Endy:PiP: Difference between revisions

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{{EndyLab}}
{{EndyLab}}
This page is for keeping track of the status of papers in the Endy Lab writing queue.<br>
This page is for keeping track of the status of papers in the Endy writing queue.<br>


===WRITING===


*'''<font color="green">Barry #1</font>''': ''A virtual machine for synthetic biology,'' or equivalent
**Authors: Barry, Drew
**Status: BC to discuss w/ various folks and propose scope of remaining work 
**<font color="red">Goal</font>: Submit before the end of August 2008


*'''<font color="green">Jason #1</font>''': ''Measurement kits and reference standards for characterizing BioBrick promoters and ribosome binding sites''
===Research Manuscripts===
**Authors: JK & DE
**Status: submitted, awaiting comments and editorial decision
**<font color="red">Goal</font>: Accepted by June 27


*'''<font color="green">Jason #2</font>''': ''Programmed selection and preferential promotion of disadvantaged bacteria,'' or equivalent
**Authors: JK & DE
**Status: JK to propose scope of modeling work
**<font color="red">Goal</font>: Submit by June 27


*'''<font color="green">Reshma #1</font>''': ''A synthetic biology approach to reprogramming bacterial odor''
**Authors: RS & DE
**Status: submitted, awaiting comments and editorial decision
**<font color="red">Goal</font>: Accepted by June 27, or revision underway


*'''<font color="green">Reshma #2</font>''': ''Signal levels, load, and error rates in engineered transcriptional devices''
===='''<font color="green">Barry #1</font>''': ''Model-based forward engineering of autocatalytic, self-regulating, and orthogonal gene expression systems in Escherichia coli''====
**Authors: RS & DE
*Authors: Barry, Drew
**Status: RS to draft a first paragraph-level outline from most recent discussions with DE
*Status: Drew drafting for PNAS
**<font color="red">Goal</font>: Submit by June 27
*Writing: On Google Docs
*[[User:Barry Canton/Notebook/T7 RNAP transcription of rRNA | Project page]] & [[Endy:Chassis engineering/Paper|Paper page]].
*<font color="red">Goal</font>: Submit June 2009


*'''<font color="green">Samantha #1</font>''': ''Engineering phosphorylation-dependent post-translational protein devices''
===='''<font color="green">Jason #2</font>''': ''Programmed selection and preferential promotion of microbes using a selectostat''====
**Authors: SS & DE
*Authors: JK & DE
**Status: SS and DE to discuss response to PLoS editors
*Status: Endy drafting for PNAS
**<font color="red">Goal</font>: Resubmit by June 4
*Main Text on Google Docs
*Figures
*Supplement
*[[Endy:Notebook/Sortostat_Paper | OWW Page]]
*<font color="red">Goal</font>: Submit June 2009


*'''<font color="green">Samantha #2</font>''': ''Signals and specifications for a family of phosphorylation-dependent devices,'' or equivalent
===='''<font color="green">Reshma #1</font>''': ''Using genetically encoded odorant reporters to engineer bacteria that smell like wintergreen and banana''====
**Authors: SS & DE
*Authors: RS & DE
**Status: SS to draft paragraph level outline, pending resubmission of SS#1
*Status: reviews received, revision complete, sent to RC3 for his comments
**<font color="red">Goal</font>: Submit by June 27
*<font color="red">Goal</font>: submitted


*'''<font color="green">Ty #1</font>''': ''Tools for making systems biology models more scientific''
===='''<font color="green">Reshma #2</font>''': ''Signal levels, load, and error rates in engineered transcriptional devices''====
**Authors: TT, DE
*Authors: RS & DE
**Status: DE to edit, send to Roger for his comments, then to Ty, then final edits and submit
*Status: RS working on figures
**<font color="red">Goal</font>: Submit by June 13
*<font color="red">Goal</font>: Submit by end of August


*'''<font color="green">Ty #2</font>''': ''Measurement and analysis of protein abundances suggests tradeoff between signaling system output and dynamic range''  
===='''<font color="green">Samantha #1</font>''': ''Controlling cellular location by engineering phosphorylation''====
**Authors: TT, DE
*Authors: SS & DE
**Status: DE to edit, send to Roger for his comments, then to Ty, then final edits and submit
*Status: In review at PLoS Biology
**<font color="red">Goal</font>: Submit by June 13
*<font color="red">Goal</font>: Have ''in press'' in 2008


*'''<font color="green">Ty #3</font>''': ''Mechanics, controls, and models of yeast mating response''
===='''<font color="green">Samantha #2</font>''': ''Signals and specifications for a family of phosphorylation-dependent devices,'' or equivalent====
**Authors: TT, DE
*Authors: SS & DE
**Status: JT and TT to edit
*Status: Outline and structure finalized, SS leading writing
**<font color="red">Goal</font>: Submit by June 27
*<font color="red">Goal</font>: Submit by end of August


*'''<font color="green">Sri #1</font>''': ''Measures & models of phage T7 mRNA''
===='''<font color="green">Ty #1</font>''': ''Tools for making systems biology models more scientific''====
**Authors: HK, DE, SK
*Authors: TT, DE
**Status: Sri needs to provide Fig 4, Drew needs to edit
*Status: DE to do final edit, send to RB and TT for final approval
**<font color="red">Goal</font>: Submit by June 27
*<font color="red">Goal</font>: Submit by end of August


*'''<font color="green">Drew #1</font>''': ''A Common Signal Carrier for Genetic Devices''
===='''<font color="green">Ty #2</font>''': ''Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range''====
**Authors: Austin, Drew, Tom, Randy, Samantha
*Authors: TT, DE
**Status: DE to review
*Status: Submitted to MSB
**<font color="red">Goal</font>: Submit by June 27
*<font color="red">Goal</font>: Get published ASAP.


===RESEARCH CONCLUDING===
===='''<font color="green">Ty #3</font>''': ''Mechanics, Controls, and Modeling of Mating Pheromone-Initiated Signaling in the Yeast Saccharomyces cerevisiae:  A Comprehensive Analysis''====
*Authors: TT, DE
*Status: JT and TT to edit (not working well, what should DE do?)
*<font color="red">Goal</font>: Submit by ???


#Deterministic cell fate selection during phage lambda infection
===='''<font color="green">Sri #1</font>''': ''Measures & models of phage T7 mRNA''====
#*Francois,Drew
*Authors: HK, DE, SK
#*Status: FSP leading experiments
*Status: Sri needs to provide Fig 4, Drew needs to edit
#**Bonus: consider what to do with right operator model paper
*<font color="red">Goal</font>: Submit by end of August


#An engineered post-translational  device
===='''<font color="green">Drew #1</font>''': ''A common signal carrier for genetic devices''====
#*Samantha, Drew
*Authors: Austin, Drew, Tom, Randy, Samantha
#*Samantha finishing microscopy, gels; revising draft
*Status: DE to expand and rewrite
#Eau d'E.coli
*<font color="red">Goal</font>: Submit by end of August
#*iGEM 06
#*Status: Stephen drafting and finishing bananas characterization
#PoPS toolkit
#*Jason and UROP army
#*Status: experiments completing, awaiting outline
#Zinc-Finger Logic Gates
#*RS, TK, DE
#*Status: experiments completing, awaiting outline
#M13.1
#*FM, BH, NK, DE
#*Status: awaiting synthetic DNA to test. Confirm completion of point mutants
#Low abundance of Ste5 scaffold protein
#*KRB, TMT, ..., DE, RB
#*Status: TMT finishing modeling work, RY varying Ste5 abundances.  Manuscript needs to be updated.


===='''<font color="green">Drew #2</font>''': ''Free as in phosphoramidites'', or equivalent====
*Authors: DG and DE
*Status: DE to write
*<font color="red">Goal</font>: Submit by end of August


*'''<font color="green">Blank #1</font>''': ''Title,'' or equivalent
===BOOKS===
**Authors: your names here
**Status: your names here
**<font color="red">Goal</font>: Submit by some date


===='''<font color="green">DE #1</font>''':CoTS====
*Authors: DE
*Status: DE outlining
*<font color="red">Goal</font>: Proposal by end of August


BOOKS
===='''<font color="green">DE #2</font>''':I2SB====
*Authors: DE
*Status: DE outlining
*<font color="red">Goal</font>: Outline by end of August


#CoTS
===BLANK===
#*Drew
 
#*Status: outlining
===='''<font color="green">Blank #1</font>''': ''Title,'' or equivalent====
#I2SB
*Authors: your names here
#*Drew
*Status: your names here
#*Status: outlining
*<font color="red">Goal</font>: Submit by some date
 
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Latest revision as of 14:04, 16 June 2009

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This page is for keeping track of the status of papers in the Endy writing queue.


Research Manuscripts

Barry #1: Model-based forward engineering of autocatalytic, self-regulating, and orthogonal gene expression systems in Escherichia coli

  • Authors: Barry, Drew
  • Status: Drew drafting for PNAS
  • Writing: On Google Docs
  • Project page & Paper page.
  • Goal: Submit June 2009

Jason #2: Programmed selection and preferential promotion of microbes using a selectostat

  • Authors: JK & DE
  • Status: Endy drafting for PNAS
  • Main Text on Google Docs
  • Figures
  • Supplement
  • OWW Page
  • Goal: Submit June 2009

Reshma #1: Using genetically encoded odorant reporters to engineer bacteria that smell like wintergreen and banana

  • Authors: RS & DE
  • Status: reviews received, revision complete, sent to RC3 for his comments
  • Goal: submitted

Reshma #2: Signal levels, load, and error rates in engineered transcriptional devices

  • Authors: RS & DE
  • Status: RS working on figures
  • Goal: Submit by end of August

Samantha #1: Controlling cellular location by engineering phosphorylation

  • Authors: SS & DE
  • Status: In review at PLoS Biology
  • Goal: Have in press in 2008

Samantha #2: Signals and specifications for a family of phosphorylation-dependent devices, or equivalent

  • Authors: SS & DE
  • Status: Outline and structure finalized, SS leading writing
  • Goal: Submit by end of August

Ty #1: Tools for making systems biology models more scientific

  • Authors: TT, DE
  • Status: DE to do final edit, send to RB and TT for final approval
  • Goal: Submit by end of August

Ty #2: Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range

  • Authors: TT, DE
  • Status: Submitted to MSB
  • Goal: Get published ASAP.

Ty #3: Mechanics, Controls, and Modeling of Mating Pheromone-Initiated Signaling in the Yeast Saccharomyces cerevisiae: A Comprehensive Analysis

  • Authors: TT, DE
  • Status: JT and TT to edit (not working well, what should DE do?)
  • Goal: Submit by ???

Sri #1: Measures & models of phage T7 mRNA

  • Authors: HK, DE, SK
  • Status: Sri needs to provide Fig 4, Drew needs to edit
  • Goal: Submit by end of August

Drew #1: A common signal carrier for genetic devices

  • Authors: Austin, Drew, Tom, Randy, Samantha
  • Status: DE to expand and rewrite
  • Goal: Submit by end of August

Drew #2: Free as in phosphoramidites, or equivalent

  • Authors: DG and DE
  • Status: DE to write
  • Goal: Submit by end of August

BOOKS

DE #1:CoTS

  • Authors: DE
  • Status: DE outlining
  • Goal: Proposal by end of August

DE #2:I2SB

  • Authors: DE
  • Status: DE outlining
  • Goal: Outline by end of August

BLANK

Blank #1: Title, or equivalent

  • Authors: your names here
  • Status: your names here
  • Goal: Submit by some date

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