Team:Newcastle/e Science

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(→Databases, services and software for Synthetic Biology)
 
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== E-Science Toolkit for Synthetic Biology (working title) ==
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== e-Science Toolkit for Synthetic Biology (working title) ==
=== Aims ===
=== Aims ===
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# Create a list of databases, services and software available for Synthetic Biology
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# The aim of this research is to apply e-Science to synthetic biology, focussing on workflows.
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# Create a set of work-flows for Synthetic Biology
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=== Objectives ===
=== Objectives ===
 +
# Explore the methodology of synthetic biologists.
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# 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.
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# Create a web site/database of available databases, services and software
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=== Databases, services and software for Synthetic Biology ===
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# Develop web services required that don't yet exist
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# Databases
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# Create Taverna work-flows
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## [http://partsregistry.org/Main_Page Registry of Standard Biological Parts]
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## [http://www.oxfordjournals.org/nar/database/a/ 2010 NAR Database Summary Paper Alpha List]
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## [http://128.240.147.145:8082/Biobricks/ Bacillus subtilis Parts]
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## [http://models.cellml.org/ Standard virtual biological parts: a repository of modular modeling components for synthetic biology. (Cooling et. al. 2010)]
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# Web sites
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## [http://www.synthetic-biology.info/ Synthetic Biology]
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## [http://syntheticbiology.org/ syntheticbiology.org]
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## [http://bioinformatics.ca/links_directory/ Bioinformatics Links Directory]
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## [http://research.ncl.ac.uk/synthetic_biology/ Synthetic Biology at Newcastle]
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# Web Services
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## [http://www.biocatalogue.org/ BioCatalogue.org]
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## eFetch parameters http://www.ncbi.nlm.nih.gov/corehtml/query/static/efetchseq_help.html
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# Publications
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## [http://nar.oxfordjournals.org/content/vol37/suppl_2/index.dtl#EDITORIAL_______WEB_SERVER_ISSUE Nucleic Acids Research annual Web Server Issue in 2009]
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=== Establish "life lines" ===
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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:
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# Taverna
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# myExperiment
=== Project Timeline ===
=== Project Timeline ===
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# Project Proposal: 22 April 2010
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# Presentation
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# Project Submission
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== Workflows ==
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=== [[Team:Newcastle_Restriction_site_finder|Restriction site finder]]===
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=== [[Team:Newcastle_Combining_virtual_parts|Combining virtual parts]]===

Latest revision as of 22:01, 25 May 2010

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Contents

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

  1. Explore the methodology of synthetic biologists.
  2. 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.
  3. Determine what computing resources are already available for use in synthetic biology
  4. Identify computational tools that can be developed.
  5. reate at least one workflow to automate the production of a biobrick
  6. If time allows and a need has been identified, create a web service for use in workflows for synthetic biology.
  7. 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

  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]
    4. [http://models.cellml.org/ Standard virtual biological parts: a repository of modular modeling components for synthetic biology. (Cooling et. al. 2010)]
  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]
    2. eFetch parameters http://www.ncbi.nlm.nih.gov/corehtml/query/static/efetchseq_help.html
  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

Project Timeline

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

Workflows

Restriction site finder

=== Combining virtual parts===
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