Endy:PiP: Difference between revisions

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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@@ Line 1: / Line 1: @@
 {{EndyLab}}
-This page is for organizing 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>
-EXPERIMENTS FINISHED
-#Deterministic cell fate selection during phage lambda infection
-#*Francois,Drew
-#*Status: Sent to Cell
-#Measures & Models of Phage T7 mRNA
-#*Heather, Drew, Sri
-#*Status: Sri needs to provide Fig 4, Drew needs to edit (send to PNAS)
-#The Lambda Right Operator is a Volume Sensor
-#*Drew
-#*Status: Drew needs to write, send to MSB, PLoS ONE, or Genetics
-#Post Synthesis Genetics
-#*Drew (invite Gil Berjarano, Radikha Nagpal, and a TBD developmental biologist)
-#*Status: Drew needs to organize (invited at Cell)
-#A Common Signal Carrier for Genetic Devices
-#*Austin, Drew, Tom, Randy, Samantha
-#*Status: DE to revise and send to MSB
-#OpenWetWare
-#*OWW Board
-#*Status: DE to edit, send to PLoS
-#A Modeler's Review of Yeast Pheromone Response
-#*Ty, Thorner, Drew
-#*Status: Ty to write, Drew to edit, JT to edit over New Years.  Find place that will publish 200 page article
-#Escherichia coliroids
-#*RS, DE, NK
-#*Status: awaiting outline
-WORK CONCLUDING
+===Research Manuscripts===
-#An engineered post-translational  device
-#*Samantha, Drew
-#*Samantha finishing microscopy, gels; revising draft
-#Eau d'E.coli
-#*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.
-BOOKS
-#CoTS
+===='''<font color="green">Barry #1</font>''': ''Model-based forward engineering of autocatalytic, self-regulating, and orthogonal gene expression systems in Escherichia coli''====
-#*Drew
+*Authors: Barry, Drew
-#*Status: outlining
+*Status: Drew drafting for PNAS
-#I2SB
+*Writing: On Google Docs
-#*Drew
+*[[User:Barry Canton/Notebook/T7 RNAP transcription of rRNA | Project page]] & [[Endy:Chassis engineering/Paper|Paper page]].
-#*Status: outlining
+*<font color="red">Goal</font>: Submit June 2009
+===='''<font color="green">Jason #2</font>''': ''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
+*[[Endy:Notebook/Sortostat_Paper | OWW Page]]
+*<font color="red">Goal</font>: Submit June 2009
+===='''<font color="green">Reshma #1</font>''': ''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
+*<font color="red">Goal</font>: submitted
+===='''<font color="green">Reshma #2</font>''': ''Signal levels, load, and error rates in engineered transcriptional devices''====
+*Authors: RS & DE
+*Status: RS working on figures
+*<font color="red">Goal</font>: Submit by end of August
+===='''<font color="green">Samantha #1</font>''': ''Controlling cellular location by engineering phosphorylation''====
+*Authors: SS & DE
+*Status: In review at PLoS Biology
+*<font color="red">Goal</font>: Have ''in press'' in 2008
+===='''<font color="green">Samantha #2</font>''': ''Signals and specifications for a family of phosphorylation-dependent devices,'' or equivalent====
+*Authors: SS & DE
+*Status: Outline and structure finalized, SS leading writing
+*<font color="red">Goal</font>: Submit by end of August
+===='''<font color="green">Ty #1</font>''': ''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
+*<font color="red">Goal</font>: Submit by end of August
+===='''<font color="green">Ty #2</font>''': ''Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range''====
+*Authors: TT, DE
+*Status: Submitted to MSB
+*<font color="red">Goal</font>: Get published ASAP.
+===='''<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 ???
+===='''<font color="green">Sri #1</font>''': ''Measures & models of phage T7 mRNA''====
+*Authors: HK, DE, SK
+*Status: Sri needs to provide Fig 4, Drew needs to edit
+*<font color="red">Goal</font>: Submit by end of August
+===='''<font color="green">Drew #1</font>''': ''A common signal carrier for genetic devices''====
+*Authors: Austin, Drew, Tom, Randy, Samantha
+*Status: DE to expand and rewrite
+*<font color="red">Goal</font>: Submit by end of August
+===='''<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
+===BOOKS===
+===='''<font color="green">DE #1</font>''':CoTS====
+*Authors: DE
+*Status: DE outlining
+*<font color="red">Goal</font>: Proposal by end of August
+===='''<font color="green">DE #2</font>''':I2SB====
+*Authors: DE
+*Status: DE outlining
+*<font color="red">Goal</font>: Outline by end of August
+===BLANK===
+===='''<font color="green">Blank #1</font>''': ''Title,'' or equivalent====
+*Authors: your names here
+*Status: your names here
+*<font color="red">Goal</font>: Submit by some date
+{{ShowGoogleExcel|id=pPNCEiE71Bq1I759bMAFhTg|width=800|height=600}}
+{{ShowGoogleWord|id=d7z7wrm_5cgnvmwcn|width=800|height=600}}