Murray Wiki - User contributions [en]

Group Schedule, Summer 2017

2017-07-10T22:18:41Z

Sguo:

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
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* [[Schedule|Richard's calendar (travel)]]
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* [[Group Schedule, Spring 2017]]
|}

The schedule for group and subgroup meetings is given below. Contact Richard if you need to change the schedule. Unless otherwise noted, here are the locations of the meetings:

:{| width=100%
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* Biocircuits subgroup - 111 Keck
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* NCS subgroup - 110 Steele
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* Group meetings - 213 ANB
|}

{| width=100% border=1
|- valign=top

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=== Week 1: 19 Jun - 23 Jun ===
'''NCS: Mon, 10a-12p'''
* Introductions
* Sofie Haesaert
<hr>
* No biocircuits meeting

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=== Week 2: 26 Jun - 30 Jun ===
'''Biocircuits: Mon, 10a-12p'''
* Ania Baetica
* George Artavanis
<hr>
* BioCon project meeting: Mon, 12p-2p - 111 Keck
* SURF kickoff meeting: Mon, 2p-3:30p - 111 Keck
* No NCS meeting

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=== Week 3: 3 Jul - 7 Jul ===
'''Biocircuits: Wed, 10a-12p'''
* Vipul Singhal
* Yong Wu
'''NCS: Wed, 1p-3p''' - 114 Steele
* Tony Fragoso
* Jake Reher (Ames)

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=== Week 4: 10 Jul - 14 Jul ===
'''Biocircuits: Mon, 10a-12p'''
* James Parkin
* Mark Prator
* Swati Agrawal
'''NCS: Tue, 10a-12p'''
* Sumanth Dathathri
* Yashwanth Nakka (Chung)

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=== Week 5: 17 Jul - 21 Jul ===
* No group meetings, Richard out of town
'''Biocircuits: Mon, 11a-12p'''
* Lab cleanup

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=== Week 6: 24 Jul - 28 Jul ===
'''Biocircuits: Tue, 10a-12p'''
* William Poole
* Shaobin Guo
'''NCS: Tue, 1p-3p'''
* Richard Cheng
* Ellen Feldman (Burdick)

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=== Week 7: 31 Jul - 4 Aug ===
'''Biocircuits: Tue, 10a-12p'''
* Leo Green
* Sam Clamons
'''NCS: Wed, 10a-12p'''
* Ioannis Filippidis
* Wen-Loong Ma (Ames)

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=== Week 8: 7 Aug - 11 Aug ===
'''Biocircuits: Tue, 10a-12p'''
* SURF students
'''NCS: Wed, 10a-12p'''
* SURF students
<hr>
* BioCon project meeting: Mon, 10a-12p

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=== Week 9: 14 Aug - 18 Aug ===
'''Biocircuits: Tue, 10a-12p'''
* Andrey Shur
* Cindy Ren
* Note: this meeting will probably shift to Thu, 10a-12p - 114 Steele
'''NCS: Wed, 10a-12p'''
* Jin Ge (tentative)
* Matt Burkhardt (Burdick)
* Note: this meeting will probably shift to Thu, 1-3p - 114 Steele

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=== Week 10: 21 Aug - 25 Aug ===
'''Biocircuits: Tue, 10a-12p'''
* Reed McCardell
* Anand Swaminathan
'''NCS: Wed, 10a-12p'''
* Karena Cai
* Thomas Gurriet (Ames)

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=== Week 11: 28 Aug - 1 Sep ===
'''Biocircuits: Tue, 10a-12p'''
* Andy Halleran
* Shan Huang
'''NCS: Wed, 10a-12p'''
* Tung Phan
* Francesca Baldini (Chung)
* Note: this meeting will likely shift to Thu (31 Aug) - 114 Steele

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=== Week 12: 4 Sep - 8 Sep ===
* No group meetings, Richard out of town

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=== Week 13: 11 Sep - 15 Sep ===
* No group meetings, Richard out of town
'''Biocircuits: Mon, 11a-12p'''
* Lab cleanup

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=== Week 14: 18 Sep - 22 Sep ===
'''Biocircuits: Mon, 12p-2p'''
* Michaelle Mayalu
* Rory Williams
<hr>
* BioCon project meeting: Mon, 10a-12p
* No NCS group meeting

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=== Week 15: 25 Sep - 29 Sep ===
* First week of classes; see [[Group Schedule, Fall 2017|fall term schedule]]
|}

May 2017 meeting schedule

2017-05-08T14:50:16Z

Sguo: /* 30 May (Tue) */

Richard will be in town several different times in May. Please sign up for a time to meet below. Please note that these are likely the last "sabbatical" meetings until Richard returns to Pasadena in early July. __NOTOC__

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==== 15 May (Mon) ====
* 9:30 am: Open
* 10:15 am: Open
* 11:00 am: Faculty meeting
* 11:30 am: Open
* 12:15 pm: Lunch
* 1:30 pm: Open
* 2:15 pm: Open
* 3:00 pm: Open
* 3:45 pm: Break
* 4:00 pm: Namita
* 4:45 pm: Open
* 5:30 pm: Open
* 6:15 pm: Done for the day

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==== 16 May (Tue)====
* 9:30 am: Open
* 10:15 am: Tung
* 11:00 am: Faculty meeting
* 12:00 pm: Lunch
* 1:30 pm: Depart
* 12:00 pm: Lunch
* 1:30 pm: Depart

|- valign=top
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====21 May (Sun) ====
* 1:45 pm: Open
* 2:30 pm: Open
* 3:15 pm: Open
* 4:00 pm: Break
* 4:15 pm: Open
* 5:00 pm: Open
* 5:45 pm: Open
* 6:30 pm: Done for the day

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==== 22 May (Mon) ====
* 10:15 am: Mark
* 11:00 am: Open
* 11:45 am: Lunch
* 12:00 pm: DARPA BioCon meeting
* 2:00 pm: Open
* 2:45 pm: Off campus
* 4:15 pm: Open
* 5:00 pm: Non-Caltech meetings
* 6:30 pm: Done for the day

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==== 23 May (Tue) ====
* 9:30 am: Faculty discussion
* 10:30 am: Hold (Susan)
* 11:30 am: Lunch
* 12:00 pm: Telecon
* 1:00 pm: Anu thesis defense
* 3:00 pm: Terri (?)
* 3:30 pm: Depart

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====28 May (Sun) ====
* 1:45 pm: Open
* 2:30 pm: Open
* 3:15 pm: Open
* 4:00 pm: Done for the day
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====29 May (Mon) ====
* 1:45 pm: Open (if needed)
* 2:30 pm: Open (if needed)
* 3:15 pm: Open (if needed)
* 4:00 pm: Done for the day
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==== 30 May (Tue) ====
* 9:30 am: Open
* 10:15 am: Shaobin
* 11:00 am: Stepan seminar
* 12:00 pm: Lunch
* 1:30 pm: Namita
* 2:15 pm: Open
* 3:00 pm: Depart
|}

Apr 2017 meeting schedule

2017-04-12T16:20:11Z

Sguo: /* 19 Apr (Wed) */

Richard will be in town 19-21 Apr. Please sign up for a time to meet below. __NOTOC__

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==== 19 Apr (Wed) ====
* 9:30 am: Hold (Sofie or Leo)
* 10:30 am: Admin meeting (SP, MC)
* 11:15 am: Shaobin
* 12:00 pm: DARPA BioCon meeting
* 2:00 pm: Candidacy exam
* 3:00 pm: CDS tea
* 3:45 pm: Open
* 4:30 pm: Admin meeting (LL)
* 5:00 pm: Open (tentative)
* 5:45 pm: Associates event

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==== 20 Apr (Thu) ====
* 9:30 am: Hold (Sofie or Leo)
* 10:30 am: Mark
* 11:15 am: Tony Fragoso
* 12:00 pm: Lunch
* 1:30 pm: EBRC telecon
* 2:30 pm: Open
* 3:15 pm: Open
* 4:00 pm: Vipul
* 4:45 pm: Break
* 5:00 pm: Tung
* 5:45 pm: Sam
* 6:00 pm: Open (if needed)
* 6:45 pm: Open (if needed)
* 7:30 pm: Done for the day

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==== 21 Apr (Fri) ====
* 9:15 am: Open
* 10:00 am: JPL CIF meeting
* 11:15 am: Karena
* 12:00 pm: Lunch
* 12:45 pm: Open
* 1:30 pm: Open
* 2:15 pm: Open
* 3:00 pm: Break
* 3:15 pm: Open
* 4:00 pm: Miki
* 4:45 pm: Open
* 5:30 pm: Done for the day

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==== 23 Apr (Sun) ====
* 1:45 pm: Open
* 2:30 pm: Open
* 3:15 pm: Open
* 4:00 pm: Break
* 4:15 pm: Open
* 5:00 pm: Open
* 5:45 pm: Shan
* 6:30 pm: Done for the day
|}

Group Schedule, Spring 2017

2017-03-16T19:12:39Z

Sguo: /* Week 4: 24 Apr - 28 Apr */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* {{RMM public schedule|Richard's calendar (travel)}}
| width=50% |
* [[Group Schedule, Winter 2017]]
|}

The schedule for group and subgroup meetings is given below. Contact Anandh if you need to change the schedule. Unless otherwise noted, here are the locations of the meetings:

:{| width=100%
|- valign=top
| width=30% |
* Group meetings - 213 ANB
| width=30% |
* Biocircuits subgroup - Keck 111
| width=30% |
* NCS subgroup - 243 ANB
|}

{| width=100% border=1

|- valign=top
| width=25% |
=== Week 1: 3 Apr - 7 Apr ===
'''Biocircuits: Mon, 10a-12p'''
* Leo Green
* Ania Baetica

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=== Week 2: 10 Apr - 14 Apr ===
'''Biocircuits: Mon, 10a-12p'''
* Vipul Singhal
* Open

'''Biocircuits: Wed, 11a-12p'''
* Lab cleanup

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=== Week 3: 17 Apr - 21 Apr ===
'''Biocircuits: Mon, 11a-12p'''
* Yong Wu
* Mark Prator
|- valign=top
| width=25% |

=== Week 4: 24 Apr - 28 Apr ===
'''Biocircuits: Mon, 10a-12p'''
* James Parkin
* Shaobin Guo (Pre-defense talk)

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=== Week 5: 1 May - 5 May ===
'''Biocircuits: Mon, 10a-12p'''
* Sam Clamons
* Andrey Shur

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=== Week 6: 8 May - 12 May===
'''Biocircuits: Mon, 10a-12p'''
* Anandh Swaminathan
* Cindy Ren

|- valign=top
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=== Week 7: 15 May - 19 May ===
'''Biocircuits: Mon, 10a-12p'''
* Reed McCardell
* William Poole
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=== Week 8: 22 May - 26 May ===
* RMM in town, no group meeting

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=== Week 9: 29 May - 2 Jun ===
'''Happy Memorial Day!'''

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=== Week 10: 5 Jun - 9 Jun ===
'''Biocircuits: Mon, 10a-12p'''
* Rotation student
* Rotation student

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=== Week 11: 12 Jun - 16 Jun ===
'''Biocircuits: Mon, 10a-12p'''
* Rotation student
* Rotation student
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=== Week 12: 19 Jun - 23 Jun ===
'''Summer'''
|}

Group Schedule, Spring 2017

2017-03-16T19:12:16Z

Sguo:

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* {{RMM public schedule|Richard's calendar (travel)}}
| width=50% |
* [[Group Schedule, Winter 2017]]
|}

The schedule for group and subgroup meetings is given below. Contact Anandh if you need to change the schedule. Unless otherwise noted, here are the locations of the meetings:

:{| width=100%
|- valign=top
| width=30% |
* Group meetings - 213 ANB
| width=30% |
* Biocircuits subgroup - Keck 111
| width=30% |
* NCS subgroup - 243 ANB
|}

{| width=100% border=1

|- valign=top
| width=25% |
=== Week 1: 3 Apr - 7 Apr ===
'''Biocircuits: Mon, 10a-12p'''
* Leo Green
* Ania Baetica

| width=25% |

=== Week 2: 10 Apr - 14 Apr ===
'''Biocircuits: Mon, 10a-12p'''
* Vipul Singhal
* Open

'''Biocircuits: Wed, 11a-12p'''
* Lab cleanup

| width=25% |

=== Week 3: 17 Apr - 21 Apr ===
'''Biocircuits: Mon, 11a-12p'''
* Yong Wu
* Mark Prator
|- valign=top
| width=25% |

=== Week 4: 24 Apr - 28 Apr ===
'''Biocircuits: Mon, 10a-12p'''
* James Parkin
* Shaobin Guo

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=== Week 5: 1 May - 5 May ===
'''Biocircuits: Mon, 10a-12p'''
* Sam Clamons
* Andrey Shur

| width=25% |

=== Week 6: 8 May - 12 May===
'''Biocircuits: Mon, 10a-12p'''
* Anandh Swaminathan
* Cindy Ren

|- valign=top
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=== Week 7: 15 May - 19 May ===
'''Biocircuits: Mon, 10a-12p'''
* Reed McCardell
* William Poole
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=== Week 8: 22 May - 26 May ===
* RMM in town, no group meeting

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=== Week 9: 29 May - 2 Jun ===
'''Happy Memorial Day!'''

|- valign=top
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=== Week 10: 5 Jun - 9 Jun ===
'''Biocircuits: Mon, 10a-12p'''
* Rotation student
* Rotation student

| width=25% |

=== Week 11: 12 Jun - 16 Jun ===
'''Biocircuits: Mon, 10a-12p'''
* Rotation student
* Rotation student
| width=25% |

=== Week 12: 19 Jun - 23 Jun ===
'''Summer'''
|}

Mar 2017 meeting schedule

2017-02-26T20:03:23Z

Sguo: /* 3 Mar (Fri) */

Richard will be in town 3-7 Mar. Please sign up for a time to meet below. __NOTOC__

{| border=1
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==== 3 Mar (Fri) ====
* 10:00 am: DENSO CPM telecon
* 11:00 am: Open
* 11:45 am: Shaobin
* 12:30 pm: Lunch
* 1:00 pm: Hold: DARPA telecon
* 2:00 pm: Open
* 2:45 pm: Open
* 3:30 pm: SBIR telecon (w/ Mark P)
* 4:00 pm: Faculty meeting
* 5:45 pm: Open
* 6:30 pm: Done for the day

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==== 5 Mar (Sun) ====
* 1:45 pm: Open
* 2:30 pm: Open
* 3:15 pm: Open
* 4:00 pm: Break
* 4:15 pm: Open
* 5:00 pm: Open
* 5:45 pm: Open
* 6:30 pm: Done for the day

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==== 6 Mar (Mon) ====
* 9:30 am: AFOSR BRI telecon
* 10:30 am: Open
* 11:15 am: Open
* 12:00 pm: Lunch
* 12:30 pm: Hold: DARPA telecon
* 1:30 pm: Open
* 2:15 pm: Open
* 3:00 pm: Open
* 3:45 pm: Break
* 4:00 pm: Open
* 4:45 pm: Open
* 5:30 pm: Open
* 6:15 pm: Done for the day

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==== 7 Mar (Tue) ====
* 9:30 am: Busy
* 10:15 am: Open
* 11:00 am: Hold: DARPA telecon
* 12:00 pm: Lunch
* 12:45 pm: Hold
* 1:15 pm: Andrew M
* 2:00 pm: Open
* 2:45 pm: Depart for airport
|}

Nov 2016 meeting schedule

2016-11-03T18:53:29Z

Sguo: /* 14 Nov (Mon) */

Richard will be in town 13-16 Nov. Please sign up for a time to meet below.
__NOTOC__

{| border=1
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==== 13 Nov (Sun) ====
 
 
<hr>
* 2 pm: Hold until needed
* 2:45 pm: Hold until needed
* 3:30 pm: Hold until needed
* 4:15 pm: Break
* 5:00 pm: Hold until needed
* 5:45 pm: Hold until needed
* 6:30 pm: Done for the day

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==== 14 Nov (Mon) ====
* 10:30 am: Open
* 11:15 am: Open
<hr>
* 1:30 pm: Open
* 2:15 pm: Open
* 3:00 pm: Shaobin
* 3:45 pm: Break
* 4:00 pm: Open
* 4:45 pm: Open
* 5:30 pm: Open
* 6:15 pm: Done for the day
| width=25% |

====15 Nov (Tue) ====
* 10:30 am: Open
* 11:15 am: Open
<hr>
* 1:30 pm: Open
* 2:15 pm: Open
* 3:00 pm: Open
* 3:45 pm: Break
* 4:00 pm: Open
* 4:45 pm: Open
* 5:30 pm: Open
* 6:15 pm: Done for the day
| width=25% |

==== 16 Nov (Wed) ====
* 10:30 am: Open
* 11:15 am: Open
<hr>
* 1:30 pm: Open
* 2:15 pm: Open
* 3:00 pm: CDS tea
* Depart for airport at ~4 pm
|}

Sep/Oct 2016 meeting schedule

2016-09-19T14:31:24Z

Sguo: /* 3 Oct (Mon) */

Richard will be in town 29 Sept - 3 Oct 2016. Please sign up for a time to meet below.
__NOTOC__

{| border=1
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==== 29 Sep (Thu) ====
* Flying in from SF in the morning
* 1:00 pm: George
* 1:45 pm: Andrey
* 2:30 pm: Tony Fragoso
* 3:15 pm: Break
* 3:30 pm: Richard C.
* 4:15 pm: Sam
* 5:00 pm: Open
* 5:45 pm: Break
* 6:00 pm: Open
* 6:45 pm: Open
* 7:30 pm: Done for the day
| width=25% |

==== 30 Sep (Fri) ====
* Morning: busy with other meetings/phone calls
* 1:30-3:30 pm: Integrase project meeting (Victoria, Andrey, George, Sam, Ania, Cindy, Jining)
* 3:30 pm: Miki
* 4:30 pm: break
* 4:45 pm: Andrew
* 5:30 pm: Anandh
* 6:15 pm: Done for the day
| width=25% |

==== 2 Oct (Sun) ====
* 1:45 pm: YONG
* 2:30 pm: Open
* 3:15 pm: Open
* 4:00 pm: Break
* 4:15 pm: Cindy
* 5:00 pm: Open
* 5:45 pm: Open
* 6:30 pm: Done for the day

| width=25% |

==== 3 Oct (Mon) ====
* 10 am - 12 pm: DARPA BioCon meeting
* 12:00 pm: Candidacy exam
* 1:45 pm: Jaymie
* 2:45 pm: Tung
* 3:30 pm: Shaobin
* 4:15 pm: Victoria
* 5:00 pm: Break
* 5:15 pm: Daniel N
* 6:00 pm: William
* 6:45 pm: Open
* 7:30 pm: Done for the day
|}

Aug 2016 meeting schedule

2016-07-31T17:19:50Z

Sguo: /* 8 Aug (Mon) */

Richard will be in town 7-10 August 2016. Please sign up for a time to meet below.
__NOTOC__

{| border=1
|- valign=top
| width=25% |
==== 7 Aug (Sun) ====
* 2:15 pm: YONG?
* 3:00 pm: Open
* 3:45 pm: Open
* 4:00 pm: Break
* 4:45 pm: Open
* 5:30 pm: Open
* 6:30 pm: Open
| width=25% |

==== 8 Aug (Mon) ====
* 9-11 am: Integrase project meeting (Victoria, Andrey, Sam, Ania, Cindy)
<hr>
* 12:45 pm: Anandh
* 1:30 pm: Shaobin (if TXTL meeting changed to today)
* 2:15 pm: Open
* 3:00 pm: Open
* 3:45 pm: Break
* 4:00 pm: Open
* 4:45 pm: Open
| width=25% |

==== 9 Aug (Tue) ====
* 8:30 am: Open
* 9:15 am: Open
* 10:00 am: Jaymie
* 11 am - 2 pm: DARPA Biological Control project meeting (Anandh, Ania, Cindy, James, Reed, Andrey, Sam?)
* 1:00 pm: Tung
* 1:45 pm: Hold: James
* 2:30 pm: Tony Fragoso
* 3:15 pm: Break
* 3:30 pm: Vipul
* 4:15 pm: Ioannis
* 5:00 pm: Open
* 5:45 pm: Break
| width=25% |

==== 10 Aug (Wed) ====
* 9-11 am: TX-TL project meeting (Clare, Mark, Shaobin, Yong, Vipul, Sam, Miki)
* 11:00 am: Shaobin
* 11:45 am: Unavailable
* 12:45 pm: Miki
* 1:45 pm: YONG?
* 2:30 pm: Leave for airport
|}

Aug 2016 meeting schedule

2016-07-31T00:27:17Z

Sguo: /* 8 Aug (Mon) */

Richard will be in town 7-10 August 2016. Please sign up for a time to meet below.
__NOTOC__

{| border=1
|- valign=top
| width=25% |
==== 7 Aug (Sun) ====
* 2:15 pm: Open
* 3:00 pm: Open
* 3:45 pm: Open
* 4:00 pm: Break
* 4:45 pm: Open
* 5:30 pm: Open
* 6:30 pm: Open
| width=25% |
==== 8 Aug (Mon) ====
* 9-11 am: Integrase project meeting (Victoria, Andrey, Sam, Ania)
<hr>
* 12:45 pm: Anandh
* 1:30 pm: Open
* 2:15 pm: Open
* 3:00 pm: Open
* 3:45 pm: Break
* 4:00 pm: Open
* 4:45 pm: Open
| width=25% |

==== 9 Aug (Tue) ====
* 8:30 am: Open
* 9:15 am: Open
* 10:00 am: Jaymie
* 11 am - 2 pm: DARPA Biological Control project meeting (Anandh, Ania, Cindy, James, Reed, Andrey, Sam)
* 1:00 pm: Tung
* 1:45 pm: Open
* 2:30 pm: Open
* 3:15 pm: Break
* 3:30 pm: Vipul
* 4:15 pm: Open
* 5:00 pm: Open
* 5:45 pm: Break
| width=25% |

==== 10 Aug (Wed) ====
* 9-11 am: TX-TL project meeting (Clare, Mark, Shaobin, Yong, Vipul, Sam, Miki)
* 11:00 am: Shaobin
* 11:45 am: Unavailable
* 12:45 pm: Miki
* 1:45 pm: Open
* 2:30 pm: Leave for airport
|}

Aug 2016 meeting schedule

2016-07-31T00:27:08Z

Sguo: /* 10 Aug (Wed) */

Richard will be in town 7-10 August 2016. Please sign up for a time to meet below.
__NOTOC__

{| border=1
|- valign=top
| width=25% |
==== 7 Aug (Sun) ====
* 2:15 pm: Open
* 3:00 pm: Open
* 3:45 pm: Open
* 4:00 pm: Break
* 4:45 pm: Open
* 5:30 pm: Open
* 6:30 pm: Open
| width=25% |
==== 8 Aug (Mon) ====
* 9-11 am: Integrase project meeting (Victoria, Andrey, Sam, Ania)
<hr>
* 12:45 pm: Anandh
* 1:30 pm: Shaobin
* 2:15 pm: Open
* 3:00 pm: Open
* 3:45 pm: Break
* 4:00 pm: Open
* 4:45 pm: Open
| width=25% |

==== 9 Aug (Tue) ====
* 8:30 am: Open
* 9:15 am: Open
* 10:00 am: Jaymie
* 11 am - 2 pm: DARPA Biological Control project meeting (Anandh, Ania, Cindy, James, Reed, Andrey, Sam)
* 1:00 pm: Tung
* 1:45 pm: Open
* 2:30 pm: Open
* 3:15 pm: Break
* 3:30 pm: Vipul
* 4:15 pm: Open
* 5:00 pm: Open
* 5:45 pm: Break
| width=25% |

==== 10 Aug (Wed) ====
* 9-11 am: TX-TL project meeting (Clare, Mark, Shaobin, Yong, Vipul, Sam, Miki)
* 11:00 am: Shaobin
* 11:45 am: Unavailable
* 12:45 pm: Miki
* 1:45 pm: Open
* 2:30 pm: Leave for airport
|}

Aug 2016 meeting schedule

2016-07-31T00:24:39Z

Sguo: /* 8 Aug (Mon) */

Richard will be in town 7-10 August 2016. Please sign up for a time to meet below.
__NOTOC__

{| border=1
|- valign=top
| width=25% |
==== 7 Aug (Sun) ====
* 2:15 pm: Open
* 3:00 pm: Open
* 3:45 pm: Open
* 4:00 pm: Break
* 4:45 pm: Open
* 5:30 pm: Open
* 6:30 pm: Open
| width=25% |
==== 8 Aug (Mon) ====
* 9-11 am: Integrase project meeting (Victoria, Andrey, Sam, Ania)
<hr>
* 12:45 pm: Anandh
* 1:30 pm: Shaobin
* 2:15 pm: Open
* 3:00 pm: Open
* 3:45 pm: Break
* 4:00 pm: Open
* 4:45 pm: Open
| width=25% |

==== 9 Aug (Tue) ====
* 8:30 am: Open
* 9:15 am: Open
* 10:00 am: Jaymie
* 11 am - 2 pm: DARPA Biological Control project meeting (Anandh, Ania, Cindy, James, Reed, Andrey, Sam)
* 1:00 pm: Tung
* 1:45 pm: Open
* 2:30 pm: Open
* 3:15 pm: Break
* 3:30 pm: Vipul
* 4:15 pm: Open
* 5:00 pm: Open
* 5:45 pm: Break
| width=25% |

==== 10 Aug (Wed) ====
* 9-11 am: TX-TL project meeting (Clare, Mark, Shaobin, Yong, Vipul, Sam, Miki)
* 11:00 am: Open
* 11:45 am: Unavailable
* 12:45 pm: Miki
* 1:45 pm: Open
* 2:30 pm: Leave for airport
|}

Group Schedule, Summer 2016

2016-06-20T18:44:51Z

Sguo:

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [[Schedule|Richard's calendar (travel)]]
| width=50% |
* [[Group Schedule, Spring 2016]]
|}

The schedule for group and subgroup meetings is given below. Contact Richard if you need to change the schedule. Unless otherwise noted, here are the locations of the meetings:

:{| width=100%
|- valign=top
| width=30% |
* Group meetings - 213 ANB
| width=30% |
* Biocircuits subgroup - 111 Keck
| width=30% |
* NCS subgroup - 243 ANB
|}

{| width=100% border=1

|- valign=top
| width=25% |
=== Week 0: 13 Jun - 17 Jun ===
'''Biocircuits: Mon, 10a-12p'''
* William Poole (long)
* Alex White (short)
'''NCS: Tue, 1:30p-3p'''
* Benson Christalin (main)
* Tung Phan (update)

| width=25% |
=== Week 1: 20 Jun - 24 Jun ===
'''NCS: Mon, 1:30p-3p'''
* Jon Åge Stakvik (update)
* Jin Ge (update)
'''Biocircuits: Tues, 10a-12p'''
* Victoria Hsiao (long)
* Clare Hayes (short)

| width=25% |

=== Week 2: 27 Jun - 1 Jul ===
'''Biocircuits: Tues, 10a-12p'''
* Mark Prator (long)
* Shaobin Guo (short)

|- valign=top
| width=25% |

=== Week 3: 4 Jul - 8 Jul ===
'''Biocircuits: Mon, 10a-12p'''
* Vipul Singhal (long)
* Anu Thubagere (short)

| width=25% |
=== Week 4: 11 Jul - 15 Jul ===
'''Biocircuits: Mon, 10a-12p'''
* Ania Baetica (long)
* James Parkin (short)

| width=25% |

=== Week 5: 18 Jul - 22 Jul ===
* SEED

|- valign=top
| width=25% |
=== Week 6: 25 Jul - 29 Jul ===
'''Biocircuits: Mon, 10a-12p'''
* Yong Wu (long)
* Open (short)

| width=25% |
=== Week 7: 1 Aug - 5 Aug ===
'''Biocircuits: Mon, 10a-12p'''
* Andrey Shur (long)
* Sam Clamons (short)

| width=25% |
=== Week 8: 8 Aug - 12 Aug ===
'''Biocircuits: Mon, 11a-12p'''
* Lab cleanup
<hr>
* Richard in town Mon-Wed (tentative)

|- valign=top
| width=25% |
=== Week 9: 15 Aug - 19 Aug ===
'''Biocircuits: Mon, 10a-12p'''
* Andrew Montequin (SURF)
* Alex White (SURF)

| width=25% |
=== Week 10: 22 Aug - 26 Aug ===
'''Biocircuits: Mon, 10a-12p'''
* Reed McCardell (long)
* Anandh Swaminathan (short)

| width=25% |

=== Week 12: 29 Aug - 3 Sep ===
'''Biocircuits: Mon, 10a-12p'''
* Cindy Ren (long)
* Open (short)

|- valign=top
| width=25% |
=== Week 12: 5 Sep - 9 Sep ===
'''Biocircuits: Mon, 10a-12p'''
* Clare Hayes (long)
* Open (short)

| width=25% |
=== Week 13: 12 Sep - 16 Sep ===
'''Biocircuits: Mon, 10a-12p'''
* [Hold: George Artavanis] (long)
* Open (short)

| width=25% |
=== Week 14: 19 Sep - 23 Sep ===
'''Biocircuits: Mon, 10a-12p'''
* [Hold: William Poole] (long)
* Open (short)
|}

Group Schedule, Winter 2016

2016-01-28T18:19:55Z

Sguo: /* Week 7: 15 Feb - 19 Feb */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [[Schedule|Richard's calendar (travel)]]
| width=50% |
* [[Group Schedule, Fall 2015]]
|}

The schedule for group and subgroup meetings is given below. Contact Richard if you need to change the schedule. Unless otherwise noted, here are the locations of the meetings:

:{| width=100%
|- valign=top
| width=30% |
* Group meetings - 213 ANB
| width=30% |
* Biocircuits subgroup - 111 Keck
| width=30% |
* NCS subgroup - 243 ANB
|}

{| width=100% border=1

|- valign=top
| width=25% |
=== Week 1: 4 Jan - 8 Jan ===
* Richard in India (Mon-Fri)

| width=25% |

=== Week 2: 11 Jan - 15 Jan ===
* Richard in India (Mon-Fri)

| width=25% |

=== Week 3: 18 Jan - 22 Jan ===
'''NCS: Tue, 1p-2:30p'''
* Ioannis Filippidis (main)
* Benson Christalin (short)
'''Biocircuits: Tue, 3p-5p'''
* Yutaka Hori (long)
* Clare Hayes (short)

|- valign=top
| width=25% |

=== Week 4: 25 Jan - 29 Jan ===
'''Biocircuits: Tue, 10a-12p'''
* Vipul Singhal (long)
* Abel Chiao (short)
'''NCS: Wed, 10:30a-12p'''
* Cat McGhan (main)
* Ioannis Filippidis (short)

| width=25% |

=== Week 5: 1 Feb - 5 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* Victoria Hsiao (long)
* Anandh Swaminathan (short)
'''NCS: Wed, 10:30a-12p'''
* Tony Fragoso (main)
* Open (short)

| width=25% |

=== Week 6: 8 Feb - 12 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* Meeting will probably shift to Mon, 10a-12p
* Ania Baetica (long)
* Anu Thubagere (short)
'''NCS: Wed, 10:30a-12p'''
* Meeting will probably shift to Mon, 1p-2:30p
* Sumanth Dathathri (main)
* Open (short)

|- valign=top
| width=25% |

=== Week 7: 15 Feb - 19 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* Yong Wu (long)
* James Parkin (short)
'''NCS: Wed, 10:30a-12p'''
* Daniel Naftalovich (main)
* Open (short)

| width=25% |

=== Week 8: 22 Feb - 26 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* Andrey Shur (long)
* Shaobin Guo (short)
'''NCS: Tue, 1:30p-3p'''
* Ivan Papusha (main)
* Open (short)

| width=25% |

=== Week 9: 29 Feb - 4 Mar ===
'''Biocircuits: Tue, 10a-12p'''
* Sam Clamons (short)
* Sean Sanchez (short)
* Tina Xu (UG)
'''NCS: Wed, 10:30a-12p'''
* Jiangang Li (main)
* Sumanth Dathathri (short)
|- valign=top
| width=25% |

=== Week 10: 7 Mar - 11 Mar ===
'''Biocircuits: Tue, 10a-12p'''
* Open (rotation)
* Tiffany Zhou (UG)
'''NCS: Wed, 10:30a-12p'''
* Benson Christalin (main)
* Open (short)

| width=25% |

=== Week 11: 14 Mar - 18 Mar ===
'''Biocircuits: Tue, 10a-12p'''
* Open (rotation)
* Andrew Montequin (UG)
'''NCS: Wed, 10:30a-12p'''
* Visitor (main)
* Open (short)

| width=25% |

=== Week 12: 21 Mar - 25 Mar ===
* Richard out of town (Mon-Fri)
|}

Group Schedule, Winter 2016

2016-01-28T18:19:38Z

Sguo: /* Week 8: 22 Feb - 26 Feb */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [[Schedule|Richard's calendar (travel)]]
| width=50% |
* [[Group Schedule, Fall 2015]]
|}

The schedule for group and subgroup meetings is given below. Contact Richard if you need to change the schedule. Unless otherwise noted, here are the locations of the meetings:

:{| width=100%
|- valign=top
| width=30% |
* Group meetings - 213 ANB
| width=30% |
* Biocircuits subgroup - 111 Keck
| width=30% |
* NCS subgroup - 243 ANB
|}

{| width=100% border=1

|- valign=top
| width=25% |
=== Week 1: 4 Jan - 8 Jan ===
* Richard in India (Mon-Fri)

| width=25% |

=== Week 2: 11 Jan - 15 Jan ===
* Richard in India (Mon-Fri)

| width=25% |

=== Week 3: 18 Jan - 22 Jan ===
'''NCS: Tue, 1p-2:30p'''
* Ioannis Filippidis (main)
* Benson Christalin (short)
'''Biocircuits: Tue, 3p-5p'''
* Yutaka Hori (long)
* Clare Hayes (short)

|- valign=top
| width=25% |

=== Week 4: 25 Jan - 29 Jan ===
'''Biocircuits: Tue, 10a-12p'''
* Vipul Singhal (long)
* Abel Chiao (short)
'''NCS: Wed, 10:30a-12p'''
* Cat McGhan (main)
* Ioannis Filippidis (short)

| width=25% |

=== Week 5: 1 Feb - 5 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* Victoria Hsiao (long)
* Anandh Swaminathan (short)
'''NCS: Wed, 10:30a-12p'''
* Tony Fragoso (main)
* Open (short)

| width=25% |

=== Week 6: 8 Feb - 12 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* Meeting will probably shift to Mon, 10a-12p
* Ania Baetica (long)
* Anu Thubagere (short)
'''NCS: Wed, 10:30a-12p'''
* Meeting will probably shift to Mon, 1p-2:30p
* Sumanth Dathathri (main)
* Open (short)

|- valign=top
| width=25% |

=== Week 7: 15 Feb - 19 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* Yong Wu (long)
* Shaobin Guo (short)
'''NCS: Wed, 10:30a-12p'''
* Daniel Naftalovich (main)
* Open (short)

| width=25% |

=== Week 8: 22 Feb - 26 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* Andrey Shur (long)
* Shaobin Guo (short)
'''NCS: Tue, 1:30p-3p'''
* Ivan Papusha (main)
* Open (short)

| width=25% |

=== Week 9: 29 Feb - 4 Mar ===
'''Biocircuits: Tue, 10a-12p'''
* Sam Clamons (short)
* Sean Sanchez (short)
* Tina Xu (UG)
'''NCS: Wed, 10:30a-12p'''
* Jiangang Li (main)
* Sumanth Dathathri (short)
|- valign=top
| width=25% |

=== Week 10: 7 Mar - 11 Mar ===
'''Biocircuits: Tue, 10a-12p'''
* Open (rotation)
* Tiffany Zhou (UG)
'''NCS: Wed, 10:30a-12p'''
* Benson Christalin (main)
* Open (short)

| width=25% |

=== Week 11: 14 Mar - 18 Mar ===
'''Biocircuits: Tue, 10a-12p'''
* Open (rotation)
* Andrew Montequin (UG)
'''NCS: Wed, 10:30a-12p'''
* Visitor (main)
* Open (short)

| width=25% |

=== Week 12: 21 Mar - 25 Mar ===
* Richard out of town (Mon-Fri)
|}

Research meetings, Jan/Feb 2016

2016-01-19T04:33:49Z

Sguo: /* 27 Jan 2016 (Wed) */

Please sign up for a slot below. __NOTOC__

{| border=1 width=100%
|- valign = top
|
=== 25 Jan 2016 (Mon) ===
* Richard in SF
|
=== 26 Jan 2016 (Tue) ===
* 1-2 pm: Andrey Shur
* 2-3 pm: Anders Knight
* 3-4 pm: Reed McCardell
* 5:30-6:30 pm: Ania Baetica
|

=== 27 Jan 2016 (Wed) ===
* 8:30-9:30 am: Vipul Singhal
* 9:30-10:30 am: Anandh Swaminathan
* 4-5 pm: Shaobin
* 5-6 pm: open
|

=== 28 Jan 2016 (Thu) ===
* 5:30-6:30 pm: open
* 6:30-7:30 pm: open
|
=== 29 Jan 2016 (Fri) ===
* 2-3 pm: Victoria Hsiao
* 3-4 pm: Clare
* 4:30-5:30 pm: Ioannis Filippidis
* 5:30-6:30 pm: open
|- valign = top
|

=== 25 Jan 2016 (Mon) ===
* Richard in Hartford
|
=== 2 Feb 2016 (Tue) ===
* 9-10 am: Yong W.
* 2-3 pm: Tony Fragoso
* 3-4 pm: open
* 4-5 pm: James Parkin
* 5:30-6:30 pm: Daniel Naftalovich
* 6:30-7:30 pm: Anu Thubagere
|

=== 3 Feb 2016 (Wed) ===
* 8:30-9:30 am: open
* 9:30-10:30 am: open
|
=== 4 Feb 2016 (Thu) ===
* Richard in SF
|
=== 5 Feb 2016 (Fri) ===
* BE visiting day
|}

Tom Ellis, May 2015

2015-05-06T00:42:04Z

Sguo: /* Schedule: 18 May (Mon) */

Tom Ellis from Imperial College will be visiting on 18 May (Mon). If you would like to meet with him, please sign up for a slot below.

=== Schedule: 18 May (Mon) ===

{{agenda begin}}
{{agenda item|12:00 pm|Lunch with Richard}}
{{agenda item|1:15 pm|Biosensors and multicellular circuits - Shaobin, Victoria and James}}
{{agenda item|2:00 pm|Open}}
{{agenda item|2:45 pm|Open}}
{{agenda item|3:30 pm|Open}}
{{agenda item|4:15 pm|Metabolic engineering - Yong, }}
{{agenda item|5:00 pm|Richard}}
{{agenda item|5:30 pm|Done for the day}}
{{agenda end}}

SURF discussions, Jan 2015

2015-01-20T18:07:06Z

Sguo: /* 26 Jan (Mon) */

Slots for talking with applicants and co-mentors about SURF projects. Please sign up for one of the slots below. All times are PST. __NOTOC__

{| width=100% border=1
|- valign=top
|
==== 21 Jan (Wed) ====
* 9:20: Samira and Nuno
* 9:50: Open
<hr>
* 14:30: Rafsan Chowdhury
<hr>
* 15:30: Open
|

==== 22 Jan (Thu) ====
* 9:00: Open
<hr>
* 17:30: Open
* 18:00: Open
|

==== 23 Jan (Fri) ====
* 10:00:Aileen Cheng
<hr>
* 14:00: Open
* 14:30: Open
<hr>
* 16:00: Open
|

==== 26 Jan (Mon) ====
* 8:00: Open
* 8:30: Phuc (Sam), Yong, Shaobin
<hr>
* 17:30: Samira, Vasu, Yuening (tentative)
* 18:00: Open
|}

The agenda for the phone call is (roughly):

# Description of the basic idea behind the project (based on applicant's understanding)
# Discussion about approaches, things to read, variations to consider, etc
# Discussion of the format of the proposal
# Questions and discussion about the process

SURF discussions, Jan 2015

2015-01-20T18:06:47Z

Sguo: /* 26 Jan (Mon) */

Slots for talking with applicants and co-mentors about SURF projects. Please sign up for one of the slots below. All times are PST. __NOTOC__

{| width=100% border=1
|- valign=top
|
==== 21 Jan (Wed) ====
* 9:20: Samira and Nuno
* 9:50: Open
<hr>
* 14:30: Rafsan Chowdhury
<hr>
* 15:30: Open
|

==== 22 Jan (Thu) ====
* 9:00: Open
<hr>
* 17:30: Open
* 18:00: Open
|

==== 23 Jan (Fri) ====
* 10:00:Aileen Cheng
<hr>
* 14:00: Open
* 14:30: Open
<hr>
* 16:00: Open
|

==== 26 Jan (Mon) ====
* 8:00: Open
* 8:30: Phuc, Yong, Shaobin (Sam)
<hr>
* 17:30: Samira, Vasu, Yuening (tentative)
* 18:00: Open
|}

The agenda for the phone call is (roughly):

# Description of the basic idea behind the project (based on applicant's understanding)
# Discussion about approaches, things to read, variations to consider, etc
# Discussion of the format of the proposal
# Questions and discussion about the process

Group Schedule, Winter 2014

2014-02-06T19:15:51Z

Sguo: /* Week 10: 10 Mar - 14 Mar */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [[Schedule|Richard's calendar (travel)]]
| width=50% |
* [[Group Schedule, Fall 2013]]
|}

The schedule for group and subgroup meetings is given below. Contact Richard if you need to change the schedule. Unless otherwise noted, here are the locations of the meetings:

:{| width=100%
|- valign=top
| width=30% |
* Group meetings - 213 ANB
| width=30% |
* Biocircuits subgroup - 111 Keck
| width=30% |
* NCS subgroup - 243 ANB
|}

{| width=100% border=1

|- valign=top
| width=30% |
=== Week 1: 6 Jan - 10 Jan ===
'''Biocircuits: Mon, 10a-12p'''
* Vipul Singhal
* Yutaka Hori
'''NCS: Thu, 3p-5p'''
* Ivan Papusha
* Vasu Raman
| width=30% |

=== Week 2: 13 Jan - 17 Jan ===
'''Biocircuits: Mon, 10a-12p'''
* Victoria Hsiao
* Marcella Gomez
'''NCS: Thu, 3p-5p'''
* Stephanie Tsuei
* Scott Livingston
| width=30% |

=== Week 3: 20 Jan - 24 Jan ===
'''Biocircuits: Tue, 10:30a-12:30p'''
* Dan Siegal-Gaskins
* Anandh Swaminathan
'''NCS: Wed, 10a-12p'''
* Yilin Mo
* iCyPhy planning
|- valign=top
| width=30% |

=== Week 4: 27 Jan - 31 Jan ===
'''Biocircuits: Tue, 10:30a-12:30p'''
* Anu Thubagere
* Zach Sun
'''NCS: Wed, 10:00a-12:00p'''
* Eric Wolff
| width=30% |

=== Week 5: 3 Feb - 7 Feb ===
'''Biocircuits: Tue, 1-3p'''
* Jongmin Kim
* Vanessa Jonsson
'''NCS: Wed, 10:00a-12:00p'''
* Matanya Horowitz
* TerraSwarm planning

| width=30% |

=== Week 6: 10 Feb - 14 Feb ===
'''Biocircuits: Tue, 10:30a-12:30p'''
* <strike> Shaobin Guo </strike>
* Emzo de los Santos
'''NCS: Wed, 10:00a-12:00p'''
* Ioannis Filippidis
* TuLiP planning
|- valign=top
| width=30% |

=== Week 7: 17 Feb - 21 Feb ===
* Richard out of town, Mon-Fri
* Biocircuits lab cleanup, Tue @ 10 am
| width=30% |

=== Week 8: 24 Feb - 28 Feb ===
'''Biocircuits: Tue, 12-1:30 pm'''
* Yong Wu
* Clare Hayes
'''NCS: Wed, 10:00a-12:00p'''
* Marcella Gomez
* Mark Milam visit (tentative)

| width=30% |

=== Week 9: 3 Mar - 7 Mar ===
'''Biocircuits: Thu, 10:30a-12:30p'''
* Enoch Yeung
* Joe Meyerowitz
'''NCS: Thu, 3p-5p'''
* Duo Han
* Anandh Swaminathan?

|- valign=top
| width=30% |

=== Week 10: 10 Mar - 14 Mar ===
'''Biocircuits: Wed, 10a-12p'''
* Zach Shao
* Ania Baetica
* Shaobin Guo
'''NCS: Wed, 1p-3p'''
* Open
* Open

| width=30% |

=== Week 11: 17 Mar - 21 Mar ===
* Richard out of town, Mon-Fri
* Biocircuits lab cleanup, Tue @ 10 am
* Vincent Noireaux visiting Caltech, 17-18 Mar
| width=30% |

=== Week 13: 24 Mar- 28 Mar ===
* Spring break

|}

Group Schedule, Winter 2014

2014-02-06T19:15:40Z

Sguo: /* Week 6: 10 Feb - 14 Feb */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [[Schedule|Richard's calendar (travel)]]
| width=50% |
* [[Group Schedule, Fall 2013]]
|}

The schedule for group and subgroup meetings is given below. Contact Richard if you need to change the schedule. Unless otherwise noted, here are the locations of the meetings:

:{| width=100%
|- valign=top
| width=30% |
* Group meetings - 213 ANB
| width=30% |
* Biocircuits subgroup - 111 Keck
| width=30% |
* NCS subgroup - 243 ANB
|}

{| width=100% border=1

|- valign=top
| width=30% |
=== Week 1: 6 Jan - 10 Jan ===
'''Biocircuits: Mon, 10a-12p'''
* Vipul Singhal
* Yutaka Hori
'''NCS: Thu, 3p-5p'''
* Ivan Papusha
* Vasu Raman
| width=30% |

=== Week 2: 13 Jan - 17 Jan ===
'''Biocircuits: Mon, 10a-12p'''
* Victoria Hsiao
* Marcella Gomez
'''NCS: Thu, 3p-5p'''
* Stephanie Tsuei
* Scott Livingston
| width=30% |

=== Week 3: 20 Jan - 24 Jan ===
'''Biocircuits: Tue, 10:30a-12:30p'''
* Dan Siegal-Gaskins
* Anandh Swaminathan
'''NCS: Wed, 10a-12p'''
* Yilin Mo
* iCyPhy planning
|- valign=top
| width=30% |

=== Week 4: 27 Jan - 31 Jan ===
'''Biocircuits: Tue, 10:30a-12:30p'''
* Anu Thubagere
* Zach Sun
'''NCS: Wed, 10:00a-12:00p'''
* Eric Wolff
| width=30% |

=== Week 5: 3 Feb - 7 Feb ===
'''Biocircuits: Tue, 1-3p'''
* Jongmin Kim
* Vanessa Jonsson
'''NCS: Wed, 10:00a-12:00p'''
* Matanya Horowitz
* TerraSwarm planning

| width=30% |

=== Week 6: 10 Feb - 14 Feb ===
'''Biocircuits: Tue, 10:30a-12:30p'''
* <strike> Shaobin Guo </strike>
* Emzo de los Santos
'''NCS: Wed, 10:00a-12:00p'''
* Ioannis Filippidis
* TuLiP planning
|- valign=top
| width=30% |

=== Week 7: 17 Feb - 21 Feb ===
* Richard out of town, Mon-Fri
* Biocircuits lab cleanup, Tue @ 10 am
| width=30% |

=== Week 8: 24 Feb - 28 Feb ===
'''Biocircuits: Tue, 12-1:30 pm'''
* Yong Wu
* Clare Hayes
'''NCS: Wed, 10:00a-12:00p'''
* Marcella Gomez
* Mark Milam visit (tentative)

| width=30% |

=== Week 9: 3 Mar - 7 Mar ===
'''Biocircuits: Thu, 10:30a-12:30p'''
* Enoch Yeung
* Joe Meyerowitz
'''NCS: Thu, 3p-5p'''
* Duo Han
* Anandh Swaminathan?

|- valign=top
| width=30% |

=== Week 10: 10 Mar - 14 Mar ===
'''Biocircuits: Wed, 10a-12p'''
* Zach Shao
* Ania Baetica
'''NCS: Wed, 1p-3p'''
* Open
* Open

| width=30% |

=== Week 11: 17 Mar - 21 Mar ===
* Richard out of town, Mon-Fri
* Biocircuits lab cleanup, Tue @ 10 am
* Vincent Noireaux visiting Caltech, 17-18 Mar
| width=30% |

=== Week 13: 24 Mar- 28 Mar ===
* Spring break

|}

TX-TL Workshop, Aug 2013: Detailed Schedule

2013-08-30T17:49:52Z

Sguo: /* Friday */

{{righttoc}}
The detailed schedule below describes that is happening in each track of the [[TX-TL Workshop, Aug 2013|TX-TL workshop]] and roughly when different groups should be doing different things. Zach and Clare are responsible for keeping track of what is going on. The master copy of this schedule is on the [https://www.cds.caltech.edu/biocircuits/index.php/TX-TL_workshop,_26-30_Aug_2013#Detailed_schedule|biocircuits wiki] (not publicly accessible). A summary of the workshop schedule is available on the [[TX-TL Workshop, Aug 2013|main workshop page]].

==== Monday ====
Goals:
* TX-TL basics: Get everyone up to speed on the basics of TX-TL and the tools we will need for the rest of the week
* TX-TL extract: Create colonies from stocks

 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL basics
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|-
| 9:30 || Optional tutorials
* Geneious (Emzo)
| || ||
|-
| 12:00 || colspan=4 align=center | Lunch at Chandler: meet outside of Keck Lab at noon
|-
| 1:30 || colspan=4 align=center | Welcome and Introductions, 114 Steele Lab
|-
| 2:00 || Overview (Richard, Vincent)
* [http://www.cds.caltech.edu/~murray/talks/breadboards_workshop-26Aug13.pdf Biomolecular breadboards], Richard
* [http://www.cds.caltech.edu/~murray/talks/noireaux_txtl-26Aug13.pdf TX-TL toolbox], Vincent
* Schedule for the week, Richard
| || ||
|-
| 3:30 || Lab safety session (Clare) || || ||
|- valign=top
| 4:00
| Set up reactions for inducible promoter reactions (Zach, Clare)
* Use the [http://www.cds.caltech.edu/~murray/talks/TXTL_e18_template.xlsx TX-TL spreadsheet] to set up reactions at 4 different inducer levels
* Pipette reactions into 384 well plate (two columns per team, run in duplicate)
* Run overnight on plate reader at 29 degC
| || ||
|-
| 5:30 || || || || Streak out colonies
|-
| 6:00 || colspan=4 align=center | Done for the day
|-
| 7:30 || Optional tutorials
* MATLAB/Simbiology (Zoltan)
* Lab techniques (Enoch)
|
|
|
|}

==== Tuesday ====
Goals:
* TX-TL basics: plot experimental data and learn about TX-TL modeling and simulation
* TX-TL implement: create and run linear DNA, create "3X" plasmid DNA plates
* TX-TL design: meet with TAs to discuss projects
* TX-TL extract: pick colonies and grow up cells
* TX-TL extras: prepare phospholipids for use on Wed
 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL basics
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|-
| 9:00 || Analyze TX-TL results from previous day
* Take data off of plate reader, plot in Excel (or MATLAB)
* [[Media:firstday_data.xlsx|Data available here]]
Golden Gate cloning overview (1 hr, Zach)
* [[Media:overallfirstGenAssembly.png|diagram]]
| || ||
|- valign=top
| 10:00 || || || || Pick colonies, start cultures
|- valign=top
| 10:30 || TX-TL modeling toolbox (Vipul, Zoltan)
* Toolbox overview (45 m)
* Hands-on demo (30 m)
* Run models of results from previous evening (script)
| || ||
|-
| 12:00 || colspan=4 align=center | Lunch
|- valign=top
| 1:00 || || DNA assembly (Zach, Clare, Shaobin)
* Assemble feedforward loop onto individual plasmids ("3X"): AraC, TetR, deGFP ([[Media:GoldenBraid Assembly 082713.png|diagram]], [http://www.cds.caltech.edu/~murray/talks/DNA_Assembly_Protocol.pdf protocol])
* Start PCR reactions to amplify linear
* Transform plasmids (3X) and streak out on plates
| ||
|- valign=top
| 3:00
| G4, G5: Vesicles prep. Reaction and feeding solutions [Vincent]
G6: ALL intro session [Enoch]
| valign=center | PCR runs (2 hr)
| G1-G3: Breakout discussions (w/ TAs)
* Each group will choose a circuit to prototype using linear DNA on Wed, Thu
* Choices: RNA circuit, negative auto-regulation, genetic switch, IFFL2
* TAs: Emzo de los Santos (vesicles), Victoria Hsiao (ALL), Dan Siegal-Gaskins (logic), Vipul Singhal (RNA), Zoltan Tuza (genetic switch), Yong Wu (vesicles)
|
|- valign=top
| 5:00 || || Set up linear DNA runs
* Run gels to confirm PCR results
* PCR cleanup linear DNA segments
* Each group will set up 2 columns of runs (duplicates). Vary aTc and arabinose (2 each + controls)
* Biotek 1: Run linear FFL overnight at 29 degC [[Media:TXTL e11 linear IFFL 082713.xlsx|Spreadsheet available here]]
[Pre-prepared linear DNA available for all circuits in case your PCR didn't work]
|
| valign=bottom| Passage cells
|-
| 7:00 || colspan=4 | Done for the day
|-
| colspan=5 align=center | Homework: Simulate feedfoward loops + individual circuits
|}

==== Wednesday ====
Goals
* TX-TL implement: analyze linear DNA, set up and run 3X plasmids in TX-TL
* TX-TL design: create circuits and set up overnight runs
* TX-TL extract: bead beating and dialysis
* TX-TL extras: set up and run vesicles, set up and run droplets
 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL extras
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|- valign=top
| 10:00
| G4, G5: Vesicles prep: phospholipids [Vincent]
G6: ALL protocol development [Enoch]
| valign=middle |
| G1-G3: Plan out circuits designs to build and test (with TAs)
* Decide on what experiments you want to run
* Check availability of parts; plan out assemblies for the day, if needed
| Pellet and wash cells (Jongmin, Anu)
* Demonstrate how to pellet and wash cells
|- valign=top
| 12:30 || || Go over data from previous night [[Media:Workday2 IFFL data 082713.xlsx|Data available here]] || ||
|- valign=top
| 1:00 || colspan=4 | Lunch
|- valign=top
| 2:00
| G4-G6: demonstration sessions (optional)
* 2:00 (prep @ 1:45): Vesicles demo (Vincent): review preparation of feeding, reaction, phospholipids + live vesicles prep [Vincent] + view pre-prepared vesicles on microscope
* 3:30: Droplets (Enoch): ALL overview + set up reactions for evening run (Keck 040 - sub-basement)

Remaining time: Meet in small groups and work on circuit
|
|
| G1-G3: bead beating, centrifugation, dialysis (Jongmin, Anu, Clare) - Keck 116
* Each student to set up at least one bead beating tube
* Run bead beating and centrifuge results
* Load dialysis cassettes

Remaining time: Meet in small groups and work on circuit
|- valign=top
| 5:00
|
* Start ALL runs (Enoch)
| colspan=2 | Set up overnight runs
* Biotek1: FFL 3X plasmids [[Media:TXTL e11 linear IFFL workshop test plasmid 082813.xlsx|Spreadsheet available here]]
* Victor: RNA circuit
* Biotek 2: Switch and logic circuits
|
|-
| 6:00 || colspan=4 | Done for the day
|-
| colspan=5 align=center | Homework: Simulate feedfoward loops + individual circuits
|}

==== Thursday ====
Goals
* TX-TL implement: analyze 3X plasmid DNA circuits, set up and run 1X plasmids in TX-TL + cells with 1X plasmid
* TX-TL design: modify circuits and/or set up plasmid versions; set up overnight runs
* TX-TL extract: bead beating and dialysis (second set of groups)
* TX-TL extras: set up and run vesicles, set up and run droplets (first set of groups)
 

{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL extras
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|- valign=top
| 10:00
| G1-G3: demonstration sessions (optional)
* 10:00: Vesicles demo (Vincent): review prep of reaction, feeding, phospholipid, vesicles + view vesicles from previous day on microscope
* 11:30: Droplets (Enoch): ALL overview + set up reactions for afternoon run (Keck 040 - sub-basement)
|
| Circuit design and preparation (if needed)
* Decide on new runs to be done with circuit variants
| G4-G6: bead beating, centrifugation, dialysis (Anu, Jongmin, Clare) - Keck 116
* Each student to set up at least one bead beating tube
* Run bead beating and centrifuge results
* Load dialysis cassettes
|- valign=top
| 12:30 || || Go over data from previous night [[Media:Workday3 IFFL data 082813.xlsx|Data available here]] || ||
|- valign=top
| 1:00 || colspan=4 | Lunch
|- valign=top
| 2:00
|
* Start ALL runs (Enoch)
|
|
| Extract prep overview (Clare) - Steele library
* Review of whole process and calibration procedure
* Discuss variability between extract batches (with data)
|- valign=top
| 3:00 || colspan=4 | Meet in small groups

|- valign=top
| 5:00
|
In vivo runs
* Dilute cells and set up in 96 well plate
* Run in Biotek 2
|
|
|
|- valign=top
| 6:00 || colspan=4 | Done for the day
|-
| colspan=5 align=center | Homework: Simulate feedfoward loops + individual circuits
|}

==== Friday ====
Goals:
* TX-TL implement: compare simulations, linear, 3X plasmid, 1X plasmid and ''in vivo'' results
* TX-TL design: analyze results and make short presentation
* TX-TL extras: present data from previous days
 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL extras
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|- valign=top
| 10:00
|
| Analyze and compare data [[Media:Workday4 IFFL in vivo data 082913.xlsx|Data available here]]
* Simulations (Tue night), linear TX-TL (Tue night), plasmid TX-TL (Wed/Thu nights), cells (Thu night)
| Analyze data
* Data analysis of in vivo FFL results
|
|- valign=top
| 10:30
| colspan=3 | Group presentations
* 10 minute presentation of circuit results to the group
* Enoch: ALL data
|
|-
| 12:00
| colspan=4 | Group lunch - Pizza! Meet in Steele library
|}

TX-TL Workshop, Aug 2013: Detailed Schedule

2013-08-30T17:49:30Z

Sguo: /* Friday */

{{righttoc}}
The detailed schedule below describes that is happening in each track of the [[TX-TL Workshop, Aug 2013|TX-TL workshop]] and roughly when different groups should be doing different things. Zach and Clare are responsible for keeping track of what is going on. The master copy of this schedule is on the [https://www.cds.caltech.edu/biocircuits/index.php/TX-TL_workshop,_26-30_Aug_2013#Detailed_schedule|biocircuits wiki] (not publicly accessible). A summary of the workshop schedule is available on the [[TX-TL Workshop, Aug 2013|main workshop page]].

==== Monday ====
Goals:
* TX-TL basics: Get everyone up to speed on the basics of TX-TL and the tools we will need for the rest of the week
* TX-TL extract: Create colonies from stocks

 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL basics
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|-
| 9:30 || Optional tutorials
* Geneious (Emzo)
| || ||
|-
| 12:00 || colspan=4 align=center | Lunch at Chandler: meet outside of Keck Lab at noon
|-
| 1:30 || colspan=4 align=center | Welcome and Introductions, 114 Steele Lab
|-
| 2:00 || Overview (Richard, Vincent)
* [http://www.cds.caltech.edu/~murray/talks/breadboards_workshop-26Aug13.pdf Biomolecular breadboards], Richard
* [http://www.cds.caltech.edu/~murray/talks/noireaux_txtl-26Aug13.pdf TX-TL toolbox], Vincent
* Schedule for the week, Richard
| || ||
|-
| 3:30 || Lab safety session (Clare) || || ||
|- valign=top
| 4:00
| Set up reactions for inducible promoter reactions (Zach, Clare)
* Use the [http://www.cds.caltech.edu/~murray/talks/TXTL_e18_template.xlsx TX-TL spreadsheet] to set up reactions at 4 different inducer levels
* Pipette reactions into 384 well plate (two columns per team, run in duplicate)
* Run overnight on plate reader at 29 degC
| || ||
|-
| 5:30 || || || || Streak out colonies
|-
| 6:00 || colspan=4 align=center | Done for the day
|-
| 7:30 || Optional tutorials
* MATLAB/Simbiology (Zoltan)
* Lab techniques (Enoch)
|
|
|
|}

==== Tuesday ====
Goals:
* TX-TL basics: plot experimental data and learn about TX-TL modeling and simulation
* TX-TL implement: create and run linear DNA, create "3X" plasmid DNA plates
* TX-TL design: meet with TAs to discuss projects
* TX-TL extract: pick colonies and grow up cells
* TX-TL extras: prepare phospholipids for use on Wed
 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL basics
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|-
| 9:00 || Analyze TX-TL results from previous day
* Take data off of plate reader, plot in Excel (or MATLAB)
* [[Media:firstday_data.xlsx|Data available here]]
Golden Gate cloning overview (1 hr, Zach)
* [[Media:overallfirstGenAssembly.png|diagram]]
| || ||
|- valign=top
| 10:00 || || || || Pick colonies, start cultures
|- valign=top
| 10:30 || TX-TL modeling toolbox (Vipul, Zoltan)
* Toolbox overview (45 m)
* Hands-on demo (30 m)
* Run models of results from previous evening (script)
| || ||
|-
| 12:00 || colspan=4 align=center | Lunch
|- valign=top
| 1:00 || || DNA assembly (Zach, Clare, Shaobin)
* Assemble feedforward loop onto individual plasmids ("3X"): AraC, TetR, deGFP ([[Media:GoldenBraid Assembly 082713.png|diagram]], [http://www.cds.caltech.edu/~murray/talks/DNA_Assembly_Protocol.pdf protocol])
* Start PCR reactions to amplify linear
* Transform plasmids (3X) and streak out on plates
| ||
|- valign=top
| 3:00
| G4, G5: Vesicles prep. Reaction and feeding solutions [Vincent]
G6: ALL intro session [Enoch]
| valign=center | PCR runs (2 hr)
| G1-G3: Breakout discussions (w/ TAs)
* Each group will choose a circuit to prototype using linear DNA on Wed, Thu
* Choices: RNA circuit, negative auto-regulation, genetic switch, IFFL2
* TAs: Emzo de los Santos (vesicles), Victoria Hsiao (ALL), Dan Siegal-Gaskins (logic), Vipul Singhal (RNA), Zoltan Tuza (genetic switch), Yong Wu (vesicles)
|
|- valign=top
| 5:00 || || Set up linear DNA runs
* Run gels to confirm PCR results
* PCR cleanup linear DNA segments
* Each group will set up 2 columns of runs (duplicates). Vary aTc and arabinose (2 each + controls)
* Biotek 1: Run linear FFL overnight at 29 degC [[Media:TXTL e11 linear IFFL 082713.xlsx|Spreadsheet available here]]
[Pre-prepared linear DNA available for all circuits in case your PCR didn't work]
|
| valign=bottom| Passage cells
|-
| 7:00 || colspan=4 | Done for the day
|-
| colspan=5 align=center | Homework: Simulate feedfoward loops + individual circuits
|}

==== Wednesday ====
Goals
* TX-TL implement: analyze linear DNA, set up and run 3X plasmids in TX-TL
* TX-TL design: create circuits and set up overnight runs
* TX-TL extract: bead beating and dialysis
* TX-TL extras: set up and run vesicles, set up and run droplets
 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL extras
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|- valign=top
| 10:00
| G4, G5: Vesicles prep: phospholipids [Vincent]
G6: ALL protocol development [Enoch]
| valign=middle |
| G1-G3: Plan out circuits designs to build and test (with TAs)
* Decide on what experiments you want to run
* Check availability of parts; plan out assemblies for the day, if needed
| Pellet and wash cells (Jongmin, Anu)
* Demonstrate how to pellet and wash cells
|- valign=top
| 12:30 || || Go over data from previous night [[Media:Workday2 IFFL data 082713.xlsx|Data available here]] || ||
|- valign=top
| 1:00 || colspan=4 | Lunch
|- valign=top
| 2:00
| G4-G6: demonstration sessions (optional)
* 2:00 (prep @ 1:45): Vesicles demo (Vincent): review preparation of feeding, reaction, phospholipids + live vesicles prep [Vincent] + view pre-prepared vesicles on microscope
* 3:30: Droplets (Enoch): ALL overview + set up reactions for evening run (Keck 040 - sub-basement)

Remaining time: Meet in small groups and work on circuit
|
|
| G1-G3: bead beating, centrifugation, dialysis (Jongmin, Anu, Clare) - Keck 116
* Each student to set up at least one bead beating tube
* Run bead beating and centrifuge results
* Load dialysis cassettes

Remaining time: Meet in small groups and work on circuit
|- valign=top
| 5:00
|
* Start ALL runs (Enoch)
| colspan=2 | Set up overnight runs
* Biotek1: FFL 3X plasmids [[Media:TXTL e11 linear IFFL workshop test plasmid 082813.xlsx|Spreadsheet available here]]
* Victor: RNA circuit
* Biotek 2: Switch and logic circuits
|
|-
| 6:00 || colspan=4 | Done for the day
|-
| colspan=5 align=center | Homework: Simulate feedfoward loops + individual circuits
|}

==== Thursday ====
Goals
* TX-TL implement: analyze 3X plasmid DNA circuits, set up and run 1X plasmids in TX-TL + cells with 1X plasmid
* TX-TL design: modify circuits and/or set up plasmid versions; set up overnight runs
* TX-TL extract: bead beating and dialysis (second set of groups)
* TX-TL extras: set up and run vesicles, set up and run droplets (first set of groups)
 

{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL extras
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|- valign=top
| 10:00
| G1-G3: demonstration sessions (optional)
* 10:00: Vesicles demo (Vincent): review prep of reaction, feeding, phospholipid, vesicles + view vesicles from previous day on microscope
* 11:30: Droplets (Enoch): ALL overview + set up reactions for afternoon run (Keck 040 - sub-basement)
|
| Circuit design and preparation (if needed)
* Decide on new runs to be done with circuit variants
| G4-G6: bead beating, centrifugation, dialysis (Anu, Jongmin, Clare) - Keck 116
* Each student to set up at least one bead beating tube
* Run bead beating and centrifuge results
* Load dialysis cassettes
|- valign=top
| 12:30 || || Go over data from previous night [[Media:Workday3 IFFL data 082813.xlsx|Data available here]] || ||
|- valign=top
| 1:00 || colspan=4 | Lunch
|- valign=top
| 2:00
|
* Start ALL runs (Enoch)
|
|
| Extract prep overview (Clare) - Steele library
* Review of whole process and calibration procedure
* Discuss variability between extract batches (with data)
|- valign=top
| 3:00 || colspan=4 | Meet in small groups

|- valign=top
| 5:00
|
In vivo runs
* Dilute cells and set up in 96 well plate
* Run in Biotek 2
|
|
|
|- valign=top
| 6:00 || colspan=4 | Done for the day
|-
| colspan=5 align=center | Homework: Simulate feedfoward loops + individual circuits
|}

==== Friday ====
Goals:
* TX-TL implement: compare simulations, linear, 3X plasmid, 1X plasmid and ''in vivo'' results
* TX-TL design: analyze results and make short presentation
* TX-TL extras: present data from previous days
 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL extras
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|- valign=top
| 10:00
|
| Analyze and compare data
* Simulations (Tue night), linear TX-TL (Tue night), plasmid TX-TL (Wed/Thu nights), cells (Thu night)
| Analyze data [[Media:Workday4 IFFL in vivo data 082913.xlsx|Data available here]]
* Data analysis of in vivo FFL results
|
|- valign=top
| 10:30
| colspan=3 | Group presentations
* 10 minute presentation of circuit results to the group
* Enoch: ALL data
|
|-
| 12:00
| colspan=4 | Group lunch - Pizza! Meet in Steele library
|}

File:Workday4 IFFL in vivo data 082913.xlsx

2013-08-30T17:49:13Z

Sguo:

TX-TL Workshop, Aug 2013: Detailed Schedule

2013-08-29T22:26:37Z

Sguo: /* Wednesday */

{{righttoc}}
The detailed schedule below describes that is happening in each track of the [[TX-TL Workshop, Aug 2013|TX-TL workshop]] and roughly when different groups should be doing different things. Zach and Clare are responsible for keeping track of what is going on. The master copy of this schedule is on the [https://www.cds.caltech.edu/biocircuits/index.php/TX-TL_workshop,_26-30_Aug_2013#Detailed_schedule|biocircuits wiki] (not publicly accessible). A summary of the workshop schedule is available on the [[TX-TL Workshop, Aug 2013|main workshop page]].

==== Monday ====
Goals:
* TX-TL basics: Get everyone up to speed on the basics of TX-TL and the tools we will need for the rest of the week
* TX-TL extract: Create colonies from stocks

 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL basics
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|-
| 9:30 || Optional tutorials
* Geneious (Emzo)
| || ||
|-
| 12:00 || colspan=4 align=center | Lunch at Chandler: meet outside of Keck Lab at noon
|-
| 1:30 || colspan=4 align=center | Welcome and Introductions, 114 Steele Lab
|-
| 2:00 || Overview (Richard, Vincent)
* [http://www.cds.caltech.edu/~murray/talks/breadboards_workshop-26Aug13.pdf Biomolecular breadboards], Richard
* [http://www.cds.caltech.edu/~murray/talks/noireaux_txtl-26Aug13.pdf TX-TL toolbox], Vincent
* Schedule for the week, Richard
| || ||
|-
| 3:30 || Lab safety session (Clare) || || ||
|- valign=top
| 4:00
| Set up reactions for inducible promoter reactions (Zach, Clare)
* Use the [http://www.cds.caltech.edu/~murray/talks/TXTL_e18_template.xlsx TX-TL spreadsheet] to set up reactions at 4 different inducer levels
* Pipette reactions into 384 well plate (two columns per team, run in duplicate)
* Run overnight on plate reader at 29 degC
| || ||
|-
| 5:30 || || || || Streak out colonies
|-
| 6:00 || colspan=4 align=center | Done for the day
|-
| 7:30 || Optional tutorials
* MATLAB/Simbiology (Zoltan)
* Lab techniques (Enoch)
|
|
|
|}

==== Tuesday ====
Goals:
* TX-TL basics: plot experimental data and learn about TX-TL modeling and simulation
* TX-TL implement: create and run linear DNA, create "3X" plasmid DNA plates
* TX-TL design: meet with TAs to discuss projects
* TX-TL extract: pick colonies and grow up cells
* TX-TL extras: prepare phospholipids for use on Wed
 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL basics
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|-
| 9:00 || Analyze TX-TL results from previous day
* Take data off of plate reader, plot in Excel (or MATLAB)
* [[Media:firstday_data.xlsx|Data available here]]
Golden Gate cloning overview (1 hr, Zach)
* [[Media:overallfirstGenAssembly.png|diagram]]
| || ||
|- valign=top
| 10:00 || || || || Pick colonies, start cultures
|- valign=top
| 10:30 || TX-TL modeling toolbox (Vipul, Zoltan)
* Toolbox overview (45 m)
* Hands-on demo (30 m)
* Run models of results from previous evening (script)
| || ||
|-
| 12:00 || colspan=4 align=center | Lunch
|- valign=top
| 1:00 || || DNA assembly (Zach, Clare, Shaobin)
* Assemble feedforward loop onto individual plasmids ("3X"): AraC, TetR, deGFP ([[Media:GoldenBraid Assembly 082713.png|diagram]], [http://www.cds.caltech.edu/~murray/talks/DNA_Assembly_Protocol.pdf protocol])
* Start PCR reactions to amplify linear
* Transform plasmids (3X) and streak out on plates
| ||
|- valign=top
| 3:00
| G4, G5: Vesicles prep. Reaction and feeding solutions [Vincent]
G6: ALL intro session [Enoch]
| valign=center | PCR runs (2 hr)
| G1-G3: Breakout discussions (w/ TAs)
* Each group will choose a circuit to prototype using linear DNA on Wed, Thu
* Choices: RNA circuit, negative auto-regulation, genetic switch, IFFL2
* TAs: Emzo de los Santos (vesicles), Victoria Hsiao (ALL), Dan Siegal-Gaskins (logic), Vipul Singhal (RNA), Zoltan Tuza (genetic switch), Yong Wu (vesicles)
|
|- valign=top
| 5:00 || || Set up linear DNA runs
* Run gels to confirm PCR results
* PCR cleanup linear DNA segments
* Each group will set up 2 columns of runs (duplicates). Vary aTc and arabinose (2 each + controls)
* Biotek 1: Run linear FFL overnight at 29 degC [[Media:TXTL e11 linear IFFL 082713.xlsx|Spreadsheet available here]]
[Pre-prepared linear DNA available for all circuits in case your PCR didn't work]
|
| valign=bottom| Passage cells
|-
| 7:00 || colspan=4 | Done for the day
|-
| colspan=5 align=center | Homework: Simulate feedfoward loops + individual circuits
|}

==== Wednesday ====
Goals
* TX-TL implement: analyze linear DNA, set up and run 3X plasmids in TX-TL
* TX-TL design: create circuits and set up overnight runs
* TX-TL extract: bead beating and dialysis
* TX-TL extras: set up and run vesicles, set up and run droplets
 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL extras
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|- valign=top
| 10:00
| G4, G5: Vesicles prep: phospholipids [Vincent]
G6: ALL protocol development [Enoch]
| valign=middle |
| G1-G3: Plan out circuits designs to build and test (with TAs)
* Decide on what experiments you want to run
* Check availability of parts; plan out assemblies for the day, if needed
| Pellet and wash cells (Jongmin, Anu)
* Demonstrate how to pellet and wash cells
|- valign=top
| 12:30 || || Go over data from previous night [[Media:Workday2 IFFL data 082713.xlsx|Data available here]] || ||
|- valign=top
| 1:00 || colspan=4 | Lunch
|- valign=top
| 2:00
| G4-G6: demonstration sessions (optional)
* 2:00 (prep @ 1:45): Vesicles demo (Vincent): review preparation of feeding, reaction, phospholipids + live vesicles prep [Vincent] + view pre-prepared vesicles on microscope
* 3:30: Droplets (Enoch): ALL overview + set up reactions for evening run (Keck 040 - sub-basement)

Remaining time: Meet in small groups and work on circuit
|
|
| G1-G3: bead beating, centrifugation, dialysis (Jongmin, Anu, Clare) - Keck 116
* Each student to set up at least one bead beating tube
* Run bead beating and centrifuge results
* Load dialysis cassettes

Remaining time: Meet in small groups and work on circuit
|- valign=top
| 5:00
|
* Start ALL runs (Enoch)
| colspan=2 | Set up overnight runs
* Biotek1: FFL 3X plasmids [[Media:TXTL e11 linear IFFL workshop test plasmid 082813.xlsx|Spreadsheet available here]]
* Victor: RNA circuit
* Biotek 2: Switch and logic circuits
|
|-
| 6:00 || colspan=4 | Done for the day
|-
| colspan=5 align=center | Homework: Simulate feedfoward loops + individual circuits
|}

==== Thursday ====
Goals
* TX-TL implement: analyze 3X plasmid DNA circuits, set up and run 1X plasmids in TX-TL + cells with 1X plasmid
* TX-TL design: modify circuits and/or set up plasmid versions; set up overnight runs
* TX-TL extract: bead beating and dialysis (second set of groups)
* TX-TL extras: set up and run vesicles, set up and run droplets (first set of groups)
 

{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL extras
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|- valign=top
| 10:00
| G1-G3: demonstration sessions (optional)
* 10:00: Vesicles demo (Vincent): review prep of reaction, feeding, phospholipid, vesicles + view vesicles from previous day on microscope
* 11:30: Droplets (Enoch): ALL overview + set up reactions for afternoon run (Keck 040 - sub-basement)
|
| Circuit design and preparation (if needed)
* Decide on new runs to be done with circuit variants
| G4-G6: bead beating, centrifugation, dialysis (Anu, Jongmin, Clare) - Keck 116
* Each student to set up at least one bead beating tube
* Run bead beating and centrifuge results
* Load dialysis cassettes
|- valign=top
| 12:30 || || Go over data from previous night [[Media:Workday3 IFFL data 082813.xlsx|Data available here]] || ||
|- valign=top
| 1:00 || colspan=4 | Lunch
|- valign=top
| 2:00
|
* Start ALL runs (Enoch)
|
|
| Extract prep overview (Clare) - Steele library
* Review of whole process and calibration procedure
* Discuss variability between extract batches (with data)
|- valign=top
| 3:00 || colspan=4 | Meet in small groups

|- valign=top
| 5:00
|
In vivo runs
* Dilute cells and set up in 96 well plate
* Run in Biotek 2
|
|
|
|- valign=top
| 6:00 || colspan=4 | Done for the day
|-
| colspan=5 align=center | Homework: Simulate feedfoward loops + individual circuits
|}

==== Friday ====
Goals:
* TX-TL implement: compare simulations, linear, 3X plasmid, 1X plasmid and ''in vivo'' results
* TX-TL design: analyze results and make short presentation
* TX-TL extras: present data from previous days
 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL extras
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|- valign=top
| 9:00
|
| Analyze and compare data
* Simulations (Tue night), linear TX-TL (Tue night), plasmid TX-TL (Wed/Thu nights), cells (Thu night)
| Analyze data
* Collect data from plate reader
* Create 10 minute presentation of results (with TAs)
|
|- valign=top
| 10:30
| colspan=3 | Group presentations
* 10 minute presentation of circuit results to the group
* Enoch: ALL data
|
|-
| 12:00
| colspan=4 | Group lunch (optional)
|}

TX-TL Workshop, Aug 2013: Detailed Schedule

2013-08-29T22:26:27Z

Sguo: /* Wednesday */

{{righttoc}}
The detailed schedule below describes that is happening in each track of the [[TX-TL Workshop, Aug 2013|TX-TL workshop]] and roughly when different groups should be doing different things. Zach and Clare are responsible for keeping track of what is going on. The master copy of this schedule is on the [https://www.cds.caltech.edu/biocircuits/index.php/TX-TL_workshop,_26-30_Aug_2013#Detailed_schedule|biocircuits wiki] (not publicly accessible). A summary of the workshop schedule is available on the [[TX-TL Workshop, Aug 2013|main workshop page]].

==== Monday ====
Goals:
* TX-TL basics: Get everyone up to speed on the basics of TX-TL and the tools we will need for the rest of the week
* TX-TL extract: Create colonies from stocks

 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL basics
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|-
| 9:30 || Optional tutorials
* Geneious (Emzo)
| || ||
|-
| 12:00 || colspan=4 align=center | Lunch at Chandler: meet outside of Keck Lab at noon
|-
| 1:30 || colspan=4 align=center | Welcome and Introductions, 114 Steele Lab
|-
| 2:00 || Overview (Richard, Vincent)
* [http://www.cds.caltech.edu/~murray/talks/breadboards_workshop-26Aug13.pdf Biomolecular breadboards], Richard
* [http://www.cds.caltech.edu/~murray/talks/noireaux_txtl-26Aug13.pdf TX-TL toolbox], Vincent
* Schedule for the week, Richard
| || ||
|-
| 3:30 || Lab safety session (Clare) || || ||
|- valign=top
| 4:00
| Set up reactions for inducible promoter reactions (Zach, Clare)
* Use the [http://www.cds.caltech.edu/~murray/talks/TXTL_e18_template.xlsx TX-TL spreadsheet] to set up reactions at 4 different inducer levels
* Pipette reactions into 384 well plate (two columns per team, run in duplicate)
* Run overnight on plate reader at 29 degC
| || ||
|-
| 5:30 || || || || Streak out colonies
|-
| 6:00 || colspan=4 align=center | Done for the day
|-
| 7:30 || Optional tutorials
* MATLAB/Simbiology (Zoltan)
* Lab techniques (Enoch)
|
|
|
|}

==== Tuesday ====
Goals:
* TX-TL basics: plot experimental data and learn about TX-TL modeling and simulation
* TX-TL implement: create and run linear DNA, create "3X" plasmid DNA plates
* TX-TL design: meet with TAs to discuss projects
* TX-TL extract: pick colonies and grow up cells
* TX-TL extras: prepare phospholipids for use on Wed
 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL basics
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|-
| 9:00 || Analyze TX-TL results from previous day
* Take data off of plate reader, plot in Excel (or MATLAB)
* [[Media:firstday_data.xlsx|Data available here]]
Golden Gate cloning overview (1 hr, Zach)
* [[Media:overallfirstGenAssembly.png|diagram]]
| || ||
|- valign=top
| 10:00 || || || || Pick colonies, start cultures
|- valign=top
| 10:30 || TX-TL modeling toolbox (Vipul, Zoltan)
* Toolbox overview (45 m)
* Hands-on demo (30 m)
* Run models of results from previous evening (script)
| || ||
|-
| 12:00 || colspan=4 align=center | Lunch
|- valign=top
| 1:00 || || DNA assembly (Zach, Clare, Shaobin)
* Assemble feedforward loop onto individual plasmids ("3X"): AraC, TetR, deGFP ([[Media:GoldenBraid Assembly 082713.png|diagram]], [http://www.cds.caltech.edu/~murray/talks/DNA_Assembly_Protocol.pdf protocol])
* Start PCR reactions to amplify linear
* Transform plasmids (3X) and streak out on plates
| ||
|- valign=top
| 3:00
| G4, G5: Vesicles prep. Reaction and feeding solutions [Vincent]
G6: ALL intro session [Enoch]
| valign=center | PCR runs (2 hr)
| G1-G3: Breakout discussions (w/ TAs)
* Each group will choose a circuit to prototype using linear DNA on Wed, Thu
* Choices: RNA circuit, negative auto-regulation, genetic switch, IFFL2
* TAs: Emzo de los Santos (vesicles), Victoria Hsiao (ALL), Dan Siegal-Gaskins (logic), Vipul Singhal (RNA), Zoltan Tuza (genetic switch), Yong Wu (vesicles)
|
|- valign=top
| 5:00 || || Set up linear DNA runs
* Run gels to confirm PCR results
* PCR cleanup linear DNA segments
* Each group will set up 2 columns of runs (duplicates). Vary aTc and arabinose (2 each + controls)
* Biotek 1: Run linear FFL overnight at 29 degC [[Media:TXTL e11 linear IFFL 082713.xlsx|Spreadsheet available here]]
[Pre-prepared linear DNA available for all circuits in case your PCR didn't work]
|
| valign=bottom| Passage cells
|-
| 7:00 || colspan=4 | Done for the day
|-
| colspan=5 align=center | Homework: Simulate feedfoward loops + individual circuits
|}

==== Wednesday ====
Goals
* TX-TL implement: analyze linear DNA, set up and run 3X plasmids in TX-TL
* TX-TL design: create circuits and set up overnight runs
* TX-TL extract: bead beating and dialysis
* TX-TL extras: set up and run vesicles, set up and run droplets
 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL extras
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|- valign=top
| 10:00
| G4, G5: Vesicles prep: phospholipids [Vincent]
G6: ALL protocol development [Enoch]
| valign=middle |
| G1-G3: Plan out circuits designs to build and test (with TAs)
* Decide on what experiments you want to run
* Check availability of parts; plan out assemblies for the day, if needed
| Pellet and wash cells (Jongmin, Anu)
* Demonstrate how to pellet and wash cells
|- valign=top
| 12:30 || || Go over data from previous night [[Media:Workday2 IFFL data 082713.xlsx|Data available here]] || ||
|- valign=top
| 1:00 || colspan=4 | Lunch
|- valign=top
| 2:00
| G4-G6: demonstration sessions (optional)
* 2:00 (prep @ 1:45): Vesicles demo (Vincent): review preparation of feeding, reaction, phospholipids + live vesicles prep [Vincent] + view pre-prepared vesicles on microscope
* 3:30: Droplets (Enoch): ALL overview + set up reactions for evening run (Keck 040 - sub-basement)

Remaining time: Meet in small groups and work on circuit
|
|
| G1-G3: bead beating, centrifugation, dialysis (Jongmin, Anu, Clare) - Keck 116
* Each student to set up at least one bead beating tube
* Run bead beating and centrifuge results
* Load dialysis cassettes

Remaining time: Meet in small groups and work on circuit
|- valign=top
| 5:00
|
* Start ALL runs (Enoch)
| colspan=2 | Set up overnight runs
* Biotek1: FFL 3X plasmids [Media:TXTL e11 linear IFFL workshop test plasmid 082813.xlsx|Spreadsheet available here]]
* Victor: RNA circuit
* Biotek 2: Switch and logic circuits
|
|-
| 6:00 || colspan=4 | Done for the day
|-
| colspan=5 align=center | Homework: Simulate feedfoward loops + individual circuits
|}

==== Thursday ====
Goals
* TX-TL implement: analyze 3X plasmid DNA circuits, set up and run 1X plasmids in TX-TL + cells with 1X plasmid
* TX-TL design: modify circuits and/or set up plasmid versions; set up overnight runs
* TX-TL extract: bead beating and dialysis (second set of groups)
* TX-TL extras: set up and run vesicles, set up and run droplets (first set of groups)
 

{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL extras
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|- valign=top
| 10:00
| G1-G3: demonstration sessions (optional)
* 10:00: Vesicles demo (Vincent): review prep of reaction, feeding, phospholipid, vesicles + view vesicles from previous day on microscope
* 11:30: Droplets (Enoch): ALL overview + set up reactions for afternoon run (Keck 040 - sub-basement)
|
| Circuit design and preparation (if needed)
* Decide on new runs to be done with circuit variants
| G4-G6: bead beating, centrifugation, dialysis (Anu, Jongmin, Clare) - Keck 116
* Each student to set up at least one bead beating tube
* Run bead beating and centrifuge results
* Load dialysis cassettes
|- valign=top
| 12:30 || || Go over data from previous night [[Media:Workday3 IFFL data 082813.xlsx|Data available here]] || ||
|- valign=top
| 1:00 || colspan=4 | Lunch
|- valign=top
| 2:00
|
* Start ALL runs (Enoch)
|
|
| Extract prep overview (Clare) - Steele library
* Review of whole process and calibration procedure
* Discuss variability between extract batches (with data)
|- valign=top
| 3:00 || colspan=4 | Meet in small groups

|- valign=top
| 5:00
|
In vivo runs
* Dilute cells and set up in 96 well plate
* Run in Biotek 2
|
|
|
|- valign=top
| 6:00 || colspan=4 | Done for the day
|-
| colspan=5 align=center | Homework: Simulate feedfoward loops + individual circuits
|}

==== Friday ====
Goals:
* TX-TL implement: compare simulations, linear, 3X plasmid, 1X plasmid and ''in vivo'' results
* TX-TL design: analyze results and make short presentation
* TX-TL extras: present data from previous days
 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL extras
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|- valign=top
| 9:00
|
| Analyze and compare data
* Simulations (Tue night), linear TX-TL (Tue night), plasmid TX-TL (Wed/Thu nights), cells (Thu night)
| Analyze data
* Collect data from plate reader
* Create 10 minute presentation of results (with TAs)
|
|- valign=top
| 10:30
| colspan=3 | Group presentations
* 10 minute presentation of circuit results to the group
* Enoch: ALL data
|
|-
| 12:00
| colspan=4 | Group lunch (optional)
|}

File:TXTL e11 linear IFFL workshop test plasmid 082813.xlsx

2013-08-29T22:26:16Z

Sguo:

TX-TL Workshop, Aug 2013: Detailed Schedule

2013-08-29T22:25:15Z

Sguo: /* Tuesday */

{{righttoc}}
The detailed schedule below describes that is happening in each track of the [[TX-TL Workshop, Aug 2013|TX-TL workshop]] and roughly when different groups should be doing different things. Zach and Clare are responsible for keeping track of what is going on. The master copy of this schedule is on the [https://www.cds.caltech.edu/biocircuits/index.php/TX-TL_workshop,_26-30_Aug_2013#Detailed_schedule|biocircuits wiki] (not publicly accessible). A summary of the workshop schedule is available on the [[TX-TL Workshop, Aug 2013|main workshop page]].

==== Monday ====
Goals:
* TX-TL basics: Get everyone up to speed on the basics of TX-TL and the tools we will need for the rest of the week
* TX-TL extract: Create colonies from stocks

 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL basics
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|-
| 9:30 || Optional tutorials
* Geneious (Emzo)
| || ||
|-
| 12:00 || colspan=4 align=center | Lunch at Chandler: meet outside of Keck Lab at noon
|-
| 1:30 || colspan=4 align=center | Welcome and Introductions, 114 Steele Lab
|-
| 2:00 || Overview (Richard, Vincent)
* [http://www.cds.caltech.edu/~murray/talks/breadboards_workshop-26Aug13.pdf Biomolecular breadboards], Richard
* [http://www.cds.caltech.edu/~murray/talks/noireaux_txtl-26Aug13.pdf TX-TL toolbox], Vincent
* Schedule for the week, Richard
| || ||
|-
| 3:30 || Lab safety session (Clare) || || ||
|- valign=top
| 4:00
| Set up reactions for inducible promoter reactions (Zach, Clare)
* Use the [http://www.cds.caltech.edu/~murray/talks/TXTL_e18_template.xlsx TX-TL spreadsheet] to set up reactions at 4 different inducer levels
* Pipette reactions into 384 well plate (two columns per team, run in duplicate)
* Run overnight on plate reader at 29 degC
| || ||
|-
| 5:30 || || || || Streak out colonies
|-
| 6:00 || colspan=4 align=center | Done for the day
|-
| 7:30 || Optional tutorials
* MATLAB/Simbiology (Zoltan)
* Lab techniques (Enoch)
|
|
|
|}

==== Tuesday ====
Goals:
* TX-TL basics: plot experimental data and learn about TX-TL modeling and simulation
* TX-TL implement: create and run linear DNA, create "3X" plasmid DNA plates
* TX-TL design: meet with TAs to discuss projects
* TX-TL extract: pick colonies and grow up cells
* TX-TL extras: prepare phospholipids for use on Wed
 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL basics
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|-
| 9:00 || Analyze TX-TL results from previous day
* Take data off of plate reader, plot in Excel (or MATLAB)
* [[Media:firstday_data.xlsx|Data available here]]
Golden Gate cloning overview (1 hr, Zach)
* [[Media:overallfirstGenAssembly.png|diagram]]
| || ||
|- valign=top
| 10:00 || || || || Pick colonies, start cultures
|- valign=top
| 10:30 || TX-TL modeling toolbox (Vipul, Zoltan)
* Toolbox overview (45 m)
* Hands-on demo (30 m)
* Run models of results from previous evening (script)
| || ||
|-
| 12:00 || colspan=4 align=center | Lunch
|- valign=top
| 1:00 || || DNA assembly (Zach, Clare, Shaobin)
* Assemble feedforward loop onto individual plasmids ("3X"): AraC, TetR, deGFP ([[Media:GoldenBraid Assembly 082713.png|diagram]], [http://www.cds.caltech.edu/~murray/talks/DNA_Assembly_Protocol.pdf protocol])
* Start PCR reactions to amplify linear
* Transform plasmids (3X) and streak out on plates
| ||
|- valign=top
| 3:00
| G4, G5: Vesicles prep. Reaction and feeding solutions [Vincent]
G6: ALL intro session [Enoch]
| valign=center | PCR runs (2 hr)
| G1-G3: Breakout discussions (w/ TAs)
* Each group will choose a circuit to prototype using linear DNA on Wed, Thu
* Choices: RNA circuit, negative auto-regulation, genetic switch, IFFL2
* TAs: Emzo de los Santos (vesicles), Victoria Hsiao (ALL), Dan Siegal-Gaskins (logic), Vipul Singhal (RNA), Zoltan Tuza (genetic switch), Yong Wu (vesicles)
|
|- valign=top
| 5:00 || || Set up linear DNA runs
* Run gels to confirm PCR results
* PCR cleanup linear DNA segments
* Each group will set up 2 columns of runs (duplicates). Vary aTc and arabinose (2 each + controls)
* Biotek 1: Run linear FFL overnight at 29 degC [[Media:TXTL e11 linear IFFL 082713.xlsx|Spreadsheet available here]]
[Pre-prepared linear DNA available for all circuits in case your PCR didn't work]
|
| valign=bottom| Passage cells
|-
| 7:00 || colspan=4 | Done for the day
|-
| colspan=5 align=center | Homework: Simulate feedfoward loops + individual circuits
|}

==== Wednesday ====
Goals
* TX-TL implement: analyze linear DNA, set up and run 3X plasmids in TX-TL
* TX-TL design: create circuits and set up overnight runs
* TX-TL extract: bead beating and dialysis
* TX-TL extras: set up and run vesicles, set up and run droplets
 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL extras
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|- valign=top
| 10:00
| G4, G5: Vesicles prep: phospholipids [Vincent]
G6: ALL protocol development [Enoch]
| valign=middle |
| G1-G3: Plan out circuits designs to build and test (with TAs)
* Decide on what experiments you want to run
* Check availability of parts; plan out assemblies for the day, if needed
| Pellet and wash cells (Jongmin, Anu)
* Demonstrate how to pellet and wash cells
|- valign=top
| 12:30 || || Go over data from previous night [[Media:Workday2 IFFL data 082713.xlsx|Data available here]] || ||
|- valign=top
| 1:00 || colspan=4 | Lunch
|- valign=top
| 2:00
| G4-G6: demonstration sessions (optional)
* 2:00 (prep @ 1:45): Vesicles demo (Vincent): review preparation of feeding, reaction, phospholipids + live vesicles prep [Vincent] + view pre-prepared vesicles on microscope
* 3:30: Droplets (Enoch): ALL overview + set up reactions for evening run (Keck 040 - sub-basement)

Remaining time: Meet in small groups and work on circuit
|
|
| G1-G3: bead beating, centrifugation, dialysis (Jongmin, Anu, Clare) - Keck 116
* Each student to set up at least one bead beating tube
* Run bead beating and centrifuge results
* Load dialysis cassettes

Remaining time: Meet in small groups and work on circuit
|- valign=top
| 5:00
|
* Start ALL runs (Enoch)
| colspan=2 | Set up overnight runs
* Biotek1: FFL 3X plasmids
* Victor: RNA circuit
* Biotek 2: Switch and logic circuits
|
|-
| 6:00 || colspan=4 | Done for the day
|-
| colspan=5 align=center | Homework: Simulate feedfoward loops + individual circuits
|}

==== Thursday ====
Goals
* TX-TL implement: analyze 3X plasmid DNA circuits, set up and run 1X plasmids in TX-TL + cells with 1X plasmid
* TX-TL design: modify circuits and/or set up plasmid versions; set up overnight runs
* TX-TL extract: bead beating and dialysis (second set of groups)
* TX-TL extras: set up and run vesicles, set up and run droplets (first set of groups)
 

{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL extras
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|- valign=top
| 10:00
| G1-G3: demonstration sessions (optional)
* 10:00: Vesicles demo (Vincent): review prep of reaction, feeding, phospholipid, vesicles + view vesicles from previous day on microscope
* 11:30: Droplets (Enoch): ALL overview + set up reactions for afternoon run (Keck 040 - sub-basement)
|
| Circuit design and preparation (if needed)
* Decide on new runs to be done with circuit variants
| G4-G6: bead beating, centrifugation, dialysis (Anu, Jongmin, Clare) - Keck 116
* Each student to set up at least one bead beating tube
* Run bead beating and centrifuge results
* Load dialysis cassettes
|- valign=top
| 12:30 || || Go over data from previous night [[Media:Workday3 IFFL data 082813.xlsx|Data available here]] || ||
|- valign=top
| 1:00 || colspan=4 | Lunch
|- valign=top
| 2:00
|
* Start ALL runs (Enoch)
|
|
| Extract prep overview (Clare) - Steele library
* Review of whole process and calibration procedure
* Discuss variability between extract batches (with data)
|- valign=top
| 3:00 || colspan=4 | Meet in small groups

|- valign=top
| 5:00
|
In vivo runs
* Dilute cells and set up in 96 well plate
* Run in Biotek 2
|
|
|
|- valign=top
| 6:00 || colspan=4 | Done for the day
|-
| colspan=5 align=center | Homework: Simulate feedfoward loops + individual circuits
|}

==== Friday ====
Goals:
* TX-TL implement: compare simulations, linear, 3X plasmid, 1X plasmid and ''in vivo'' results
* TX-TL design: analyze results and make short presentation
* TX-TL extras: present data from previous days
 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL extras
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|- valign=top
| 9:00
|
| Analyze and compare data
* Simulations (Tue night), linear TX-TL (Tue night), plasmid TX-TL (Wed/Thu nights), cells (Thu night)
| Analyze data
* Collect data from plate reader
* Create 10 minute presentation of results (with TAs)
|
|- valign=top
| 10:30
| colspan=3 | Group presentations
* 10 minute presentation of circuit results to the group
* Enoch: ALL data
|
|-
| 12:00
| colspan=4 | Group lunch (optional)
|}

File:TXTL e11 linear IFFL 082713.xlsx

2013-08-29T22:25:05Z

Sguo:

TX-TL Workshop, Aug 2013: Detailed Schedule

2013-08-29T20:22:07Z

Sguo: /* Thursday */

{{righttoc}}
The detailed schedule below describes that is happening in each track of the [[TX-TL Workshop, Aug 2013|TX-TL workshop]] and roughly when different groups should be doing different things. Zach and Clare are responsible for keeping track of what is going on. The master copy of this schedule is on the [https://www.cds.caltech.edu/biocircuits/index.php/TX-TL_workshop,_26-30_Aug_2013#Detailed_schedule|biocircuits wiki] (not publicly accessible). A summary of the workshop schedule is available on the [[TX-TL Workshop, Aug 2013|main workshop page]].

==== Monday ====
Goals:
* TX-TL basics: Get everyone up to speed on the basics of TX-TL and the tools we will need for the rest of the week
* TX-TL extract: Create colonies from stocks

 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL basics
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|-
| 9:30 || Optional tutorials
* Geneious (Emzo)
| || ||
|-
| 12:00 || colspan=4 align=center | Lunch at Chandler: meet outside of Keck Lab at noon
|-
| 1:30 || colspan=4 align=center | Welcome and Introductions, 114 Steele Lab
|-
| 2:00 || Overview (Richard, Vincent)
* [http://www.cds.caltech.edu/~murray/talks/breadboards_workshop-26Aug13.pdf Biomolecular breadboards], Richard
* [http://www.cds.caltech.edu/~murray/talks/noireaux_txtl-26Aug13.pdf TX-TL toolbox], Vincent
* Schedule for the week, Richard
| || ||
|-
| 3:30 || Lab safety session (Clare) || || ||
|- valign=top
| 4:00
| Set up reactions for inducible promoter reactions (Zach, Clare)
* Use the [http://www.cds.caltech.edu/~murray/talks/TXTL_e18_template.xlsx TX-TL spreadsheet] to set up reactions at 4 different inducer levels
* Pipette reactions into 384 well plate (two columns per team, run in duplicate)
* Run overnight on plate reader at 29 degC
| || ||
|-
| 5:30 || || || || Streak out colonies
|-
| 6:00 || colspan=4 align=center | Done for the day
|-
| 7:30 || Optional tutorials
* MATLAB/Simbiology (Zoltan)
* Lab techniques (Enoch)
|
|
|
|}

==== Tuesday ====
Goals:
* TX-TL basics: plot experimental data and learn about TX-TL modeling and simulation
* TX-TL implement: create and run linear DNA, create "3X" plasmid DNA plates
* TX-TL design: meet with TAs to discuss projects
* TX-TL extract: pick colonies and grow up cells
* TX-TL extras: prepare phospholipids for use on Wed
 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL basics
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|-
| 9:00 || Analyze TX-TL results from previous day
* Take data off of plate reader, plot in Excel (or MATLAB)
* [[Media:firstday_data.xlsx|Data available here]]
Golden Gate cloning overview (1 hr, Zach)
* [[Media:overallfirstGenAssembly.png|diagram]]
| || ||
|- valign=top
| 10:00 || || || || Pick colonies, start cultures
|- valign=top
| 10:30 || TX-TL modeling toolbox (Vipul, Zoltan)
* Toolbox overview (45 m)
* Hands-on demo (30 m)
* Run models of results from previous evening (script)
| || ||
|-
| 12:00 || colspan=4 align=center | Lunch
|- valign=top
| 1:00 || || DNA assembly (Zach, Clare, Shaobin)
* Assemble feedforward loop onto individual plasmids ("3X"): AraC, TetR, deGFP ([[Media:GoldenBraid Assembly 082713.png|diagram]], [http://www.cds.caltech.edu/~murray/talks/DNA_Assembly_Protocol.pdf protocol])
* Start PCR reactions to amplify linear
* Transform plasmids (3X) and streak out on plates
| ||
|- valign=top
| 3:00
| G4, G5: Vesicles prep. Reaction and feeding solutions [Vincent]
G6: ALL intro session [Enoch]
| valign=center | PCR runs (2 hr)
| G1-G3: Breakout discussions (w/ TAs)
* Each group will choose a circuit to prototype using linear DNA on Wed, Thu
* Choices: RNA circuit, negative auto-regulation, genetic switch, IFFL2
* TAs: Emzo de los Santos (vesicles), Victoria Hsiao (ALL), Dan Siegal-Gaskins (logic), Vipul Singhal (RNA), Zoltan Tuza (genetic switch), Yong Wu (vesicles)
|
|- valign=top
| 5:00 || || Set up linear DNA runs
* Run gels to confirm PCR results
* PCR cleanup linear DNA segments
* Each group will set up 2 columns of runs (duplicates). Vary aTc and arabinose (2 each + controls)
* Biotek 1: Run linear FFL overnight at 29 degC
[Pre-prepared linear DNA available for all circuits in case your PCR didn't work]
|
| valign=bottom| Passage cells
|-
| 7:00 || colspan=4 | Done for the day
|-
| colspan=5 align=center | Homework: Simulate feedfoward loops + individual circuits
|}

==== Wednesday ====
Goals
* TX-TL implement: analyze linear DNA, set up and run 3X plasmids in TX-TL
* TX-TL design: create circuits and set up overnight runs
* TX-TL extract: bead beating and dialysis
* TX-TL extras: set up and run vesicles, set up and run droplets
 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL extras
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|- valign=top
| 10:00
| G4, G5: Vesicles prep: phospholipids [Vincent]
G6: ALL protocol development [Enoch]
| valign=middle |
| G1-G3: Plan out circuits designs to build and test (with TAs)
* Decide on what experiments you want to run
* Check availability of parts; plan out assemblies for the day, if needed
| Pellet and wash cells (Jongmin, Anu)
* Demonstrate how to pellet and wash cells
|- valign=top
| 12:30 || || Go over data from previous night [[Media:Workday2 IFFL data 082713.xlsx|Data available here]] || ||
|- valign=top
| 1:00 || colspan=4 | Lunch
|- valign=top
| 2:00
| G4-G6: demonstration sessions (optional)
* 2:00 (prep @ 1:45): Vesicles demo (Vincent): review preparation of feeding, reaction, phospholipids + live vesicles prep [Vincent] + view pre-prepared vesicles on microscope
* 3:30: Droplets (Enoch): ALL overview + set up reactions for evening run (Keck 040 - sub-basement)

Remaining time: Meet in small groups and work on circuit
|
|
| G1-G3: bead beating, centrifugation, dialysis (Jongmin, Anu, Clare) - Keck 116
* Each student to set up at least one bead beating tube
* Run bead beating and centrifuge results
* Load dialysis cassettes

Remaining time: Meet in small groups and work on circuit
|- valign=top
| 5:00
|
* Start ALL runs (Enoch)
| colspan=2 | Set up overnight runs
* Biotek1: FFL 3X plasmids
* Victor: RNA circuit
* Biotek 2: Switch and logic circuits
|
|-
| 6:00 || colspan=4 | Done for the day
|-
| colspan=5 align=center | Homework: Simulate feedfoward loops + individual circuits
|}

==== Thursday ====
Goals
* TX-TL implement: analyze 3X plasmid DNA circuits, set up and run 1X plasmids in TX-TL + cells with 1X plasmid
* TX-TL design: modify circuits and/or set up plasmid versions; set up overnight runs
* TX-TL extract: bead beating and dialysis (second set of groups)
* TX-TL extras: set up and run vesicles, set up and run droplets (first set of groups)
 

{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL extras
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|- valign=top
| 10:00
| G1-G3: demonstration sessions (optional)
* 10:00: Vesicles demo (Vincent): review prep of reaction, feeding, phospholipid, vesicles + view vesicles from previous day on microscope
* 11:30: Droplets (Enoch): ALL overview + set up reactions for afternoon run (Keck 040 - sub-basement)
|
| Circuit design and preparation (if needed)
* Decide on new runs to be done with circuit variants
| G4-G6: bead beating, centrifugation, dialysis (Anu, Jongmin, Clare) - Keck 116
* Each student to set up at least one bead beating tube
* Run bead beating and centrifuge results
* Load dialysis cassettes
|- valign=top
| 12:30 || || Go over data from previous night [[Media:Workday3 IFFL data 082813.xlsx|Data available here]] || ||
|- valign=top
| 1:00 || colspan=4 | Lunch
|- valign=top
| 2:00
|
* Start ALL runs (Enoch)
|
|
| Extract prep overview (Clare) - Steele library
* Review of whole process and calibration procedure
* Discuss variability between extract batches (with data)
|- valign=top
| 3:00 || colspan=4 | Meet in small groups

|- valign=top
| 5:00
|
In vivo runs
* Dilute cells and set up in 96 well plate
* Run in Biotek 2
|
|
|
|- valign=top
| 6:00 || colspan=4 | Done for the day
|-
| colspan=5 align=center | Homework: Simulate feedfoward loops + individual circuits
|}

==== Friday ====
Goals:
* TX-TL implement: compare simulations, linear, 3X plasmid, 1X plasmid and ''in vivo'' results
* TX-TL design: analyze results and make short presentation
* TX-TL extras: present data from previous days
 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL extras
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|- valign=top
| 9:00
|
| Analyze and compare data
* Simulations (Tue night), linear TX-TL (Tue night), plasmid TX-TL (Wed/Thu nights), cells (Thu night)
| Analyze data
* Collect data from plate reader
* Create 10 minute presentation of results (with TAs)
|
|- valign=top
| 10:30
| colspan=3 | Group presentations
* 10 minute presentation of circuit results to the group
* Enoch: ALL data
|
|-
| 12:00
| colspan=4 | Group lunch (optional)
|}

File:Workday3 IFFL data 082813.xlsx

2013-08-29T20:22:00Z

Sguo:

TX-TL Workshop, Aug 2013: Detailed Schedule

2013-08-29T20:21:23Z

Sguo: /* Wednesday */

{{righttoc}}
The detailed schedule below describes that is happening in each track of the [[TX-TL Workshop, Aug 2013|TX-TL workshop]] and roughly when different groups should be doing different things. Zach and Clare are responsible for keeping track of what is going on. The master copy of this schedule is on the [https://www.cds.caltech.edu/biocircuits/index.php/TX-TL_workshop,_26-30_Aug_2013#Detailed_schedule|biocircuits wiki] (not publicly accessible). A summary of the workshop schedule is available on the [[TX-TL Workshop, Aug 2013|main workshop page]].

==== Monday ====
Goals:
* TX-TL basics: Get everyone up to speed on the basics of TX-TL and the tools we will need for the rest of the week
* TX-TL extract: Create colonies from stocks

 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL basics
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|-
| 9:30 || Optional tutorials
* Geneious (Emzo)
| || ||
|-
| 12:00 || colspan=4 align=center | Lunch at Chandler: meet outside of Keck Lab at noon
|-
| 1:30 || colspan=4 align=center | Welcome and Introductions, 114 Steele Lab
|-
| 2:00 || Overview (Richard, Vincent)
* [http://www.cds.caltech.edu/~murray/talks/breadboards_workshop-26Aug13.pdf Biomolecular breadboards], Richard
* [http://www.cds.caltech.edu/~murray/talks/noireaux_txtl-26Aug13.pdf TX-TL toolbox], Vincent
* Schedule for the week, Richard
| || ||
|-
| 3:30 || Lab safety session (Clare) || || ||
|- valign=top
| 4:00
| Set up reactions for inducible promoter reactions (Zach, Clare)
* Use the [http://www.cds.caltech.edu/~murray/talks/TXTL_e18_template.xlsx TX-TL spreadsheet] to set up reactions at 4 different inducer levels
* Pipette reactions into 384 well plate (two columns per team, run in duplicate)
* Run overnight on plate reader at 29 degC
| || ||
|-
| 5:30 || || || || Streak out colonies
|-
| 6:00 || colspan=4 align=center | Done for the day
|-
| 7:30 || Optional tutorials
* MATLAB/Simbiology (Zoltan)
* Lab techniques (Enoch)
|
|
|
|}

==== Tuesday ====
Goals:
* TX-TL basics: plot experimental data and learn about TX-TL modeling and simulation
* TX-TL implement: create and run linear DNA, create "3X" plasmid DNA plates
* TX-TL design: meet with TAs to discuss projects
* TX-TL extract: pick colonies and grow up cells
* TX-TL extras: prepare phospholipids for use on Wed
 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL basics
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|-
| 9:00 || Analyze TX-TL results from previous day
* Take data off of plate reader, plot in Excel (or MATLAB)
* [[Media:firstday_data.xlsx|Data available here]]
Golden Gate cloning overview (1 hr, Zach)
* [[Media:overallfirstGenAssembly.png|diagram]]
| || ||
|- valign=top
| 10:00 || || || || Pick colonies, start cultures
|- valign=top
| 10:30 || TX-TL modeling toolbox (Vipul, Zoltan)
* Toolbox overview (45 m)
* Hands-on demo (30 m)
* Run models of results from previous evening (script)
| || ||
|-
| 12:00 || colspan=4 align=center | Lunch
|- valign=top
| 1:00 || || DNA assembly (Zach, Clare, Shaobin)
* Assemble feedforward loop onto individual plasmids ("3X"): AraC, TetR, deGFP ([[Media:GoldenBraid Assembly 082713.png|diagram]], [http://www.cds.caltech.edu/~murray/talks/DNA_Assembly_Protocol.pdf protocol])
* Start PCR reactions to amplify linear
* Transform plasmids (3X) and streak out on plates
| ||
|- valign=top
| 3:00
| G4, G5: Vesicles prep. Reaction and feeding solutions [Vincent]
G6: ALL intro session [Enoch]
| valign=center | PCR runs (2 hr)
| G1-G3: Breakout discussions (w/ TAs)
* Each group will choose a circuit to prototype using linear DNA on Wed, Thu
* Choices: RNA circuit, negative auto-regulation, genetic switch, IFFL2
* TAs: Emzo de los Santos (vesicles), Victoria Hsiao (ALL), Dan Siegal-Gaskins (logic), Vipul Singhal (RNA), Zoltan Tuza (genetic switch), Yong Wu (vesicles)
|
|- valign=top
| 5:00 || || Set up linear DNA runs
* Run gels to confirm PCR results
* PCR cleanup linear DNA segments
* Each group will set up 2 columns of runs (duplicates). Vary aTc and arabinose (2 each + controls)
* Biotek 1: Run linear FFL overnight at 29 degC
[Pre-prepared linear DNA available for all circuits in case your PCR didn't work]
|
| valign=bottom| Passage cells
|-
| 7:00 || colspan=4 | Done for the day
|-
| colspan=5 align=center | Homework: Simulate feedfoward loops + individual circuits
|}

==== Wednesday ====
Goals
* TX-TL implement: analyze linear DNA, set up and run 3X plasmids in TX-TL
* TX-TL design: create circuits and set up overnight runs
* TX-TL extract: bead beating and dialysis
* TX-TL extras: set up and run vesicles, set up and run droplets
 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL extras
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|- valign=top
| 10:00
| G4, G5: Vesicles prep: phospholipids [Vincent]
G6: ALL protocol development [Enoch]
| valign=middle |
| G1-G3: Plan out circuits designs to build and test (with TAs)
* Decide on what experiments you want to run
* Check availability of parts; plan out assemblies for the day, if needed
| Pellet and wash cells (Jongmin, Anu)
* Demonstrate how to pellet and wash cells
|- valign=top
| 12:30 || || Go over data from previous night [[Media:Workday2 IFFL data 082713.xlsx|Data available here]] || ||
|- valign=top
| 1:00 || colspan=4 | Lunch
|- valign=top
| 2:00
| G4-G6: demonstration sessions (optional)
* 2:00 (prep @ 1:45): Vesicles demo (Vincent): review preparation of feeding, reaction, phospholipids + live vesicles prep [Vincent] + view pre-prepared vesicles on microscope
* 3:30: Droplets (Enoch): ALL overview + set up reactions for evening run (Keck 040 - sub-basement)

Remaining time: Meet in small groups and work on circuit
|
|
| G1-G3: bead beating, centrifugation, dialysis (Jongmin, Anu, Clare) - Keck 116
* Each student to set up at least one bead beating tube
* Run bead beating and centrifuge results
* Load dialysis cassettes

Remaining time: Meet in small groups and work on circuit
|- valign=top
| 5:00
|
* Start ALL runs (Enoch)
| colspan=2 | Set up overnight runs
* Biotek1: FFL 3X plasmids
* Victor: RNA circuit
* Biotek 2: Switch and logic circuits
|
|-
| 6:00 || colspan=4 | Done for the day
|-
| colspan=5 align=center | Homework: Simulate feedfoward loops + individual circuits
|}

==== Thursday ====
Goals
* TX-TL implement: analyze 3X plasmid DNA circuits, set up and run 1X plasmids in TX-TL + cells with 1X plasmid
* TX-TL design: modify circuits and/or set up plasmid versions; set up overnight runs
* TX-TL extract: bead beating and dialysis (second set of groups)
* TX-TL extras: set up and run vesicles, set up and run droplets (first set of groups)
 

{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL extras
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|- valign=top
| 10:00
| G1-G3: demonstration sessions (optional)
* 10:00: Vesicles demo (Vincent): review prep of reaction, feeding, phospholipid, vesicles + view vesicles from previous day on microscope
* 11:30: Droplets (Enoch): ALL overview + set up reactions for afternoon run (Keck 040 - sub-basement)
|
| Circuit design and preparation (if needed)
* Decide on new runs to be done with circuit variants
| G4-G6: bead beating, centrifugation, dialysis (Anu, Jongmin, Clare) - Keck 116
* Each student to set up at least one bead beating tube
* Run bead beating and centrifuge results
* Load dialysis cassettes
|- valign=top
| 12:30 || || Go over data from previous night || ||
|- valign=top
| 1:00 || colspan=4 | Lunch
|- valign=top
| 2:00
|
* Start ALL runs (Enoch)
|
|
| Extract prep overview (Clare) - Steele library
* Review of whole process and calibration procedure
* Discuss variability between extract batches (with data)
|- valign=top
| 3:00 || colspan=4 | Meet in small groups

|- valign=top
| 5:00
|
In vivo runs
* Dilute cells and set up in 96 well plate
* Run in Biotek 2
|
|
|
|- valign=top
| 6:00 || colspan=4 | Done for the day
|-
| colspan=5 align=center | Homework: Simulate feedfoward loops + individual circuits
|}

==== Friday ====
Goals:
* TX-TL implement: compare simulations, linear, 3X plasmid, 1X plasmid and ''in vivo'' results
* TX-TL design: analyze results and make short presentation
* TX-TL extras: present data from previous days
 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL extras
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|- valign=top
| 9:00
|
| Analyze and compare data
* Simulations (Tue night), linear TX-TL (Tue night), plasmid TX-TL (Wed/Thu nights), cells (Thu night)
| Analyze data
* Collect data from plate reader
* Create 10 minute presentation of results (with TAs)
|
|- valign=top
| 10:30
| colspan=3 | Group presentations
* 10 minute presentation of circuit results to the group
* Enoch: ALL data
|
|-
| 12:00
| colspan=4 | Group lunch (optional)
|}

File:Workday2 IFFL data 082713.xlsx

2013-08-29T20:20:34Z

Sguo:

TX-TL Workshop, Aug 2013: Detailed Schedule

2013-08-27T20:00:22Z

Sguo: /* Tuesday */

{{righttoc}}
The detailed schedule below describes that is happening in each track of the [[TX-TL Workshop, Aug 2013|TX-TL workshop]] and roughly when different groups should be doing different things. Zach and Clare are responsible for keeping track of what is going on. The master copy of this schedule is on the [https://www.cds.caltech.edu/biocircuits/index.php/TX-TL_workshop,_26-30_Aug_2013#Detailed_schedule|biocircuits wiki] (not publicly accessible). A summary of the workshop schedule is available on the [[TX-TL Workshop, Aug 2013|main workshop page]].

==== Monday ====
Goals:
* TX-TL basics: Get everyone up to speed on the basics of TX-TL and the tools we will need for the rest of the week
* TX-TL extract: Create colonies from stocks

 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL basics
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|-
| 9:30 || Optional tutorials
* Geneious (Emzo)
| || ||
|-
| 12:00 || colspan=4 align=center | Lunch at Chandler: meet outside of Keck Lab at noon
|-
| 1:30 || colspan=4 align=center | Welcome and Introductions, 114 Steele Lab
|-
| 2:00 || Overview (Richard, Vincent)
* [http://www.cds.caltech.edu/~murray/talks/breadboards_workshop-26Aug13.pdf Biomolecular breadboards], Richard
* [http://www.cds.caltech.edu/~murray/talks/noireaux_txtl-26Aug13.pdf TX-TL toolbox], Vincent
* Schedule for the week, Richard
| || ||
|-
| 3:30 || Lab safety session (Clare) || || ||
|- valign=top
| 4:00
| Set up reactions for inducible promoter reactions (Zach, Clare)
* Use the [http://www.cds.caltech.edu/~murray/talks/TXTL_e18_template.xlsx TX-TL spreadsheet] to set up reactions at 4 different inducer levels
* Pipette reactions into 384 well plate (two columns per team, run in duplicate)
* Run overnight on plate reader at 29 degC
| || ||
|-
| 5:30 || || || || Streak out colonies
|-
| 6:00 || colspan=4 align=center | Done for the day
|-
| 7:30 || Optional tutorials
* MATLAB/Simbiology (Zoltan)
* Lab techniques (Enoch)
|
|
|
|}

==== Tuesday ====
Goals:
* TX-TL basics: plot experimental data and learn about TX-TL modeling and simulation
* TX-TL implement: create and run linear DNA, create "3X" plasmid DNA plates
* TX-TL design: meet with TAs to discuss projects
* TX-TL extract: pick colonies and grow up cells
* TX-TL extras: prepare phospholipids for use on Wed
 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL basics
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|-
| 9:00 || Analyze TX-TL results from previous day
* Take data off of plate reader, plot in Excel (or MATLAB)

Golden Gate cloning overview (1 hr, Zach)
| || ||
|- valign=top
| 10:00 || || || || Pick colonies, start cultures
|- valign=top
| 10:30 || TX-TL modeling toolbox (Vipul, Zoltan)
* Toolbox overview (45 m)
* Hands-on demo (30 m)
* Run models of results from previous evening (script)
| || ||
|-
| 12:00 || colspan=4 align=center | Lunch
|- valign=top
| 1:00 || || DNA assembly (Zach, Clare, Shaobin) [[File:GoldenBraid Assembly 082713.png|20px]]
* Assemble feedforward loop onto individual plasmids ("3X"): AraC, TetR, deGFP
* Start PCR reactions to amplify linear
* Transform plasmids (3X) and streak out on plates
| ||
|- valign=top
| 3:00
| G4, G5: Vesicles prep. Reaction and feeding solutions [Vincent]
G6: ALL intro session [Enoch]
| valign=center | PCR runs (2 hr)
| G1-G3: Breakout discussions (w/ TAs)
* Each group will choose a circuit to prototype using linear DNA on Wed, Thu
* Choices: RNA circuit, negative auto-regulation, genetic switch, IFFL2
* TAs: Emzo de los Santos (vesicles), Victoria Hsiao (ALL), Dan Siegal-Gaskins (logic), Vipul Singhal (RNA), Zoltan Tuza (genetic switch), Yong Wu (vesicles)
|
|- valign=top
| 5:00 || || Set up linear DNA runs
* Run gels to confirm PCR results
* PCR cleanup linear DNA segments
* Each group will set up 2 columns of runs (duplicates). Vary aTc and arabinose (2 each + controls)
* Biotek 1: Run linear FFL overnight at 29 degC
[Pre-prepared linear DNA available for all circuits in case your PCR didn't work]
|
| valign=bottom| Passage cells
|-
| 7:00 || colspan=4 | Done for the day
|-
| colspan=5 align=center | Homework: Simulate feedfoward loops + individual circuits
|}

==== Wednesday ====
Goals
* TX-TL implement: analyze linear DNA, set up and run 3X plasmids in TX-TL, create 1X plasmids for use on Thursday
* TX-TL design: create circuits and set up overnight runs
* TX-TL extract: bead beating and dialysis
* TX-TL extras: set up and run vesicles, set up and run droplets
 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL extras
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|- valign=top
| 9:00 || || Analyze TX-TL results from previous day
* Grab and analyze linear DNA results
Pick colonies and start cultures for plasmid FFL circuits
* Pick colonies for 3X FFL circuits
* Set up colony PCR + start cell cultures
[Pre-prepared plates available for all circuits in case you didn't get any colonies]
| ||
|- valign=top
| 10:00
| G4, G5: Vesicles prep: phospholipids [Vincent]
G6: ALL protocol development [Enoch]
| valign=middle | PCR runs
| G1-G3: Plan out circuits designs to build and test (with TAs)
* Decide on what experiments you want to run
* Check availability of parts; plan out assemblies for the day, if needed
| Pellet and wash cells (Jongmin, Anu)
* Demonstrate how to pellet and wash cells
|- valign=top
| 12:00 || || Run gels to check colony PCR || ||
|- valign=top
| 1:00 || colspan=4 | Lunch
|- valign=top
| 2:00
| G4-G6: demonstration sessions (optional)
* Vesicles demo (Vincent): review preparation of feeding, reaction, phospholipids + live vesicles prep [Vincent] + view pre-prepared vesicles on microscope
* Droplets (Enoch): ALL overview + set up reactions for evening run
|
|
| G1-G3: bead beating, centrifugation, dialysis (Jongmin, Anu, Clare)
* Each student to set up at least one bead beating tube
* Run bead beating and centrifuge results
* Load dialysis cassettes
|- valign=top
| 4:00
|
| Prepare plasmid DNA
* Mini-prep 3X plasmids
* Transform 1X plasmid (from Shaobin) and streak plates
[Pre-prepared plasmid and linear versions of all circuits available as a backup]
| Circuit design and preparation (if needed)
|
|- valign=top
| 5:00
|
* Start ALL runs (Enoch)
| colspan=2 | Set up overnight runs
* Biotek1: FFL 3X plasmids
* Victor: student-designed circuits (linear DNA)
|
|-
| 6:00 || colspan=4 | Done for the day
|}

==== Thursday ====
Goals
* TX-TL implement: analyze 3X plasmid DNA circuits, set up and run 1X plasmids in TX-TL + cells with 1X plasmid
* TX-TL design: modify circuits and/or set up plasmid versions; set up overnight runs
* TX-TL extract: bead beating and dialysis (second set of groups)
* TX-TL extras: set up and run vesicles, set up and run droplets (first set of groups)
 

{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL extras
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|- valign=top
| 9:00
|
| Analyze TX-TL results from previous day
* Grab and analyze 3X plasmid FFL results
Pick colonies and start cultures for plasmid FFL circuits
* Pick colonies for 1X plasmid FFL circuit
* Set up colony PCR + start cell cultures
[Pre-prepared plates of all circuits available as backups]
| Analyze TX-TL results from previous day
* Grab and analyze linear DNA results
|
|- valign=top
| 10:00
| G1-G3: demonstration sessions (optional)
* Vesicles demo (Vincent): review prep of reaction, feeding, phospholipid, vesicles + view vesicles from previous day on microscope
* Droplets (Enoch): ALL overview + set up reactions for afternoon run
|
| Circuit design and preparation (if needed)
* Decide on new runs to be done with circuit variants
| G4-G6: bead beating, centrifugation, dialysis (Anu, Jongmin, Clare)
* Each student to set up at least one bead beating tube
* Run bead beating and centrifuge results
* Load dialysis cassettes
|- valign=top
| 1:00 || colspan=4 | Lunch
|- valign=top
| 2:00
|
* Start ALL runs (Enoch)
|
|
| Extract prep overview (Clare)
* Use slides to go through whole process and calibration procedure
* Discuss variability between extract batches (with data)
|- valign=top
| 4:00
|
| 1X plasmid runs
* Mini-prep plasmids; run gel to verify
In vivo runs
* Dilute cells and set up in 96 well plate
[Pre-prepared 1X plasmids available as backup]
|
|
|- valign=top
| 5:00
|
| colspan=2 | Set up overnight runs
* Biotek1: FFL 1X plasmids
* Biotek2: FFL in vivo
* Victor: student-designed circuits
|
|-
| 6:00 || colspan=4 | Done for the day
|}

==== Friday ====
Goals:
* TX-TL implement: compare simulations, linear, 3X plasmid, 1X plasmid and ''in vivo'' results
* TX-TL design: analyze results and make short presentation
* TX-TL extras: present data from previous days
 
{| width=100% border=1
|-
| Time
! width=25% align=center | TX-TL extras
! width=25% align=center | TX-TL implement
! width=25% align=center | TX-TL design
! width=25% align = center | TX-TL extract
|- valign=top
| 9:00
|
| Analyze and compare data
* Simulations (Tue night), linear TX-TL (Tue night), plasmid TX-TL (Wed/Thu nights), cells (Thu night)
| Analyze data
* Collect data from plate reader
* Create 10 minute presentation of results (with TAs)
|
|- valign=top
| 10:30
| colspan=3 | Group presentations
* 10 minute presentation of circuit results to the group
* Enoch: ALL data
|
|-
| 12:00
| colspan=4 | Group lunch (optional)
|}

File:GoldenBraid Assembly 082713.png

2013-08-27T19:59:04Z

Sguo:

September 2013 Meetings

2013-08-27T06:27:28Z

Sguo: /* Thu, 12 Sep */

The list below has times that I am available to meet between 3 and 13 September. Please pick a time that works and fill in your name. If none of the times work, send me e-mail (or find someone else who has a slot that does work and figure out how much of a bribe is required to get them to switch). __NOTOC__

{| border=1 width=100%
|- valign=top
| width=20% |
2 Sep - Labor Day
| width=20% |
==== Tue, 3 Sep ====
{{agenda begin}}
{{agenda item|2:00p|Emzo}}
{{agenda item|3:00p|Joe Levine}}
{{agenda item| | }}
{{agenda item|4:30|Enoch}}
{{agenda item|5:30|Zach}}
{{agenda end}}
| width=20% |

==== Wed, 4 Sep ====
{{agenda begin}}
{{agenda item| | }}
{{agenda item| | }}
{{agenda item| | }}
{{agenda item|4:30|Joe}}
{{agenda item|5:30|Jongmin}}
{{agenda end}}
| width=20% |

==== Thu, 5 Sep ====
{{agenda begin}}
{{agenda item|2:00p|Open}}
{{agenda item|3:00p|Open}}
{{agenda item| | }}
{{agenda item|4:30|Open}}
{{agenda item|5:30|Ioannis}}
{{agenda end}}
| width=20% |
6 Sep - Richard out of town
|- valign=top
| colspan=2 width=40% |

==== Mon, 9 Sep / Tue, 10 Sep ====
{| cellspacing=0 cellpadding=0
|- valign=top
| width=50% |
{{agenda begin}}
{{agenda item|2:00p|dsg}}
{{agenda item|3:00p|Scott Livingston}}
{{agenda item| | }}
{{agenda item|4:30|Ivan Papusha}}
{{agenda item|5:30|Zoltan}}
{{agenda end}}
| width=50% |
Note: I may need to travel on either Mon or Tue {{implies}} please only sign up for a slot if you can make that time on both days.
|}
| width=20% |

==== Wed, 11 Sep ====
{{agenda begin}}
{{agenda item|1:00p|Clare}}
{{agenda item|2:00p|Yong}}
{{agenda item| | }}
{{agenda item|4:00|Anandh}}
{{agenda item|5:00|Anu}}
{{agenda end}}
| width=20% |

==== Thu, 12 Sep ====
{{agenda begin}}
{{agenda item|2:00p|Stephanie}}
{{agenda item|3:00p|Victoria}}
{{agenda item| | }}
{{agenda item|4:30|Shaobin}}
{{agenda item|5:30|Open}}
{{agenda end}}
| width=20% |

==== Fri, 13 Sep ====
{{agenda begin}}
{{agenda item|1:00p|Vanessa}}
{{agenda item|2:00p|Open}}
{{agenda end}}
|}

March 2013 meeting schedule

2013-03-03T03:08:26Z

Sguo: /* 11 Mar (Mon) */

The list below has times that I am available to meet between 4 March and 13 March. Please pick a time that works and fill in your name. If none of the times work, send me e-mail (or find someone else who has a slot that does work and figure out how much of a bribe is required to get them to switch). Please only sign up for one time slot. __NOTOC__

{| width=100% border=1
|- valign=top
| width=30% |
==== 6 Mar (Wed) ====
{{agenda begin}}
{{agenda item|8:45-9:45|Ophelia}}
{{agenda item||}}
{{agenda item|1:15-2:00|Stephanie}}
{{agenda item||}}
{{agenda item|5:00-5:45|Open}}
{{agenda item|5:45-6:00|UG advisee}}
{{agenda item|6:00-6:45|Open}}
{{agenda item|6:45-7:30|Open}}
{{agenda end}}
| width=30% |
==== 7 Mar (Thu) ====
{{agenda begin}}
{{agenda item|2:00-3:30|DARPA breadboards}}
{{agenda item|4:00-4:15|UG advisee}}
{{agenda item|4:15-5:00|Open}}
{{agenda item|5:00-5:45|Open}}
{{agenda item|5:45-6:00|UG advisee}}
{{agenda item|6:00-6:45|Open}}
{{agenda item|6:45-7:30|Open}}
{{agenda end}}
| width=30% |
==== 8 Mar (Fri) ====
{{agenda begin}}
{{agenda item|8:45-9:30|Open}}
{{agenda item||}}
{{agenda item|11:00-11:45|ALL telecon (Enoch, Joe M)}}
{{agenda item||}}
{{agenda item|12:00-1:15|NCS group meeting}}
{{agenda item|1:15-2:00|Open (might get shortened)}}
{{agenda item||}}
{{agenda item|5:00-5:45|Open}}
{{agenda item|5:45-6:30|Open}}
{{agenda end}}

|- valign=top
|
==== 10 Mar (Sun) ====
{{agenda begin}}
{{agenda item|2:30-2:45|UG advisee}}
{{agenda item|2:45-3:00|UG advisee}}
{{agenda item|3:00-4:00|Open}}
{{agenda item|4:00-5:00|Open}}
{{agenda item|5:00-6:00|Open}}
{{agenda item|6:00-6:15|UG advisee}}
{{agenda item|6:15-6:30|UG advisee}}
{{agenda end}}
|
==== 11 Mar (Mon) ====
{{agenda begin}}
{{agenda item|3:30-4:15|Open}}
{{agenda item|4:15-5:00|Shaobin}}
{{agenda item|5:00-5:15|UG advisee}}
{{agenda item|5:15-6:00|Open}}
{{agenda item|6:00-6:45|Open}}
{{agenda item|6:45-7:30|Open}}
{{agenda end}}
|

==== 12 Mar (Tue) ====
{{agenda begin}}
{{agenda item|11:00-11:45|Open}}
{{agenda item||}}
{{agenda item|1:00-3:00|Biocircuits meeting}}
{{agenda item||}}
{{agenda item|3:30-4:15|Nathan Belliveau}}
{{agenda item|4:15-5:00|Open}}
{{agenda item|5:00-5:15|UG advisee}}
{{agenda item|5:15-6:00|Open}}
{{agenda item|6:00-6:45|Open}}
{{agenda item|6:45-7:30|Open}}
{{agenda end}}
|}