| Date | Message |
|---|
2025-09-12 |
MotifLab version 2.0 is finally here!
After many years in pre-production and several pre-release teaser versions,
the official release of MotifLab 2.0 is here at last.
Version 2 includes hundreds of major and minor updates and improvements over version 1.
Here is a list of the most significant additions:
New data types
- A new data type to represent cis-regulatory Modules
- Nested regions
- Support for long-range chromatin interaction data
- General Maps (that can also be used for text and not just numbers)
- Possibility to annotate Sequence objects with additional properties,
including GO annotations
Data input / output
- Support for Excel formats for input and output
- Images can be embedded in HTML files rather than being saved to separated
files
- More options for loading feature data from SQL databases, files (BigBED,
BigWIG or 2bit) and the UCSC Genome Browser API
- Protocol-specific report templates can be defined in HTML and
text-format. These includes placeholders that can be filled in with results
from analyses
Protocol Editor
- It is now possible to define macros for use in protocols
GUI
- Faster and more responsive GUI, especially when visualizing many
sequences
- New ways to visualize tracks with different graph types, such as the
"DNA Graph" track type for numeric datasets
- Nested regions (including motifs in modules) can be visualized with
different connector styles, and UTR regions can be indicated for genes
- Tracks can be grouped and displayed on top of each other
- Improved performance of UNDO/REDO system and local data caching
- The GUI now includes a "Sequence Browser" tool to list all sequences and
filter sequences based on properties (analogous to the Motif Browser and
Module Browser tools), and also a Region Browser
Configurations
- It is now much easier to configure new organisms, genome builds and data
sources
Plugins
- MotifLab 2 features a plugin system that allows it to be easily extended
with new features
|
2017-01-11 |
New plugins
We kick off the new year with some new plugins for MotifLab (version 2).
- Region Decorator – colors, hides or decorates regions based on their properties
- Smart Board – allows you to draw shapes on top of the visualization panel
- SNP Highlighter – highlights the location of SNPs (or other regions) across all tracks
- Gibbs Sampler Demo – an animated demonstration of the Gibbs Sampler algorithm
To install these plugins, go to the "Configure" menu in MotifLab and select "Plugins".
Then press the "Add From Repository" button, select the plugin from the list and click "Install".
|
2016-08-10 |
Bug Alert!
A serious bug was discovered in version 2 of MotifLab affecting the default map values produced by
the "statistic" operation. The default values usually represent overall numbers across all sequences.
E.g. for the "region count" statistic the default value is the total number of regions in all sequences,
and for the "maximum value" statistic the default is the maximum across all sequences.
However, these default values cannot be trusted. Values for individual sequences are not affected by the bug.
The problem has been resolved in version 2.0.-1,
which was released immediately after the bug was discovered and fixed.
|
2016-08-01 |
New motif collections
Several updated motif collections, including JASPAR, HOCOMOCO, HOMER and Cis-BP have been published in the
resources section.
|
2014-09-15 |
MotifLab web site is up again!
In the past few weeks, the MotifLab web site has been down due to hardware
malfunction.
The site has now been relocated to a new server and all the
functionality should be restored and work properly again.
|
2014-03-10 |
Configuring BioMart services
MotifLab relies on BioMart web services
to map gene names to their genomic locations,
but the default BioMart server only returns gene coordinates for the latest genome
build of an organism.
If you want to work with older genome builds or analyze genes
from organisms not supported by BioMart, make sure you have configured the
right archived BioMart service to use (or set up your own gene mapping file) as explained in
this new tutorial
|
2014-02-03 |
Bug Alert!
A serious bug was discovered in MotifLab v1.07 related to local caching of downloaded Region Dataset
tracks. Read more
|