Difference between revisions of "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.
  
==Lab safety==
+
==Design==
'''All people working in a biological research lab must undergo safety training.'''
+
===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.
  
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.)
+
===Abstraction hierarchy & standardization===
 
+
*Parts - zinc fingers?
Heather will be giving the lab-specific training.
+
*Devices - receiver?, inverter?
 
+
*Systems - bacterial photography?
==Wiki==
 
'''How-to on wiki's'''
 
 
 
*[[OpenWetWare:Getting started | Getting started]] --> Quick tutorial on using the OpenWetWare wiki
 
*Populate the official iGEM wiki
 
 
 
==Abstraction hierarchy==
 
 
*PoPS and composability
 
*PoPS and composability
  
==Registry==
+
==Build==
*Obtain accounts
+
===Construction methods===
*Making a part (both basic and subpart)
+
*[[BioBricks]] <font color=red>- Day 1, Week 1</font>
*BLAST
+
*Standard assembly <font color=blue>- Day 2, Week 1</font>
*Sequence alignments
 
 
 
==BioBricks assembly==
 
*[[BioBricks]]
 
*Standard assembly
 
 
*3A assembly
 
*3A assembly
 
*In frame assembly
 
*In frame assembly
 
*Direct synthesis
 
*Direct synthesis
  
==Part and device characterization==
+
===Construction tools===
 +
*Registry
 +
*#Obtain accounts <font color=red>- Day 1, Week 1</font>
 +
*#Making a part (both basic and composite) <font color=red>- Day 1, Week 1</font>
 +
*#BLAST
 +
*#Sequence alignments
 +
*NCBI Entrez  <font color=red>- Day 1, Week 1</font>
 +
*VectorNTI
 +
*Others?
 +
 
 +
==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
  
==Searching and reading the literature==
+
==Necessary skills==
*[[Searching the literature]]
+
===Lab notebooks & documentation===
 +
*[[OpenWetWare:Getting started | Getting started with wiki editing]] <font color=red>- Day 1, Week 1</font>
 +
*Populate the [http://parts.mit.edu/wiki/index.php/MIT_2006 official MIT iGEM 2006 wiki page]
 +
*The online lab notebook framework
 +
 
 +
===Searching and reading the literature===
 +
*[[Searching the literature]] <font color=green>- Day 3, Week 1</font>
  
==Lab techniques==
+
===Lab safety===
 +
*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.
 +
*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'''
 
 
#[[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]
  
==Week 1==
 
Goals -
 
*Do one assembly stage
 
*Make a biobrick
 
*Necessary software - VectorNTI, Registry, Wiki
 
*Literature searching
 
  
===Day 1===
+
==Schedules==
====Dry Lab====
+
*[[IGEM:MIT/2006/Introduction/Week 1]]
*Safety training
 
*Lab tour
 
*Registry accounts
 
====Wet Lab====
 
*Pick a gene and design primers
 
**Introduces parts
 
*Start overnights
 
**Introduces sterile technique, culturing,
 
===Day 2===
 
====Dry Lab====
 
*BioBricks Construction
 
====Wet Lab====
 
*Prep & Digest
 

Latest revision as of 11:14, 2 June 2006

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

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