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, [...]
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…)
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!
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?
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!!!
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…
(Re)Started developing the variant reader. IDbases and other general databases are almost there. More on tomorrow!
MySQL is OK so far!
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!
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.
Finally finished LOVD importer based on their REST Atom Feeds API. It takes a long time to import everything and even more time to get the PubMed publications associated with each gene (only genes with variants: 91 minutes).
Also started preparing the “Semantic Web in 20 minutes” keynote. Due on tuesday.
Current WAVe status: 232 diseases, 750 [...]
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