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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 build 04 released |
Ivo Fokkema, 2013-04-18 |
Today, LOVD 3.0 build 04 has been released. New features implemented, amongst others: Updated the manual; Custom columns can now be downloaded; Import script now has a "simulate" mode; Added an custom column and updated one other.
Bugs fixed, amongst others: Fixed possible password issue directly after registering; LOVD could match the wrong NG reference sequence; Fixed issue with selecting the correct gene in the configuration area; Fixed problem with disabling a VariantOnTranscript column; When changing the order of curators, the changes were applied system wide.
See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-beta-11
Manual version included: April 16th, 2013. |
| LOVD 3.0 build 03 released |
Ivo Fokkema, 2013-03-06 |
Today, LOVD 3.0 build 03 has been released. New features implemented, amongst others: Updated the manual; Improved support for large import files; Multiple speed improvements: HGVS syntax check, variant mapper and all views affected by large data sets.
Bugs fixed, amongst others: The public could not see any contents in VariantOnTranscript fields in the "View all variants affecting transcripts" custom viewlist; Fixed some issues occurring with large LOVD installations (~22.000 genes).
See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-beta-11
Manual version included: February 20th, 2013. |
| Opening the LOVD3 support forum |
Ivo Fokkema, 2013-02-27 |
Today we installed a forum integrated into our Trac developers environment, where LOVD3 users can ask questions or suggest and discuss improvements. Registration is necessary to post, to protect us from spam submissions, but of course no registration is required for reading the forums. We will be inserting some common questions we get, and the respective answers, to help our users find answers faster, and to allow community discussion. All users are strongly encouraged to use the forum for asking questions, since others may have the same question!
There are currently three forums: LOVD3 support, LOVD3 suggestions, and LOVD3 announcements.
https://humgenprojects.lumc.nl/trac/LOVD3/discussion |
| Celebrating 10 years of LOVD (2) |
Ivo Fokkema, 2013-02-04 |
Once a month, we have a joint morning coffee break of the entire Human Genetics department at the Leiden University Medical Center. This time we had nice small LOVD3 cakes celebrating the LOVD3 release and the 10th anniversary of LOVD. Johan den Dunnen named a few of LOVD's main successes over the last 10 years and LOVD's main developer Ivo Fokkema got a nice gift: a sweater with the LOVD3 logo and the text "LOVD's main brain", which he claims to wear with great pride. |
| LOVD 3.0 build 02 released |
Ivo Fokkema, 2013-01-30 |
Today, LOVD 3.0 build 02 has been released. New features implemented, amongst others: Several improvements to the download options such as a gene-specific download option; Improved the menus; Improved custom column removal; Implemented the "Empty gene database" feature; dbSNP IDs in the special dbSNP field are now links.
Bugs fixed, amongst others: Fixed numeric reference to user in emails sent out when screenings had been edited; The "Download selected entries" option failed; Fixed issue with created genes caused by a change on the HGNC website.
See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-beta-11
Manual version included: November 19th, 2012. |
| Power failure affecting chromium.liacs.nl server |
Ivo Fokkema, 2013-01-14 |
Due to a major power failure this morning at the Leiden University and Leiden University Medical Center, one of our LOVD servers (chromium.liacs.nl) is only responding to its IP address 132.229.137.16. So you can find the LOVD databases for instance on:
http://132.229.137.16/LOVD2/colon_cancer/
instead of:
http://chromium.liacs.nl/LOVD2/colon_cancer/
This is a temporary problem that we hope will be fixed soon.
Update 16:18 CET: Everything is fixed now, chromium.liacs.nl is up again! |
| LOVD 3.0 build 01 released!!! |
Ivo Fokkema, 2012-12-19 |
LOVD 3.0 build 01 has been released! After more than three years of hard work, LOVD 3.0 has now reached the stable phase. We believe LOVD 3.0 now is stable enough to be used in production environment. If you're interested in using LOVD 3.0, but rather not want to deal with installing it yourself on a server of your own, contact us! Our shared LOVD 3.0 installation, where 20 curators currently supervise 1744 genes with 16871 variants, is available to you.
Bugs fixed, amongst others: The variant type graphs analyzed an incorrect set of variants; Genes created when importing SeattleSeq files didn't get their Entrez Gene and OMIM IDs stored; Fixed multiple problems with MySQL's strict mode; Fixed several issues with the variant mapper.
See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-beta-11
Manual version included: November 19th, 2012. |
| LOVD 3.0 beta 12 (RC2) released |
Ivo Fokkema, 2012-12-10 |
Today, LOVD 3.0-beta-12 (Release Candidate 2) has been released. There will be no significant changes to the code anymore until the first stable release of LOVD3. New features implemented, amongst others: The gene-specific data listings now also mention the data owner just like most other data listings; Modified LOVD scripts to accept changed warning codes from Mutalyzer; When mapping variants, LOVD now also predicts the RNA field.
Bugs fixed: Importing data didn't work anymore since it was asking for the password to be provided for every entry; Individuals without any diseases selected could not be published using the quick curate option.
See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-beta-11
Manual version included: November 19th, 2012. |
| LOVD 3.0 beta 11 (RC1) released |
Ivo Fokkema, 2012-12-03 |
Today, LOVD 3.0-beta-11 (Release Candidate 1) has been released. There will be no significant changes to the code anymore until the first stable release of LOVD3. New features implemented, amongst others: Added spam protection to the submitter registration form using the StopForumSpam.com API; Added support for XR reference sequences; Added color coding and a quick-publish (curate) option to the detailed views of entries that have a status; Added the current LOVD 3.0 manual, which is still work in progress; Added short and full legend from data listings - move the mouse cursor over a column's header, or click on the help icon to open the full legend.
Bugs fixed, amongst others: Fixed some minor issues with the "Sort curators" page; Fixed possible query error and notices in the import script; Fixed some issues with the emails sent after data submission.
See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-beta-11
Manual version included: November 19th, 2012. |
| Gene Variant Database (LSDB) course using LOVD |
Ivo Fokkema, 2012-11-22 |
| On December 18th 2012, a gene variant database (LSDB) curation course using LOVD will take place in London, UK. See the Gen2Phen website for more information. |
| LOVD 3.0 beta 10 released |
Ivo Fokkema, 2012-11-13 |
Today, LOVD 3.0-beta-10 has been released. New features implemented, amongst others: Added basic ORCID ID integration in the submitter registration form; When creating a user account, you can have the account details mailed to him/her; Added support for non-coding genes with NR transcript reference sequences; Updated jQuery library; Added links to the HGVS nomenclature rules from the submission form; Adding, editing or deleting a variant now also affects the gene's "Updated" timestamp; Implemented an RESTful API with equal input and output as the LOVD 2.0 API; Added links from the gene homepages to the major genome browsers, using LOVD's BED file output track.
Bugs fixed, amongst others: Many fixes in the import script; Fixed problem with the DBID prediction; Fixed query error when mapping an unrecognized variant to a transcript.
See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-beta-10 |
| Celebrating 10 years of LOVD |
Ivo Fokkema, 2012-11-01 |
We're celebrating 10 years of LOVD! Today 10 years ago, we laid out the foundation of what was to become LOVD. Back then, LOVD was developed for running the databases of the Leiden Muscular Dystrophy pages, and was as a not-so-modular system with lots of characteristics specific for that website only. Now, LOVD is the world's most popular LSDB with users all over the world.
A special thank you to all our users, especially those who helped by sending us suggestions, bug reports, code changes, positive or even negative feedback. Without you, we wouldn't have gotten anywhere. |
| LOVD 3.0 beta 09 released |
Ivo Fokkema, 2012-10-11 |
Today, LOVD 3.0-beta-09 has been released. New features implemented, amongst others: Improved the display of diseases without abbreviations; Added support for SQL strict mode; Implemented first version (alpha) of the data import feature - this requires a new format compared to LOVD 2.0, that can be obtained by making a full data download from the LOVD setup area. Currently implemented is an "insert all" mode that regards any data in the file as new, and tries to import it.
Bugs fixed, amongst others: Fixed problem during installation of LOVD 3.0-beta-08; Curators of many genes didn't have an overview of all genes curated on their account page; Fixed problem with download format; The owner of a screening could not be changed by editing the field.
Closes #17.
See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-beta-08 |
| LOVD 3.0 beta 08 released |
Ivo Fokkema, 2012-09-05 |
Today, LOVD 3.0-beta-08 has been released. New features implemented, amongst others: Added the quick gene switcher on the top of the page; Implemented the gene-specific page header & footer; Proxy servers requiring basic authentication are now also supported; Updated the whole submission workflow; Submitters can continue previously unfinished submissions; Added color highlighting based on the status on the data listings; Updated all menu's on data's detailed listings to the newer dropdown format; Curators can now also create, edit or delete diseases; LOVD will send out emails also when data has been edited.
Bugs fixed, amongst others: Submitters and curators had trouble editing their own data; Curators couldn't delete their own data.
See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-beta-08 |
| LOVD 3.0 beta 07 released |
Ivo Fokkema, 2012-07-26 |
Today, LOVD 3.0-beta-07 has been released. New features implemented, amongst others: Added the LOVD Reference Sequence Parser script; Added support for gene aliases while creating new genes; Improved the full download format; Added the LOVD Configuration area; Added possibility of marking individuals als healthy controls; Reviewed and improved descriptions of virtually all custom columns; Added new custom column: Phenotype/Additional.
Bugs fixed, amongst others: Fixed problems with Internet Explorer 7 and authorizing curators or and the Mutalyzer tools on the variant data entry form; Fixed some possible Javascript errors on the variant entry forms; Some fields that should have be hidden based on the user's level, are now actually hidden.
Also changed: Submitters are no longer allowed to add submissions without adding individual data also.
See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-beta-07 |
| LOVD 3.0 beta 06 released |
Ivo Fokkema, 2012-06-22 |
Today, LOVD 3.0-beta-06 has been released. New features implemented, amongst others: Added easy way to manage phenotype columns from the disease detailed view; Added new custom columns: Individual/Age_of_death, Individual/Death/Cause, Phenotype/Age and Phenotype/Length; Made some improvements when importing VCF files; Added link to genome browsers from the variant detailed view; Added first version of full data download; Added some graphs on the LOVD status page and added a page with graphs about a gene's data; Added the protein change prediction option on variant data entry forms.
Bugs fixed, amongst others: Fixed missing data when importing SeattleSeq annotated files; Fixed several problems handling the Mutalyzer webservice; Fixed some problems handling DECIMAL database fields; Fixed problems with JavaScript redirects in Internet Explorer; Fixed problems with submissions for submitters and curators.
Closes #14.
See the changelog.
Download the new build. |
News older than 12 months can be found in the archive.
| Last modified 2013/04/18 16:47:25 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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