Lovd Setup

Modules

Available LOVD modules

These are the modules included with LOVD. Of each of the modules, the functionality is described in detail.

Mutalyzer module

The Mutalyzer software was developed to guide researchers in using the correct HGVS nomenclature for their variants. LOVD helps by connecting to the Mutalyzer module from the submitter form, to allow both submitters and curators to check their nomenclature.

For Mutalyzer to work correctly, a GenBank file is necessary.
You can upload one through the Mutalyzer GenBank uploader or even have Mutalyzer generate one for you, after which you can configure LOVD to use the Mutalyzer GenBank ID by editing the gene's settings.
You can also upload a GenBank file to LOVD, after which it can be used by the Mutalyzer module and for the LOVD Reference Sequence parser.

Using the Mutalyzer module
Once the module is enabled, the variant submission form for every gene which has a GenBank file associated to it, will include a button "Check variant with Mutalyzer 1.0.4" directly below the "DNA change" field. Fill in a value in the "DNA change" field, and click the button. A new window will pop up, where the results of the query to the Mutalyzer service will appear.

Troubleshooting
Every day, Mutalyzer cleans up his GenBank file cache and removes all GenBank files which are older than one month. This implies that the link between Mutalyzer and your gene database in LOVD may be broken every month, and need to be re-established. This happens with either of the following two conditions:

You have a GenBank file uploaded to LOVD, or
You have uploaded a GenBank file into Mutalyzer, and have supplied LOVD with the generated Mutalyzer UD identifier

To fix this, do either of the following:

Don't download a GenBank file, but configure LOVD to use an official NCBI GenBank ID, or
Uninstall and reinstall the Mutalyzer module. Reinstallation may take some time, as the module is contacting Mutalyzer to generate new ID's for every gene's GenBank files. Remember that you'll have to do this once a month.

This problem will be fixed in a future version of Mutalyzer in which the GenBank file cache will be handled in a more efficient way.

ShowMaxDBID

This module is useful for curators, as it mentions the first free DBID value on the variant submission form and allows curators to quickly insert it into the DBID field. Do this by clicking the link "copy to field".

reCAPTCHA

This module is an implementation of a CAPTCHA functionality in the submitter registration form, used to block fake submitter registrations done by spambots or similar programs. CAPTCHA stands for "Completely Automated Public Turing test to tell Computers and Humans Apart". It is a technique nowadays used widespread over the internet to protect data entry forms, such as registration forms or contact forms, to be filled in by computers by presenting a question that is regarded currently not possible for a computer to answer. This could be a simple mathematical equation or, more often used, a distorted image that contains text.

This module is based on the reCAPTCHA project that is currently the recommended standard of the CAPTCHA method. It combines a CAPTCHA test with the digitalisation of books, by using the answers given by human beings using reCAPTCHA modules all over the world, to solve words which could not be digitized properly.

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