Thursday, December 11, 2008
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.
Wednesday, November 12, 2008
Version 1.07
== STREAM reads and writes XML files ==
The state of the program can be saved as an XML file, which contains all information of TFBS-map, gene and TF expression, as-well as the optimization settings and results.
== STREAM can now scan ==
You can provide the binding specificity of the TFs and scan a sequence with them directly, rather than using an external program to generate the TFBS-map. Stream supports two
formats a) count matrix (Jaspar format) and b) meme format. The sequence must be in
fasta format.
== Direction of the TFBSs are displayed ==
The direction (strand, anti-strand) of the TFBS can be displayed if the information was given.
== Joint training and visualization of multiple problems ==
A model can now be trained on more than one dataset. A dataset or "problem" has a TFBS-map, TF expression and Target expression information. You can combine any number of problems, as long as they are regulated by a similar set of TFs (no need to be exactly the same). The list of problems that are trained together and their properties are displayed in a table.
== Complexes can be generated ==
TF can co-operate and activate (or repress) transcription differently (e.g. stronger) if they have
formed a complex. The new version of STREAM therefore offers the user to specify which TFs can form a complex and what the task of the complex is. The concentration of the complex is
then the minimum of the expression levels of the two involved TFs. The expression levels of the individual TFs is then reduced accordingly. The binding sites of the complexes can be chosen to be
a) all sites of either TF (which means the TF-complex will compete with the individual TF for the TFBS)
b) new sites are generated for the complex at each location where the TFBS of both TFs are present within a certain distance
c) new sites at position where TFBSs exist of both TFs and no other TFBS in-between.
== Training can be stopped rather than canceled ==
Stopping the training will give you the current state of the optimization and the progress since start and stop is not lost.
The state of the program can be saved as an XML file, which contains all information of TFBS-map, gene and TF expression, as-well as the optimization settings and results.
== STREAM can now scan ==
You can provide the binding specificity of the TFs and scan a sequence with them directly, rather than using an external program to generate the TFBS-map. Stream supports two
formats a) count matrix (Jaspar format) and b) meme format. The sequence must be in
fasta format.
== Direction of the TFBSs are displayed ==
The direction (strand, anti-strand) of the TFBS can be displayed if the information was given.
== Joint training and visualization of multiple problems ==
A model can now be trained on more than one dataset. A dataset or "problem" has a TFBS-map, TF expression and Target expression information. You can combine any number of problems, as long as they are regulated by a similar set of TFs (no need to be exactly the same). The list of problems that are trained together and their properties are displayed in a table.
== Complexes can be generated ==
TF can co-operate and activate (or repress) transcription differently (e.g. stronger) if they have
formed a complex. The new version of STREAM therefore offers the user to specify which TFs can form a complex and what the task of the complex is. The concentration of the complex is
then the minimum of the expression levels of the two involved TFs. The expression levels of the individual TFs is then reduced accordingly. The binding sites of the complexes can be chosen to be
a) all sites of either TF (which means the TF-complex will compete with the individual TF for the TFBS)
b) new sites are generated for the complex at each location where the TFBS of both TFs are present within a certain distance
c) new sites at position where TFBSs exist of both TFs and no other TFBS in-between.
== Training can be stopped rather than canceled ==
Stopping the training will give you the current state of the optimization and the progress since start and stop is not lost.
Wednesday, September 10, 2008
STREAM publication
An application note about STREAM has been published in Bioinformatics :
STREAM: Static Thermodynamic REgulAtory Model of transcription.
STREAM: Static Thermodynamic REgulAtory Model of transcription.
Bioinformatics. 2008 Sep 6. [Epub ahead of print]
PMID: 18776194
The publication will be open access (so stay tuned...)
PMID: 18776194
The publication will be open access (so stay tuned...)
Thursday, September 4, 2008
Version 1.05.1
This is just a bug-fix...
== Fixed disrupted gradient descent settings dialog ==
== Fixed cross-validation handler to be reusable ==
== Added fixed length for the iteration input field in optimization settings dialog ==
== Fixed disrupted gradient descent settings dialog ==
== Fixed cross-validation handler to be reusable ==
== Added fixed length for the iteration input field in optimization settings dialog ==
Tuesday, July 15, 2008
Version 1.05
== Categorical data can be displayed ==
For visualization purposes, STREAM allows the user to label the expression data points with up to two "features" (e.g. the "condition" under which the measurements were made). Features may be "continuous" (real numbers), or "categorical" such as cell types, tissue types or experimental treatments (as in the example).
STREAM utilizes the values of the features or visualization only, and the user may interactively select either feature as the X axis for plots of the data.
== Expandable ToolTips are included ==
The ToolTips for every program feature (e.g. button or text field) were included. These ToolTips can be expanded to display, conveniently, the help entry for this specific feature in a scrollable popup window.
The implementation of the ExpandableToolTip class is available here.
== Highlight inactive expression objects ==
Expression elements, which are not used by a TFBS in the map are shown to be "inactive" by displaying the associated graph in the Expression Viewer with a lighter and desaturated color.
== Application adjust to resizing and screen ==
The application now allows the panels to be customized in size to adjust for any screen resolution.
== Parameter string can be collected from the ParamsViewer Panel ==
The formated parameter string can be collected with the "Collect" button in the ParamsViewer panel. It is the same format as required to read in using the Edit -> Set Params - Dialog. That way trained parameter settings can be comfortably imported into different models.
== Target and prediction color fixed ==
The target function (values) are always displayed in red, while the associated prediction is displayed in blue in the ExpressionViewer.
== Dimension names can be customized ==
Name of the first and second dimension of the data can be chosen by the user. The name can contain letters and numbers as well es '-' it can also contain a space but then the name must be in '' ''. The name can be changed while the program is running and will appear in the .stream file. To change the name make a right-click on the Expression image -> Properties -> Plot -> Label.
== Target name can be customized ==
If there is only one column in the target expression file and the target colum is therefore unambiguous, any name can be specified (valid names contain letters numbers or '-', they may also contain white spaces but then the name must be in the name must be in '' '')
If more than one expression value column is in the file, the column containing the target for the optimization needs to be labeled as ''target''.
For visualization purposes, STREAM allows the user to label the expression data points with up to two "features" (e.g. the "condition" under which the measurements were made). Features may be "continuous" (real numbers), or "categorical" such as cell types, tissue types or experimental treatments (as in the example).STREAM utilizes the values of the features or visualization only, and the user may interactively select either feature as the X axis for plots of the data.
== Expandable ToolTips are included ==
The ToolTips for every program feature (e.g. button or text field) were included. These ToolTips can be expanded to display, conveniently, the help entry for this specific feature in a scrollable popup window.
The implementation of the ExpandableToolTip class is available here.
== Highlight inactive expression objects ==
Expression elements, which are not used by a TFBS in the map are shown to be "inactive" by displaying the associated graph in the Expression Viewer with a lighter and desaturated color.
== Application adjust to resizing and screen ==
The application now allows the panels to be customized in size to adjust for any screen resolution.
== Parameter string can be collected from the ParamsViewer Panel ==
The formated parameter string can be collected with the "Collect" button in the ParamsViewer panel. It is the same format as required to read in using the Edit -> Set Params - Dialog. That way trained parameter settings can be comfortably imported into different models.
== Target and prediction color fixed ==
The target function (values) are always displayed in red, while the associated prediction is displayed in blue in the ExpressionViewer.
== Dimension names can be customized ==
Name of the first and second dimension of the data can be chosen by the user. The name can contain letters and numbers as well es '-' it can also contain a space but then the name must be in '' ''. The name can be changed while the program is running and will appear in the .stream file. To change the name make a right-click on the Expression image -> Properties -> Plot -> Label.
== Target name can be customized ==
If there is only one column in the target expression file and the target colum is therefore unambiguous, any name can be specified (valid names contain letters numbers or '-', they may also contain white spaces but then the name must be in the name must be in '' '')
If more than one expression value column is in the file, the column containing the target for the optimization needs to be labeled as ''target''.
Version 1.04
== Displayed TFBS information ==
The TFBS information is displayed when mouse is moved over a TFBS in the TFBS Viewer.
== Unused expression objects can be saved ==
If a expression object is loaded into STREAM but not used by a TFBS site it is not contributing to the calculated prediction. In prior versions these expression objects are not saved in the .stream file. Now, there is a dialog prompting whether or not to save it.
== Changes to the GUI dialog ==
Minor improvements of the dialog system.
== Version ==
An About-popup containing the version of the program instance is added.
The TFBS information is displayed when mouse is moved over a TFBS in the TFBS Viewer.== Unused expression objects can be saved ==
If a expression object is loaded into STREAM but not used by a TFBS site it is not contributing to the calculated prediction. In prior versions these expression objects are not saved in the .stream file. Now, there is a dialog prompting whether or not to save it.
== Changes to the GUI dialog ==
Minor improvements of the dialog system.
== Version ==
An About-popup containing the version of the program instance is added.
Friday, July 11, 2008
Version 1.03
==Improved "cancel" functionality==
It is now possible to abort training for GD and SA. While training some of the GUI is inactivated to prevent changes by the user e.g. parameter settings, which would effect the training.
==Improved read-in function==
More robust read function for expression files. Tab or space delimitation should work as well as space or no space between tissue and time points.
==.stream file crash==
Solved issue of program crashing when not .stream file given as problem file
==User interface polished==
The user interface looks prettier.
It is now possible to abort training for GD and SA. While training some of the GUI is inactivated to prevent changes by the user e.g. parameter settings, which would effect the training.
==Improved read-in function==
More robust read function for expression files. Tab or space delimitation should work as well as space or no space between tissue and time points.
==.stream file crash==
Solved issue of program crashing when not .stream file given as problem file
==User interface polished==
The user interface looks prettier.
Welcome to STREAM Blog
This Blog is about STREAM - Static Thermodynamic REgulAtory Model of transcription - a bioinformatics application for researchers, who want to model the transcriptional regulation of a specific gene and predict its transcriptional output in different situations.
It will contain information about the program, conducted experiments and informs about new Versions of STREAM.
It will contain information about the program, conducted experiments and informs about new Versions of STREAM.
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