LOVD 3.0 News - Archived news

More recent news can be found in the current news.

LOVD proposing to share variant effect through APIs Ivo Fokkema, 2017-01-20
The following message has been sent last week to all LOVD curators known to us. So far, we only got positive replies! If you have any comments on our proposed update on sharing variant effect in LOVDs, please let us know!

Dear LOVD Curators,

Times are changing, also for LOVD. In this mail, sent to all registered curators we have on record, we would like to mention some of the latest developments and, IMPORTANT TO NOTE FOR YOU, to ask for your permission to proceed with these plans. We will repeat this request in 2-3 weeks and when you then do not reply within 2 weeks we will assume you have no objection. Important to note that also after this date you, as owner of the data you have submitted, can still change your mind and grant or withdraw permission.

While initially genes were studied one at a time, the standard now quickly develops towards gene panel, whole exome and whole genome sequencing. As a consequence, while our databases were initially used to check existing knowledge on one or a few variants per gene, users now want to check hundreds to thousands of variants. Although we built an automated tool for this, LOVD's API, this tool currently only answers the question "is this variant known in an LOVD database". Helpful, but the essential information missing is the reported classification of the variant; does the variant affect the function of the gene/protein and is it associated with a phenotype? This information is not shared because we did not yet ask your permission to do so. With this mail we now ask your permission.

      LOVD will start to share variant classification

When you do not agree with this policy, please let us know as soon as possible. Please note that the classification is already publicly available using the LOVD website. What will change, is that we will start to share this automatically using LOVD's API. This allows people to annotate variants automatically without having to go to the website and look. You can imagine that this will greatly facilitate data analysis for all our users, including yourself.

LOVD's API has a "fair use policy". Our servers have a limited capacity and will not be able to cope with the demand of many users that would all like to annotate variants from whole exome or even full genome sequencing. We have been approached by several parties with the request to share, on a regular basis, a copy of the data that is available in the API. There are two reasons for this; 1) the fair use policy, 2) privacy issues. LOVD has started to share this information but charges a fee for the service provided. We will use these fees to keep LOVD alive and further extend the possibilities offered. We are in the process of establishing an oversight committee (in collaboration with the Human Variome Project) that will annually review our work and the way we spend any income from these services.

When you see any problems with these developments, please let us know.

Best regards,
Johan den Dunnen
Ivo Fokkema
LOVD-team

LOVD 3.0 build 18 released Ivo Fokkema, 2016-12-23
Today, LOVD 3.0 build 18 has been released. New features implemented, amongst others: The LOVD header now will stick to the top of the browser's viewport, such that the links in the header are always visible; LOVD now includes a submission API, that can take VarioML formatted JSON data and convert this into an LOVD3 import file (not yet documented); When a Database administrator creates a new user, the level now selected by default will be Submitter instead of Manager; When variants are imported without position fields or variant type filled in, LOVD will now predict them.
Bugs fixed, amongst others: The "Manage transcripts for this variant" feature didn't allow the removal of a transcript anymore; When a user needed to change the password, the force option didn't work properly, and could be circumvented; The variant effect fields didn't have a default value when importing; Variants that were imported with empty intron positions, didn't group together with variants that had a 0 filled in; LOVD3 is now compatible with the ONLY_FULL_GROUP_BY MySQL setting.
Closes #140 and #144.

See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-12
Manual version included: August 31st, 2016.

LOVD 3.0 build 17 patch 02 released Ivo Fokkema, 2016-09-27
We have released a patch due to two bugs introduced in the latest LOVD release. Custom columns could no longer be edited, and some data views had entries that couldn't be clicked.
To apply this patch, either:
  1. If you hadn't updated your LOVD installation yet, just download the latest build, which includes this fix, and update your installation. See the manual on how to update your LOVD installation.
  2. Otherwise, if you already updated your LOVD installation to the latest build before the publication of this new item, then either redownload the latest build, or download the patch (GZIPped TARball or ZIP archive) and extract the files in your LOVD folder.
  3. If you've downloaded the latest version after publication of this news item, then you already have this patch included in that download.
We apologize for the inconvenience.

LOVD 3.0 build 17 patch 01 released Ivo Fokkema, 2016-09-22
We have released a patch due to a bug introduced in the latest LOVD release. Custom links no longer functioned in most columns in custom data listings.
To apply this patch, either:
  1. If you hadn't updated your LOVD installation yet, just download the latest build, which includes this fix, and update your installation. See the manual on how to update your LOVD installation.
  2. Otherwise, if you already updated your LOVD installation to the latest build before the publication of this new item, then either redownload the latest build, or download the patch (GZIPped TARball or ZIP archive) and extract the files in your LOVD folder.
  3. If you've downloaded the latest version after publication of this news item, then you already have this patch included in that download.
We apologize for the inconvenience.

LOVD 3.0 build 17 released Ivo Fokkema, 2016-09-21
Today, LOVD 3.0 build 17 has been released. New features implemented, amongst others: Added a remarks field for transcripts, and tissues, features and remarks fields to diseases; Added the option to block submitter registrations; Added the option to create announcements within LOVD; Described these two new features in the manual, and added a new chapter "Updating LOVD"; The Find & Replace feature from LOVD2 has been improved and incorporated into LOVD3 (still in Beta, only on selected data listings, see the data listing's menu).
Bugs fixed, amongst others: Solved various problems with the new access sharing feature; Solved two problems with the update import feature; The proxy server settings were often ignored by LOVD, and proxy servers could not be used when using HTTPS, such as with Mutalyzer resources; For curators, editing a disease could result in a fatal error in some conditions; Fixed issue with creating genes with some database settings.
Closes #53, #61, #65, #67, #72, #77, #80, #87, #88, #101, #105, #109, #112, #121 and #124.

See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-12
Manual version included: August 31st, 2016.

LOVD 3.0 build 16 released Ivo Fokkema, 2016-06-24
Today, LOVD 3.0 build 16 has been released. New features implemented, amongst others: Clarified the IP address allow list feature and added more warnings about the risks of this feature; Added possibility for sharing access to one's data with others - one can make another user a 'colleague' and let them view (and optionally edit) their submissions.
Bugs fixed, amongst others: RNA prediction of a variant affecting splicing was incorrect; Fixed problem with the DBID generation; Fixed problem with the update import overwriting the Owned By field under certain conditions and with it throwing errors about fields that were not defined; Fixed problem with Mutalyzer providing unstable transcript IDs, which resulted in incorrect protein descriptions or false errors on the DNA variants.
Closes #51, #53, #66, #69 and #76.

See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-12
Manual version included: February 5th, 2016.

Loading large numbers of genes, transcripts and diseases into LOVD3 Ivo Fokkema, 2016-05-09
We would like to draw your attention to the LOVD3 Gene Loader, a tool developed to load large numbers of genes, transcripts and optionally diseases into an LOVD3 installation.
For more information, see the LOVD3 Gene Loader GitHub page. This tool downloads gene data from the HGNC automatically, discovers transcripts for the selected genes, and when data from OMIM has been obtained, it can insert diseases and links to the genes as well. It can optionally be restricted to a certain set of genes and/or transcripts.
For questions about the script, check the LOVD3 Gene Loader GitHub page or contact us if you can't find the answer to your question.

LOVD 3.0 build 15 released Ivo Fokkema, 2016-05-02
Today, LOVD 3.0 build 15 has been released. New features implemented, amongst others: Mitochondrial genes are now supported; The view 'Individuals screened for gene X' has been replaced by the view 'Individuals with variants in gene X'; LOVD now allows more transcripts to be stored; up to 16 million; The geneswitcher in the header is now an autocomplete field for large databases; Updated the manual; On data entry forms, the "Owner of this data" field now has the user's ID visible as well, to distinguish between two users with the same name; For each shared custom column, the list of genes or diseases that this column is active for, is now shown on the column's detailed view; Automatic filling of certain password fields in forms is now blocked, and the automatically filled in username will no longer cause issues; When assigning or changing the curators for a certain gene, the LOVD logs now contain information on the exact changes; Implemented a speed optimization in LOVD when showing data listings, which should speed up any data listing.
Bugs fixed, amongst others: When a new transcript was created, variants from other chromosomes were selected to be remapped as well; Lowered spam score of emails sent out by LOVD; Fixed several issues with the importer; Variant counts on the gene homepage were counted using the gene's first transcript only; Fixed some missing and incorrect links in the tab dropdown menus.
Closes #6, #7, #9, #17, #25, #26, #27, #29, #39, #42, #43, #52 and #54.

See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-12
Manual version included: February 5th, 2016.

Moved to GitHub Ivo Fokkema, 2016-01-26
Our code respository has been moved from our own SVN server to the GitHub service, to make it easier for others to collaborate on improving LOVD as well as to increase our visibility to the open source community in general. We will also be using GitHub as our major bug tracker.

LOVD 3.0 build 14 patch 01 released Ivo Fokkema, 2015-10-19
We have released a patch due to a bug introduced in the latest LOVD release. The diseases detailed view showed a query error.
Closes #41.
To apply this patch, either:
  1. If you hadn't updated your LOVD installation yet, just download the latest build, which includes this fix, and update your installation. See the manual on how to update your LOVD installation.
  2. Otherwise, if you already updated your LOVD installation to the latest build before the publication of this new item, then either redownload the latest build, or download the patch (GZIPped TARball or ZIP archive) and extract the files in your LOVD folder.
  3. If you've downloaded the latest version after publication of this news item, then you already have this patch included in that download.
We apologize for the inconvenience.

LOVD 3.0 build 14 released Ivo Fokkema, 2015-10-09
Today, LOVD 3.0 build 14 has been released. New features implemented, amongst others: Curators can now simulate the import of an LOVD tab-delimited file; Several speed improvements of views and the import function; Major update to gene-specific graph page; The unique variant view is now available - when the variant tab is selected, only unique variants are displayed now; Updating entries via an import file is now available (still in beta); Added support for hg38 for new LOVD3 installations only, and it is also the new default for new LOVD3 installations; Several other changes related to the genome builds.
Bugs fixed, amongst others: Fixed several bugs in the import function; Fixed problem when LOVD is behind a proxy communicating over HTTPS; When creating a download file, filters applied would sometimes overwrite previously set filters, for instance causing the gene-specific download to sometimes not contain all related diseases; When downloading variant data, the given Variant_On_Transcripts effectid had been overwritten in the file by the Variants_On_Genome effectid; When gene symbols with wrong capitalization are used in URLs, some features and pages caused errors; Fixed several bugs related to the new genome build.

See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-12
Manual version included: July 31st, 2015.

LOVD 3.0 build 13 released Ivo Fokkema, 2015-03-23
Today, LOVD 3.0 build 13 has been released. New features implemented, amongst others: Updated the manual by adding a new chapter about adding data and improving the manual in various other chapters; Data entry forms are extended with the fields' legend texts; Improved the submission process by adding a possibility to return to a screening during submission; Improved data import in various ways, more files are supported and and import speed is improved; Improved the way a new disease can be created through the individual and gene data entry forms.
Bugs fixed, amongst others: Given parent IDs were not properly checked during import; Importing a file with phenotype or screening data without a given individual ID caused a fatal error instead of an error message; Fixed problems with spaces in the LOVD installation path; When genes overlap, the protein change prediction predicted by the variant mapper was sometimes incorrect; Diseases could not be linked to a big number of genes (hundreds); The ORCID integration during user registration had to be updated due to a discontinued service; The gene-specific page for listing individuals sometimes showed individuals screened for other genes.

See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-12
Manual version included: March 19th, 2015.

LOVD 3.0 build 12 released Ivo Fokkema, 2014-10-09
Today, LOVD 3.0 build 12 has been released. This fixes an important issue that new LOVD 3.0-11 installations have with the updated Mutalyzer webservice, such as the inability to create genes. Installations upgraded to 3.0-11 from previous versions, should not have this problem.
New features implemented, amongst others: The Gene homepage now shows a link to PubMed, showing articles linked to the gene; Improved the speed of the update checker; Updated the country list.
Bugs fixed, amongst others: When manually mapping a variant to a transcript, transcripts on the reverse strand did not display the correctly calculated distance; Some numbers on the Gene homepage were not displayed correctly (non-public variants, individuals with public variants); The SeattleSeq importer caused errors due to the recent changes to the Mutalyzer interface; The reference sequence parser couldn't download files from Mutalyzer anymore due to their recent server update; New LOVD 3.0-11 installations didn't connect to the correct Mutalyzer webservice, whereas installations upgraded from 3.0-10, did.
Closes #35.

See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-12
Manual version included: May 6th, 2014.

LOVD 3.0 build 11 released Ivo Fokkema, 2014-08-07
Today, LOVD 3.0 build 11 has been released. It is critical that you update your LOVD installation to this version, as one month from now, Mutalyzer will release an update, that removes the communication method we have been using so far. In order to keep a fully functional LOVD, you need to update your LOVD installation before September, 2014.
New features implemented, amongst others: Added "Not classified" as a value for the variant effect option list, which is selected by default; Added navigation to the full disease list from the individuals data entry form, in installations with many diseases configured; Improved the LOVD Reference Sequence Parser: you can now choose wich genomic reference sequence file is used; Restyled the Configuration area and included the names and email addresses of the managers of the LOVD installation; Rewrote all communication with Mutalyzer to the new standard, which will be required starting from the next Mutalyzer release, planned in September 2014.
Bugs fixed, amongst others: DB-IDs for genes containing a hyphen followed by a number, were rejected by LOVD; Due to changes in the ORCID API you could no longer register using an ORCID ID; Variants with many genes associated with it could not be edited; The variant mapper sometimes did not return any RNA or Protein prediction; Due to the HGNC changing their REST webservice output format, there were problems with creating multiple genes starting from Thursday, July 31th.

See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-11
Manual version included: May 6th, 2014.

LOVD 3.0 build 10 patch 20140806 released Ivo Fokkema, 2014-08-06
We have released a patch due to the recent change in the output of the HGNC webservice, that caused problems with creating genes.

To apply this patch:
First, make sure your LOVD installation is up to date (version LOVD 3.0-10). See the manual on how to update your LOVD installation.
Then, download the patch (GZIPped TARball or ZIP archive) and extract the files in your LOVD folder.

LOVD 3.0 build 10 released Ivo Fokkema, 2014-04-28
Today, LOVD 3.0 build 10 has been released. New features implemented, amongst others: Added a chapter on the LOVD API to the manual; Sped up the SeattleSeq import by preventing unnecessary Mutalyzer webservice calls; Improved the protein description prediction for the SeattleSeq import format; The owned_by and statusid fields are no longer mandatory while importing; More information is shown when viewing your own account page.
Bugs fixed, amongst others: The API didn't return a proper date of last update; The "Individuals" and "Phenotypes" columns in the Disease listing were not handled as numeric columns by LOVD; Fixed problem with links to the collaborators shown on the gene homepage; The VOG and Genes tables could not be sorted on the chromosome field; Collaborators lost authorization when dynamically reloading a data view, by searching, sorting or navigating the view.

See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-beta-11
Manual version included: January 16th, 2014.

LOVD 3.0 build 09 released Ivo Fokkema, 2014-01-13
Today, LOVD 3.0 build 09 has been released. New features implemented, amongst others: The variant checker (protein predictor) using the Mutalyzer services can now also work with an NG reference sequence; Improved views for diseases associated with many genes; From the "Your account" link in the top right-hand side of the screen, links are provided to view the data owned by you; Improved the speed of the variant overview on the Screenings or Individuals detailed pages.
Bugs fixed, amongst others: Fixed errors showing up when editing variants under certain conditions; LOVD was uninstallable on MySQL 5.6 due to a changed variable we use to check a mandatory setting; Fixed issue with created genes caused by a change on the HGNC website.
Closes #26.

See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-beta-11
Manual version included: September 3rd, 2013.

LOVD 3.0 build 08 released Ivo Fokkema, 2013-10-16
Today, LOVD 3.0 build 08 has been released. New features implemented, amongst others: Applied speed improvements to the disease list, and the numbers of related entries on the genes and disease lists now also include non-public entries for authorized users; When managing the transcripts for a certain variant, the distance between the variant and the transcripts are now shown; LOVD can now fetch the average variant frequency of any variant in the database from various studies and populations, which can then be viewed in the variant's detailed view, including a link for a detailed view; IDs in the logs recognized by LOVD are now turned into links, allowing quick navigation.
Bugs fixed, amongst others: Importing is no longer restricted in time by PHP; Users with special characters in their name could sometimes not receive email from LOVD; The StopForumSpam check at user registration could not deal with multiple email addresses per user; Custom links could not be assigned to all custom columns when the number of columns had increased to large numbers; When directly publishing a variant, the DBID assigned to it was ignoring the mapping to any transcripts; Whenever a variant is not recognized because it's not correct HGVS syntax, it couldn't be manually mapped to a different transcript; For large gene databases, the gene homepages showed an incorrect number for individuals with public variants; Quick-curating entries sometimes triggered an incorrect error.

See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-beta-11
Manual version included: September 3rd, 2013.

LOVD variant track in the UCSC genome browser Ivo Fokkema, 2013-08-19
The UCSC genome browser now contains the LOVD variant track, listed under "Phenotype and Disease Associations". It provides access to more than 150.000 unique variants stored in public LOVDs, with curated disease associations.
Try it out: http://genome.ucsc.edu/cgi-bin/hgTracks

LOVD curators: To enable this feature, make sure the "Include in the global LOVD listing" setting is enabled in the LOVD system settings, and in case you're using LOVD2, that all reference sequences are configured properly. LOVD3 does this automatically.
All public LOVDs are listed here:
http://www.lovd.nl/3.0/public_list.

LOVD 3.0 build 07 released Ivo Fokkema, 2013-08-15
Today, LOVD 3.0 build 07 has been released. New features implemented, amongst others: Added chapters to the manual on downloading & importing data, data security and troubleshooting and added additional sections to the chapter on custom columns; All age fields now also support shorter input formats; The individuals view and the gene-specific full data view now allow sorting on the disease column as well; From a variant detailed view, you can now easily view all reports for that variant; Submitters can now also see their non-public data in the gene-specific variant views.
Bugs fixed, amongst others: Fixed error in explanation on data listing which can't be sorted because it's too slow; Data owners had an option in the menu to publish their data themselves, and clicking this resulted in an unclear error message; Searching full-match on text including an underscore didn't return the expected results; Fixed problem with variant position offset in Ensembl genome browser; The welcome email for a new user who was created by another user contained an incorrect link to the user's account page.
Closes #23.

See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-beta-11
Manual version included: August 15th, 2013.

LOVD 3.0 build 06 released Ivo Fokkema, 2013-06-28
Today, LOVD 3.0 build 06 has been released. New features implemented, amongst others: LOVD3 now requires PHP/5.3.0; The variant listings below individual and screenings detailed views now also show the variant's effect on transcript level; Added several sections to the custom column chapter in the manual; A disease-specific phenotypes listing is now available from the disease detailed view.
Bugs fixed, amongst others: Removed links to user account pages when these are not viewable, and opened up the user account pages for those who should be able to see them; When removing custom columns, sometimes the number of values reported to be lost was wrong; Curators can now again remove phenotype columns that still contain values; The gene-specific overviews (variants and full data view) were not showing some non-public columns to curators due to a overly strict security check; Through certain manipulations, collaborators and curators would be able to see (not edit) non-public data of genes they had no authorization for.
Closes #18.

See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-beta-11
Manual version included: April 16th, 2013.

Please re-download 3.0 build 05 Ivo Fokkema, 2013-05-31
We just noticed that an error has occurred while packaging release LOVD 3.0 build 05 yesterday. The file individuals.php was overwritten by an incomplete version. There have been a few downloads already, please re-download LOVD 3.0 build 05 if you had already downloaded it. The files currently on the download page is the correct release.
If you are using the SVN repository, you do not need to do anything; the version uploaded to the repository yesterday did not contain the error.
Our apologies for the inconvenience.

LOVD 3.0 build 05 released Ivo Fokkema, 2013-05-30
Today, LOVD 3.0 build 05 has been released. New features implemented, amongst others: Variants can now be imported without specifying the DBID; Improved error message during import when not specifying a field's value correctly; Custom columns can now also be imported using the LOVD3 import format; The detailed view of an individual entry now shows links to the parents when they are in the database as well; The list of diseases now shows the number of individuals in the database having those diseases.
Bugs fixed, amongst others: Fixed a problem with quoted data and some minor issues with the import script; Fixed various problems with the data listing navigation.

See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-beta-11
Manual version included: April 16th, 2013.

LOVD receives status of HVP Recommended System Ivo Fokkema, 2013-05-29
HVP Recommended System Last week, LOVD was given the status of HVP Recommended System by the International Scientific Advisory Committee of the Human Variome Project. It was the first time that such a recommendation was issued. Alongside with LOVD, the HGVS sequence variant nomenclature received the same status.
This makes LOVD the first software project to become a recommended system of the Human Variome Project.
Currently still under review to become a recommended system as well is the Mutalyzer software package, which provides a collection of tools aimed at checking or generating the HGVS sequence variant nomenclature.
LOVD and Mutalyzer together integrate to ensure the quality of sequence variants stored in LOVD instances.
More information about HVP Recommended Systems.

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
Nice LOVD3 cakes! The LOVD3 sweater 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.

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
The HGVS award received by Johan den Dunnen 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!

Progress of LOVD 3.0 development Ivo Fokkema, 2011-01-05
Since December, we have a new team member working full time on the LOVD 3.0 development. As such, we are proceeding quite rapidly now. Our test versions do require a bit more work to be useful to users, but if you'd like to take a look at what LOVD 3.0 looks like right now, please contact us and we'll explain you how to get to our SVN repository.
For more information on what will change in LOVD 3.0 versus LOVD 2.0, please visit the Frequently Asked Questions (FAQ).

Website opened Ivo Fokkema, 2010-05-19
The website of LOVD 3.0 has been opened, almost 4 years after we opened the website for LOVD 2.0. There is no download or screenshots available yet, but you can expect some screenshots in the future before release. We are working hard on the software, but a first release will take at least 6 more months, so please be patient! More information on what will change in LOVD 3.0 versus LOVD 2.0, please visit the Frequently Asked Questions (FAQ).

Announcing LOVD 3.0 Ivo Fokkema, 2009-10-29
We would like to announce that the development has started of a new LOVD branch, LOVD 3.0. In the last year, we have refined the data model, which allows for more flexibility in data storage and data sharing. The look and feel of the system will not change too much; however the way data can be viewed will change according to the new data model.

Because the focus in development will move somewhat, releases of LOVD 2.0 will not be as frequent as normal.

Last modified 2018/03/21 04:43:07 CET

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.

A recommended system of the Human Variome Project LOVD has received funding from the European Community's Seventh Framework Programme
(FP7/2007-2013) under grant agreement nº 200754 - the GEN2PHEN project.
©2004-2018 Leiden University Medical Center, Netherlands
Ivo F.A.C. Fokkema BSc., Prof. Johan T. den Dunnen PhD