Timina / News: Recent posts

Timina 0.12.1: fixes some bugs found in the previous version.

Fixes bugs:

[ 2777751 ] - Error in automatic annotation if no plugins defined

[ 2770823 ] - Annotation summary page shows inappropriate options

[ 2731676 ] - HTML in assembly execution log is truncated

[ 1919694 ] - Database is not cleaned if an automatic annotation fails

For more information about Timina see http://timina.sourceforge.net .

This new version includes four bug fixes and introduces annotation tools interface.

Fixes bugs:

[ 2513735 ] - Unable to execute Fasta program in pipelines
[ 2273005 ] - HTTP Status 500 when an user with few privileges log in
[ 2219422 ] - Fail in tabbed file with all automatic annotation best hits
[ 2219396 ] - Annotation form shows field of length zero

Implements planned features:

[ 1962109 ] - Blast tool
[ 1962108 ] - Search tool
[ 1962106 ] - Annotation tools interface... read more

Timina 0.10.0 released. This new version includes two bug fixes and introduces some new features requested by our users.

Bug fixed:

- [ 1958409 ] - Long gene names are truncated in Blast hits
- [ 1940262 ] - NullPointerException at AnnotationReportServlet

Requested features implemented:

- [ 1936372 ] - Download of a tabbed file with all automatic annotation hits
- [ 1936370 ] - Direct access to contigs, singlets and ORFs
- [ 1936369 ] - Download of plaque sequences in FASTA file

This new version attempts to fix two critical bugs. All users must update their installations by this version.

Bugs fixed:

- [ 1934966 ] - Assembly fails (AssemblyPipelineException) for transcriptome

- [ 1934987 ] - Assembly for trancriptome seems not create tables

Timina 0.8.3 now available. This new release fixes one important bug. All users must update their installations by this version.

Bug fixed:

-[ 1933998 ] - Assembly fail to clean tables if its processing fail

This new release fixes several bugs, including some critical problems. All users must update their installations by this version.

Bugs fixed:

- [1928747] - Automatic annotation don't generates base sequence file
- [1928717] - Automatic annotation fails with AnnotationPipelineException
- [1928693] - Projects into the same servlet container shares databases
- [1928415] - Programs execution error: java.lang.IllegalMonitorStateExcep
- [1919723] - Automatic annotation continues when external programs fails
- [1919694] - Database is not cleaned if an automatic annotation fails
- [1919095] - Annotation plugins execution fails without plugins
- [1916132] - Assembly continues without confirmed sequences... read more

Timina is a Java web-based framework for automation of all steps of a genome sequencing project: submission, assembly and annotation of sequences.

This is Timina third release! This package provides resources for sequences submission, assembly and annotation and fixes bugs in Timina 0.8. People using Timina 0.1 or 0.8 should request
detailed information before update.

This package provides resources for sequences submission, assembly and annotation. People using Timina 0.1 should request detailed information before update.

Changes:
- Some changes in database definitions for submission.
- Fixes some undocumented bugs in submission and users subsystems.
- Adds sequences assembly.
- Adds sequences annotation (automatic and manual).
- Adds annotation plug-ins interface.
- Updates all classes and database modeling.
- Updates all classes and database documentation.... read more

Work in modules for assembly and ORFs identification was concluded last night. However a new package will not be released now. The new features can be used from CVS code tagged as "Timina-0-3" version. Details about assembly and ORFs identification are in Javadoc comments. More details will be presented in the next release, that will include annotation of sequences (contigs, singlets and ORFs).

Timina is a Java web-based framework for automation of all steps of a genome sequencing project: submission, assembly and annotation of sequences. This release provides resources for sequences submission. Assembly and annotation will be avaiable in the next version.