IGEM:MIT/2006/Introduction

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This page contains links to introductory information for the MIT iGEM team.
This page contains links to introductory information for the MIT iGEM team.
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==Synthetic Biology==
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==Design==
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'''General introduction to ideas in Synthetic Biology'''
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===System Design considerations===
 +
*Feasible system scale (numbers of parts, plasmids, chassis types)
 +
*Design tools - models, network diagrams
 +
*Moving from system->devices->parts->DNA specification
 +
*Likelihood of success - protein engineering, cloning, new biological techniques and new science etc.
 +
===Abstraction hierarchy & standardization===
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*Parts - zinc fingers?
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*Devices - receiver?, inverter?
 +
*Systems - bacterial photography?
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*PoPS and composability
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==Build==
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===Construction methods===
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*[[BioBricks]] <font color=red>- Day 1, Week 1</font>
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*Standard assembly <font color=blue>- Day 2, Week 1</font>
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*3A assembly
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*In frame assembly
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*Direct synthesis
 +
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===Construction tools===
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*Registry
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*#Obtain accounts <font color=red>- Day 1, Week 1</font>
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*#Making a part (both basic and composite) <font color=red>- Day 1, Week 1</font>
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*#BLAST
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*#Sequence alignments
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*NCBI Entrez  <font color=red>- Day 1, Week 1</font>
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*VectorNTI
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*Others?
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==Test==
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*Plate reader characterization (i.e. Receiver)
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*Flow cytometry (i.e. Screening plasmid)
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*Microscopy
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*RT-PCR and Westerns
 +
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==Necessary skills==
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===Lab notebooks & documentation===
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*[[OpenWetWare:Getting started | Getting started with wiki editing]] <font color=red>- Day 1, Week 1</font>
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*Populate the [http://parts.mit.edu/wiki/index.php/MIT_2006 official MIT iGEM 2006 wiki page]
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*The online lab notebook framework
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===Searching and reading the literature===
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*[[Searching the literature]] <font color=green>- Day 3, Week 1</font>
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===Lab safety===
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*Complete the [[Endy:Safety_Training | '''Endy lab safety training''']].  (Even if you have worked in a lab before, you should visit this page and verify that your training is up to date.)  This should be done before your first day in lab.
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*Heather will be giving the lab-specific training <font color=red>- Day 1, Week 1</font>
 +
 +
==Links==
 +
'''General introduction to ideas in Synthetic Biology'''
#[[Adventures | Adventures in synthetic biology comic]] --> Learn about PoPS
#[[Adventures | Adventures in synthetic biology comic]] --> Learn about PoPS
#[http://openwetware.org/images/0/0d/Nature04342.pdf Foundations for engineering biology] --> rant by Drew Endy
#[http://openwetware.org/images/0/0d/Nature04342.pdf Foundations for engineering biology] --> rant by Drew Endy
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#MIT iGEM 2004 presentation ([[:Image:Mit-2004-iGEM-final.ppt|.ppt]],[[:Image:Mit-iGEM-2004-final.pdf|pdf]])
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#UT Austin and UCSF 2004 project ([http://parts.mit.edu/registry/index.php/Featured_Parts:Light_Sensor coliroids])
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#Find descriptions of [http://parts2.mit.edu/wiki/index.php/Igem_2005 2005 projects]
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==Wiki==
 
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'''How-to on wiki's'''
 
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#[[OpenWetWare:Getting started | Getting started]] --> Quick tutorial on using the OpenWetWare wiki
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==Schedules==
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*[[IGEM:MIT/2006/Introduction/Week 1]]

Current revision

This page contains links to introductory information for the MIT iGEM team.

Contents

Design

System Design considerations

  • Feasible system scale (numbers of parts, plasmids, chassis types)
  • Design tools - models, network diagrams
  • Moving from system->devices->parts->DNA specification
  • Likelihood of success - protein engineering, cloning, new biological techniques and new science etc.

Abstraction hierarchy & standardization

  • Parts - zinc fingers?
  • Devices - receiver?, inverter?
  • Systems - bacterial photography?
  • PoPS and composability

Build

Construction methods

  • BioBricks - Day 1, Week 1
  • Standard assembly - Day 2, Week 1
  • 3A assembly
  • In frame assembly
  • Direct synthesis

Construction tools

  • Registry
    1. Obtain accounts - Day 1, Week 1
    2. Making a part (both basic and composite) - Day 1, Week 1
    3. BLAST
    4. Sequence alignments
  • NCBI Entrez - Day 1, Week 1
  • VectorNTI
  • Others?

Test

  • Plate reader characterization (i.e. Receiver)
  • Flow cytometry (i.e. Screening plasmid)
  • Microscopy
  • RT-PCR and Westerns

Necessary skills

Lab notebooks & documentation

Searching and reading the literature

Lab safety

  • Complete the Endy lab safety training. (Even if you have worked in a lab before, you should visit this page and verify that your training is up to date.) This should be done before your first day in lab.
  • Heather will be giving the lab-specific training - Day 1, Week 1

Links

General introduction to ideas in Synthetic Biology

  1. Adventures in synthetic biology comic --> Learn about PoPS
  2. Foundations for engineering biology --> rant by Drew Endy
  3. MIT iGEM 2004 presentation (.ppt,pdf)
  4. UT Austin and UCSF 2004 project (coliroids)
  5. Find descriptions of 2005 projects


Schedules

Personal tools