Stream 1.1

-- Updated documentation --
The documentation of how to run STREAM from the command line was improved (thanks Philip)

-- Improved calculate start parameter function --
The way the initial parameter values are picked was improved.

Deciphering the regulatory code in the genome

Recent presentation about STREAM.

Deciphering the regulatory code in the genome

View more documents from all Power.

Missing supplementary now online

The link to the supplementary information seems to be missing for our latest publication in Bioinformatics ("Optimizing static thermodynamic models of transcriptional regulation."). So, please find the supplementary information on our stream web page instead.

Stream 1.09.1

Bugfix
The "Edit TFs" GUI was scrambled when the Logo of the PWM was displayed. This is fixed.

Stream 1.09

== Edit TFBS-map with STREAM ==
Stream now allows you to delete a TFBS or edit its PWM score. These changes have an undo-function.

== Edit DNA sequence with STREAM ==
Stream displays the provided DNA sequence in an editor for you to introduce changes directly to the sequence. The editor also highlights the TFBSs as colored landmarks. These changes have an undo-function.

== Save PWMs in the xml file ==
Stream now saves the provided position weight matrices (PWMs) in the xml file. It also stores the background and PWM threshold you specified.

== Python scripts ==
There are also some python-scripts available on the webpage, which supports the generations of xml files. These python-scripts can:
- extract subsequences from a larger FASTA-file
- generate xml files from STREAM friendly sequence, PWM, expression, TFBS-map files
- merge .xml files
- generate new .xml files containing only a subset of the expression data
- calculate the theoretical maximal PWM-score given a PWM
- generate random data given a xml file

Bugfix:
- section corrected so that xml files generated after training can be read in again.

Citeulike group about transcriptional regulation by thermodynamic models

I created a public group for collecting papers relevant to the topic of modeling transcriptional regulation using thermodynamic approaches. Everyone can see the entries and should be able to extend the current collection. The group is available at :

http://www.citeulike.org/group/8624/library

Top 10 Applications of STREAM

STREAM was presented at the GIW 2008. I uploaded the handout I had there, which summarizes STREAM and list some applications for STREAM.