ResSpecies Web Application

Web Application to access data in the resSpecies database.

Current Release: 3.5.2 (4765) (Wed, Jun 30, 2010)

Release History

3.5.2 (4765) (Wed, Jun 30, 2010)

Bug Fixes

• Fixed a problem with the Genotype Submission pages incorrectly reporting that individuals were not part of the population against which genotypes were being submitted. This was due to a change in the that the populations were being pre-loaded. Thanks to Fenge Li and Atia Bashir for reporting the problem. (Ticket 4763)
• Added configuration so that the application redirects back to the top-level species list page if an incorrect species is supplied. This should never happen but is added as a defensive measure against manual URL hacking (Ticket 4764)

3.5.1 (4733) (Tue, May 25, 2010)

Bug Fixes

• Fixed the Genotype Coverage Query option. This was failing with an error message complaining about trying to format infinity as a number. Turns out that the population was not being loaded properly, so it appeared to have zero members. Calculating the percentage coverage then resulted in a division by zero which is widely recognised as a Bad Thing. Thanks to Mick Watson for reporting the problem. (Ticket 4732)

3.5.0 (4721) (Fri, May 14, 2010)

New Features

• Added the Genotype Grid Export option. This option allows the user to select individuals and markers and have genotypes exported in a text-based grid with individuals in rows and markers in column. The genotypes are exported in the "cells" of the grid with the alleles specified as names separated with a hyphen (-). An optional setting allows individual name to be exported as well as ID.

3.4.4 (4716) (Mon, May 10, 2010)

New Features

• Added code (plus pretty interface elements) to allow the user to select which columns are to be included in the Pedigree Export. If the user has javascript enabled then he/she can not only choose what is included, but also the order in which the columns are exported. This functionality degrades nicely to a set of tick-boxes when javascript is not available. Credit to Damon Querry for the prettiness of the interface. (Ticket 4634)
• Changed the default setting for the "Just Check" option in Genotype Submissions. Previously users had to explicitly uncheck this in order to get their data added to the database which led to confusion in multiple instances (where data was not submitted when users believed that it had been). Since the prime intention of this route is to add data to the database and since data that breaks Mendelian inheritance will be trapped by the checking code anyway, we decided to change the default setting accordingly. (Ticket 4670)
• Changes under the hood to the way in which the application establishes connections to the database. (Ticket 4678)

Bug Fixes

• Modified the logic inside the application so that only populations with genotypes for SNP markers are presented for the GenAbel export. GenAbel assumes bi-allelic markers. Although the code checked this property later in the export, it was confusing for users to see populations and then be told that there were no genotypings. (Ticket 4638)

3.4.3 (4647) (Fri, Mar 19, 2010)

New Features

• Added the Adding your data section to the species menu.

3.4.2 (4612) (Fri, Mar 05, 2010)

New Features

• Added Dog to the available species

3.4.1 (4603) (Thu, Mar 04, 2010)

New Features

• Added an option to filter the genotype coverage query on the strength of the coverage
• Added a graphical repesentation of the coverage to the genotype coverage query

3.4.0 (4596) (Fri, Feb 26, 2010)

New Features

• Added the Genotype Coverage Query option to the main menu

3.3.2 (4583) (Tue, Feb 16, 2010)

Bug Fixes

• Fixed a permissions problem for certain users
• Fixed a bug where a population with no families was causing an error
• Fixed a bug where the pick marker step was listing populations rather than marker types.

3.3.1 (4557) (Wed, Feb 03, 2010)

New Features

• [COSMETIC] Improved the look and feel of the release notes page

Bug Fixes

• Altered an application configuration that was preventing email export from working under certain circumstances
• Changed the unknown phenotype value in the GenAbel Export from * to the correct value of NA

3.3.0 (4533) (Thu, Jan 21, 2010)

New Features

• Added email functionality to the export routines. If a user is logged in then an option is offered at the final data selection stage to email the data to their registered email address. Data is exported as separate attachments to a single email message to simplify the handling
• [COSMETIC] Improved the look and feel of the error pages

Bug Fixes

• Corrected various grammatical and spelling errors in the interface

3.2.1.38709.4504 (Mon, Jan 11, 2010)

New Features

• Added validation to the genotype submission option so that multiple genotype entries in the submission file are now ignored if the alleles are the same or reported as an error if the alleles are different

Bug Fixes

• Fixed a bug in the genotype submission error code that reported all the individuals as not being members of the population if an unknown marker was included in the submission file
• Sorted the order of the output in the QTLExpress Export report so that the individuals are now sorted on generation/accession this makes the report more readable and also fixes the order of the generation header line of the marker genotypes/pedigree file

3.2.0.38684.4485 (Thu, Dec 17, 2009)

New Features

• Added a Genotype Export tool to extract genotypes in 'ID Marker A1 A2' format
• Added an option to all the Export tools that allows individuals to be ignored by either name or accession
• [COSMETIC] Tidied the Release notes section on the top-level page and also fixed the formatting on the Release History page
• [COSMETIC] Added round edges and drop-shadows for browsers that support it
• [COSMETIC] Amended the GenAbel Export so that locations that were displayed in scientific notation are now displayed as decimals

3.1.3.38674.4468 (Mon, Dec 07, 2009)

Bug Fixes

• Changed the interpretation and reporting of 'novel alleles' in the inheritance checker. 'Novel allele' now means 'an allele was seen in the individual that was not seen in either parent.

3.1.2.38671.4467 (Fri, Dec 04, 2009)

Bug Fixes

• Fixed a bug in the genotype submission error reporting code that was causing only one error to be reported per marker.

3.1.1.38658.4443 (Wed, Nov 25, 2009)

New Features

• Added release notes for current version to the intro page.

3.1.0.38656.4439 (Mon, Nov 23, 2009)

New Features

• Added release notes page.
• Added new export option to output files in GenAbel format.
• Fixed the pick markers for alleles step so that the alleles are now sorted by symbol.

Bug Fixes

• Fixed Bug RT 4436: removed leftover references to the test species.