• Version 0.18.0
    • Plots:
      • A new plot system has been implemented. This new system will make it easier to compose new, specialized plots.
      • The fullowing plots are supported in the new plot node: Image, Density and Scatter Plot.
    • GOBrowser:
      • Downloaded genes can now be saved to file and later reloaded.
      • Target genes can now be selected from the master gene list.
    • R:
      • The R interaction has been optimized.
      • New graphical toul for isntalling R libraries used in SciCraft. Can be accessed from the "Touls" menu.
    • Misc:
      • TextFileReader: The user interface of the TextFileReader has been improved.
      • Function Nodes: the title can now be change and is no longer dependant on the filename of the function.
      • New connection line between nodes.
      • The documentation has been updated.
    • Bugfixes:
      • Data sent from the EditNode can now be used in R functions.
      • SciCraft will no longer crash if it finds an unreadable file when loading nodes.
      • SciCraft will now remember ports that has been disconnected from multiinputports and no longer auto connect these when opening a diagram.
      • it is now possible to open node documentation from the node tree.
      • RData will now convert python lists to Numeric arrays to prevent problems.
      • the TextFileReader will now update the variable info when changing separators.
      • You can now filter RData that does not have a dim attribute in the Plot2DNode.
      • GOBrowser will now download the genes in batches to prevent the db backend from crashing.
      • SciCraft will no longer show multiple popups when it finds multiple function nodes with the same name.
  • Version 0.17.0
    • Plots:
      • Input for dendrogram plot have been changed to cluster objects.
      • Scatter, line and normal qq plot have been updated so that they can pick data from structs and R objects.
    • Misc:
      • Data filter: data seen in a plot (currently only scatter plot) can be filtered out from providing nodes.
      • DataComposer: browse data by selected indices in plot.
      • Added support for 4 new ID types in GOBrowser (affy, uligo, agilent and IMAGE clone).
    • Bugfixes:
      • Several bugs fixed in the ZMLCreator.
      • Default values on parameters was in come cases ignored.
      • Cached RData could not be loaded and resulted in a crash when loading a diagram.
      • Not all attributes on an RData object was stored when saving to file.
      • Experiment files (*.exp) saved on Windows could not be loaded in the Linux version of SciCraft.
      • A single scalar as input to a plot node resulted in an exception.
      • Textfile reader no longer ignores empty lines.
  • Version 0.16.0
    • Misc:
      • Gene Ontulogy Browser: added toul for looking up gene IDs in a gene ontulogy tree.
      • FileWriterNode and OutputNode has been combined to one node.
      • When loading a file in the input node the file is read in a background process that can be aborted.
      • ZMLCreator: added buttons for adding ports and parameters.
      • The tab-order on several widgets has been reworked to be more logical.
      • DebugNodes are now only show if environment variable SCDEBUG is set or SciCraft is started with "-D"/"--debug".
      • When staring SciCraft with a non-existing filename as argument the newly created diagram will use this filename when saved.
      • The structure of the node tree has been changed.
      • SciCraft will now warn the user if he/she tries to close an unsaved diagram.
      • The R-interface has been completely rewritten. SciCraft should now support all the data types used in R and the performance should also be higher.
      • RDissectionNode and StructDissectionNode has been removed and replaced with DissectionNode.
      • Nodes in a diagram can now be renamed.
    • Bugfixes:
      • The input node will no longer give an exception if it can not find the file name saved in this node.
      • SciCraft will notice if a relative path is no longer correct and try to fix it.
      • The user will now get a warning if SciCraft was unable to save a diagram.
      • Fixed a possible Unicode problem on OS X. This problem prevented SciCraft from populating the 'Recently opened diagram' list.
      • The default node dialog is now showing the name of the parameter in the parameter group box title.
      • Relative paths are converted if the diagram is saved in new directory.
      • Fixed a problem that on occasions would leave the Run and Stop buttons disabled.
      • When using marker toultip in plots the user got an IndexError if the label input contained less labels than markers.
      • Diagram comments was not shown on screenshot when exporting to EPS.
  • Version 0.15.0
    • Plots:
      • Improved scatterplot. Uses curves instead of markers thus enhancing the performance.
      • Densityplot can now use Gaussian smoothing.
      • The vtk package is now optional.
    • Misc:
      • MADesigner: filenames for Raw Data Files can now be edited.
      • Node connections can now be marked as hidden, making them "invisible".
      • The default dialog widgets for nodes has been changed. The new widgets should be easier to use.
    • Bugfixes:
      • SciCraft crashed if one of the xml files for the function nodes was invalid.
      • when setting axis labels in an image plot, the plot was resized incorrectly.
      • the input node did not clear the 'Chosen Ports' list of the content
      • if the data file changed.
      • when printing a plot to an EPS file, the size was incorrect.
      • if you pressed 'Cancel' when you were asked for a filename during export to EPS, the file was created anyway.
      • Density plot was not able to highlight markers in other plots when mapped.
      • When saving a custom plot an unhandeled exception was thrown, preventing the saved plot to be added to the node tree.
      • Labels where not properly added in line and scatter plot. A repaint of the plot was missing.
      • When using culour mapping in scatter plot, the scatter plot forced a usage of the default size for markers.
      • The recently opened files-list no longer add relative paths.
      • The spreadsheat node will now show the row numbers properly when displaying a large data set with more that 99 rows.
      • Density plot will now save and load resulution properly.
      • Empty strings can now be used as markers in line and scatter plot.
      • Image plot will now save and load selection mode like it should.
      • Fixed a problem on the Windows version that prevented SciCraft from using the R-function nodes.
  • Version 0.14.1
    • Misc:
      • On Windows we have started to use VendorID to sign the Qt/PyQt module. This was done to restrict dynamic loading of the PyQt module shipped with SciCraft
    • Bugfixes:
      • MADesigner: fixed so that names on bio materals can be changed properly.
      • MADesigner: renaming bio materials did not update comparison lines.
  • Version 0.14.0
    • Touls:
      • Micro Array Designer: a toul used for setting up micro array experiments.
      • File handling:
      • Added support for reading and writing structs.
      • Faster Octave and Mat file readers.
    • Plots:
      • Added blur as a functionality for density plot.
    • Nodes:
      • StructDissectionNode: node used for dissecting structs.
    • Bugfixes:
      • RFileReader was not able to read R-files containing a list.
      • Fixed a problem that caused the plot node to exit with an exception. if you deleted the input to culour and/or size mapping.
      • When saving a new diagram to file, the file name is now added to the list of recently opened files.
      • When loading a diagram from the command line with invalid xml, SciCraft will no longer crash.
      • Selected markers in a plot are forced to be redrawn and will be easier to see.
  • Version 0.13.0
    • Plots:
      • NaN (Not a Number) values are support in selected plots.
      • Mulitline and Histogram plot have been optimised with regards to time and large datasets.
    • Nodes:
      • UserQueryNode: allows the user to set values for each input and send these as output.
      • VectorSpreadsheetNode and SpreadSheetNode have been combined into one node.
      • It is now possible to copy data from the SpreadsheetNode to the clipboard.
      • Parameters can now have the type directories.
    • Functions:
      • ZMLCreator can now set icon for function nodes. This icon can be an absulute path or relative to the zml file.
    • Misc:
      • The file menu will now show the 5 most recently opened files.
      • The line drawing between nodes have been changed. It is now updated 'in real-time' and should be faster.
      • Added 'Close diagram' to the File menu.
    • Bugfixes:
      • Fixed a problem with the R plugin where two identical functions could end up with the same result when executed in debug mode.
      • Fixed a problem where SciCraft did not start on Debian unless the package python-dev was installed.
      • Histogram plot would some times not use the largest value when counting data.
      • When printing several plots, image plots would be blank.
      • When trying to execute an invalid diagram, the dialog showing the error message could not be shown.
      • Opening the dendrogram settings window should be possible again.
      • Normal QQ plot did not show labels when using a saved diagram.
      • Several plots crashed if it received strings as input.
      • Autoupdate was not working on Density plot.
      • Density Plot threw an exception when trying to use illegal indices.
      • When enabling automapping only one plot mapping was shown. To see the rest the user had to select Apply or reopen the dialog box.
      • Image plot can now use a vector as input.
  • Version 0.12.0
    • Plots:
      • Added image density plot
      • Added multi line plot
      • Added normal probability plot
      • Changed defualt size on markers in scatter and line plot.
    • Nodes:
      • New node, VectorComparisonSpreadSheet.
      • New output node that support multiple input port.
      • Inspect input and output data on nodes.
      • Option for saving to file in the spreadsheet node.
      • Option for refreshing nodes in node tree.
    • Functions:
      • Option for viewing output from function nodes.
      • Option for refreshing nodes in node tree.
      • New and improved ZMLCreator which is used for creating function nodes.
      • Rewrote several of our Octave scripts to make them faster.
    • Misc:
      • Testrunner automatically finds new test modules.
    • Bugfixes:
      • The SciCraft debian package will now depend on python-qwt and Octave.
      • Fixed a problem where adding and removing plots in Plot2D node caused some plots to end up ontop of each other.
      • When redusing the numver of windows in the plot node, the incorrect plot was removed.
      • RDissection node will now remove uld output ports when the data set changes.
      • Fixed a problem where the image plot assumed that the id of saved ports stayed the same.
      • Fixed a problem where parts of deleted plots got stored in the zmd file and prevented the diagram from being loaded the next time.
  • Version 0.11.1
    • Bugfixes:
      • Bugfix: octave node optimalization failed if one input port had the same name as one of the output ports.
      • Bugfix: connecting two incompatible nodes will give a better error message.
      • Bugfix: function nodes will now show an error message if one or more of the parameters have a wrong type.
      • Bugfix: fixed so that you could open dendrogram plots even if they have no data.
      • Bugfix: in some cases the texfilereader would show two output ports, while it should have been only one. This is now fixed.
      • Bugfix: path to function nodes was not properly created on Windows.
      • Bugfix: plot nodes could not use ports with two or more words in the name.
      • Bugfix: SciCraft will now check if R is installed properly before importing rpy.
  • Version 0.11.0
    • GUI:
      • Creating links between nodes will now choose the left side for entry and right side for exit. This is preventing new users from getting confused.
      • Data kept in nodes can be inspected through menu on links.
      • Status window in bottom right corner showing state of all nodes during run.
    • Plot:
      • New image plot for visualizing matrices with selectable culormaps and mapping against other plots.
      • New histogram plot.
    • Bugfixes:
      • Fixed AttributeError raised when clicking in empty dendrogram.
      • Removing plotwidget while having several mappings, left one or more mappings (fixed).
      • Cut-off setting in dendrogram is now stored.
      • Dendrogram now cleans up axis on removal.
      • Creating nodes in "wrong" order stopped zmd files with plotnode from loading (fixed).
      • Was unable to restart diagram if one out of two running function nodes crash (fixed).
      • Octave plugin now handles functions without output.
      • Y axis in dendrogram plot is now removed properly.
      • Dendrogram mapping should now be working properly (correct values highlighted).
      • Labels are now inserted when loading a saved dendrogram plot.
      • Plugins should be able to execute when installed from the windows installer.
      • Function nodes that crash with optimalization enabled does not bring scicraft back to a runnable state.
      • Impossible to delete links to a multiport.
      • Impossible to delete a node connected to a multiinputport.


  • Version 0.10.0
    • FileHandlers:
      • Added enhanced text file reader
    • Functions:
      • New directory structure for toulboxes
    • GUI:
      • Added functionality for html based help info for nodes
      • Added splashscreen
    • Misc:
      • Removed test diagrams from the examples directory
      • Added more realistic examples
    • ModuleDiagram:
      • Data from 'Cullect&Run' can now be saved to disk and can be used again the next time the diagram is opened
    • Plot
      • Added toultip-style labels in plot. These labels will be shown when the mouse is above a plot marker
      • Added input ports which can handle multiple connections for plotnode
      • Improved dendrogram plot, it is now horizontal oriented and can use labels
      • Added option for chaning font size on plot labels
      • Added range selection for data in plot using the Matlab notation
    • Plugin:
      • Rewritten RPlugin to use files instead of pickling, making it more stable
      • Added debug mode to RPlugin so that the user can view possible errors from R
      • Added functionality for contrulling output from R function nodes that return complex objects
      • Added option for debugging R in the Preferences window
    • Bugfixes:
      • Robj objects from RPlugin caused pickling to fail in RPlugin
      • Plot mapping list was not updated when enabling auto mapping
      • Trying to remove an empty function path in the preferences window caused an exception
      • It was possible to add an empty path as function path
      • Plot window can now be made as small as the user wants
      • Clicking anchor-links in the help viewer threw an exception and showed an empty window
      • When loading a diagram using non-existing functions, SciCraft threw an exception, but no user message was given
      • Dendrogram plots were not correctly displayed when zooming out
      • RDissectionNode would in some cases fail with the error message 'fields' in consule.
      • Connections from RDissectionNode were in some cases deleted
      • OctaveRunner could not use functions with a title that was not the same as the function name
      • Error messages were printed when using relative links in the help viewer
      • Reducing the number of plot windows in Plot2D did not resize the plot area
      • When adding new plot windows in the 2D plot node, the windows were too small
      • Plot labels were removed when changing row or culumn
      • Plots were not updated when data was changed
      • Using R, "character" vectors added to data.frames were converted to "factor"
      • Changed so that the first X-value used in lineplots is 1 when using Indexed
      • Changed default X-source value to Indexed in lineplot
      • Incorrect zml function file caused scicraft to crash during startup
      • RObjectHandler did not handle lists that returned incorrect length parameter
      • Fixed a problem where running 'Cullect&Run' on a node without a connected input port caused an error
      • Changing value of row/culunm spinbox with keyboard was sometimes ignored when pressing update in the plot
      • Changing filename made output ports disappear in InputNode


  • Version 0.9.0
    • FileHandlers:
      • When a file type is unknown, the input node no longer selected 'Unknown' file type
    • GaussDal:
      • Store/retrieve mapping to/from port
      • Automatically highlight the next atom in the reference mulecule to be mapped
      • Added procrastes routine
      • Arbitrary mapping based on sequence in input
      • Keep the orientation of each mulecule rendered independently
    • GUI
      • GUI: Better user interface for the preferences window
    • ModuleDiagram:
      • Cullect & Run, features that allows you to store data on nodes and run connected nodes without running the entire diagram again.
    • Nodes:
      • Removed obsulete logic-nodes
    • Plot:
      • Show info on selected items in plot, mapped against a database
      • User can set cutoff level on vertical axis in dendrogram plots
      • User can select all objects part of cluster in dendrogram plots
      • Added printing of plot, vector graphics
      • Added the possibility to save plot setups to custom plot and reuse these later
      • Added toulbar for plot node
    • Plugin
      • Optimized speed on octave functions by combining nodes into one octave process
      • Improve speed of octave scripts by adding ;
    • Windows:
      • Added icon for SciCraft.exe
      • Associated SciCraft Module Diagrams with SciCraft
      • Warning window when starting scicraft without R and/or octave changed to be in front when it starts
    • Bugfixes:
      • Empty list as first row of input matrix to spread sheet made the node fail.
      • Deleted dendrogram plot was not removed from the plot window
      • Octave warnings were treated as errors in SciCraft.
      • Octave variables were saved in reversed order from ZML-creator.
      • Fixed the error output from the Octave plugin.
      • BASEFileReader does did not read file correctly
      • The EditNode did not handle string/text matrices correctly
      • Fixed missing response when validating a correct diagram
      • Settings for plotwindow is now reset when adding a new plot
      • Windows, SciCraft had to be started in the SciCraft directory
      • GaussDal filereader lacked sanity checks - caused exception when trying o read unreadable files
      • SciCraft crashed on windows when you imported rpy if R was not installed
      • New port got deleted in the input node if a port with the same name existed
      • ParamNode could not use the value '0'
      • OctavePlugin could not separate between input variables that had the same name.
      • Plot node had wrong number of culumns available given certain conditions.
      • Plot data descriptions were not updated on run.
      • Fixed converting matrix from octave to R format
      • 2Dplot were not updated when datasource changes
      • Not able to add R the PATH environment with Norwegian (and probably others) Windows XP


  • Version 0.8.0
    • New 2D plot
      • 2D scatter plot
      • 2D line plot
      • 2D dendrogram plot
      • The plot node can show several plots side by side or on top of each other
      • Advanced marker options, marker size and culour can be define by an input vector.
      • Zoom functionality
      • Select rows/culumns in the plot
      • Possibility to change axis ranges/ratio for any plot
      • Support string matrix as labels
      • Possibility to set axis labels and title for each plot
      • Enable selection of values individually or with selection rectangle in 2D plot
      • Enabled selection/marking of values in one plot to select values in other plots
    • New RDissection node
      • capable to dissecting complex R objects into data types that can be used with other plugins within SciCraft
      • Store dissection settings for use with other diagrams
    • Support for non-number matrices in the matlab reader
    • You can now start SciCraft with a diagram from the command line and make SciCraft run this diagram as soon as the program is started
    • Window style can now be updated "on-the-fly"
    • Saving an unconfigured 3D plot in a MD and reopening crashed SciCraft
    • Workaround for a bug which caused many diagrams to hang with PyQt 3.12
    • Having two InputNodes reading R data caused exceptions to occur
    • Removed uld 2D Scatterplot based on VTK
    • Optimized node loading at startup


  • Version 0.7.0
    • Adding nodes to diagram spreads them out
    • When choosing input files, dimensions of/info on data is shown
    • Mouse usage separated into two touls, edit and link
    • Added function path editing in preferences
    • Data in links can now be inspected with popup menu
    • All file readers/writes have been integrated into InputNode/OutputNode
    • Simple EPS can be generated from module diagram via PyX
    • Added Drag'n'Drop from node tree to diagram
    • Added spreadsheet node to inspect numeric data
    • Stop button added
    • Added 2D scatter plot node with label support
    • Added text reader to read ascii files (used with labels)
    • Added SciCraft icon in application
    • Implemented selection rectangle and move multiple nodes.
    • Replaced pca-function using ParamNode with pca-function setting aMax as parameter
    • PyMul is now optional, but recommended.
    • SciCraft now recommends python-qwt and python-pyx for plots and EPS generation
    • Fixed resizing of canvas window which among others made it possible to have nodes outside the view area and not accessible for the user
    • Fixed problem that made SciCraft crash when opening a non-existent file
    • Filedialog will open current working directory and not home directory
    • Disabled dimensions of/info on R data files on Windows due to problem with R and rpy


  • Version 0.6.3
    • Fixed problem with selecting and deleting induvidual links


  • Version 0.6.2
    • Fixed problem with deleting a node and then clicking on a node label
    • Fixed problems with link contruller GUI
    • Added "..." to buttons and menus that opens a new window
    • Fixed problem with file readers where it was unable to find specified file
    • Added "Minimize all" and "Maximize all" to the window menu
    • Fixed so that when adding a new port in plot nodes no longer changes selected port in uld plots
    • Fixed problem with window menu not updating active window


  • Version 0.6.1
    • problem with objects swapping their relative position in the Z-plane after picking (single mode).
    • Windows version quitting without any feedback if R is not found in the Windows path environment.


  • Version 0.6.0
    • Parameters on Octave function nodes
    • Better link drawing


  • Version 0.5.0
    • Possibility to have several windows open and running at the same time
    • Progress bar when running a diagram
    • Error checking when running a diagram
    • Improved support for R
    • 2D plotting
    • Easier Windows installation
    • ++ many smaller new features and bug fixes