Phenex 1.0.3 released

February 23, 2010

Phenex 1.0.3 is now available.  This release fixes a serious bug which caused Phenex to append modified phenotype annotations within files, instead of replacing the previous data. Phenex will now read and write NeXML files correctly. It should also automatically recover the latest data from files saved with older versions of Phenex.

All Phenex users should replace their current copy of Phenex with the latest release. It can be downloaded from the Phenex homepage on the Phenoscape wiki.

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Posted by Jim

Phenex 1.0.2 released

January 20, 2010

Phenex 1.0.2 is now available.  This is a minor update which fixes an interface problem caused by a recent Mac OS X Java update.  It also fixes a file loading bug which occurred on specific older versions of Mac OS X.  Phenex can be downloaded from its homepage on the Phenoscape wiki.

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Posted by Jim

Announcing Phenex 1.0

November 25, 2009

Phenoscape is proud to announce the immediate availabiity of Phenex 1.0, the first public release of our platform-independent desktop application for annotating character-by-taxon matrices with ontology terms.  Phenex has been in development and available in beta form for over a year, while we used it to curate more than 50 publications for inclusion in the Phenoscape Knowledgebase. Read the rest of this entry »

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Posted by Jim

Our summer of code project

August 27, 2009

Phenoscape has mentored, under the auspices of NESCent, another Google Summer of Code student this year.  Kasia Hayden developed a plugin package for Mesquite that allows users to view character matrices and EQ (ontology-based) annotations produced using the Phenex tool.  The primary purpose was to allow curators to share their annotation work with others in the context of a more familiar tool.  Users can select cells in a Mesquite character matrix and, using two new cell tools, see EQ annotations either as text in the bottom pane of the matrix window, or as a graph in a separate pop-up window. Read the rest of this entry »

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Posted by pmidford

Phenex 1.0-beta24 released

August 14, 2009

Phenex 1.0-beta24 is now available for download.

This release has a few new features and a number of bug fixes:

Features:

  • The Search panel from OBO-Edit is now available in Phenex, under the View > Ontology menu.  This allows the user to do a textual search of all loaded terms, and view a results list.
  • There is a “quick editing” mode for the character matrix interface.  The user can type the name of a state symbol, without first double-clicking the cell, and Tab or Return to the next cell to edit.
  • If the quality “count” has been used in a phenotype for any state for a character, it will be auto-filled for subsequent states.
  • Open/Save panel starts at the previously visited directory.

Bugs fixed:

  • Copy and paste of terms in the Phenotypes table works consistently now.
  • The post-composition editor no longer disappears after tabbing out of the genus field when running on Java 6.
  • The menubar no longer disappears after using the post-composition editor.

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Posted by Jim

Introducing Phenex

October 30, 2008

After a summer of intensive development, at our recent Data Roundup we introduced curators to our new phenotype annotation software, Phenex. Phenex is an application for annotating character matrix files with ontology terms. Character states can be annotated using the Entity-Quality syntax for ontologically describing phenotypes. In addition, taxon entries can be annotated with identifiers from a taxonomy ontology. Phenex saves ontology annotations alongside traditional character matrix data using the new NeXML format standard for evolutionary data. Read the rest of this entry »

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Posted by Jim