FLUX CAPACITOR
FLUX CAPACITOR is a project that focuses on abundancy prediction for splice forms, transcripts and alternative splicing events from reads generated by applying new sequencing technologies (e.g., the Illumina Genome Analyzer, Roche 454-sequencing, etc. ...) to RNA molecules extracted from a population of cells.
Orientation
The Flux Capacitor pages include the external resources listed below.
 To get some basic information, see our SciVee video about RNAseq, deconvolution of short sequencing reads and abundance prediction for single transcripts or alternative splicing events.
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You can find a steadily growing amount of documentation about the Flux Capacitor and the Flux Simulator in the Flux Wiki. There is also a joint Flux Forum to discuss the current design and future steps. |
The download repository and the issue tracker with bugs and planned improvemens is hosted by Google Code. In order to file new bugs, you have to obtain a free google account. |
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News
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The RSS reader widget is from Grazr. You can create similar ones, for instance by using the  Google Reader, a widget that also fits on your iGoogle homepage. Whatever gadget you use, the RSS/Atom feed to read the news of the Flux Capacitor and Flux Simulator, you have to provide the feed URL:
http://5562148.de.strato-hosting.eu/cgi-data/rss/feeds/flux.rss
Alternatively you can simply click on the RSS symbol  in your browsers address bar (usually at the top of the window). |
Navigation
The programs available in the "Download" section are:
The FLUX CAPACITOR itself is a high-throughput computational tool to predict abundancies of spliceforms and AS events based on an reference annotation and reads from an RNAseq experiment. You can find a quick overview how to use the program in the section "Getting Started". The program formulates linear constraints from both pieces of information, deconvolution and segregation into single transcript species is achieved by solving these constraints by a so-called linear program solver. Section "Benchmarks" gives an impression up to which degree the current version of the FLUX CAPACITOR is able to cope with RNAseq data. The program is implemented in system independent Java technology, but requires platform-specific compilations of the linear program solver libraries, as described in section "Installation"". FLUX CAPACITOR adopts the GTF and BED formats as described in section "Data Formats".
The FLUX SIMULATOR is an in silico simulation of the biological and experimental background that influences the distribution of reads in an RNAseq experiment. Starting by assigning a generic gene expression profile for the interrogated cells, the FLUX SIMULATOR can mimicry different orders and parameters of standard sequencing preparation protocols. In the end, read distributions are presented visually and the obtained reads can be used to evaluate abundancy prediction methods.
Also, have a look at the forum pages for ongoing discussions and the most complete version of the FAQ (frequently asked questions). Feel free to anonymously file a bug report whenever you encounter suspicious behaviour of one of my programs, or contact me with the information on my homepage.
Have fun, cheers!
Michael Sammeth
