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Old 05-15-2012, 07:00 PM   #3
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Location: US

Join Date: Nov 2009
Posts: 437

Hi gringer,

Certainly one aspect of OpenGE will be the management of analysis pipelines composed of existing tools. Much like the recently released bpipe project, the aim would be to incorporate existing tools into workflows. We want to eventually build a web-based GUI (in development right now) that allows for the dynamic creation of workflows (currently this is implemented at the command line) and we would like it to feature things like: versioning of tools, progress tracking, recovery and restarting from errors, etc.

Rewriting everyone's code is inefficient and unnecessary, but OpenGE also will feature modifications of existing code from projects like bamtools. We have implemented a multithreaded BAM compression method, a multithread combined merge-sort, and some other low-level tools for operating on BAM files. I know Heng Li has begun introducing some of this into samtools and I believe Nils Homer may be working on this as well. I would love to see how our code stacks up since a secondary goal of the project is to accelerate the analysis of genomes.

One nice thing about the project is that we will have funding to continue development of the GUI as well as optimization and addition of other tools to the software. I am hoping that via SEQanswers we can get direction from the community on prioritizing what to do next. Furthermore we hope to write adapters/plugins for existing tools and to encourage others to join in the development, etc.

The project is completely open source and will be hosted on GitHub. We are hoping that the combination of fast code and a easy to use package manager/workflow GUI will put all this analysis in the hands everyone...

Sorry for the long post, but hopefully that sort answers your question?
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