LOVD v.2.0 - Leiden Open Variation Database
Online gene-centered collection and display of DNA variants
|Please note that LOVD2 is no longer supported. The last security release is from October 2020. Upgrade to LOVD3 to continue receiving updates.
If your question is not in the list, please send your question to Ing. Ivo F.A.C. Fokkema at I.F.A.C.Fokkema@LUMC.nl.
What operating systems will the CD run on?
This CD runs on Windows 98 (some limitations), NT, 2000, 2003, XP and Vista (32 bit). The CD also requires a webbrowser, such as Mozilla Firefox, Safari, Google Chrome or Microsoft Internet Explorer.
What about Linux/Macintosh?
Mostly, users of Linux or Macintosh are more experienced computer users who are more likely to know how to install Apache, PHP and MySQL. We may still plan to release a Linux or Mac version, but we currently doubt the popularity of such a CD. If you feel differently, please let us know.
What do you mean, the CD is not recommended for production environments?
With production environments we mean an actual webserver that you will use to publish your LOVD installation to the world via the world wide web. The standard settings for Apache, PHP and MySQL on this CD may not be optimized for safety. Additionally, some LOVD security measures have been sacrificed on the CD to improve the easy of use. If you want to publish your LOVD on the web, have a local expert install and set up Apache, PHP, MySQL and a Mail Transfer Agent to make sure your installation is safe.
But I already have Apache, PHP and MySQL installed!
Great, in that case you don't need this CD! Just download LOVD without all the other software, extract it into your document root and follow the steps explained in the included INSTALL.txt file.
I have downloaded the file, but my computer however does not recognize the file type.
The file you downloaded is an ISO image, a file that is used to create CDs with. You will need to have CD burning software installed on your computer to convert the ISO image into an actual CD.
I have installed the CD. Now how do I start it?
There should be an LOVD icon on your desktop. If you can't find it, run:
I see LOVD on my screen. Now how do I log in?
The default username / password combination to get into the system is admin / admin.
Can I upgrade the LOVD version installed with this CD?
To upgrade an outdated LOVD that came with the Local install CD, just download the newest build from our website and overwrite all files in C:\xampp\htdocs\LOVDv.2.0\. After you log in, LOVD will upgrade itself to the latest build.
If you download a new LOVD Local install CD image, you can only install it after you remove the C:\xampp directory, which means you will lose all of your data in your LOVD installation.
Do all the features work like an LOVD installed on a server?
Most features are just the same. However, because the LOVD on your computer can not be reached by the internet by default, there are some features who do not work. Also, if you have a locally installed firewall blocking outgoing connections, some additional features may be affected.
Features not working using the local install CD:
In case a firewall is blocking outgoing connections:
- If you upload your own GenBank file in LOVD, the Mutalyzer nomenclature check will not work. Use a NCBI ID in stead of a local file or upload your GenBank file manually in Mutalyzer and fill in the Mutalyzer UD number to fix this.
- Your LOVD installation can not be listed on the list of public LOVDs on our website.
- The link to the UCSC genome browser doesn't work because the UCSC can't reach the BED file that your installation provides. Download the BED file (the link the UCSC tells you cannot be found) manually and upload it into the UCSC browser to circumvent this.
- LOVD cannot notify you of updates, and the icon on the bottom right-hand side of the screen indicates an error.
- LOVD cannot reach the Mutalyzer variant mapping service and therefore cannot map your variants to the genome. When creating or editing gene databases, errors may pop up about not being able to check the reference sequence, and links to the UCSC and NCBI viewers don't work.
I get this error on the screen: Error 404 - Not Found
This error message may also look like "The requested URL /LOVDv.2.0/account_login.php was not found on this server".
Look for a black window which name ends with "c:\xampp\apache_start.exe" - does it contain an error similar to "Could not bind to address 127.0.0.1:80"? In that case, there is already a webserver installed on your computer! If you don't need that webserver, remove it from your computer and try again. Otherwise, contact us.
I get this error on the screen: Access denied for user 'root'@'localhost' (using password: YES)
Look for a black window which name ends with "c:\xampp\mysql_start.exe" - does it contain an error similar to "Do you already have another mysqld server running on port: 3306"? In that case, you already have a MySQL database installed on your computer! If you don't need that MySQL installation, remove it from your computer and try again. Otherwise, contact us.
I get this error on the screen: Can't connect to MySQL server at 'localhost'
Look for a black window which name ends with "c:\xampp\mysql_start.exe" - does it contain an error similar to "Can't start server: can't create PID file: Permission denied"? In that case, the MySQL database was not closed properly the last time it was used. First close all of the LOVD services using the LOVD startup window, then go to this directory: C:\xampp\mysql\data\. Remove any files in the directoy which are ending in .pid, and restart the LOVD services using the icon on your desktop.
|Last modified 2014/08/25 14:48:36 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