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Jenkins-CI 
automating lab processes 
Science Cafe 
Maastricht, 2 October 2014 
Department of Bioinformatics - BiGCaT 1
CI := Continuous Integration 
• Continuous 
– Automation: while you write grants or 
teach 
– Reactive: when people commit...
What is Jenkins-CI? 
Department of Bioinformatics - BiGCaT 3
Just software? No. 
• “Jenkins High throughput Screening” 
Department of Bioinformatics - BiGCaT 4
Just software? No. 
• “Jenkins High throughput Screening” 
Department of Bioinformatics - BiGCaT 5
Department of Bioinformatics - BiGCaT 6
Jenkins 4 BiGCaT 
Department of Bioinformatics - BiGCaT 7
BridgeDb: alternative builds 
• Ant + Maven 
• Branches 
• R package 
– builds when ... 
Department of Bioinformatics - Bi...
PathVisio plugins 
• Recompile for 
every new 
PathVisio build 
Department of Bioinformatics - BiGCaT 9
What if the build fails? 
Department of Bioinformatics - BiGCaT 10
Unit / regression / ... testing? 
Department of Bioinformatics - BiGCaT 11
Computer-Assisted WikiPathways 
Curation 
Department of Bioinformatics - BiGCaT 12
Detect common problems 
Department of Bioinformatics - BiGCaT 13
What problems? 
Department of Bioinformatics - BiGCaT 14
Example “error message” 
Department of Bioinformatics - BiGCaT 15
Source code 
Department of Bioinformatics - BiGCaT 16
Jenkins 4 eNanoMapper 
Department of Bioinformatics - BiGCaT 17
Ontology integration & testing 
Department of Bioinformatics - BiGCaT 18
Department of Bioinformatics - BiGCaT 19
User Authentication 
• BiGCaT 
– unimaas! 
• Jenkins 
– OpenTox LDAP 
Department of Bioinformatics - BiGCaT 20
Big thanks Nuno! 
PS. this presentation show what Jenkins 
can do. All things running as jobs are 
work from others. Make ...
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Jenkins-CI: automating lab processes

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Jenkins, a digital butler, is a web site platform that supports automation of processes. While originally developed to compile software, its flexibility allows for a wide variety of processes to be automated. In this Science Cafe I will show how I am using Jenkins in my daily scientific research, supporting some repetitive tasks I no longer have to do manually. For example, it compile a wide range of software tools, including BridgeDb, PathVisio plugins, R packages, the Chemistry Development Kit, and other libraries. It is important to note, that Jenkins will attempt to recompile these software libraries each time a change is made. In fact, it will email me, if it failed to compile. But besides building these tools, it also automatically runs test suites, that find regressions, caused by unexpected side effects (or by many other reasons).

Furthermore, Jenkins is not limited to software. Of course, automation needs something a computer can execute, but this need not be compiling and testing of source code alone. I will also show how I use Jenkins to daily create RDF versions of WikiPathways, and how I use this for automated curation of WikiPathways content. I will also show how we use Jenkins in the EU FP7 eNanoMapper project for ontology development.

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Jenkins-CI: automating lab processes

  1. 1. Jenkins-CI automating lab processes Science Cafe Maastricht, 2 October 2014 Department of Bioinformatics - BiGCaT 1
  2. 2. CI := Continuous Integration • Continuous – Automation: while you write grants or teach – Reactive: when people commit changes • Integration – Compile starts when something else (successfully) compiled – Plugins... Department of Bioinformatics - BiGCaT 2
  3. 3. What is Jenkins-CI? Department of Bioinformatics - BiGCaT 3
  4. 4. Just software? No. • “Jenkins High throughput Screening” Department of Bioinformatics - BiGCaT 4
  5. 5. Just software? No. • “Jenkins High throughput Screening” Department of Bioinformatics - BiGCaT 5
  6. 6. Department of Bioinformatics - BiGCaT 6
  7. 7. Jenkins 4 BiGCaT Department of Bioinformatics - BiGCaT 7
  8. 8. BridgeDb: alternative builds • Ant + Maven • Branches • R package – builds when ... Department of Bioinformatics - BiGCaT 8
  9. 9. PathVisio plugins • Recompile for every new PathVisio build Department of Bioinformatics - BiGCaT 9
  10. 10. What if the build fails? Department of Bioinformatics - BiGCaT 10
  11. 11. Unit / regression / ... testing? Department of Bioinformatics - BiGCaT 11
  12. 12. Computer-Assisted WikiPathways Curation Department of Bioinformatics - BiGCaT 12
  13. 13. Detect common problems Department of Bioinformatics - BiGCaT 13
  14. 14. What problems? Department of Bioinformatics - BiGCaT 14
  15. 15. Example “error message” Department of Bioinformatics - BiGCaT 15
  16. 16. Source code Department of Bioinformatics - BiGCaT 16
  17. 17. Jenkins 4 eNanoMapper Department of Bioinformatics - BiGCaT 17
  18. 18. Ontology integration & testing Department of Bioinformatics - BiGCaT 18
  19. 19. Department of Bioinformatics - BiGCaT 19
  20. 20. User Authentication • BiGCaT – unimaas! • Jenkins – OpenTox LDAP Department of Bioinformatics - BiGCaT 20
  21. 21. Big thanks Nuno! PS. this presentation show what Jenkins can do. All things running as jobs are work from others. Make sure to follow the links to the GitHub projects for many of these jobs to see the heroes of that project! Department of Bioinformatics - BiGCaT 21

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