Update Log (official releases)

Date	Updates
2014-02-06 version 1.08	This update fixes a serious bug discovered in earlier versions related to local caching of downloaded Region data tracks. (Read more)
2013-04-24 version 1.07	Support for some of the tools from MotifSuite led to the discovery of a bug in v1.0 of MotifLab which was subsequently fixed in v1.05. However, this bugfix actually resulted in problems with the ChIPMunk program. With this new version 1.07, all programs should hopefully work once more.
2013-04-16 version 1.06	Added new statistic to "Compare motif track to numeric track" analysis which will count the number of motif instances (TFBS) where the average value of the numeric track within the TFBS is greater than or equal to a specified threshold value. Fixed a bug in the "Compare motif track to numeric track" analysis which caused the "sum" column to be output instead of the "min" column when outputting the analysis to HTML or RawData formats (the "sum" column was hence output twice). Added an extra "Help" button to the dialogs for the "analysis" and "output" operations which will display the HELP page for the selected analysis or data format respectively (note that the documentation itself might not be completed yet for every analysis/data format). Added functionality to create Sequence Numeric Maps based on statistics Added functionality to extract either "assigned entries" or "unassigned" entries from a Map object. The "assigned entries" are those entries that have explicitly assigned values in the map, whereas unassigned entries do not have explicitly assigned values and will thus return the default value. Changed the MapFormat and MapExpression data formats so that the "Include entries" parameter now refers to a Collection containing the entries to include in the output.
2013-04-09 version 1.05	Added "Center" sequence alignment anchor to "Motif position distribution" analysis. Added "Center" sequence alignment anchor to Positional Distribution Viewer tool and added possibility to only base the histgram on a (sub)collection of sequences. (Also fixed some additional minor problems with this tool). Fixed some layout issues in "Configure Data Tracks" dialog and also included functionality to add new tracks and data sources from an XML-based configuration file (or by directly copy/pasting or editing XML-formatted configuration entries in a simple text editor) Made several additions to the EvidenceGFF data format: Added a "skip standard fields" option which will omit the standard GFF fields and only output the evidence column(s) Added new "sequence" evidence codes to output different sequence properties (e.g. sequence name, gene name, sequence location, organism and genome build, etc.) Added a "text" evidence code to output literal text. Added a "percentage overlapping" code which will output how large fraction of a TFBS is overlapped by a region from another track. Added MapExpression data format for (numeric) Maps which can output maps in arbitrary user defined formats and input maps based on user defined regular expressions. Added "Include/Exclude Marked Sequences" options to the context menu in the Sequence Collection dialog Fixed a serious bug which caused MotifLab to crash when "Execute Current Line" was selected in the Protocol menu. Added option to use only a (sub)collection of the sequences when creating a new Background Model based on a DNA track Fixed problems when importing motif collections in TRANSFAC format Fixed rendering problems in Motifs Panel when motifs are updated Fixed a minor bug for the draw tool so that regions can now be deleted by pointing at them with the mouse and pressing the DELETE key (previously this worked for all tools except the draw tool). Fixed a problem with parsing the condition for the "interpolate" operation and also changed the command for this operation somewhat Added option to draw borders around the regions in region tracks. These borders can either be in black or in a darker shade of the color of the region. To enable borders for a specific track, select the chosen border style from the context menu in the Features Panel or select the track in the panel and press the "B" key to cycle between the three different styles (no border, darker color or black). The current implementation of the border is not very nice in close-up (since the width of the border increases as you zoom in), but I will try to improve this in the future. Added "Info" button to External Programs Repository dialog which makes it possible to display information about a selected program in the repository in a popup dialog without actually installing the program first. Added support for several of the programs from MotifSuite, including MotifLocator, MotifSampler, MotifComparison and CreateBackgroundModel. The configuration files needed are available in the repository. Most of these programs will also work with earlier versions of MotifLab. However, use of positional priors in MotifSampler requires this new version to function properly.
2012-12-20 version 1.0	Official release of version 1.0
2012-12-17 version 0.9999	Fixed bug in "rank" functionality for Modules and Sequences (the rank operation would previously always return Motif Numeric Maps rather than maps for the correct type) Fixed bug regarding "span" statements in WIG data format. Changed command syntax for "count" operation Added possibility to use literal constant as 'anchor' position for "distance" operation For sequences specified in BED format, we have added the possibility to base the sequence names on the coordinates (chr_start_end) rather than assigning them default incremental names (SequenceX) Added even more "extract" options, such as extracting "top/bottom X" entries from maps as collections, extracting "size" from collections and to extract random subcollections. Plus additional minor improvements and bugfixes.
2012-11-23 version 0.9998	Just some minor additions. Added more "extract" options for Collections and Numeric Maps. Added optional "flanks" for base cursor (set in sequence window context menu).
2012-11-15 version 0.9997	Added ScerTF as a predefined Motif Collection Added possibility to specify "preferred mirror" servers that will be used instead of the original server specified in the data sources. This is very useful if you have created your own mirror of the UCSC Genome Browser (or just want to use a mirror with less traffic). See the "tips & tricks" section for how to do this. Added "-config" (or "-c" for short) option to the CLI-client that can be used to set certain MotifLab configuration settings without going through the Options dialog in the GUI. Minor bugfixes and GUI improvements
2012-10-26 version 0.9996	Fixed bug in SimpleModuleScanner Added tool to extend sequences Added new keyboard short-cut "U" to Features Panel which will sort the sequences in a region track according to the number of visible regions in each sequence (descending) Fixed a very embarrassing bug which led to bundled motif discovery/scanning programs being unusable the first time MotifLab was started. (After that they would work normal.) Improved the performance of the bundled motif scanning program 'SimpleScanner' by using multi-threading to take advantage of multiple CPU cores. Added new bundled motif scanning program 'ConsensusScanner' which searches for matches to IUPAC representations of motifs (rather than using the PWM representation). Changed the 'Include' output-parameter used by many analyses to be based on user-defined collections rather than predefined criteria. A lot of other smaller bugfixes and GUI improvements
2012-10-01 version 0.9995	Finally added support for compound conditions (multiple conditions connected by the boolean operators AND/OR). The conditions can be grouped and nested to arbitrary levels. Added "motif similarity" analysis which compares a single motif to a collection of motifs using all available comparison metrics. Also made a distinction beetween "similarity metrics" (which give higher scores to more similar motifs) and "difference/distance metrics" (which give lower scores to more similar motifs). Improved the GUI appearance of Benchmark analyses with sortable tables. Added a few more performance metrics and the possibility to specify the minimum required overlap in order to call a prediction "true positive" on the site-level. Also improved calculation of Matthews Correlation Coefficient (nCC) which could previously sometimes fail due to precision-problems in some extreme cases. Results for single operations that are executed interactively in the GUI are now shown immediatly in popup dialogs when appropriate. (Previously, only the results for the "analyze" operation appeared in this way.) This behavior can be suppressed by holding down the SHIFT-key when clicking the OK-button in the operation-dialog. Added "max distance" parameter to "interpolate" operation Fixed bugs affecting training/validation dataset sampling for PriorsGenerators Fixed bug affecting external programs that output results to STDOUT rather than writing the results to files Updated the protocol language for a few operations in order to make the commands seem closer to natural english language Additional minor bugfixes and GUI improvements
2012-08-29 version 0.9994	Fixed a few bugs (including some serious ones affecting execution of external programs that were introduced in the previous release).
2012-08-13 version 0.9993	Added support for ChIPMunk motif discovery tool Improved support for user-defined properties for regions in conditions and arithmetic operations. Added "BED" tab in Sequence Dialog which allows sequences to be specified as genomic regions in BED-format. Updated the "score" operation so that it can now score direct/reverse/relative/opposite strand in addition to the best score from both strands. Added "color boxes" as optional first column in HTML-output for all motif- and module-analyses Added new type of evidence to EvidenceGFF-format which outputs the distance from the target region to some other region in a track. The syntax "<regiontrack>=distance to closest" (or distance to 'any') will output the distance to the nearest region in the specified region track. "<regiontrack>=distance to <Selected>" will output the distance to the closest region whose type is listed in the 'Selected' data object (which can be a Collection or Text Variable). "<regiontrack>=distance to interaction partner" will output the distance to the nearest interaction partner in the given track. It is possible to use the 'non-overlapping' qualifier with either of these. Fixed a +/-1 mistake in the "merge" operation
2012-07-02 version 0.9992	Added "Favorites" dialog to the Data menu where users can register often used data items for easy access. Added new 4-field input/output format to "Location" data format for sequences. Also added possibily to specify custom output format. Added new output data format for modules: HTML_ModuleTable. Added optional drop-shadow effect for expanded region tracks in close-up view. This is blatant eye candy and is disabled by default. To toggle this setting, select the track in the Features Panel and press the W-key. Added functionality to select the whole sequence or invert the selection windows in a sequence. This functionality is available from the sequence context menu or by pressing keys A or I. Minor bugfixes and improvements to the GUI.
2012-05-18 version 0.999	Added a new configuration dialog which allows users to configure which organisms and gene identifiers MotifLab will recognize. Added possibility to edit the "startup script" which is executed when MotifLab's GUI is started (from the Configuration menu) Added "sort/group" buttons to the Features Panel and Data Objects Panel. These buttons link to functionality to sort data objects alphabetically and/or group them by data type. Improved the "Benchmark" analysis by adding site-level statistics for sensitivity, PPV and ASP. Also, switched to using a "format" string to specify which statistics to include in the output (and their order) rather than using a bunch of checkboxes. Improved the wildcard functionality available for some display settings by allowing wildcards to be used in combination with a prefix or suffix rather than just a single wildcard. Added a tooltip to the logo column of the "compare motifs panel" which shows the pairwise alignment of the selected motif and the target motif. Added a button to the Motif Score Filter which can be used to specify whether the filter should hide regions with scores ABOVE (or equal to) the selected cutoff value or BELOW the value. Improved the Crop Tool by allowing Numeric Variables or Maps to be used to specify the number of bases to crop off the start/end of sequences. Fixed bug in GTF data format for attributes containing spaces and added support for referencing user-defined properties in the alternative "format" string for GFF data format. Additional bugfixes and GUI improvements.
2012-04-25 version 0.998	Drastically improved performance when saving sessions (especially when saving to 'slow' devices such as network discs). Fixed a somewhat serious problem in regard to using external programs (affecting users of "Weeder") Minor bugfixes and improvements to the GUI
2012-04-16 version 0.997	New operation: "rank". Can be used to extract the rank order of motifs, modules or sequences based on a Numeric Map, a numeric column in an Analysis or a numeric property of the data objects themselves. It is also possible derive a combined rank order based on the (weighted) rank sum of several properties. Added two new motif comparison metrics based on symmetric Kullback-Leibler divergence and Chi-squared test. Minor bugfixes
2012-03-23 version 0.996	This version contains quite a number of major updates and corrections and some of the new functionality is no longer compatible with earlier version (this can also affect saved sessions). If you need to use the previous version (v0.995) you can find it here. New operation: "copy". Can be used to create identical copies of any data object New operation: "difference". Can be used to compare two data objects and highlight the differences between them. New operation: "collate". Can be used to combine data-columns from several different analyses into a single "meta" analysis. New operation: "discriminate". Can be used to convert a "regular" priors track into a "discriminative prior". New operation: "prune". Can be used to remove duplicate regions or similar overlapping regions from Region Datasets. New analysis: "Region Dataset Coverage". Can be used to assess how large portion of each sequence is covered by the regions of a Region Dataset. New analyses: "Count Module Occurrences","Count Region Occurrences" and "Compare Region Occurrences" which works the same way as the old "Count Motif Occurrences" and "Compare Motif Occurrences" except that they work for modules and general regions instead of motifs. Replaced StringVariable and StringCollection with a single new TextVariable data type Added possibility to reuse images created for motif and module logos across multiple analysis when output to HTML. Added support for Cascading Style Sheets for HTML-output and JavaScript to sort HTML-tables. (this only works when viewed in external browsers). Added "type-replace" transform which can be used to replace the region type of region based on regular expressions. Added possibility to create random collections with size specified in either absolute or relative terms (undocumented feature only available in protocol). Added several new "display setting" statements including "restoreSession", "saveOutput" and the general "setting". Added optional "-saveSession" and "-inputSession" arguments to CLI-client Added possibility to display several independent histograms on top of each other in the Positional Distribution Viewer tool, and also added auto-update functionality so that histograms are updated if the visibility of regions changes. Added "within region" parameter to "Count Motif Occurrences" Added pie-chart to "Compare Region Datasets" analysis Added possibility to specify default programs to use for motif/module scanning/discovery. Made context menus and keyboard shortcuts more consistent throughout. Grouped together operations in context menus in the data panels and made it possible to select applicable analyses through context menus. Added option to mark parameters as being "advanced". Advanced parameters are hidden by default in parameter panels. Added possibility to assign values to, and change values of, custom region properties throught the use of arithmetic operations. Added possibility to control the appearance of bar-charts (colors, borders, shadows, gradient fill). This is so far an undocumented feature. Added possibility to change the colors used by the protocol editor. Added option to sort sequences based on selected criteria to the context menu for feature datasets. (This sort of works as a short-cut to the functionality in the Sort Tool). Added functionality to create a Numeric Variable based on the size of a collection: X = new Numeric Variable(somecollection) Improved the SimpleModuleSearcher algorithm with several new options Added functionality to create Motif Partitions based on known alternatives for each motif (creating "equivalence clusters" of similar motifs) Added functionality to automatically create Modules based on known motif interactions. Added functionality to create Sequence Collections based on a chosen statistic, e.g. which sequences contains a given motif(s), or which sequences have GC-content>50%. Added proper support for the FIMO motif-scanning algorithm. Fixed problems with UNC-paths when executing external programs. Improved SimpleModuleScanner so that it now can use Module Collections as input rather than a single Module. (It is still rather slow for many modules, though). Added functionality to create and display histograms in Motif Position Distribution Analysis. Added column header tooltips for most tables with numeric data which shows information about the values in the columns, such as min, max and average values and also a histogram. Added possibility to have "horizontal gradient fill" for regions Added functionality to extract the rank-order of values in a Numeric Map as a new Numeric Map. Added new output-format for motif tracks: MATCH Added a few more "clear data" options to the top-level menu in the GUI.
2011-12-21 version 0.995	Implemented support for making concurrent download request to data servers so that data for several sequences can be downloaded in parallel rather than just one at a time. This can significantly speed up the download time for larger datasets. However, since it also places additional strain on the data servers, this option is disabled by default. Implemented functionality to allow new Priors Generator classifiers to be trained 'on-the-fly' in a protocol script by specifying the setup of the classifier and training process in a configuration file. Fixed an embarrasing bug in many Motif-dataformats which lead files containing only a single motif to be unparsable Made it possible to specify the preferred order of 'mirror datasources' (different sources for the same feature+genomebuild) by reordering sources in the 'DataTrack Configuration'-dialog through drag'n'drop. Added a new type of transform (to the transform operation) called 'odds' which is the same as 'logit' but without the log: F(p)=p/(1-p) Added possibility to 'extract' a list of the types of regions that are present in a Region Dataset as a String Collection Added support for TSS-relative coordinates in GFF and EvidenceGFF data formats Added option to place TSS at either position '0' or '+1' (default). If the latter option is selected, a TSS-relative coordinate system will skip the 0-position and proceed directly from position -1 to +1. Added option to show cumulative histogram instead of normal histogram for the 'Numeric Dataset Distribution' analysis Added possibility to "skip unrecognized gene IDs" in the Sequence Dialog Added '-retry off\|prompt\|<seconds>' option to the CLI-client which specifies how the client should react when MotifLab encounters errors. Plus several minor improvements and bugfixes
2011-11-08 version 0.994	Added some minor features and fixed a few embarrassing bugs. Added support for embedded bedGraph lines within WIG files. Added "Import" button to the "Manual Entry"-tab in Sequences Dialog so that locations of sequences to analyze can be imported from a file. (Either 8-field or 10-field formats) Added support for parsing Motifs in TAMO format (but not for writing output) Improved speed-performance of "show reverse complement" option in Motif Dialog. The range of values for Motif Score Filter is henceforth only based on visible sequences in visible tracks, and the range will be updated whenever the visibility of any tracks or sequences are changed. Fixed problems with initialization of consensus motif, IC-content and GC-content from log-odds matrices read from file. Fixed Compare Region Datasets analysis (which did not work at all because of a newly introduced bug). Fixed protocol parse error complaint caused by <= operator in conditions Added support for extracting "top:X" and "bottom:X" entries in a Map as a Collection, and to extract "_DEFAULT_" value as Numeric Variable. (This was actually already possible, but only as a "hidden feature") Fixed bug in argument for Transform operation (affecting GUI) Fixed bug in Priority format so that it is now possible to use SPACE as field separator (this did not work properly before). Allowing double-stranded priors in Priority formatted files. However, in these cases only the first half of the values will be used.
2011-10-28 version 0.993	Updated AffinityScanner motif scanning algorithm, so that it can use either raw or log-likelihood scores (both absolute and relative). Made the Motif_Properties data format more general and expressive (but perhaps slightly less user-friendly)
2011-10-18 version 0.992	Minor bugfixes and improvements to the GUI Added "welcome screen" which is shown the first time MotifLab is started (Also available under the Help menu)
2011-10-06 version 0.991	A few more minor updates and improvements Improved performance when adding duplicate sequences (which is not really allowed) Added option to skip unrecognized identifiers when entering a list of gene IDs in Sequence Dialog Fixed bug when creating Motif Numeric Map from a track Added new display settings: regionColor, regionvisible, showRegion, hideRegion, updates and refresh Added "verbose mode" to CLI-client Added possibility to sort output from "count motif occurrences" analysis by p-value
2011-09-30 version 0.99	This release comprises several updates and improvements. Although I plan to add some additional support for a few external programs in the immediate future (ModuleSearcher, ClusterBuster and ChIPMunk), with this version MotifLab is now considered to finally be stable, feature-complete and free of known bugs. The version number will therefore be upgraded to version 1.0 after a short period of testing. Added "DAS wizard" to Datatracks configuration dialog. The wizard allows users to easily search and add new Region Datasets found in the DAS-registry (www.dasregistry.org) Added dataformat CisML for output-formatting and parsing region datasets (especially motif tracks) Added possibility to create Motif Collections based on motif properties Added support for motif scanning tools MATCH and CLOVER Made all arithmetic operations, including transform and threshold applicable to Expression Profiles and Numeric Maps Added several new display settings statements Added option to show/edit motif representation (matrix, consensus and logo) in reverse complement Fixed persistant GUI state for the data side panel (containing features, motifs and data panels) Made context menus for tables showing sequences, motifs and modules more consistent Added support for headers in Expression Profiles Added possibility to create Motif Numeric Maps based on motif comparison scores (via context menu in motif comparison panel) Changed the orientation setting called 'From Sequence' to 'Relative' Added option to include constituent single motif sites when outputting and parsing module tracks. This will store all relevant data in the GFF-file so that module tracks can be completely restored from file. Added possibility to return either raw or log-likelihood scores when using the score operation, and to return either absolute or relative scores. Added new motif-comparison function: IC-weighted Pearson's correlation Finished implementing prompts for all data types in CLI-client Added support for mirror servers for data sources Added possibility to comment/uncomment selected lines in protocols (in Protocol menu) Added option of converting regular region tracks to Module tracks (in Features panel context menu) Attempting automatic conversion of all loaded Region datasets to Motif or Module tracks if possible Added "anchor" setting to Positional Distribution Viewer Added possibility to specify anchor and relative start/end coordinates for each sequence in Sequence Input Dialog Added possibility to view and edit additional region properties (by double-clicking on a region site while holding down CTRL) Added possibility to define which colors to use to represent up/down-expressed sequences in Expression Profiles Added possibility to delay resolving references when creating collections or partitions "From List" (this will keep the original references in the protocol) Finished tooltips for non-expanded module tracks Fixed faulty implementations of ROC and Precision/Recall curves Hopefully, fixed problems with motif sequence logos across platforms Renamed some of the analyses Updated descriptions of operations (used for tooltips etc.) Fixed several minor bugs and made improvements to the GUI Added new Welcome screen which will be shown on first startup (also available from the Help-menu)
2011-08-22 version 0.983	Added support for user-defined properties for motifs Updated context menus for tables and panels containing sequences, motifs and modules to make them more consistent Fixed a few syntactic errors in the `README.txt` and `runMotifLab.bat` files that are included in the downloadable ZIP-file
2011-08-15 version 0.982	Added two new condition operators applicable to regions: weighted average and weighted sum. The new operators are alternatives to the earlier 'average' and 'sum' operators that considered the average value (or sum value) of a numeric datatrack inside the sequence segment spanned by the region. The new operators are meant to be used with motif tracks and will default to the standard non-weighted operators for other region tracks. In the weighted instances, the numeric track value in each position is weighted by the (normalized) IC-content of the aligned motif in the corresponding position. E.g.: Consider a binding site for a motif with consensus "nnnCACGTGnnn" (size=12bp) which is being compared to a numeric datatrack with phylogenetic conservation values. In the conservation track the six middle bases are perfectly conserved while the other bases are not conserved at all. According to the standard 'average' operator the average conservation score of this TFBS will be 0.5 since only six of the twelve bases are conserved. However, if we use the 'weighted average' the six middle bases will be given more weight than the flanks since the middle part has higher IC-content. In this example the weighted average will be closer to 1.0, which signifies that the 'important part' of the motif is conserved (while the non-important parts are not considered). Renamed the old condition operators upstreamValue and downstreamValue which considered the most upstream (or downstream) value within a region relative to the orientation of the sequence to sequenceUpstreamValue and sequenceDownstreamValue. At the same time, two new operators were introduced which considers the most upstream (or downstream) values of the region relative to the orientation of the region itself. These were then called regionUpstreamValue and regionDownstreamValue. Changed the orientation setting called "From Gene" which is used by many data formats to "From Sequence" (but the old setting can still be used to retain backwards compatibility).
2011-08-12 version 0.981	Introduced new data types for Module Partitions and Module Numeric Maps Updated the dialog interface for Sequence Collections to be more like other collections, partitions and numeric maps Updated the dialog interface for Modules by introducing more controls for functionality that was previously only available through context menus. This will hopefully make the options for configuring Modules more visible to the user. Added a new output format for Region tracks called EvidenceGFF Minor bugfixes and improvements to the GUI
2011-07-13	Made first BETA-version of MotifLab publicly available