COPE (Connecting Overlapped Pair-End reads) is a method to align and connect the illumina sequenced Pair-End reads of which the insert size is smaller than the sum of the two read length.The connected reads can be used in genome assembly, resequencing and transcriptome research.
The full citation:
COPE: An accurate k-mer based pair-end reads connection tool to facilitate genome assembly
Binghang Liu; Jianying Yuan; Siu-Ming Yiu; Zhenyu Li; Yinlong Xie; Yanxiang Chen; Yujian Shi; Hao Zhang; Yingrui Li; Tak-Wah Lam; Ruibang Luo
Bioinformatics (2012) 28(22): 2870-2874; doi: 10.1093/bioinformatics/bts563
The OsMoSys Framework is a research project implementing a multi-formalism multi-solution framework for defining and analysing complex systems models. It uses model composition to cope with systems complexity.
...It can handle highly non-linear dependencies between multivariate random variables. The particle based inference can answer arbitrary questions given the provided evidence and can even cope with multimodal densities. The library supports the most common types of densities and conditional densities, like uniform or normal densities and facilitates user defined density functions.
To enable easy use the library is taking account of modern development techniques like policy based design and template programming.
All these properties make it applicaple for a wide range of applications.