PPIXpress Files

ATTENTION:
Due to a bug in their pipeline, Ensembl release 88 misses data that is important for PPIXpress. 
The problem is fixed in release 89.
Ensembl release 92 handles ’nonsense-mediated decay’ and ’non-stop decay’ transcripts differently.

PPIXpress_1.23.zip contains
    - PPIXpress.jar and PPIXpress_GUI.jar Java 8 binaries
    - helper scripts to start the GUI for both Windows and Unix operating systems
    - source code
    - user guide
    - example data for human and mouse
    - GNU GPL V3 license information

Changes from 1.22 to 1.23:
    - option to also integrate data from the Eukaryotic Linear Motif (ELM) resource
    
Changes from 1.21 to 1.22:
    - STRING retrieval updated to v11

Changes from 1.20 to 1.21:
    - fixes regarding output of abundances for gene input data
    - MySQL ConnectorJ updated to 8.0.15

Changes from 1.19 to 1.20:
    - some retrieval fixes (Uniprot switched to https-only)
    - MySQL ConnectorJ updated to 8.0.11

Changes from 1.18 to 1.19:
    - small bugfix regarding the output of PPIXpress' version with "-version"
    - MySQL ConnectorJ updated to 5.1.45
    
Changes from 1.17 to 1.18:
    - completely overhauled UCSC/Ensembl mapping,
      mapping now retrieves transcript-version dependent data from UCSC 
      and enforces Ensembl's GRCh37 server
    - count normalization by transcript length added as an option in de cmd-binary
    
Changes from 1.16 to 1.17:
    - improved UCSC/Ensembl mapping, can make a slight difference when
      removal of ’nonsense-mediated decay’ or ’non-stop decay’ transcript 
      is activated or length normalization (only in framework) is used
    - version can be shown with "-version"
    
Changes from 1.15 to 1.16:
    - updated 3did retrieval to their new https servers
      
Changes from 1.14 to 1.15:
    - the abundance of the most abundant transcript (or the sum of 
      all expressed transcripts coding for the protein) is now 
      reported in the major_transcript outputs
    - MySQL ConnectorJ updated to 5.1.42
    
Changes from 1.13 to 1.14:
    - UK-based Ensembl MySQL server is now the default for queries
    - internal optimization of queries
    - MySQL ConnectorJ updated to 5.1.40
      
Changes from 1.12 to 1.13:
    - compatibility-fix for correct behaviour of ’nonsense-mediated decay’ or ’non-stop decay’
      loss of interactions in PPICompare

Changes from 1.11 to 1.12:
    - transcript-biotype additionally retrieved, proteins represented by transcripts that are
      tagged with biotype ’nonsense-mediated decay’ or ’non-stop decay’
      are by default not included in the constructed network

Changes from 1.10 to 1.11:
    - reference PPIN, full DDIN and associated transcripts from mapping-stage can be reported
    - MySQL ConnectorJ updated to 5.1.39
    - compiled with Java 8 in mind

Changes from 1.09 to 1.10:
    - iPfam release 1.0 is added to the local DDI data and not retrieved anymore

Changes from 1.08 to 1.09:
    - due to recent downtimes of iPfam, the option to
      turn of automatic retrieval of DDI data was added to GUI version

Changes from 1.07 to 1.08:
    - optimization of gene/transcript(s)/protein(s) - association query

Changes from 1.06 to 1.07:
    - by default, protein interaction data can now be retrieved from mentha,
      which is regularly updated and hosts the most complete compilation of physical interactions,
      IntAct is only used as a fallback for less common organisms
    - small aesthetical fixes in GUI-version

Changes from 1.05 to 1.06:
    - optional compressed output
    - MySQL ConnectorJ updated to 5.1.38
    - small internal changes like optimization of some queries

Changes from 1.04 to 1.05:
    - in addition to IntAct, iRefIndex data can be retrieved
    - outdated UniProt accessions can be automatically
      updated to their current primary accessions
    - optional output of assumed major transcript per protein
    - added support for new expression fileformat: native Kallisto output
    - several small fixes in GUI-version

Changes from 1.03 to 1.04:
    - added support for new expression fileformat: native RSEM output
    - Ensembl identifiers with version-suffixes
      are now broadly supported for expression data

Changes from 1.02 to 1.03:
    - more robust GTF parsing
    - MySQL ConnectorJ updated to 5.1.36

Changes from 1.01 to 1.02:
    - more robust inference of expression data file types
    - some refactoring

Changes from 1.00 to 1.01:
    - current 3did and iPfam interaction data is now automatically retrieved to enhance
      the precompiled domain interaction data given by IDDI/DOMINE (switchable)
    - expression threshold can be set according to a given percentile
      of the values in the sample
    - protein-protein interaction networks can now also be given as HGNC symbols,
      ENSEMBL genes or directly retrieved from the most current IntAct release
    - STRING retrieval updated to v10, MySQL ConnectorJ updated to 5.1.35
    - percentage of proteins and protein interactions associated with
      non-artificial domain interactions is reported in the mapping stage
    - a standalone version with a simple GUI is provided