B Kinoshita - Creating biology pipelines with BioUno
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BioUno is an open source project that uses continuous integration tools like Jenkins to create biology pipelines. It was created by Bruno Kinoshita in Brazil as a way to apply DevOps practices to biology. BioUno uses Jenkins for its jobs, notifications, and integration with other tools. The next steps are to enhance documentation, find new developers and users, and compare BioUno to other similar biology tools.
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B Kinoshita - Creating biology pipelines with BioUno
- 1. Creating Biology Pipelines with BioUno Bru n o P. Kin o sh ita - b ru n o @ tu p ilab s.co m – kin o w@ ap ach e .o rg h ttp ://www.tu p ilab s.co m
- 2. Who a m I B r u n o P . K in o s h it a 27 yo, Brazilian, from Sao Paulo, Sao Paulo Software P r o g r a m m e r @ T u p i L a b s Participating in several OSS (Apache Commons, tap4j, Jenkins, TestLink, TunesViewer, …) k in o w @ p a c h e . o r g a @ i n o w – Twitter/GitHub/FreeNode k Bru n o P. Kin o sh ita - b ru n o @ tu p ilab s.co m – kin o w@ ap ach e .o rg h ttp ://www.tu p ilab s.co m
- 3. W h a t ' s B io U n o ? A n O p e n S o u r c e p r o je c t t h a t u s e s c o n t in u o u s in t e g r a t io n t o o ls a n d t e c h n iq u e s t o c r e a t e b io lo g y p ip e lin e s One of the tools used is J e n k i n s , an O p e n S o u r c e build server It has p l u g - i n s ... And an update center... Bru n o P. Kin o sh ita - b ru n o @ tu p ilab s.co m – kin o w@ ap ach e .o rg Then why didn't you name it bio-j h ://www.tu p ilab s.co m ttp enkins?
- 4. B io U n o . W h o c r e a t e d it ? H o w ? W h e n ? It is an interesting story that started some time ago in Brazil... in an Irish Pub Bru n o P. Kin o sh ita - b ru n o @ tu p ilab s.co m – kin o w@ ap ach e .o rg h ttp ://www.tu p ilab s.co m
- 5. W h y J e n k in s ? An a w e s ome O pe n S ourc e c o m m u n i t y (more than 100 developers) Simple w e b interface J o b s c h e d u le a n d m a n a g e m e n t N o t if ic a t io n s C l o u d computing B i g D a t a (Hadoop) no Bru Existing integration with many programming P. Kin o sh ita - b ru n o @ tu p ilab s.co m – kin o w@ ap ach e .o rg h ttp ://www.tu p ilab s.co m
- 6. N e xt s te p s Finish the u p d a t e c e n t e r infrastructure Write more p l u g -i n s Enhance the user/developer d o c u m e n t a t io n Prepare a small public c o m p u t e r f a c i l i t y for BioUno Find new d e v e l o p e r s & u s e r s Comparison with Taverna, Galaxy and other Bru n o P. Kin o sh ita - b ru n o @ tu p ilab s.co m – kin o w@ ap ach e .o rg similar tools h ttp ://www.tu p ilab s.co m
- 7. DEMO Bru n o P. Kin o sh ita - b ru n o @ tu p ilab s.co m – kin o w@ ap ach e .o rg h ttp ://www.tu p ilab s.co m
- 8. A n y q u e s t io n s ? Bru n o P. Kin o sh ita - b ru n o @ tu p ilab s.co m – kin o w@ ap ach e .o rg h ttp ://www.tu p ilab s.co m
- 9. Th a n k yo u ! D a n k e ! O b r ig a d o ! G r a c ia s ! M e r c i! A r ig a t o u ! w w w . b io u n o . o r g k in o w @ p a c h e . o r g a @ in o w , @ u p ila b s k t Bru n o P. Kin o sh ita - b ru n o @ tu p ilab s.co m – kin o w@ ap ach e .o rg h ttp ://www.tu p ilab s.co m