EMMAWiki/NewsAndUpdates

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Revision as of 14:36, 27 December 2005 by imported>MichaelDondrup
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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(2005-12-27T13:36:13Z) (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.

-- 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

  • 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.

Bugfixes

Stable

-- 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

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