Databases

A fully updated and complete database of all environmental data as well as disease data is now available on info-kan under the 'bloomology' database. The eight coral genomes available still need to be input into the database.

Genome Module

The latest module to be implemented is to compare the genomes of coral in the area that are diseased and compare the genomes of those coral to look for orthologous genes amongst the coral species. The goal is to speculate that the functionality of the common genes that are under stress can tell us about what is happening in the ecosystem. Also, a coral reef disease ontology can be created. Coral genomes are available here, here and here.

Sources of Data

The our demo will come from two sources: one source being the coral reef data from ReefBase which is a GIS map of the Global Coral Disease Database, and second, the environmental data for each of the coral locations of interest will come from the National Oceanic and Atmospheric Administration.

Demo

A basic layout of what we will be looking at and working from is available here to view.

Notes on this project

The goal of this project to create an assessment of ecosystem health based on the relationship between observation data and disease data within specific locations within the ecosystem using the DDont. The DDont algorithm was developed to reconstruct gene ontologies based on gene and gene networks and extant annotation terms. For this demonstration we will focus on coral reef ecosystems. An extended abstract of our work is presented here. The paper's authors are Chris Rosenthal, Mehmet Dalkilic, Susan Coleman Morse, and Claudia Johnson.

Quick Instuctions for Subversion

Subversion is used essentially like CVS. You say 

svn co svn://info-kan.ads.iu.edu/ddont/ddont/trunk ddont

(the trunk is now available to anyone) and once that is done you can do 

cd ddont

and 

svn update

or 

svn commit

Welcome to Trac 0.11.3

Trac is a minimalistic approach to web-based management of software projects. Its goal is to simplify effective tracking and handling of software issues, enhancements and overall progress.

All aspects of Trac have been designed with the single goal to help developers write great software while staying out of the way and imposing as little as possible on a team's established process and culture.

As all Wiki pages, this page is editable, this means that you can modify the contents of this page simply by using your web-browser. Simply click on the "Edit this page" link at the bottom of the page. WikiFormatting will give you a detailed description of available Wiki formatting commands.

"trac-admin yourenvdir initenv" created a new Trac environment, containing a default set of wiki pages and some sample data. This newly created environment also contains documentation to help you get started with your project.

You can use trac-admin to configure Trac to better fit your project, especially in regard to components, versions and milestones.

TracGuide is a good place to start.

Enjoy!
The Trac Team

Starting Points

For a complete list of local wiki pages, see TitleIndex.