Posts tagged with events

JUC SP 2012 - Jenkins User Conference São Paulo (Call For Papers)

Oct 24, 2012 in events, jenkins, news | blog

O primeiro encontro de usuários Jenkins no Brasil vai acontecer em São Paulo, em Dezembro. Neste evento você vai poder conhecer mais sobre integração contínua, builds em diferentes linguagens de programação (Java, PHP, Ruby, Python, entre outras), cloud, boas práticas e muitos casos sobre o uso de Jenkins. Você vai também poder conversar com pessoal da CloudBees, TupiLabs e de outras empresas que participarão do evento.

O call for papers já está aberto, então se você tem um caso interessante, ou gostaria de falar sobre algum tópico de integração contínua, automatização, cloud computing e Jenkins, envie sua proposta:

Você pode submeter palestras e lighting talks, mas também estamos organizando um hackathon com o pessoal do projeto do Jenkins (aqueles que você encontra sempre pelo canal IRC #jenkins na Freenode) e com alguns dos participantes. Se você tiver uma idéia para o Hackathon, como uma feature nova, ou algum bug que você sempre quis ter corrigido, pode entrar em contato comigo e enviar sua sugestão. Sua idéia pode ser realizada lá no hackathon, contribuindo com o projeto e com a comunidade :-)

The slides from JUC SF are coming

Oct 02, 2012 in jenkins, events | news

Watch the news for more upcoming slides from JUC SF (Jenkins User Conference San Francisco). You can already check Kohsuke Kawaguchi‘s slides. The link is for the reddit thread, so you can comment there and give karma to @agentdero who posted the link.

Another interesting news is that now CloudBees Jenkins can deploy to GoogleAppEngine. I believe that in the near future BuildHive will have integration with other platforms and will be able to build software written in many programming languages too.

BOSC 2012 and BioUno

Aug 10, 2012 in jenkins, bioinformatics, events | blog

Few weeks ago TupiLabs participated of BOSC 2012 , with a talk about BioUno . BioUno is a project that applies techniques and tools from Continuous Integration in Bioinformatics, in special Jenkins . In the very beginning, the project was a ” hey, look what I can do with Jenkins “. Later on we defined that we would like to create biology pipelines with Jenkins , using plug-ins. This was the topic of our talk in BOSC 2012 - Creating biology pipelines with Jenkins . The main advantage of using Jenkins, is its distributed environment with master and slaves , the plug-ins and the documentation and community available .

In the talk, we showed a demo using vanilla Jenkins, MrBayes , with mrbayes-plugin , and R and ape for plotting, using r-plugin . It was a very simple pipeline, without using Cloud services or any NGS tool. What was great in BOSC 2012 is that we could catch up with people that work on Galaxy , Taverna , Mobyle and other workflow management systems, as well as lads from other interesting projects, like CloudGene (MapReduce interface for researchers, pretty cool). When we returned to Brazil, we had more items to include in BioUno TODO list, but also a realization. That BioUno is not only a biology workflow management system. Its roles intersect with Galaxy, Taverna and Mobyle, as a workflow management system , but also intersect with BioHPC , as a bioinformatics computer management system .

With Jenkins you can start and monitor slaves remotely (in your local network or in a cloud), execute parts of your build in one machine and serialize results back to the master, display graphs, monitor usage and execute other things that give you the possibility to use Jenkins to create very customized pipelines . Sometimes a researcher has to use tools like stacks , samtools , structure , beast and so it goes. But sometimes he has need of a very specific routine, maybe for plotting something or adjusting data output from one tool, before inputting it into the next tool in the pipeline. These routines are not always worth a tool, as they would be used very rarely . This is possible with Jenkins. Or a job may demand five computers. Common computer facilities would delegate the machine provision to cluster management systems, like PBS , LSF or some cloud based system . With Jenkins, you can manage your computer, maybe even use Puppet to help you. We have a long way ahead, we are reorganizing our servers at Linode to install JIRA and Confluence , and have a more Jenkins-like web site (as this is the principal tool in BioUno). And we are still creating plug-ins. If you have any interested in the project, feel free to join us , your help will be very welcome :-)