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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==Lab safety==
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==Design==
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'''All people working in a biological research lab must undergo safety training.'''
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===System Design considerations===
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*Feasible system scale (numbers of parts, plasmids, chassis types)
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*Design tools - models, network diagrams
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*Moving from system->devices->parts->DNA specification
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*Likelihood of success - protein engineering, cloning, new biological techniques and new science etc.
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To complete your online safety training, visit the [[Endy:Safety_Training | '''Endy lab safety training guide''']].  (Even if you have worked in a lab before, you should visit this page and verify that your training is up to date.)
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===Abstraction hierarchy & standardization===
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This should be done before your first day in lab.
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*Parts - zinc fingers?
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*Devices - receiver?, inverter?
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Heather will be giving the lab-specific training <font color=red>- Day 1, Week 1</font>
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*Systems - bacterial photography?
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==Wiki==
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'''How-to on wiki's'''
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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 official iGEM wiki
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==Abstraction hierarchy==
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*PoPS and composability
*PoPS and composability
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==Registry==
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==Build==
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*Obtain accounts <font color=red>- Day 1, Week 1</font>
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===Construction methods===
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*Making a part (both basic and subpart) <font color=red>- Day 1, Week 1</font>
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*BLAST
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*Sequence alignments
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==BioBricks assembly==
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*[[BioBricks]] <font color=red>- Day 1, Week 1</font>
*[[BioBricks]] <font color=red>- Day 1, Week 1</font>
*Standard assembly <font color=blue>- Day 2, Week 1</font>
*Standard assembly <font color=blue>- Day 2, Week 1</font>
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*Direct synthesis
*Direct synthesis
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==Part and device characterization==
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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==
*Plate reader characterization (i.e. Receiver)
*Plate reader characterization (i.e. Receiver)
*Flow cytometry (i.e. Screening plasmid)
*Flow cytometry (i.e. Screening plasmid)
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*RT-PCR and Westerns
*RT-PCR and Westerns
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==Searching and reading the literature==
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==Necessary skills==
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*[[Searching the literature]]
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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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==Lab techniques==
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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==
==Links==
'''General introduction to ideas in Synthetic Biology'''
'''General introduction to ideas in Synthetic Biology'''
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#[[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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#Find descriptions of [http://parts2.mit.edu/wiki/index.php/Igem_2005 2005 projects]
#Find descriptions of [http://parts2.mit.edu/wiki/index.php/Igem_2005 2005 projects]
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==Week 1==
 
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Goals -
 
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*Do one assembly stage
 
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*Make a biobrick
 
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*Necessary software - VectorNTI, Registry, Wiki
 
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*Literature searching
 
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===Day 1===
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==Schedules==
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====Dry Lab====
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*[[IGEM:MIT/2006/Introduction/Week 1]]
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*Safety training
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*Lab tour
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*Registry accounts
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====Wet Lab====
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*Pick a gene and design primers
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**Introduces parts
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*Start overnights
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**Introduces sterile technique, culturing,
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===Day 2===
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====Dry Lab====
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*BioBricks Construction
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====Wet Lab====
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*Prep & Digest
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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