GEN2PHEN Web2.0 Conference

Promote conference or workshop focused on Web2.0 and its integration in bioinformatics (User eXperience, usability, interface). It is important to explore this convergence. The idea is not an internation conference, but a closed workshop where specialists in biology and web applications can interact and exchange experiences.

Google Maps LSDB Locator

LSDB locator could use Google Maps API to generate a worldwide map about LSDB locations and display relevant information about the LSDBs. We could use myLSDB API to gather this information or use LSDB Locator inside myLSDB (as a feature, users could provide their location).

Google Maps Variation Viewer

Use Google Maps API to create a state-of-the-art visual variation viewer. We could use Google’s features to navigate through sequence variations and obtain more informations about a specific variation, based on the  navigational GPS metaphor: show nearby locations, monuments, similar variations…

myLSDB | myVar

myLSDB could become the first LSDB curators online community! We could use ideas from myExpriment (and traditional social  networks) to create a LSDB-related social network. Users could share information about their databases, the genes they have, experiment details, relevant scientific discoveries…

LSDB Connector

Create a “semi-manual” LSDB integration engine, using Arabella crawler to gather links and HGVS list as a base. Do some case-by-case work and convert to a pseudo-LRG format. Having the data mined and categorized would enable a search mechanism among variations: inclusion in GeneBrowsers as an API and the creation a simple variation search engine.

Google BioSearch + QuExT

Once again, we could use Google Search API to improve QuExT engine results. The first step would be to include GeNS in the query expansion mechanism. Then, there would be a larger number of terms that could be searched in Google. After this process, we could rank the results, crossing the several result lists and verifying the hits that appear in more than one list. Merging these results with traditional QuExT results would generate a better result set.

Google BioSearch API

Use Google Search API to gather results for a given topic, then categorize the results according to a predefined ontology and display the results in an attractive interface.

WikiConceptExpander + Finder

From a simple Wikipedia entry point, search for other wiki terms in the document and create a simple navigation map. The navigation map should be something like Mac OS X Finder… which leads to another idea: create a simple data browser that links concepts and displays the navigation interface like Mac OS X Finder Columns view.

BioCappuccino

Cappuccino is the first Objective-J framework. It is a Javascript framework that eases the process of creating RIA. 280slides is the first example of applications built in cappuccino. Cappuccino can be connected to Java web services allowing the development of applications involving both client and server side components. BioCappuccino could be used to migrate trivial desktop applications to the web environment or promote the creation of new solutions.

BioWikifier + BioWikifier API

Using ConceptWeb Linker ideas, we could create a simple text parsing mechanism that could be added as an extension to DiseaseCard that would search the original application pages for a list of terms and would then create an interface above them. It would involve changing the original applications but could be used to extend the reality of the integrated applications (whatever they are). Additionally, there could be an API that developers could use to customize the content that is presented in the wikified interface of their application.