GcatWiki - User contributions [en]

File:Msb gene.docx

2013-07-29T16:35:14Z

Msbrown: Msbrown uploaded a new version of "File:Msb gene.docx"

Biology

2013-07-24T18:19:44Z

Msbrown:

[[Davidson Protocols]] 
[[MWSU_protocols]] 

[[J-GGA Scaffold Design]]

[[Origin of Replication]]

[[File:Gelpouring.jpg|200px|thumb|right|Look, Mom, no EtBr!]]

[//gcat.davidson.edu/SynBio13/primer GGA Primer Designer]

'''Topics to Investigate'''

High Priority = more people

* '''Phoebe and Claire:''' eCDM8 working to make theophylline with biosensor and fitness modules (TetR) to report out. 
Which plasmid carries which device? 
Biosensor 
Fitness (tetA) 
feeds into stress module 
* '''Sachii and Jess:''' Determine the junction sequences and associated primers 
(use existing rules) 
build scaffold for insert segments 
include orI (collaborate with copy number research) 
include drug resistance gene 
test JGG design 
* '''Spencer and Sara:''' test fitness module with adhE
compare with tetA 
fine tune tetA resistance 
combine with tetA 
Does theophylline diffuse across the membrane and thus the system fails? 
* '''Brandon and Erich:''' Copy number of plasmids 
Can we alter Ori to produce a range of plasmid densities in ''E. coli''? 

Second Order Priority = one person
* produce different CDM alleles
* swap out different components (promoters, RBS, alleles)
* test out programmed evolution
* Stress module needs more work (see eCDM8 outputs)

Mathematics

2013-07-24T18:19:15Z

Msbrown:

Nucleotide Sequence Alignment website (EMBOSS Water): [http://bit.ly/10LvziF EMBOSS Water]

[http://modelingcommons.org/browse/one_model/3772 netlogo model]

-micah

Tm Calc for Oligos: [http://bit.ly/13fT96P BioMath Oligos Temp Calc]

Sachii's graphs:

[[File:Tet.xlsx]]

[[File:Graph 2.xlsx]]

[[File:Graph3.xlsx]]

Calculators:

Frequency of desirable results during transformation [https://dl.dropboxusercontent.com/u/16663498/Frequency%20calculator.xlsm excel file]

Population dominating time [https://dl.dropboxusercontent.com/u/16663498/Ecoli%20dominating%20time.xlsx excel file] (work in progress)

Transformation distribution experimental calculator [https://dl.dropboxusercontent.com/u/16663498/distributions%20calculator.xlsm excel file]

[https://dl.dropboxusercontent.com/u/16663498/PCN_calculator.xlsx PCN Calculator]

[//gcat.davidson.edu/SynBio13/GGAJET GGAJET Tool] (J-GGA Junction Generator)

[//gcat.davidson.edu/SynBio13/primer GGA Primer Designer]

Dream Gene

2013-07-16T16:12:07Z

Msbrown:

'''Dream Gene
'''

Upload documents here.

[[File:msb_gene.docx]]

File:Msb gene.docx

2013-07-16T16:11:01Z

Msbrown:

Dream Gene

2013-07-16T12:47:11Z

Msbrown:

'''Dream Gene
'''

Upload documents here.

Dream Gene

2013-07-16T12:46:57Z

Msbrown:

'''Dream Gene
'''

Summer 2013 SynBio Project (Davidson and MWSU)

2013-07-16T12:46:41Z

Msbrown:

Google Hangout 11 am Wednesday (10 Central)

 
<center>
[[File:TeamPhoto_2013b.jpg]]
</center>
<center>==[[Biology]]==</center>

<center>==[[Mathematics]]==</center>

<center>==[[Dream Gene]]==</center>

GGA results 
[[Media:DC-MWSU_GGA_results_2013.pptx]]

Summer 2013 SynBio Project (Davidson and MWSU)

2013-07-16T12:46:22Z

Msbrown:

Dream Gene

2013-07-16T12:46:01Z

Msbrown: Created page with "Page for the Dream Gene"

Page for the Dream Gene

Mathematics

2013-06-27T13:57:52Z

Msbrown:

Nucleotide Sequence Alignment website (EMBOSS Water): [http://bit.ly/10LvziF EMBOSS Water]

[http://modelingcommons.org/browse/one_model/3772 netlogo model]

-micah

Tm Calc for Oligos: [http://bit.ly/13fT96P BioMath Oligos Temp Calc]

Sachii's graphs:

[[File:Tet.xlsx]]

[[File:Graph 2.xlsx]]

[[File:Graph3.xlsx]]

Calculators:

Frequency of desirable results during transformation [https://dl.dropboxusercontent.com/u/16663498/Frequency%20calculator.xlsm excel file]

Population dominating time [https://dl.dropboxusercontent.com/u/16663498/Ecoli%20dominating%20time.xlsx excel file] (work in progress)

Transformation distribution experimental calculator [https://dl.dropboxusercontent.com/u/16663498/Frequency%20calculator.xlsm excel file]

PCN calculator [[File:PCN calculator.xlsx]]

[//gcat.davidson.edu/SynBio13/GGAJET GGAJET Tool] (J-GGA Junction Generator)

Mathematics

2013-06-27T13:53:26Z

Msbrown:

Nucleotide Sequence Alignment website (EMBOSS Water): [http://bit.ly/10LvziF EMBOSS Water]

[http://modelingcommons.org/browse/one_model/3772 netlogo model]

-micah

Tm Calc for Oligos: [http://bit.ly/13fT96P BioMath Oligos Temp Calc]

Sachii's graphs:

[[File:Tet.xlsx]]

[[File:Graph 2.xlsx]]

[[File:Graph3.xlsx]]

Calculators:

Frequency of desirable results during transformation [https://dl.dropboxusercontent.com/u/16663498/Frequency%20calculator.xlsm excel file]

Population dominating time [https://dl.dropboxusercontent.com/u/16663498/Ecoli%20dominating%20time.xlsx excel file] (work in progress)

Transformation distribution experimental calculator [https://dl.dropboxusercontent.com/u/16663498/Frequency%20calculator.xlsm excel file]

PCN calculator [[File:PCN calculator.xlsx]]

[gcat.davidson.edu/SynBio13/GGAJET GGAJET Tool ](J-GGA Junction Generator)

Mathematics

2013-06-27T13:49:20Z

Msbrown:

Nucleotide Sequence Alignment website (EMBOSS Water): [http://bit.ly/10LvziF EMBOSS Water]

[http://modelingcommons.org/browse/one_model/3772 netlogo model]

-micah

Tm Calc for Oligos: [http://bit.ly/13fT96P BioMath Oligos Temp Calc]

Sachii's graphs:

[[File:Tet.xlsx]]

[[File:Graph 2.xlsx]]

[[File:Graph3.xlsx]]

Calculators:

Frequency of desirable results during transformation [https://dl.dropboxusercontent.com/u/16663498/Frequency%20calculator.xlsm excel file]

Population dominating time [https://dl.dropboxusercontent.com/u/16663498/Ecoli%20dominating%20time.xlsx excel file] (work in progress)

Transformation distribution experimental calculator [https://dl.dropboxusercontent.com/u/16663498/Frequency%20calculator.xlsm excel file]

PCN calculator [[File:PCN calculator.xlsx]]

[https://gcat.davidson.edu/SynBio13/GGAJET GGAJET Tool ](J-GGA Junction Generator)

Mathematics

2013-06-12T21:23:19Z

Msbrown:

Mathematics

2013-06-06T15:57:21Z

Msbrown:

Nucleotide Sequence Alignment website (EMBOSS Water): [http://bit.ly/10LvziF EMBOSS Water]

Tm Calc for Oligos: [http://bit.ly/13fT96P BioMath Oligos Temp Calc]

Sachii's graphs:

[[File:Tet.xlsx]]

[[File:Graph 2.xlsx]]

[[File:Graph3.xlsx]]

File:Makers-moochers.zip

2013-06-06T15:33:00Z

Msbrown: Msbrown uploaded a new version of "File:Makers-moochers.zip"

Mathematics/Netlogo Models

2013-06-06T14:42:40Z

Msbrown: /* Here's a page to post NetLogo models */

== Here's a page to post NetLogo models ==

----

Model: '''Maker cells vs. Moocher cells''' This is a model I made to address problem three that we discussed at MWSU. To review, it deals with the issue of theophylline crossing the membrane and being absorbed by "moocher" cells which use the theophylline to increase their fitness, even though they are '''not''' the cells that wee are hoping for. See the info tab in the actual model for further detail. --Micah

[[File:Makers-moochers.zip]]

Mathematics

2013-06-06T14:42:18Z

Msbrown:

'''NetLogo Models Page''': [http://gcat.davidson.edu/mediawiki-1.19.1/index.php/Mathematics/Netlogo_Models '''NetLogo Models Page:''']

Nucleotide Sequence Alignment website (EMBOSS Water): [http://bit.ly/10LvziF EMBOSS Water]

Tm Calc for Oligos: [http://bit.ly/13fT96P BioMath Oligos Temp Calc]

Sachii's graphs:

[[File:Tet.xlsx]]

[[File:Graph 2.xlsx]]

[[File:Graph3.xlsx]]

File:Makers-moochers.zip

2013-06-06T14:40:20Z

Msbrown:

Mathematics/Netlogo Models

2013-06-06T14:40:03Z

Msbrown: Created page with " == Here's a page to post NetLogo models == ---- Model: '''Maker cells vs. Moocher cells''' This is a model I made to address problem three that we discussed at MWSU...."

Mathematics

2013-06-03T12:19:10Z

Msbrown:

Mathematics

2013-06-03T12:16:57Z

Msbrown:

Nucleotide Sequence Alignment website (EMBOSS Water): [http://bit.ly/10LvziF EMBOSS Water]

Sachii's graphs:

[[File:Tet.xlsx]]

[[File:Graph 2.xlsx]]

[[File:Graph3.xlsx]]

Mathematics

2013-06-03T12:15:58Z

Msbrown:

Nucleotide Sequence Alignment website (EMBOSS Water): bit.ly/10LvziF

Sachii's graphs:

[[File:Tet.xlsx]]

[[File:Graph 2.xlsx]]

[[File:Graph3.xlsx]]

Mathematics

2013-05-31T15:01:58Z

Msbrown:

Nucleotide Sequence Alignment website: http://www.ebi.ac.uk/Tools/psa/emboss_needle/nucleotide.html

Sachii's graphs:

[[File:Tet.xlsx]]

[[File:Graph 2.xlsx]]

[[File:Graph3.xlsx]]

Summer 2013 SynBio Project (Davidson and MWSU)

2013-05-31T14:58:30Z

Msbrown:

Google Hangout 11 am Wednesday (10 Central)

 

[[File:DC-MWSU_2013.JPG|800px|thumb|left|alt=text|DC-MWSU 2013]] 

[[File:DC-MWSU_2013.JPG]] 

<center>==[[Biology]]==</center>

<center>==[[Mathematics]]==</center>

GGA results 
[[Media:DC-MWSU_GGA_results_2013.pptx]]

File:Graph3.xlsx

2013-05-31T13:41:53Z

Msbrown:

File:Graph 2.xlsx

2013-05-31T13:40:34Z

Msbrown:

File:Tet.xlsx

2013-05-31T13:39:30Z

Msbrown: sachii's tet data

sachii's tet data

Mathematics

2013-05-31T03:46:28Z

Msbrown: sequence alignment

Nucleotide Sequence Alignment website: http://www.ebi.ac.uk/Tools/psa/emboss_needle/nucleotide.html