Team:Newcastle/e Science

E-Science Toolkit for Synthetic Biology (working title)

Aims

1. The aim of this research is to apply e-Science to synthetic biology, focussing on workflows.

Objectives

Create a web site/database of available databases, services and software

1. Databases
   1. [http://partsregistry.org/Main_Page Registry of Standard Biological Parts]
   2. [http://www.oxfordjournals.org/nar/database/a/ 2010 NAR Database Summary Paper Alpha List]
   3. [http://128.240.147.145:8082/Biobricks/ Bacillus subtilis Parts]
2. Web sites
   1. [http://www.synthetic-biology.info/ Synthetic Biology]
   2. [http://syntheticbiology.org/ syntheticbiology.org]
   3. [http://bioinformatics.ca/links_directory/ Bioinformatics Links Directory]
   4. [http://research.ncl.ac.uk/synthetic_biology/ Synthetic Biology at Newcastle]
3. Web Services
   1. [http://www.biocatalogue.org/ BioCatalogue.org]
4. Publications
   1. [http://nar.oxfordjournals.org/content/vol37/suppl_2/index.dtl#EDITORIAL_______WEB_SERVER_ISSUE Nucleic Acids Research annual Web Server Issue in 2009]

Establish "life lines"

Documentation for open source software is sometimes limited, especially when the software is still quite new. Getting online help can be a real life saver but it takes time to find all the sources, register with them and be ready to ask questions when required. Find mailing lists and on-line forums for the following and start following them:

1. Taverna
2. myExperiment

Develop web services required that don't yet exist

Create Taverna work-flows

Project Timeline

1. Project Proposal: 22 April 2010
2. Presentation
3. Project Submission