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Effectopedia Changelog

What's new in Effectopedia 1.2.61 Beta

Feb 9, 2019
  • New Save Selected AOPs Option is available in the file command bar. It allows users to select the AOPs form the currently open data source that will be saved in a file.
  • The default option is to save the AOP currently visible in the pathway viewer. Another option is select the AOPs which share common elements (like (key) events, links, initiators...) with the AOP currently visible in the viewer. Last option is to manually select AOPs to be saved.
  • Global shortcuts for file open (Ctrl+O) and file save (Ctrl+S) were added.
  • Update of AOP-Wiki daily dump endpoint location settings.

New in Effectopedia 1.2.4 Beta (Nov 27, 2017)

  • The initial support of current pre-release version of QSAR Toolbox WebAPI has been introduced. Currently the available QSAR Toolbox profiles can be viewed in Effectopedia and imported as StructuralAlert object. The profiler structured description is mapped to StructuralAler object properties. Single category output of a given profiler is selected and used as title of the StructuralAlert. Current implementation does not provide user feedback while loading the available profilers and has not been fully tested in case the web services are not available or return unexpected results. StructuralAlert interface has been updated to handle the new metadata object properties, has additional description section and references.
  • Existing Chemical dialog has been updated and now supports the three type of initiators: Chemicals, StrucuturalAlerts and BiologicalPerturbations. In case of StructuralAlerts both import of QSAR Toolbox profiles and use of existing SA is supported. The dialog now uses a single configurable panel which changes with respect to the type of the object.
  • New data fitting capability was introduced allowing the execution of (R, MATLAB, Java) scripts which optimize parameter values instead of calculating the output of the model. The new functionality is available under Data Fit tab in the in-silico dose response models. Current version allows the use of in lab (in-chemico, in-vitro, in-vivo) test method as source of the data for fitting or data file embedded in the description of the global model. Minimum three executable sources are needed for the data fitting: Effectopedia generated init script, the model and data fitting algorithm. The interface automatically switches between the model and fitting algorithm to be executed depending on the currently selected tab Currently only single record of data can be passed to the data fitting model - future versions can be expanded to pass multiple tested substances. This can be currently done only with embedded data file.
  • The link interface between two chemical structures has been updated. It now supports two new type of links: metabolic transformation and transportation. These two new types of links allow entering nonlinear data. Supporting evidences are also available in a form of reference to test method for experimental and in-silico model execution interface for in-silico support.
  • New data type concentration-time relationship was introduced along with all necessary data templates. The new data type is used in the structure to structure links.
  • The dose response interface has also been updated to allow execution of in silico models. Empirical support evidences need to be extended to allow the use of test response mapping for the MIE.
  • HTML rendering component now supports rendering of embedded png images within the HTML content. The new functionality has been tested with the HTML files imported from QSAR Toolbox
  • Two new data base types have been introduced DataValue_Text - for multi line text properties and DataValue_HTML for HTML properties. ObjectProperties view interface has been updated to show both new types in scrollable text component. Currently there is no interface for editing the HTML code.
  • Test methods user interface was modified to include structured test properties and is now showing after the textual description. By default, the list of properties is empty.
  • BugFix: owner was not properly initialized in Factors class when constructed with the default constructor.
  • BugFix: Element editor did not support loading of StructuralAlert or BiologicalPerturbation.
  • BugFix: Resizing of ObjectProperties list is now fixed and does not stay fixed with the original width of the component.
  • BugFix: Metadata of DocumentedKnowledge object did not clone by default along with all other properties of the object.

New in Effectopedia 1.2 Beta (Oct 19, 2017)

  • This release of Effectopedia introduces Phase II of the changes in the user interface targeted at improved user experience while reducing the chances for errors.
  • The single element pathway modes have been redesigned to show temporary image of the element which is going to be added/modified if the user clicks at the current position. Using this approach, it is always evident what will happen, however there are two drawbacks of the implementation - 1) currently the inserting of the new object is not smooth and cause jittering effect 2) when the final intended change is made there is no elegant exit of the mode (currently escape key or right click cancel). Element wizard mode (previously known as CLET) now inserts links between the elements automatically so the user can only cho?se the location of the elements that have coordinates. In all new implementations the most recently added element is automatically loaded in the element editor.
  • Newly created elements in the new CELT pathway wizard mode are automatically loaded in the element editor panel.
  • Context sensitive help for the former CLET wizard was updated with new help for the Pathway Element Wizard.
  • Recently added context sensitive pop up menu has been updated. Right click on temporary object now allows the current element placement mode to be terminated.

New in Effectopedia 1.075 Beta (Jul 31, 2017)

  • This version introduces the initial implementation of AOP-XML import compatible with the latest 0.9.7. schema. In this import all structured fields form AOP-XML is transferred into Effectopedia and attempt is made for some free HTML fields to be parsed into separate objects (e.g. References). Default values for Key Event biological context are established if not specified in the AOP-XML.
  • New (key) event meta information was introduced allowing the description of the short name (originating in AOP-Wiki) and event components types. The user interface for Effectopedia header was changed to use the object properties list editor.
  • Context sensitive help was updated to show “no help available” when no help is provided for the current context.
  • BugFix: Searching of keywords and groups for adverse effects was not producing results due to wrong name of the index (without the plural s)
  • BugFix: experimentalEvidenceUI was not updating the functional relationship user interface (fnRelUI) when loading new data. Current version bonds the two interfaces together
  • BugFix: Generation of response response data in the absence of time data was causing an error when trying to transfer the values for time. Current version does not attempt to transfer time data if they are not available.

New in Effectopedia 0.9.85 Beta (Sep 19, 2016)

  • KER (Links between effects) interface was updated and now allows the use of in-silico models as support evidences. These models have different set of input parameters compared to Dose Response models. While DR models use only chemical concentrations as input RR models include the state of the upstream element of the link (response in case of effect or concentration in case of chemical) and list of modifying factors. Modifying factors is defined as list of general Effectopedia objects that can be key events / effects / biological perturbations. Future versions will also provide interface allowing more general factors definition such as temperature, radiation, etc. The modifying factors interface is still not implemented and execution of in-silico RR models is not possible. - Local model settings user interface now allows the selection of the associated global model in a drop down list. Earlier versions used the first item from the list of associated global models. - BugFix: Address bar no longer hides the command toolbar when the file name is too long. - BugFix: The pathway viewer user interface was not initialized properly to update the newly introduced help context and caused null pointer exception on every mouse click in the interface modes - BugFix: Pathway editor modes now handle the case where no previous element is available (in the reset state of the editor mode) while determining the context for the help system. - BugFix: Source generator did not escape the " symbol from the descriptions which was leading to non functional Java code.

New in Effectopedia 0.9.4 Alpha (Mar 12, 2014)

  • Revision navigation is now implemented and needs further testing. The file location URL now contains the loaded pathway/pathway element besides the revision number. Earlier versions of the currently shown element - loaded in the pathway viewer - can be displayed by simply clicking on back button for revision navigation.
  • Local files now keep the location of the last edited pathway or element and automatically load it in the editor when file is opened.
  • Default Objects in Effectopedia file now have a fixed creation date which will change when new default object is introduced into the system (until now the current application execution time stamp was used)
  • Several internal optimizations were performed reducing the number of archival objects created and subsequently stored in files. The overall size of Effectopedia database was reduced to less than 2.4 Mb uncompressed (form more than 7.0Mb). As a result of the changes old Effectopedia files can not be browsed for their edit history.
  • DataSourceID was introduced which is provided by the Effectopedia.org server. The ID is obtained once and kept the same during the multiple revisions of the file.
  • Search results are now sorted by the order of creation of the elements.
  • DefaultObjects are now ignored in the search results
  • Server version of Effectopedia database was re-created from script in the new internal format 0.9.4. Old Effectopedia jar and executable files will give a warning for the file format version and need to be upgraded to the current Effectopedia version.
  • Multiple bug fixes related to the loading of the revision history, reference and default objects from local or remote XML files.

New in Effectopedia 0.9.38 Alpha (Jul 13, 2013)

  • New System Console was added as a feedback interface. Current version of the console becomes visible on the first error. It shows both the Java console and the error log. The new interface also allows copying the content of the console along with the list of mouse and keyboard actions, and the error stream to the clipboard. Additionally the user can launch the default e-mail client and paste the content of the report and send it as a feedback.
  • The cycling of the effect type (with single click on a preselected generic object) was updated and now switches only between types allowed for the current object. For example MIEs connected to a chemical could not be cycled, AdverseOutcomes are excluded from the cycle when the element has outgoing associations, MIEs are also excluded from the cycle if the previous component is not a Substance subclass.
  • Bug Fix: the problem of loading links as a segment root or disconnected links was eliminated by assigning default segment.
  • Bug Fix: Newly inserted references are editable when the whole object is not in the read only mode.
  • Bug Fix: The use of type cycling was prone to visual errors since the arcs were connected to the original visual element (which have been substituted by a object of a new type). The problem did manifest itself when the position of the new object becomes different than the original. In this case arcs were hanging in the void - which did not cause any logical errors (the pathway could be correctly displayed if the viewer is reloaded). In the current release the arcs are substituted with new ones connected to the new visual object
  • Bug Fix: The new elements added to the pathway space always had the default size, indiscriminately of the current zoom level. In the new release the elements are pre-scaled with the respect of the zoom level.
  • Bug Fix: Switching the pathway axis to different dimension often caused parts of the vertical axis to become unreachable with scrolling down. The new version calculates the available space correctly and updates the size of all synchronized headers and footers.

New in Effectopedia 0.9.37 Alpha (May 22, 2013)

  • New script version of the DNA Intercalation Mediated Cardiomyopathy pathway was added to the source. The pathway is not published yet.
  • Bug fix: ?Ctrl+del? deletion of the elements caused complete disconnection the selected elements. The new version disconnects the pathway elements only if all the pathways they are associated with are currently visible. In all cases the deleted elements are disassociated from the currently visible pathways
  • Bug fix: The VisulaOptions menu is now updated with the loaded data and aligning and visual properties of the pathway elements can be adjusted as before.
  • Internal sorting of the pathway elements was rewritten and no longer uses recursive methods. This should avoid possible stack overflow problems.
  • New internal function for batch assigning of context dimension for all elements of a certain pathway was added.

New in Effectopedia 0.9.36 Alpha (May 11, 2013)

  • Biological perturbations were introduced. This new pathway element provides the means to encode the cases in which higher level of biological organization effect has molecular level consequences and would require backward connection (which is not allowed for clarity). The current implementation allows the pathway editor to work with the new element and support all the existing features.
  • Bug Fix: The zoom level is reset to default when new information is loaded in the PathwayViewer
  • XMLFile version was updated to 0.936. New version control check was introduced (executed when file is loaded). Warning messages are generated when file format version is greater than currently supported.

New in Effectopedia 0.9.35 Alpha (May 11, 2013)

  • New feature was added to CLET mode allowing the insertion of intermediate effect up or downstream from existing link. The link is automatically reconnected and a second link is inserted to maintain the pathway connectivity.
  • The true delete method is now partially implemented, allowing the deletion of non-generic objects. The objects are disassociated from the currently visible pathways but still remain accessible trough search and show up in the list of existing elements.
  • Substance type cycler now starts the cycle with a chemical instead of structural alert.
  • The order of the elements in Effect in Terms Axis was changed to "unknown,long-term,mid-term,short-term,mixed"
  • PathwayViewer now renders correctly connected fragments of PathwayElements that are not associated with a pathway. The problems occurred in older version when user switched the view space projection containing fragments not associated with any pathway
  • The address bar user interface was modified to show tooltip with the current file name, and its layout was changed to allowing better resizing behavior.
  • Bug fix:When changing one of the pathway space axis the other might not have been initialized. The current version verifies that both dimensions are set before rebuilding the view
  • Bug fix: Multiple phenomena pronounced when changing the pathway space axis, data sources, creating a new pathway with the selected data source, etc were all fixed by complete re-loading of the DataView in all related classes.
  • Bug fix: Associated pathways list is once again modifiable with the toolbar menu. The function of redirecting the interface on double click was also maintained.
  • Bug Fix:When existing element is inserted into the pathway viewer the replaced element and all its arcs are now completely removed from the view
  • Big fix: When pathway elements were deleted their links to other objects remained untouched. The current version unliks the currently deleted object from other objects.
  • Bug fix: The showing of full caption now verifies against for empty text and does cause division by zero and no rendering of the element.
  • Bug fix: When title and ID are selected to be visible in the Effect depiction and the title is empty the ID was ignored and not displayed. Current version shows the ID even in case the title is empty.
  • Bug fix: Each new pathway element created in CLET mode when cyclic over element type replaces the old element and reassign the existing links to the new object.

New in Effectopedia 0.9.34 Alpha (May 11, 2013)

  • Pathway space axis labels are now automatically extened or shrunk in synchrone with the size of the content.
  • Bug fix: The list of associated pathways can be successfully modified with the list editor toolbar. In the last revision readolny flag was raised preventing the Existing pathway dialog from showing.
  • Bug fix: Interrupting the workflow of CLET interface mode was reversing the direction of the workflow by default. Now the direction of the new cycle is evaluated based on the the exact user action. This caused generation of two Structural Alerts instead of one Structural Alert and link.

New in Effectopedia 0.9.33 Alpha (Mar 22, 2013)

  • Bug Fix: The new script generated versions of Effectopedia pathways were affected by the disabled search indices which in their turn resulted in creating of duplicate objects. (The internal searches failed during the script execution preventing the system to reuse the existing objects)
  • Bug Fix: location external or internal ID of the object caused a crash in case of non assigned locationObject
  • Effectopedia now supports unlinking of objects which currently can be used only internally.
  • Bug Fix: The list of associated pathways in PathwaysListUI was not read-only. This is required in order for double clicking to work and load the existing pathway editing interface.
  • Bug Fix: QualityAssuranceUI was crashing when the list of contributors is empty. This was manifested when a new Chemical was edited for the first time.
  • Some additional internal fixes were made which could become problematic in future usage scenarios.

New in Effectopedia 0.9.3 Alpha (Feb 5, 2013)

  • CommandToolbarUI was moved to the top of the application in order to emphasize that all commands are executed for the the currently selected datasource. - New address bar with location and navigation was designed and implemented. The location combobox shows the list of available data sources. During program loading the location combobox is initialized with connection to the centralized database string and upon successful download it does display the current revision number. - Bug Fix: Coordinates of Sex axis were not correcly read from old files still using the Gender name for the same axis. Small patch was added to make the new version backward compatible

New in Effectopedia 0.9.27 Alpha (Dec 13, 2012)

  • Effectopedia no longer uses FTP protocol for communication with the server and instead uses HTTP for all of its transactions.
  • New list capability was added to the search tab showing all elements form a certain type in the search results
  • Multiple changes to both server side processing and generation of notifications were made. The new capabilities are still undergoing testing and not active in the current release.
  • Big list of MIEs, Adverse Outcomes and Endpoints was prepared as a script for adding into the Effectopedia database. Further refinement will be performed on the list before the list is published.

New in Effectopedia 0.9.235 Alpha (Aug 30, 2012)

  • Pathway editors now display "- read only" in their captions when a flagged object is loaded.
  • The read-only inheritance was modified for the nested EffectopediaObjects. The read only status is determined as a conjunction between the "Load" function parameter (often reflecting parent read-only flag) and self readonly flag.
  • Bug fix. The new locking mechanism was not protecting references from editing.
  • Script version of Lhasa pathway examples was updated.