3,981 research outputs found
Bioconductor: open software development for computational biology and bioinformatics.
The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples
A resource-frugal probabilistic dictionary and applications in (meta)genomics
Genomic and metagenomic fields, generating huge sets of short genomic
sequences, brought their own share of high performance problems. To extract
relevant pieces of information from the huge data sets generated by current
sequencing techniques, one must rely on extremely scalable methods and
solutions. Indexing billions of objects is a task considered too expensive
while being a fundamental need in this field. In this paper we propose a
straightforward indexing structure that scales to billions of element and we
propose two direct applications in genomics and metagenomics. We show that our
proposal solves problem instances for which no other known solution scales-up.
We believe that many tools and applications could benefit from either the
fundamental data structure we provide or from the applications developed from
this structure.Comment: Submitted to PSC 201
- …