Team:Newcastle/e Science
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e-Science Toolkit for Synthetic Biology (working title)
Aims
- The aim of this research is to apply e-Science to synthetic biology, focussing on workflows.
Objectives
- Explore the methodology of synthetic biologists.
- Explore the use of workflows in synthetic biology and determine what can be done computationally – identifying tasks that are best suited to an e-Science solution.
- Determine what computing resources are already available for use in synthetic biology
- Identify computational tools that can be developed.
- reate at least one workflow to automate the production of a biobrick
- If time allows and a need has been identified, create a web service for use in workflows for synthetic biology.
- If time allows investigate the possibility of identifying design patterns, in principle similar to that used in software engineering, in synthetic biology.
Databases, services and software for Synthetic Biology
- Databases
- [http://partsregistry.org/Main_Page Registry of Standard Biological Parts]
- [http://www.oxfordjournals.org/nar/database/a/ 2010 NAR Database Summary Paper Alpha List]
- [http://128.240.147.145:8082/Biobricks/ Bacillus subtilis Parts]
- [http://models.cellml.org/ Standard virtual biological parts: a repository of modular modeling components for synthetic biology. (Cooling et. al. 2010)]
- Web sites
- [http://www.synthetic-biology.info/ Synthetic Biology]
- [http://syntheticbiology.org/ syntheticbiology.org]
- [http://bioinformatics.ca/links_directory/ Bioinformatics Links Directory]
- [http://research.ncl.ac.uk/synthetic_biology/ Synthetic Biology at Newcastle]
- Web Services
- [http://www.biocatalogue.org/ BioCatalogue.org]
- eFetch parameters http://www.ncbi.nlm.nih.gov/corehtml/query/static/efetchseq_help.html
- Publications
- [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:
- Taverna
- myExperiment
Project Timeline
- Project Proposal: 22 April 2010
- Presentation
- Project Submission