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LOVD v.3.0 - Leiden Open Variation Database
Online gene-centered collection and display of DNA variations
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LOVD 3.0 News
| LOVD 3.0 beta 05 released |
Ivo Fokkema, 2012-05-16 |
Today, LOVD 3.0-beta-05 has been released. New features implemented, amongst others: Implemented a drop down menu for genes and disease entries; Implemented a drop down menu for almost all data listings, for authorized users only; Almost all data can now be downloaded from LOVD in tab-delimited format; Many improvements on custom column management, such that curators can easily add, remove edit and sort the custom columns for their genes and diseases; Log entries can now be deleted in groups.
Bugs fixed, amongst others: Fixed problem with the "External link" field for genes; Fixed some issues with PDO; Fixed multiple issues with custom column management; Fixed some Javascript issues, mostly with Internet Explorer; Fixed problem with valid input being denied in the dbSNP and DBID variant fields; Variants will now no longer linger in the database by default when an individual or screening is removed.
Closes #10, #11, #12.
See the changelog.
Download the new build. |
| LOVD now on Facebook |
Ivo Fokkema, 2012-05-15 |
| LOVD is now also represented on Facebook: facebook.com/LeidenOpenVariationDatabase. If you are on Facebook, be sure to stop by, "Like" us, and if you wish, leave a comment! |
| LOVD 3.0 beta 04 released |
Ivo Fokkema, 2012-04-25 |
Today, LOVD 3.0-beta-04 has been released. New features implemented, amongst others: Log entry listing under each user's detailed view; Several improvements to the automated mapping script; Added new custom columns; Updated some variant listings; Improved DBID predicting.
Bugs fixed, amongst others: Fixed various bugs in the VCF and SeattleSeq import features, and the automatic mapper script; Fixed problem with submission email when the submitter had more than one email address filled in; Fixed wrong number of variants in the individuals listing; Fixed problem with viewing Variants On Transcript detailed views; Fixed two XSS security issues; Fixed problem with searching in Owner fields.
See the changelog.
Download the new build. |
| Final report on student project NGS data |
Ivo Fokkema, 2012-04-17 |
| This week, our bioinformatics student Jerry Hoogenboom, finished his 5 month internship in the LOVD 3.0 team. His project report, titled "Importing Next Generation Sequencing Data in LOVD 3.0", and also the project's poster, are put online with his permission. We're very glad with his work, which introduced VCF and SeattleSeq annotated file import in LOVD 3.0. Thanks, Jerry! |
| LOVD 3.0 beta 03 released |
Ivo Fokkema, 2012-03-28 |
Today, LOVD 3.0-beta-03 has been released. New features implemented, amongst others: Improved messages when a viewList does not return any entries; Added option for mapping a variant to any transcript on the same chromosome; Added "imprinting" field to genes; Custom columns can now be deleted, if they are inactive; ViewLists can now have checkboxes allowing specific actions on only some entries; Variants can now be confirmed by other screenings of the same individual; Added the option to import VCF files and SeattleSeq annotated files; Variants on genomic level can be mapped automatically to genes and transcripts; Added an option to search for a variant in other LOVD databases.
Bugs fixed, amongst others: Fixed sorting problems on some viewLists; LOVD can now connect through a proxy server; Fixed problem editing or enabling custom columns on some MySQL settings; Fixed authorization problem for certain data for curators and submitters; Certain settings could not be enabled using the System Settings form; Fixed DB-ID prediction issues.
Closes #3, #8.
See the changelog.
Download the new build. |
| LOVD 3.0 beta 02 released |
Ivo Fokkema, 2012-02-09 |
Today, LOVD 3.0-beta-02 has been released. We have managed to get a lot of work done in the little time since beta-01, already worth a new release. LOVD 3.0 now requires PHP's libxml and mbstring extensions to be enabled.
New features implemented, amongst others: Searching should be faster now because of a database efficiency improvement; Improved the dropdown menu a bit; Improved the DBID value check and prediction.
Bugs fixed, amongst others: The installation process now checks for MultiViews or mod_rewrite (or something equivalent on non-Apache servers) and mod_rewrite support was improved; Fixed problem with searching for empty values or negative (NOT) searching in the database; Fixed problem with data type wizard; Genes were not editable; Fixed some missing permission checks (there are still more to be fixed).
Closes #4.
See the changelog.
Download the new build. |
| LOVD 3.0 beta 01 released!!! |
Ivo Fokkema, 2012-01-31 |
LOVD v.3.0-beta-01 has been released! Although it's still not fully featured and completely free of bugs, but we feel comfortable inviting you to try it out.
LOVD 3.0 now requires MySQL version 4.1.2 and up.
New features implemented, amongst others: Implemented custom column edit; New submission mailing process; Implemented the DBID check & prediction; Added support for mitchondrial genes; The gene-specific full data view now also shows the individuals' disease(s). Bugs fixed, amongst others: Fixed warning during LOVD install; Fixed problem with loading time variant forms; Fixed problem with password reset feature; Fixed problem when trying to create a selection list custom column.
Closes #6.
See the changelog.
Download the new build. |
| LOVD 3.0 alpha 07 released |
Ivo Fokkema, 2011-12-14 |
Today, LOVD 3.0-alpha-07 has been released. New features implemented, amongst others: Improved data views by improving /variants/GENE and implementing /view/GENE; Improved linking between data views; Implemented a /transcripts/NM_ID URL; Added the "Affects function" field (LOVD 2.0 called this "Pathogenicity"); Added support for editing a variant that affects transcripts of more than one gene. Bugs fixed, amongst others: The disease tab was linking to the wrong page when a gene was selected; Fixed issues with value checking in DECIMAL, INT and DATETIME type columns; Values of checkbox custom columns were not stored in the database.
See the changelog.
Download the new build. |
| LOVD 3.0 alpha 06 released |
Ivo Fokkema, 2011-11-18 |
Today, LOVD 3.0-alpha-06 has been released. New features implemented, amongst others: Added gene-specific page header when appropiate; When gene has been selected, the tabs lead to gene-specific pages automatically; Improvements to the PDO wrapper; Improvements to Variant viewList; Built in various security measures; Curators are now emailed after a successful data submission; Variants on transcripts can now be edited. Bugs fixed, amongst others: Problem with variants on X or Y chromosome in the Mutalyzer Syntax Checker; Fixed problem with the menu that IE users might have had; Fixed issues with viewLists; Fixed some notices; Fixed problem in password checking on some data entry forms.
See the changelog.
Download the new build. |
| Johan den Dunnen receives HGVS award |
Ivo Fokkema, 2011-10-28 |
 During the recent HGVS meeting in Montreal, Canada, which was a sattelite meeting of the ICHG/ASHG 2011 meeting, Johan den Dunnen received the HGVS award for his work in the field of human genome variation in general, and more specifically for "the establishment of international mutation nomenclature standards and to celebrate the 1000th download of the LOVD software".
According to Johan, as stated on the award, the whole LOVD team is honoured through this award. "Although I received the award, I believe the honour is for the entire LOVD team, especially Ivo Fokkema, my right hand from day 1 on this project". When we just checked LOVD has now already been downloaded more than 2000 times!
To see a bigger picture of the award, click the small picture. |
| LOVD 3.0 alpha 05 released |
Ivo Fokkema, 2011-10-18 |
Today, LOVD 3.0-alpha-05 has been released. New features implemented, amongst others: Users can now register themselves as submitters; During submission you can check the HGVS syntax of the variants and map them to the genome or other transcripts; Improved the way LOVD sends email; Improved advanced searching; Improved some of the internal works of LOVD. Bugs fixed, amongst others: Fixed minor error messages during user delete and individual create or when working in PHP's safe mode.
See the changelog.
Download the new build. |
| LOVD 3.0 alpha 04 released |
Ivo Fokkema, 2011-09-02 |
Today, LOVD 3.0-alpha-04 has been released. New features implemented, amongst others: Added more and better ways of viewing data and improved navigation from data type to data type; Started changes to make LOVD communicate with the database backend through PDO (requires PHP >= 5.1.0); Added dropdown menu to all menu tabs (proper tab highlight will follow); Added JQuery Javascript framework; Implemented full submission workflow. Bugs fixed, amongst others: Fixed password reset feature; Fixed drag and drop sorting issues and other Javascript related problems in Internet Explorer; Fixed memory leak problem in genes.php and transcripts.php permanently.
Closes #1.
See the changelog.
Download the new build. |
| LOVD 3.0 alpha 03 released |
Ivo Fokkema, 2011-08-03 |
Today, LOVD 3.0-alpha-03 has been released. New features implemented, amongst others: Curators can sort the list of curators for their genes; Implemented lovd_isAuthorized() for checking a user's authorization for different data types; Added various navigation links for curators to configure their gene database; Various code optimizations; Links to OMIM are now to OMIM.org; Columns can now be re-ordered; Implemented tooltips for custom links in the viewLists. Bugs fixed, amongst others: Fixed various issues with the curator/collaborator selection script; Fixed problem with simple drop down list custom columns; Fixed various typos; Fixed improper checks on data entry's status and owner; All custom columns can now be removed properly; Variants can be linked to a screening again; Fixed user level display in users viewList.
See the changelog.
Download the new build. |
| LOVD 3.0 alpha 02 released |
Ivo Fokkema, 2011-07-05 |
Today, LOVD 3.0-alpha-02 has been released. New features implemented, amongst others: Phenotype handling (create, edit, delete), improved settings of various viewlists, added some new icons, added more screening methods, prepared database for handling of panels (group of individuals), improved security in password handling. Bugs fixed, amongst others: Mail problems on Windows, memory leak in create genes form, fixed order of custom columns, custom columns can now be removed, problem with searching on date columns, list of collaborators and hidden curators should only be visible from collaborator level.
See the changelog.
Download the new build. |
| LOVD 3.0 alpha 01 released!!! |
Ivo Fokkema, 2011-05-26 |
LOVD v.3.0-alpha-01 has been released! You can now try out LOVD 3.0 and see how it looks. I would like to stress that this is alpha software, so do not expect everything to work correctly. Actually, there is a long list of issues that we know are present in this release.
From now on, we will be releasing updates to LOVD 3.0 monthly.
If you would like to try LOVD 3.0, check out this version online or download the first release! |
News older than 12 months can be found in the archive.
| Last modified 2012/05/16 18:00:23 CEST |
When using or discussing LOVD please refer to:
Fokkema IF, Taschner PE, Schaafsma GC, Celli J, Laros JF, den Dunnen JT (2011). LOVD v.2.0: the next generation in gene variant databases.
Hum Mutat. 2011 May;32(5):557-63.
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