XMLPipeDB / News: Recent posts

GenMAPP Builder 2.0 Beta 43 Released

GenMAPP Builder 2.0b43 has been released. This release includes the initial version of a major change in how GenMAPP Builder is used: instead of reading the GOA file at export time, it can now be imported into the relational database just like the UniProt and GO XML files. This change makes exports more streamlined and, based on preliminary testing, speeds up the export process.

Posted by dondi 2010-04-24

S. aureus GenMAPP Gene Database Released

The XMLPipeDB project has released a standard Staphylococcus aureus (strain MRSA252) Gene Database. Detailed information on this database is contained in the included ReadMe.

Posted by dondi 2010-04-15

P. aeruginosa GenMAPP Gene Database Released

The XMLPipeDB project has released a standard Pseudomonas aeruginosa str. PAO1 Gene Database. Detailed information on this database is contained in the included ReadMe.

Posted by dondi 2010-04-15

GenMAPP Builder 2.0 Beta 42 Released

GenMAPP Builder 2.0 Beta 42 has been released. This release of GenMAPP Builder updates the UniProt XML support to coincide with the 2/23/2010 version of the UniProt XSD.

Posted by dondi 2010-03-30

GenMAPP Builder 2.0 Beta 41 Released

GenMAPP Builder 2.0 Beta 41 has been released. This release of GenMAPP Builder introduces a new customization for Staphylococcus aureus.

Posted by dondi 2010-02-17

GenMAPP Builder 2.0 Beta 40 Released

GenMAPP Builder 2.0 Beta 40 has been release. This release of GenMAPP Builder restores customizations when exporting
Saccharomyces cerevisiae that have been lost for the prior 2 releases, and introduces a new customization for Pseudomonas aeruginosa.

Posted by dondi 2010-02-08

GenMAPP Builder 2.0 Beta 39 Released

GenMAPP Builder 2.0 Beta 39 has been released. This release of GenMAPP Builder includes customizations when exporting Saccharomyces cerevisiae and when running the tally engine on Staphylococcus aureus.

Posted by dondi 2010-01-29

GenMAPP Builder 2.0 Beta 38 Released

GenMAPP Builder 2.0 Beta 38 has been released. This release of GenMAPP Builder includes preliminary versions of four new species profiles, including Mycobacterium tuberculosis, Staphylococcus aureus, Pseudomonas aeruginosa, and Saccharomyces cerevisiae.

Posted by dondi 2009-12-14

GenMAPP Builder 2.0 Beta 37 Released

GenMAPP Builder 2.0 Beta 37 has been released. This version includes fixes to various aspects of the TallyEngine (taken from XMLPipeDB Utilities 2.1.4).

Posted by dondi 2009-11-02

Vibrio cholerae GenMAPP Gene Database Now Available

The XMLPipeDB project has released a standard Vibrio cholerae O1 biovar El Tor str. N16961 Gene Database. Detailed information on this database is contained in the included ReadMe.

Posted by dondi 2009-06-24

Arabidopsis thaliana GenMAPP Gene Database Now Available

The XMLPipeDB project has released a standard Arabidopsis thaliana Gene Database. Detailed information on this database is contained in the included ReadMe.

Posted by dondi 2009-06-12

Plasmodium falciparum GenMAPP Gene Database Now Available

The XMLPipeDB project has released a standard Plasmodium falciparum (isolate 3D7) Gene Database. Detailed information on this database is contained in the included ReadMe.

Posted by dondi 2009-06-09

Escherichia coli K12 GenMAPP Gene Database Update: 20090529

The XMLPipeDB project's Escherichia coli K12 GenMAPP Gene Database has been updated to 20090529. This release is the first major update to the standard Escherichia coli K12 Gene Database. The data are updated according to the Data Source and Version information contained in the included ReadMe. In this release, the following proper ID systems were added: GeneId (NCBI), RefSeq (protein), and W3110. Affymetrix probe set identifiers from the Affy table in the Ec-K12-Std_External_20060731x.gdb Gene Database were directly copied into this database without further annotation or verification of the data. Additional details are provided in the included ReadMe PDF.

Posted by dondi 2009-06-08

GenMAPP Builder 2.0 Beta 29 Released

Allows for the creation and use of multiple profiles per species.

Posted by geocoso2 2009-03-20

GenMAPP 2.0b26 Released

The new version contains an updated Tally Engine along with a new species table for E. Coli.

Posted by geocoso2 2009-02-24

GenMAPP Builder 2.0 Beta 22 Released

GenMAPP Builder 2.0 Beta 22 has been release. This release updates the Gene Ontology XML/database loading code to accommodate the latest daily term OBO XML downloads that are available from geneontology.org.

Posted by dondi 2009-01-21

GenMAPP Builder 2.0 Beta 21 Released

GenMAPP Builder 2.0 Beta 21 has been released. This version retrieves the function field based on the latest UniProt XML schema, and includes initial compatibility with Java 6 under Windows Vista. To run GenMAPP Builder under this environment, use the gmbuilder-vista.bat script that is now included with the release.

Posted by dondi 2009-01-08

GenMAPP Builder 2.0 Beta 20 Released

GenMAPP Builder 2.0 Beta 20 has been released. This version includes additional code for retrieving more IDs from a Plasmodium falciparum UniProt data set.

Posted by dondi 2008-12-02

XMLPipeDB Match Utility 1.1 Released

The XMLPipeDB Match utility has been released for the first time as a direct download. The utility has existed and been used for a while in the source code repository.

match is a utility that was developed specifically to assist in vetting and debugging GenMAPP Builder-exported Gene Database files for GenMAPP. When inspecting an exported Gene Database, specific ID counts are needed, with IDs tracked from the original XML file to the final .gdb file. To do this count properly, the equivalent of a "select distinct" must be performed: matching patterns should be found in the XML file, with duplicate matches taken into consideration as an individual ID.... read more

Posted by dondi 2008-11-29

GenMAPP Builder 2.0 Beta 19 Released

GenMAPP Builder 2 Beta 19 has been released. This release adds a Blattner record to the Systems table template in support of the special handling needed by E. coli K12. This table has System Code Ln, with the System Code for OrderedLocusNames changing to N.

In addition, very preliminary support has been added for a new species, Plasmodium falciparum. This support takes the form of special handling of PFxxxxxx IDs, such that, regardless of their origin, they appear in the OrderedLocusNames table.... read more

Posted by dondi 2008-11-25

GenMAPP Builder 2.0 Beta 18 Released

GenMAPP Builder 2 Beta 18 has been released. This release reflects continuing work at restoring custom handling of E. coli K12 UniProt data.

Posted by dondi 2008-11-12

GenMAPP Builder 2.0 Beta 17 Released

GenMAPP Builder 2 Beta 17 has been released. This release represents another try at addressing two issues: the Other table date field and the restoration of E. coli Blattner tables.

Posted by dondi 2008-11-10

GenMAPP Builder 2.0 Beta 16 Released

GenMAPP Builder 2.0 Beta 16 has been released. This release fills out the Date field of the Other record in the Systems table, and attempts to restore correct Blattner ID handling when exporting E. coli.

Posted by dondi 2008-11-06

GenMAPP Builder 2.0 Beta 15 Released

GenMAPP Builder 2.0 Beta 15 has been released. This release makes a few more adjustments caused by the change in UniProt's XSD (and thus to the corresponding relational schema). Protein count should work again, as should the "function" text field.

Posted by dondi 2008-11-03

GenMAPP Builder 2.0 Beta 14 Released

GenMAPP Builder 2.0 Beta 14 has been released. This release updates the database loading code to the 9/25/2008 version of the UniProt XSD.

Posted by dondi 2008-10-31