GcatWiki - User contributions [en]

Summer 2014 SynBio Project (Davidson and MWSU)

2014-07-23T15:23:37Z

Mospencer:

=== Final Presentations at End of Summer ===
* [[File:Math wrap-up.pptx]]
* [[File:Liquid Broth.pptx]]
* [[fitness genes]]
* [[tClone/ammeline]]

=== Presentations during MWSU visit to Davidson ===

Central Dogma presentation [[File:Central_dogma.pptx]]

PCR presentation [[File:PCR.pptx]]

Cloning presentation [[File:Cloning.pptx]]

Riboswitch presentation [[File:Riboswitch_function.pptx]]

Agent based modeling presentation [[File:AgentBased_Modeling.pptx]]

Competition presentation [[File:Competition_Modeling.xlsx]]

Programmed evolution presentation [[File:Programmed_Evolution.pdf]]

Caffeine results [[File:Caffeine_Disk.pptx]]

Ammeline presentation [[File:Ammeline.pptx]]

Repressilator modeling exercises [[File:repressilator_modeling.docx]]

Repressilator modeling Excel file [[File:Repressilator_model.xls]]

Repressilator modeling Netlogo file [[File:Repressilator_mod.nlogo.zip]]

=== Biology Files ===

Chaperone plasmid DNA sequences [[File:Chaperone_plasmid_DNA_sequences.docx]]

Origin PCR Gels 5-26-14[[File:5-26-14 Orig PCR Elecpho Gel Pic.doc]]

Chaperone PCR and Repeat Origin PCR 5-27-14[[File:5-27-14_Chap_PCR_and_Repeat_Ori_PCR.doc]]

Chaperone PCR of original clones 5-27-14[[File:5-27-14_chaperone_pcr_clones_1-24.doc]]

Origin PCR of original clones 5-27-14[[File:5-27-14 Ori PCR 1-24.doc ]]

New Chap PCR clones 1-5[[File:5-28-14_New_Chap_PCR_1-5.doc ]]

Combinations Labeling System [[File:Labeling.xlsx]]

ThyA Fitness Module [[File:ThyA fitness module.docx]]

Alternative Riboswitches[[File:Alternative Riboswitches.docx]]

Origin PCR Pictures 6-5-14 [[File:6-5-14 Origin PCR.docx]]

Chaperone PCR PA 6-5-14 [[File:6-5-14 Chaperone PCR.docx]]

Broth Growth Experiments [[File:Broth Growth Experiment Reports Revised.docx]]
===Sub-pages on various topics===

'''
[[MATH]]
'''

[[Catherine Doyle Thesis Materials]]

[[Repeating 20 Clone Experiments]]

[[Extending theophylline application]]

[[Melamine iteration]]

[[Ramping up Programmed Evolution]]

[[Rational Design of Riboswitches: papers to read]]

[[ThyA Fitness Module]]

[[Caffeine Disk Replication Data]]

=== Programmed Evolution Paper ===

[[References]]

Summer 2014 SynBio Project (Davidson and MWSU)

2014-07-23T15:23:20Z

Mospencer:

=== Final Presentations at End of Summer ===
* [[File:Math wrap-up.pptx]
* [[File:Liquid Broth.pptx]]
* [[fitness genes]]
* [[tClone/ammeline]]

=== Presentations during MWSU visit to Davidson ===

Central Dogma presentation [[File:Central_dogma.pptx]]

PCR presentation [[File:PCR.pptx]]

Cloning presentation [[File:Cloning.pptx]]

Riboswitch presentation [[File:Riboswitch_function.pptx]]

Agent based modeling presentation [[File:AgentBased_Modeling.pptx]]

Competition presentation [[File:Competition_Modeling.xlsx]]

Programmed evolution presentation [[File:Programmed_Evolution.pdf]]

Caffeine results [[File:Caffeine_Disk.pptx]]

Ammeline presentation [[File:Ammeline.pptx]]

Repressilator modeling exercises [[File:repressilator_modeling.docx]]

Repressilator modeling Excel file [[File:Repressilator_model.xls]]

Repressilator modeling Netlogo file [[File:Repressilator_mod.nlogo.zip]]

=== Biology Files ===

Chaperone plasmid DNA sequences [[File:Chaperone_plasmid_DNA_sequences.docx]]

Origin PCR Gels 5-26-14[[File:5-26-14 Orig PCR Elecpho Gel Pic.doc]]

Chaperone PCR and Repeat Origin PCR 5-27-14[[File:5-27-14_Chap_PCR_and_Repeat_Ori_PCR.doc]]

Chaperone PCR of original clones 5-27-14[[File:5-27-14_chaperone_pcr_clones_1-24.doc]]

Origin PCR of original clones 5-27-14[[File:5-27-14 Ori PCR 1-24.doc ]]

New Chap PCR clones 1-5[[File:5-28-14_New_Chap_PCR_1-5.doc ]]

Combinations Labeling System [[File:Labeling.xlsx]]

ThyA Fitness Module [[File:ThyA fitness module.docx]]

Alternative Riboswitches[[File:Alternative Riboswitches.docx]]

Origin PCR Pictures 6-5-14 [[File:6-5-14 Origin PCR.docx]]

Chaperone PCR PA 6-5-14 [[File:6-5-14 Chaperone PCR.docx]]

Broth Growth Experiments [[File:Broth Growth Experiment Reports Revised.docx]]
===Sub-pages on various topics===

'''
[[MATH]]
'''

[[Catherine Doyle Thesis Materials]]

[[Repeating 20 Clone Experiments]]

[[Extending theophylline application]]

[[Melamine iteration]]

[[Ramping up Programmed Evolution]]

[[Rational Design of Riboswitches: papers to read]]

[[ThyA Fitness Module]]

[[Caffeine Disk Replication Data]]

=== Programmed Evolution Paper ===

[[References]]

File:Math wrap-up.pptx

2014-07-23T15:22:06Z

Mospencer:

File:Caffeine Results.pptx

2014-06-13T18:33:26Z

Mospencer: Mospencer uploaded a new version of "File:Caffeine Results.pptx"

File:Caffeine Results.pptx

2014-06-11T20:47:00Z

Mospencer: Mospencer uploaded a new version of "File:Caffeine Results.pptx"

MATH

2014-06-11T20:09:29Z

Mospencer:

Nava:
"NAVA is a tool for visualising and analysing annotated secondary structures of large single-stranded RNA or DNA sequences (such as full-length virus genomes). The purpose of this tool is to assist investigators in evaluating the biological relevance of RNA or DNA secondary structures within particular sequences."
[https://sites.google.com/site/cbiomichael/software Nava Link]

StatAlign:
"StatAlign is an extendable software package for Bayesian analysis of Protein, DNA and RNA sequences. Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable measurement of the accuracy of the results.
This approach eliminates common artifacts that traditional methods suffer from, at the cost of increased computational time. These artifacts include the dependency of the constructed phylogeny on a single (probably suboptimal) alignment and bias towards the guide tree upon which the alignment relies.
The models behind the analysis permit the comparison of evolutionarily distant sequences: the TKF92 insertion-deletion model can be coupled to an arbitrary substitution model. A broad range of models for nucleotide and amino acid data is included in the package and the plug-in management system ensures that new models can be easily added."
[http://statalign.github.io/index.html StatAlign link]

UNAFold:
"UNAFold is a comprehensive software package for nucleic acid folding and hybridization prediction."

Statistics work:
[[File:Statistics_ChiSquared.xlsx‎]]

Excel File for Calculation of Probabilities of Sampling Error: [[File:Sample Probabilities.xlsx]]

Fisher's Exact Test [[File:Fishers_Exact_Test.ppt]]

Caffeine Experiment Results Statistics: [[File:Caffeine Results.pptx]]

'''Markov Chains:'''

An introduction to Markov Chains and Hidden Markov Models. [[File:Markov_Chains.pptx]]

Hidden Markov Models [[File:HiddenMarkovModels.pdf‎]]

A Presentation on Hidden Markov Models: [[File:Hidden_Markov_Models.pptx]]

File:Caffeine Results.pptx

2014-06-11T20:08:25Z

Mospencer:

File:Replication Results Template.xlsx

2014-06-04T19:05:07Z

Mospencer: Mospencer uploaded a new version of "File:Replication Results Template.xlsx"

Template to enter results of replicated experiments.

Repeating Eckdahl's 20-clone selection

2014-06-04T18:38:39Z

Mospencer:

We need to replicate Dr. Eckdahl’s 20-clone experiment twice on both campuses and mathematically analyze the data. Continue adding arabinose to induce the chaperones.

We need to grow the surviving clones on individual plates: no antibiotic, amp, amp+chlor. This will enable us to determine whether both plasmids (CDM+amp, chaperone+chlor) are still present and being transcribed.

Depending on the survivorship of the clones in the previous step, set up plates to run head-to-head competition between two surviving clones, and determine which strain is most competent. This will confirm the results of the 20-clone experiment, in a more controlled environment than a plate with all 20 clones.

Protocol created on 05/21/14: [[Eckdahl-replication-protocol]]

[https://www.dropbox.com/sh/2jqkqfz755ng0vc/AAA26M9kEeYii0pFtFlCQ17na Photos from Davidson's first replication (four plates)] (Updated May 31, 2014)

Template for results: [[File:Replication Results Template.xlsx]]
Upload a file for each campus with the results displayed in the table. There is a tab in the file for each trial.

File:Replication Results Template.xlsx

2014-06-04T18:36:34Z

Mospencer: Mospencer uploaded a new version of "File:Replication Results Template.xlsx"

Template to enter results of replicated experiments.

Repeating Eckdahl's 20-clone selection

2014-06-04T18:33:39Z

Mospencer:

We need to replicate Dr. Eckdahl’s 20-clone experiment twice on both campuses and mathematically analyze the data. Continue adding arabinose to induce the chaperones.

We need to grow the surviving clones on individual plates: no antibiotic, amp, amp+chlor. This will enable us to determine whether both plasmids (CDM+amp, chaperone+chlor) are still present and being transcribed.

Depending on the survivorship of the clones in the previous step, set up plates to run head-to-head competition between two surviving clones, and determine which strain is most competent. This will confirm the results of the 20-clone experiment, in a more controlled environment than a plate with all 20 clones.

Protocol created on 05/21/14: [[Eckdahl-replication-protocol]]

[https://www.dropbox.com/sh/2jqkqfz755ng0vc/AAA26M9kEeYii0pFtFlCQ17na Photos from Davidson's first replication (four plates)] (Updated May 31, 2014)

Template for results: [[File:Replication Results Template.xlsx]]
Upload a file for both campuses with the results displayed in the table. There is a tab in the file for each trial.

File:Replication Results Template.xlsx

2014-06-04T18:20:00Z

Mospencer: Template to enter results of replicated experiments.

Template to enter results of replicated experiments.

MATH

2014-06-03T19:24:31Z

Mospencer:

Nava:
"NAVA is a tool for visualising and analysing annotated secondary structures of large single-stranded RNA or DNA sequences (such as full-length virus genomes). The purpose of this tool is to assist investigators in evaluating the biological relevance of RNA or DNA secondary structures within particular sequences."
[https://sites.google.com/site/cbiomichael/software Nava Link]

StatAlign:
"StatAlign is an extendable software package for Bayesian analysis of Protein, DNA and RNA sequences. Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable measurement of the accuracy of the results.
This approach eliminates common artifacts that traditional methods suffer from, at the cost of increased computational time. These artifacts include the dependency of the constructed phylogeny on a single (probably suboptimal) alignment and bias towards the guide tree upon which the alignment relies.
The models behind the analysis permit the comparison of evolutionarily distant sequences: the TKF92 insertion-deletion model can be coupled to an arbitrary substitution model. A broad range of models for nucleotide and amino acid data is included in the package and the plug-in management system ensures that new models can be easily added."
[http://statalign.github.io/index.html StatAlign link]

UNAFold:
"UNAFold is a comprehensive software package for nucleic acid folding and hybridization prediction."

An introduction to Markov Chains and Hidden Markov Models. [[File:Markov_Chains.pptx]]

Statistics work:
[[File:Statistics_ChiSquared.xlsx‎]]

Excel File for Calculation of Probabilities of Sampling Error: [[File:Sample Probabilities.xlsx]]

MATH

2014-06-03T19:24:21Z

Mospencer:

Nava:
"NAVA is a tool for visualising and analysing annotated secondary structures of large single-stranded RNA or DNA sequences (such as full-length virus genomes). The purpose of this tool is to assist investigators in evaluating the biological relevance of RNA or DNA secondary structures within particular sequences."
[https://sites.google.com/site/cbiomichael/software Nava Link]

StatAlign:
"StatAlign is an extendable software package for Bayesian analysis of Protein, DNA and RNA sequences. Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable measurement of the accuracy of the results.
This approach eliminates common artifacts that traditional methods suffer from, at the cost of increased computational time. These artifacts include the dependency of the constructed phylogeny on a single (probably suboptimal) alignment and bias towards the guide tree upon which the alignment relies.
The models behind the analysis permit the comparison of evolutionarily distant sequences: the TKF92 insertion-deletion model can be coupled to an arbitrary substitution model. A broad range of models for nucleotide and amino acid data is included in the package and the plug-in management system ensures that new models can be easily added."
[http://statalign.github.io/index.html StatAlign link]

UNAFold:
"UNAFold is a comprehensive software package for nucleic acid folding and hybridization prediction."

An introduction to Markov Chains and Hidden Markov Models. [[File:Markov_Chains.pptx]]

Statistics work:
[[File:Statistics_ChiSquared.xlsx‎]]
Excel File for Calculation of Probabilities of Sampling Error: [[File:Sample Probabilities.xlsx]]

File:Sample Probabilities.xlsx

2014-06-03T19:22:50Z

Mospencer: Calculates probabilities related to sampling in replications of clone experiments.

Calculates probabilities related to sampling in replications of clone experiments.

MATH

2014-05-22T20:44:12Z

Mospencer:

Nava:
"NAVA is a tool for visualising and analysing annotated secondary structures of large single-stranded RNA or DNA sequences (such as full-length virus genomes). The purpose of this tool is to assist investigators in evaluating the biological relevance of RNA or DNA secondary structures within particular sequences."
[https://sites.google.com/site/cbiomichael/software Nava Link]

StatAlign:
"StatAlign is an extendable software package for Bayesian analysis of Protein, DNA and RNA sequences. Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable measurement of the accuracy of the results.
This approach eliminates common artifacts that traditional methods suffer from, at the cost of increased computational time. These artifacts include the dependency of the constructed phylogeny on a single (probably suboptimal) alignment and bias towards the guide tree upon which the alignment relies.
The models behind the analysis permit the comparison of evolutionarily distant sequences: the TKF92 insertion-deletion model can be coupled to an arbitrary substitution model. A broad range of models for nucleotide and amino acid data is included in the package and the plug-in management system ensures that new models can be easily added."
[http://statalign.github.io/index.html StatAlign link]

UNAFold:
"UNAFold is a comprehensive software package for nucleic acid folding and hybridization prediction."

An introduction to Markov Chains and Hidden Markov Models. [[File:Markov_Chains.pptx]]

Statistics work:
[[File:Statistics_ChiSquared.xlsx‎]]

MATH

2014-05-22T20:43:18Z

Mospencer:

Nava:
"NAVA is a tool for visualising and analysing annotated secondary structures of large single-stranded RNA or DNA sequences (such as full-length virus genomes). The purpose of this tool is to assist investigators in evaluating the biological relevance of RNA or DNA secondary structures within particular sequences."
[https://sites.google.com/site/cbiomichael/software Nava Link]

StatAlign:
"StatAlign is an extendable software package for Bayesian analysis of Protein, DNA and RNA sequences. Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable measurement of the accuracy of the results.
This approach eliminates common artifacts that traditional methods suffer from, at the cost of increased computational time. These artifacts include the dependency of the constructed phylogeny on a single (probably suboptimal) alignment and bias towards the guide tree upon which the alignment relies.
The models behind the analysis permit the comparison of evolutionarily distant sequences: the TKF92 insertion-deletion model can be coupled to an arbitrary substitution model. A broad range of models for nucleotide and amino acid data is included in the package and the plug-in management system ensures that new models can be easily added."
[http://statalign.github.io/index.html StatAlign link]

UNAFold:
"UNAFold is a comprehensive software package for nucleic acid folding and hybridization prediction."

An introduction to Markov Chains and Hidden Markov Models. [[File:Markov_Chains.pptx]]

Statistics work:
[[File:Statistics_Chi-squared.xlsx‎]]

File:Statistics ChiSquared.xlsx

2014-05-22T20:43:00Z

Mospencer:

MATH

2014-05-22T19:06:03Z

Mospencer:

Nava:
"NAVA is a tool for visualising and analysing annotated secondary structures of large single-stranded RNA or DNA sequences (such as full-length virus genomes). The purpose of this tool is to assist investigators in evaluating the biological relevance of RNA or DNA secondary structures within particular sequences."
[https://sites.google.com/site/cbiomichael/software Nava Link]

StatAlign:
"StatAlign is an extendable software package for Bayesian analysis of Protein, DNA and RNA sequences. Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable measurement of the accuracy of the results.
This approach eliminates common artifacts that traditional methods suffer from, at the cost of increased computational time. These artifacts include the dependency of the constructed phylogeny on a single (probably suboptimal) alignment and bias towards the guide tree upon which the alignment relies.
The models behind the analysis permit the comparison of evolutionarily distant sequences: the TKF92 insertion-deletion model can be coupled to an arbitrary substitution model. A broad range of models for nucleotide and amino acid data is included in the package and the plug-in management system ensures that new models can be easily added."
[http://statalign.github.io/index.html StatAlign link]

UNAFold:
"UNAFold is a comprehensive software package for nucleic acid folding and hybridization prediction."

An introduction to Markov Chains and Hidden Markov Models. [[File:Markov_Chains.pptx]]

Statistics work:
[[File:Statistic_Chi-squared.xlsx‎]]

MATH

2014-05-22T19:04:36Z

Mospencer:

Nava:
"NAVA is a tool for visualising and analysing annotated secondary structures of large single-stranded RNA or DNA sequences (such as full-length virus genomes). The purpose of this tool is to assist investigators in evaluating the biological relevance of RNA or DNA secondary structures within particular sequences."
[https://sites.google.com/site/cbiomichael/software Nava Link]

StatAlign:
"StatAlign is an extendable software package for Bayesian analysis of Protein, DNA and RNA sequences. Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable measurement of the accuracy of the results.
This approach eliminates common artifacts that traditional methods suffer from, at the cost of increased computational time. These artifacts include the dependency of the constructed phylogeny on a single (probably suboptimal) alignment and bias towards the guide tree upon which the alignment relies.
The models behind the analysis permit the comparison of evolutionarily distant sequences: the TKF92 insertion-deletion model can be coupled to an arbitrary substitution model. A broad range of models for nucleotide and amino acid data is included in the package and the plug-in management system ensures that new models can be easily added."
[http://statalign.github.io/index.html StatAlign link]

UNAFold:
"UNAFold is a comprehensive software package for nucleic acid folding and hybridization prediction."

An introduction to Markov Chains and Hidden Markov Models. [[File:Markov_Chains.pptx]]

Statistics work:
Statistic_Chi-squared.xlsx‎

File:Statistic Chi-squared.xlsx

2014-05-22T19:03:43Z

Mospencer: