wrapper! ❖ bio-hmmer3_report! ❖ bio-dbla-finder! ❖ bio-newbler_outputs! ❖ bio-sra_fastq_dumper! ❖ bigbio!
  58. 58. Data parser / analyser - protein ❖ protk! ❖ mascot-dat! ❖ bio-protparam! ❖ bio-plasmoap! ❖ bio-signalp! ❖ bio-exportpred! ❖ bio-hydropathy! ❖ bio-epitope! ❖ bio-bio-orthomcl! ❖ bio-isoelectric_point! ❖ bio-octopus! ❖ bio-tm_hmm! ❖ bio-aliphatic_index!
  59. 59. Database / Web API ❖ ruby-ensembl-api! ❖ bio-ucsc-api! ❖ bio-liftover! ❖ intermine! ❖ bio-eupathdb! ❖ bio-krona! ❖ bio-sra! ❖ bio-sradl http://www.ensembl.org
  60. 60. Statistics ❖ statsample! ❖ statsample-sem! ❖ statsample-optimization! ❖ statsample-timeseries! ❖ distribution! ❖ rinruby http://www.ncss.com/software/ncss/survival-analysis-in-ncss
  61. 61. SVG & Graph ❖ rubyvis! ❖ plotrb! ❖ bio-svgenes! ❖ bio-vis! ❖ gnuplot http://rubyvis.rubyforge.org
  62. 62. Tools ❖ minimization! ❖ integration! ❖ quorum - rails engine
  63. 63. I am Not Analyst,
 I am Programmer.
  64. 64. What can I get involved?
  65. 65. Pipeline / Workflow Galaxy - python! Taverna - java! ??? - Ruby
  66. 66. Web System ❖ Data warehouse! ❖ Pipeline management! ❖ Coordination center! ❖ Visualisation
  67. 67. Cloud / Distributed / Parallel http://www.mynamesnotmommy.com/yes-there-are-dumb-questions/question-mark/
  68. 68. What We Are Doing By Ruby?
  69. 69. Ensembl Virtual Machine ❖ Powered by VeeWee, Vagrant and Chef! ❖ Automatic build versioned Ensembl system (perl)! ❖ Include database, queuing services and analysis tools! ❖ Multi sites, multi species in one virtual machine! ❖ Help to build local & custom system from Tse-Ching Ho
  70. 70. Ensembl Virtual Machine Use existed vagrant box Prepare SOP for Chef recipes Provision VM with Chef recipes Write Chef recipes Export VM by Virtualbox Setup Vagrantfile Create Vagrant box by Veewee Write definition of Vagrant box by Veewee Ensembl VM Automation from Tse-Ching Ho
  71. 71. Ensembl Virtual Machine Web view of Ensembl from Tse-Ching Ho
  72. 72. DR. RAW ❖ Derived from DRAW and SneakPeek! ❖ Composed of C/C++, bash, perl, java, ruby! ❖ Have both DNA and RNA re-sequence analysis! ❖ Enhanced quality control for DNA and RNA! ❖ Distributed computing pipeline! ❖ Support PBS, LSF, SGE platforms (queuing system) from Hannah Lin
  73. 73. DR. RAW Analysis Tools Analysis Pipeline Quality Control Resource Manager System DNA QC
 Forward : Reverse RNA QC! Forward : Reverse BWA-0.7.7! Samtools-0.1.19! GATK-3.1 GSNAP-13-10-25! Cufflink-13-11! FusionGene … DNA Sequencing data RNA Sequencing data SGE (Sun Grid Engine) PBS (Portable Batch System)! LSF (Load Sharing Facility) Green: new components! Red: updated components from Hannah Lin
  74. 74. DR. RAW Web view by Rails from Hannah Lin
  75. 75. Neo4j - JRuby Data Parser ❖ Graph database for data integration of discrete clinical research documents! ❖ Origin data are excel/csv files collected in different time, by different people! ❖ Neo4j is good for cleanup such massive data set! ❖ Cooperation between biologist and programmer from Wei-Ming Wu, Chia-Hsuan Lee
  76. 76. Neo4j - JRuby Data Parser from Wei-Ming Wu, Chia-Hsuan Lee
  77. 77. Neo4j - JRuby Data Parser from Wei-Ming Wu, Chia-Hsuan Lee Collision Rate of Input Data: 1.3 %
  78. 78. API Server for Third Party Firm ❖ API server based on Rails, run by JRuby! ❖ ActiveRecord models for Oracle database! ❖ activerecord-oracle_enhanced-adapter gem! ❖ Import excel files to third party GUI client ! ❖ Third party server send XML request to API server from Wei-Ming Wu, Sean Wang
  79. 79. API Server for Third Party Firm TCHC server API server
 (rails, jruby) CSIS (java, oracle) Send data by XML Write into database Read data by client program Upload data Parse request Third Party Our Servers Windows GUI from Wei-Ming Wu, Sean Wang
  80. 80. Daily Checking Rule ❖ Based on Rails, run by JRuby! ❖ ActiveRecord models for Oracle database! ❖ activerecord-oracle_enhanced-adapter gem! ❖ User can define rules for checking data, usually values in filled forms! ❖ Run checking rules daily, not before filling forms from Wei-Ming Wu, Sean Wang
  81. 81. Daily Checking Rule from Wei-Ming Wu, Sean Wang
  82. 82. Daily Checking Rule from Wei-Ming Wu, Sean Wang
  83. 83. Daily Checking Rule from Wei-Ming Wu, Sean Wang
  84. 84. Daily Checking Rule from Wei-Ming Wu, Sean Wang
  85. 85. Patient Randomization ❖ Based on Rails, run by JRuby! ❖ ActiveRecord models for Oracle database! ❖ activerecord-oracle_enhanced-adapter gem! ❖ Assign patients into different groups by randomization method! ❖ Cooperation between statistician and programmer from Wei-Ming Wu, Sean Wang
  86. 86. Patient Randomization from Wei-Ming Wu, Sean Wang
  87. 87. Patient Randomization from Wei-Ming Wu, Sean Wang
  88. 88. Patient Randomization from Wei-Ming Wu, Sean Wang Assign patients to treatment groups
  89. 89. Database Statistics Dashboard ❖ Based on Rails, run by JRuby! ❖ ActiveRecord models for Oracle database! ❖ activerecord-oracle_enhanced-adapter gem! ❖ google_visualr gem for visualization! ❖ Count number of projects, forms, fields, records and patients from Wei-Ming Wu, Winnie Lui
  90. 90. Database Statistics Dashboard from Wei-Ming Wu, Winnie Lui
  91. 91. Education
  92. 92. Learning Bioinformatics ❖ http://www.nature.com/nbt/journal/v31/n11/full/ nbt.2740.html! ❖ http://www.liacs.nl/~hoogeboo/mcb/ nature_primer.html! ❖ http://www.mygoblet.org - python, R! ❖ http://www.biotnet.org
  93. 93. Books for Beginners http://practicalcomputing.org Python
  94. 94. Python Book for Bioinformatics http://shop.oreilly.com/product/9780596154516.do
  95. 95. Python is very successful in Teach than Ruby
  96. 96. Do we lack a killer application by Ruby? http://www.witardroadbaptist.org/im-new/im-not-sure-im-ready-for-church-yet/
  97. 97. We Need Human !!
  98. 98. Are You Ready 
 To Be A Data Scientist Or A Binformactis?
  99. 99. Markets http://www.genengnews.com/gen-articles/personalized-medicine-health-economic-aspects/4824/
  100. 100. http://www.bccresearch.com/market-research/biotechnology/bioinformatics-market-technology-bio051b.html Under developing Do Asia have enough market sharing?
  101. 101. Topics to take in action ❖ data generation and data management! ❖ data analysis and software! ❖ data processing and storage! ❖ application of bioinformatics in pharma research and development http://www.giichinese.com.tw/report/bc268909- bioinformatics-technologies-global-markets.html
  102. 102. Health Care in Cloud ❖ Health promotion cloud! ❖ Vaccination cloud! ❖ Exercise cloud! ❖ Workplace wellness! ❖ Physical checkup cloud! ❖ Welfare cloud from Dr. Chi-Hung Lin
  103. 103. Code For Bioinformatics
  104. 104. Q & A
  1. A particular slide catching your eye?

    Clipping is a handy way to collect important slides you want to go back to later.

×