EMMAWiki/NewsAndUpdates

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Revision as of 10:29, 21 March 2006 by imported>MichaelDondrup
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News and Updates

This page lists updates, newly improved features and bugfixes. The updates, listed under Testing are only available on the internal test web-server at http://seraph.cebitec.uni-bielefeld.de/software/emma/ . Please note that the test-webserver is available from inside the CeBiTec-network only. The test-server is subject to modification, down-times and non-operational pages without notice!

Once updates have become stable, they will be moved to the production server as well.

(!) You may subscribe to this page to keep informed about news and changes.
You will be notified by email, whenever this page is updated. If you are asked to create a Wiki profile, please fill in the form and click Create Profile.

New Features

Stable

-- MichaelDondrup DateTime(2006-02-18T17:36:01Z) 

 (!) The EMMA production webserver has been updated to EMMA 2.2
  • The Reporter Datamining Tool allows to search all experiments within a Project for transformed data. The tool allows to search for Reporter names and identifiers using wildcards and also it allows for Google style fulltext search in Descriptions. The resulting datamatrix may be exported as tab-separated file. Have a look at Reporter Datamining in the Advanced Actions menue. Please note that the maximum number of Reporters to be displayed is limited to 400.
  • Cluster Viewer: Now, you can resort the data in the Show reporters window. Click on the columnheader to sort by that column, click more often to toggle descending, ascending and no sorting. You can also sort by Reporter Name and Description.
  • A new history function allows to go back several steps at once. It is locate at the top of the main window. It's working with most of the pages now,

but in rare cases the link in the history might go wrong, displaying an empty page. Errors can also occur if try to go back to a deleted object. No data will be lost as delete operations are not stored in the history.

  • Chiefs can configure the links to external databases like EMBL, TREMBL, TIGR. Use the Configure DB links dialogue to edit these settings. This is most useful if in the Sequence Details there is no hyperlink to the external resource. For eg. TIGR medicago gene index the link is: http://www.tigr.org/tigr-scripts/tgi/tc_report.pl?species=medicago&tc=
  • ! The Advanced Actions menue now opens and closes only on click not on mouse over. The old behaviour was too annoying.
  • The login page checks for activated Cookies and JavaScript. If one of them is not activated or the user tries to use InternetExplorer, a warning message is displayed
  • Cluster browser: Cluster browser now shows Factor/Values, you can activate a Factor/Value label for the tree view also
  • Cluster browser has new auto-expand option, zooming the whole tree to have readable row-labels
  • Setting the status of an Experiment to Locked or Finished now protects the Experiment against accidential deletion, even for roles Chief and higher
  • Normal users may only edit an Experiment in Status Locked if they own it. Only Chiefs and higher may edit an Experiment in Status Finished. This is necessary to make deletion of finished Experiments possible: Set status back to In progress
  • Data Viewer: The Filter dialog now gives you the option to build boolean queries using AND and OR. Queries can be grouped by parenthesis '()'.
You still need to define filter conditions. They are named E1 ... En. A sample boolean query looks like this:  { (E1 AND E2) OR E3 }
See feature request: https://bugs.cebitec.uni-bielefeld.de/show_bug.cgi?id=511

The layout of the filter dialog is changed, take a look at the AND and OR buttons at the end of the line. They will add an entry to the expression field.

  • New Filters operators within interval and not within interval. Define a range by two numbers.
  • Array View: Now the red-green overlay images can be created on the fly. You may specify gamma, contrast and brightness. This only works for newly imported images. (Cutspotpix program is no longer needed) according to feature request https://bugs.cebitec.uni-bielefeld.de/show_bug.cgi?id=517
  • If you click on a spot in the zoom window, now, Reporter details will be displayed.
  • Pipeline: EMMA can now do Normalization on Controls, the necesary functions have been added to the system. (https://bugs.cebitec.uni-bielefeld.de/show_bug.cgi?id=528) Like always: If you need Normalization on Controls in your project, you have to request the function to be added.
  • Hierarchical clustering now uses the amap package instead of hclust. The cluster pipeline should now be more memory efficient and also faster, for large datasets
  • Manual data-set selection under Advanced-options shows more information
  • Experiment: The number of clusterings performed is listed on the overview page
  • Array Design: Link to documentation is now fixed https://bugs.cebitec.uni-bielefeld.de/show_bug.cgi?id=523
  • Object Permissions: Now shows dependent object by default, when adding a permissions set https://bugs.cebitec.uni-bielefeld.de/show_bug.cgi?id=498
  • Search: You can now also search descriptions
  • KEGG browser: You can view the available KEGG maps under advanced options. Expression data can be projected on these pathways. Therefor, an analysis step is required, which computes a GeneExpressionMatrix from the normalized data. In the results page you will find a link to the KEGG projection. The necessary pipelines will be added to these projects.

-- MichaelDondrup DateTime(2005-12-27T13:36:13Z) (from Testing DateTime(2005-09-22T11:17:01Z))

  • Documentation: links to HTML help pages can now be found in the info-text (on the left) on almost each page
  • Cluster browser (Java applet) is improved (This applet deserves its own page, in fact)
    • You can cut the tree into clusters
    • Plot line-graphs, bar and star charts of expression profiles
    • Zoom into any region
    • Change colors
    • Export the graphics as image files and data files
    • ...
  • Cluster page: speed up in loading the tree and matrix data: data is cached, reloading a cluster will be much faster, now
  • Clusters can now be deleted, and have their permissions changed
  • Clusters are now under the control of the permission system
  • Array layout: The ArrayLayout import is now more verbose, when a problem with missing or unknown columns is discovered.
  • Experiment Wizzard: More information (name and identifier) under link arrays
  • Pipeline: The significance test can now do a two.sample test, the old one, was lacking the parameter. To profit from that, a new pipline has to be imported.
  • Experiment page: More editable descriptions (Quality control, Normalization and Replication)

-- MichaelDondrup DateTime(2005-09-07T16:06:39Z)

  • Renamed this page, updated links to it to EMMAWiki/NewsAndUpdates. Now other documentations may have NewsAndUpdates, too.

-- MichaelDondrup DateTime(2005-09-07T15:55:43Z) (from Testing: DateTime(2005-08-30T17:59:41Z))

  • slight improvement of the layout and function of the Dataset Viewer. Filter Data button moved to the top of the page. Drop sorting can now be re-done, and the drop button is only displayed, when data was filtered or sorted. Note: the Drop sorting button will also drop a filtering step.

-- MichaelDondrup DateTime(2005-08-19T14:58:48Z)

  • LIMMA[[FootNote(Smyth, G. K., Yang, Y.-H., Speed, T. P. (2003). Statistical issues in microarray data analysis. In: Functional Genomics: Methods and Protocols, M. J. Brownstein and A. B. Khodursky (eds.), Methods in Molecular Biology Volume 224, Humana Press, Totowa, NJ, pages 111-136.)]] statistical test functions should now be available in every project. LIMMA is a (probably) superior alternative to a simple t-test for identifying differentially expressed genes. Chiefs may create a new pipeline with this function. For more information, refer to the LIMMA user's guide by the authors of the R-package.

-- MichaelDondrup DateTime(2005-08-19T14:41:48Z) (from Testing: DateTime(2005-08-17T20:41:06Z))

  • added possibility to change owner of an object under View permissions B-) only for Chiefs B-)
  • added a 'More help' link under the info box on a few pages
  • added icon to menu->bug report
  • edit and delete buttons are now displayed only when the user has approriate right, to perform the action

-- MichaelDondrup DateTime(2005-08-19T14:41:48Z) (from Testing: DateTime(2005-08-15T08:11:31Z))

  • Added link to news and updates to the login pages
  • Adjusted the maximum length of Name and Identifier fields in Edit Experiment page to 400 and 200.
  • Added a utility to add and edit groups under 'Settings->Manage Groups' in the top menu.

-- MichaelDondrup DateTime(2005-08-19T14:41:48Z) (from Testing: DateTime(2005-08-15T08:11:31Z))

  • Improved 'Experiment->View permissions' can now also change permissions of dependent object (aka: Arrays, Datasets)
  • Pipeline should now be more efficient and require less memory, speed up of normalization. It should now be possible to normalize more than 100 arrays in parallel.
  • Cluster browser now shows Factor/Value headers in '(right click on tree node)->show reporters', when available. If not, please re-run the clustering to see them. The Factor/Value headers will also be present in the 'export data-matrix' export

Testing

-- MichaelDondrup DateTime(2006-02-18T17:36:01Z)

  • Webserver has been updated to EMMA 2.2(final)
  • There was a small bug in the Data Viewer (Filter-function) causing not all Expressions to be evaluated

-- MichaelDondrup DateTime(2006-01-24T10:34:57Z)

  • Webserver has been updated to EMMA 2.2 Release Candidate 2

Bugfixes

Stable

-- MichaelDondrup DateTime(2006-03-21T09:29:05Z)

  • Sequence Viewer (GenDB links): BRIDGE-links to GenDB via View Contig, Jump to Region, and View Annotation did not work correctly. The direkt links to GenDB have been fixed (see Bug 612). Still, due to some deficiencies in GenDB, only the link 'Jump to Region' will work correctly (see GenDB Bug 620 and GenDB Bug 621)

-- MichaelDondrup DateTime(2006-03-20T10:47:27Z)

  • Cluster Viewer: There was a minor bug, that caused the image export of the tree to be disfunct, see Bug 608. Re-starting your browser might be necessary.

-- MichaelDondrup DateTime(2006-02-23T17:39:02Z)

  • There was a little bug, causing the Genepix import to be disfunct. (Bug 596)

-- MichaelDondrup DateTime(2006-02-18T17:36:01Z)

  • There was a bug in the filter settings of the FilterHClust module, causing overly strict filtering on hierarchical clustering pielines.

-- MichaelDondrup DateTime(2006-01-26T18:57:31Z)

-- MichaelDondrup DateTime(2006-01-24T10:34:57Z)

  • Cluster Viewer: small bug fixed in the search window. That bug would cause the text entry field to grow proportionally when resizing the window.
  • Normalization on Controls (new in 2.2rc1) had a bug that prevented it from being effective. It took all the data and computed median or mean normalization, not only the control set.
  • Analysis Pipeline: The reconfiguration dialogue displayed by clicking on Change configuration in Analyse
Arrays had a bug that would cause multi-valued parameters (like the filter flags in the Normalization pipeline) to be ingnored except for the first value. The predefined pipelines were not affected by that. (See https://bugs.cebitec.uni-bielefeld.de/show_bug.cgi?id=550)

-- MichaelDondrup DateTime(2005-12-28T10:45:57Z)

-- MichaelDondrup DateTime(2005-12-30T15:13:27Z)

-- MichaelDondrup DateTime(2005-12-27T13:36:13Z) (from Testing DateTime(2005-09-22T11:17:01Z))

  • Fixed a bug, that would cause more trouble than neccessary for chiefs, when trying to delete objects they did not own
  • Fixed a bug in the Pipeline, that would cause mixed Factor Value assignments and lead to wrong results, when more than one Factor was defined.
  • Changed confusing links to 'Create experiment (wizzard)'
  • Changed confusing help links
  • Removed a bug that prevented the two sample t-test from working
  • Typos...

-- MichaelDondrup DateTime(2005-09-07T15:55:43Z) (from Testing: DateTime(2005-08-30T17:54:44Z))

  • Fixed a bug in a new feature of the Data Viewer, that would cause an exception when trying to sort a dataset.

-- MichaelDondrup DateTime(2005-08-19T14:41:48Z) (from Testing: DateTime(2005-08-17T20:41:06Z))

  • fixed a bug in ArrayLimsImport now access rights should always be respected
  • News and Updates now also works in logout page

-- MichaelDondrup DateTime(2005-08-19T14:41:48Z) (from Testing: DateTime(2005-08-15T08:11:31Z))

  • Fixed a bug, that would cause several Arrays/ datasets not to be added to the current experiment in rare cases, during parallel import from arraylims, or parallel execution of multiple pipelines.
  • Fixed a minor bug on the cluster list page, now the return to link is functional, while viewing descriptions.

-- MichaelDondrup DateTime(2005-08-19T14:41:48Z) (from Testing: DateTime(2005-08-15T11:49:36Z))

  • Removed a bug that would break arraylims import in rare cases. When the uploaded data file has been processed under a Windows/DOS operating system,sometimes CR/LF will be added as line-break indicator. The linebreak indicators are now converted to UNIX style during parsing.
  • Made the ArrayLayoutImport more robust, against empty lines. Now the layout import will ignore empty input lines and also remove quotes (aka: "").

Testing

-- MichaelDondrup DateTime(2006-01-26T19:01:07Z)

-- MichaelDondrup DateTime(2006-01-24T10:34:57Z)

  • Import from Arraylims failed in RC1.
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