The FLUX SIMULATOR

The FluxSimulator is the part of the FLUX project that aims at providing an in silico reproduction of the experimental pipelines for RNA-Seq, adopting a minimal set of parameters. Corresponding models were established after analyzing RNA-Seq experiments from different cell types, sample preparation protocols and sequencing platforms. The first step of the FLUX project is-in fact-a transcriptome simulator. Subsequently, common sources of systematic bias in the abundance and distribution of produced reads are mimicked-whether they incur during library construction, or, in the sequencing process. The FluxSimulator provides a flexible base to design benchmark experiments based on the new sequencing technologies, as for instance abundance predictions of the FluxCapacitor.

Availability

The FluxSimulator is available following the links from the download page. It provides a command line interface for batch mode, as well as a graphical user interface for introspection of each step while being carried out. Sample files are provided with the correspondingly marked download bundles.

Bug tracking

The FluxSimulator shares together with the FluxCapacitor the system available via the Bugtracker for tracking issues (i.e., bugs, requests for enhancement, etc.). You are welcome to report abnormal program behaviour, or to share ideas about improvement there. Alternatively, you may contact me directly by email: michaATsammethDOTnet.

Further Information

The input and output formats of the FluxSimulator are standardized. Additionally, a couple of intermediary files are adopted to allow for introspection of each steps. An in-depth description of all file formats is available following the links from the Forum/FAQ pages. Additionally, you can find discussions of the community about the FLUX project models. For a general overview of this site, refer to Sitemap.