IC Bioinfs/Project1

=Project Overview= Summary of D. Huntley's sheet

=Project Timeline=
 * For now a meeting plan, will include a flow-chart of our project.

LOGBOOK

 * Filling this in is a must!

=Brainstorming= Here we shall put in our ideas- things that may need improving on.

=Resources= Section summarizing reading/sources of information for the project.

Parts Registry
Mainly the summary from the googledoc on DNA assembly methods and other stuff from the registry. Key to understand the context!

Other existing programs
There's stuff here now!

BioSQL
Info about the BioSQL project, and its schema.

Toy Database
The SQL database that will be used during the project.

Tomcat: Servlets and JSPs
Tomcat didn't quite work... so trying to implement servlets in FLEX directly:
 * Resource for reading XML files in JAVA
 * Reading in a text file using mySQL
 * Deploying a flex program on Tomcat
 * Servlets in FLEX
 * connect jsp mysql

Adobe Flex
A program to develop Rich Internet Applications.

DAS
Contains a summary of notes. It will be useful to include information about other DAS servers and how they work (eg Ensembl) as they may be useful in helping us understand what to do and how.

DAZZLE
Introduction to DAS and how to setup a DAS server. Here are links to do this in DAZZLE or PROSERVER
 * How to set up a DAS server with DAZZLE in Eclipse
 * How to write plugins for Dazzle

Google App Engine
OK, so in order to use this app engine we are going to have to create the database here using the datastore.
 * The idea is to set up this connection: Datastore-JSP-FLEX
 * Things to look at within the googleapp engine:
 * Getting started using datastore
 * Overview of the datastore
 * NEED TO CREATE THE DATABASE WITHIN THE GOOGLE APP ENGINE.
 * Defining Data Classes on GAE!
 * link abt persistence
 * GAE home page - Download, "Getting Started" guide, and more.
 * BioSQL on GAE
 * Definition of an API

Bits of code
Any useful, if somewhat basic, code we write.

BLAST IN JAVA

 * NCBI-BLAST JAVA
 * BLAST/JAVA interface
 * BIOJAVA BLAST TO HTML REQUESTS
 * HOW TO ACCESS NCBI BLAST USING JAVA?
 * http request in perl to blast
 * GET CONTENTS OF A URL- JAVA

Links
Do contribute to these sections by adding more sub-pages.


 * A review of current methods and obstacles in Synthetic Biology.
 * DAS info from parts registry
 * DAS resource from Vincent Rouilly's OWW
 * BioSQL information on Googleapp
 * Biobricks help pages
 * Dazzle
 * Drew Endy video- What is a biobrick?
 * BioJava Cookbook- Download BioJava
 * Link to Tom Knight's pdf on biobricks
 * More general stuff on biobricks- OWW