Dear de novo assembler users:
Just to be open, I wish to inform you that I started to work on a new distributed assembler focusing on metagenomics. It's called spate [spate]. spate runs on top of the thorium distributed actor engine and is built using reusable actor components from the biosal (biological sequence actor library) library. Here are the reasons: 1. After 4 years working on Ray and RayPlatform, I was beginning to be bored. Ray uses MPI for the only programming model, which can be hard to maintain in the long run. The design of RayPlatform is somehow limited. 2. Rick Stevens (my new supervisor) is very interested in better ways of expressing distributed algorithms. I am also interested in this. I think that the actor model does exactly that and is just superior to MPI in every way. 3. C (C 1999) is a technical requirement for the SAL project at Argonne for "vendor-friendliness" so that they can eventually provide better implementation for specific kernels (in biosal, these kernels are actors). Ray and RayPlatform were implemented in C++. spate, thorium, and biosal genomics are all in C 1999. 4. Ray, ABySS, Kiki, PASHA, YAGA, and SWAP (those are the distributed assemblers I know about) are not scalable enough to tackle the DOE soil Grand Challenge [GrandChallenge]. The good news is that spate takes the same arguments so the learning curve should be minimal for those who desire to try it. To get started: git clone https://github.com/sebhtml/biosal.git cd biosal make ./applications/spate_metagenome_assembler/spate -help Thank you ! --- [spate] https://github.com/sebhtml/biosal [GrandChallenge] http://dskernel.blogspot.com/2014/08/the-public-datasets-from-doejgi-great.html ------------------------------------------------------------------------------ Infragistics Professional Build stunning WinForms apps today! Reboot your WinForms applications with our WinForms controls. Build a bridge from your legacy apps to the future. http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
