WAVe

2010 begun with a new challenge: plan and develop, as fast as possible, a simple variant integration application based on DiseaseCard’s navigation concept. The idea was to reach GEN2PHEN’s goals with a new DiseaseCard-like application focused on integrating LSDBs (no one does it!) and variants contained in those LSDBs. Moreover, relevant gene-related information (pathways, proteins…) should be provided in the elegant navigation mechanism.

WAVe | Web Analysis of the Variome (version 1.0beta) is online and I consider it a success. There is plenty of room for improvements and new features which, I believe, will make WAVe a key application in GEN2PHEN.

Enough talking, WAVe is a variome integration application, focused on providing a centralized access to online available locus-specific databases and genomic variants. If you have any interest in life sciences you should visit at http://bioinformatics.ua.pt/WAVe. In case you really know something about genes, go directly to a  gene by providing its HGNC symbol: for instance, BRCA2 is at http://bioinformatics.ua.pt/WAVe/gene/BRCA2.

Feel free to give your comments/critics/opinions/suggestions, they are welcome! Comment here or send it to pdrlps@gmail.com!

WAVe

WAVe style 2

Yay! After many many many hours of web design, finally found a good-looking style to use in WAVe. Is almost everything done, except typography, autocomplete boxes and the tree!

Now it’s time to put everything in the Java application and start writing “the stuff”. (for “the stuff” I mean disclaimers, tutorials, help, content…)

WAVe 0.1: almost there!

I’m getting near version 0.1. In ideal conditions there is search, browsing, navigation… for all the genes… looking good so far!

The tree was almost finished today, time to add more and more features!

Houston, we have a Gene Tree!

There is a gene tree working on WAVe finally. Only missing the empty data types issue… I’ll try to correct it later… Content is only loaded in an iFrame also, it should be AJAX in a div, but for now it works!

Time for greater things: features, features, features! And a theme?

XmlCard Up

Today developed the algorithm for reading the tree for each gene… so many stuff to test (LSDB? no leafs? gene values or GeNS values? statis or dynamic?)

Therefore, XML card methods are done… and there is a lot of code to comment!!!

VarCrawler finito

Finally managed to finish the VarCrawler (sub)application for WAVe.

Deploy calls Creator and then Builder.

Creator for starting up and loading default values, Builder will read variants from all the web and load information from GeNS.

It is running now… for 6 hours and is at COLA63…

Back on builder

(Re)Started developing the variant reader. IDbases and other general databases are almost there. More on tomorrow!

MySQL is OK so far!

LSDB list final

Finalized the LSDB-Gene list with verification against IDBases, LOVD and UMD datbases.

Plenty more genes now (also removed lots of “dead” genes and other erroneous links! Sent it to Adam at Leicester… ask him to share with the world?

On other news, tomorrow time to migrate the system to MySQL!

Gene-LSDB list

Finished Stage 1 of the list containing LSDB and Gene relations. I won’t leave it like it is.
Next step will include careful verifications for each IDbases, UMD and LOVD (include version number) and a normalization of the list.

One file with all the lists will be easier to maintain.

Then, send it to Leicester.

DiseaseCard GeneCards Update

Updated DiseaseCard database to fit the new GeneCards link. And this was accomplished before UniProt!

(note: first post from MacJournal)