EMMAWiki/NewsAndUpdates
News and Updates
Here, we list updates with newly improved features and bugfixes. The ones, listed under 'Testing' are only available on the internal test web-server. Once they have stabilized, the updates will be moved to the production server as well.
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New Features
Stable
-- 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
Bugfixes
Stable
-- 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: "").