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Team:KULeuven/Modeling
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Inspirational websites:
- Most basic dropdown menu, with no submenu's
- The javascript library used to add effects and optimise the dropdown
- How to center a ul list effectively
The dropdown has been created and developed by the KULeuven team.
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<ul>
<li>
<a href="http://2008.igem.org/Team:KULeuven">Home</a>
</li>
<li>
<a>The Team</a>
<div>
<a href="http://2008.igem.org/Team:KULeuven/Team/LabsandGroups">Research Labs and Groups</a>
<a href="http://2008.igem.org/Team:KULeuven/Team/Students">Students</a>
<a href="http://2008.igem.org/Team:KULeuven/Team/Instructors">Instructors</a>
<a href="http://2008.igem.org/Team:KULeuven/Team/Advisors">Advisors</a>
<a href="http://2008.igem.org/Team:KULeuven/Team/Pictures">Pictures</a>
</div>
</li>
<li>
<a>The Project</a>
<div>
<a href="http://2008.igem.org/Team:KULeuven/Project">Summary</a>
<span>
<a>Components</a>
<div>
<a href="http://2008.igem.org/Team:KULeuven/Project/Input">Input</a>
<a href="http://2008.igem.org/Team:KULeuven/Project/Output">Output</a>
<a href="http://2008.igem.org/Team:KULeuven/Project/Filter">Filter</a>
<a href="http://2008.igem.org/Team:KULeuven/Project/Inverter">Invertimer</a>
<a href="http://2008.igem.org/Team:KULeuven/Project/Reset">Reset</a>
<a href="http://2008.igem.org/Team:KULeuven/Project/CellDeath">Cell Death</a>
<a href="http://2008.igem.org/Team:KULeuven/Project/Memory">Memory</a>
</div>
</span>
<a href="http://2008.igem.org/Team:KULeuven/Evaluation">End Evaluation</a>
<a href="http://2008.igem.org/Team:KULeuven/Literature">Literature</a>
<a href="http://2008.igem.org/Team:KULeuven/Brainstorm">Brainstorm</a>
</div>
</li>
<li>
<a>Ethics</a>
<div>
</div>
</li>
<li>
<a>Submitted Parts</a>
<div>
<a href="http://2008.igem.org/Team:KULeuven/Parts">Listing</a>
<a href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2008&group=KULeuven">Sandbox</a>
</div>
</li>
<li>
<a>Modeling</a>
<div>
<a href="http://2008.igem.org/Team:KULeuven/Model/Overview">Overview</a>
<a href="http://2008.igem.org/Team:KULeuven/Model/KineticConstants">Kinetic Constants</a>
<span>
<a>Components</a>
<div>
<a href="http://2008.igem.org/Team:KULeuven/Model/Output">Output</a>
<a href="http://2008.igem.org/Team:KULeuven/Model/Filter">Filter</a>
<a href="http://2008.igem.org/Team:KULeuven/Model/Inverter">Invertimer</a>
<a href="http://2008.igem.org/Team:KULeuven/Model/Reset">Reset</a>
<a href="http://2008.igem.org/Team:KULeuven/Model/CellDeath">Cell Death</a>
<a href="http://2008.igem.org/Team:KULeuven/Model/Memory">Memory</a>
</div>
</span>
<a href="http://2008.igem.org/Team:KULeuven/Model/FullModel">Full Model</a>
<a href="http://2008.igem.org/Team:KULeuven/Model/Sensitivity">Sensitivity Analysis</a>
<a href="http://2008.igem.org/Team:KULeuven/Model/MultiCell">Multi-cell Model</a>
<a href="http://2008.igem.org/Team:KULeuven/Model/Diffusion">Diffusion</a>
</div>
</li>
<li>
<a>Data Analysis</a>
<div>
<a href="http://2008.igem.org/Team:KULeuven/Data/Overview">Overview</a>
<span>
<a>New Parts</a>
<div>
<a href="http://2008.igem.org/Team:KULeuven/Data/GFP">GFP (LVA-tag)</a>
<a href="http://2008.igem.org/Team:KULeuven/Data/T7">T7 (UmuD-tag)</a>
<a href="http://2008.igem.org/Team:KULeuven/Data/Antisense">Antisense LuxI</a>
<a href="http://2008.igem.org/Team:KULeuven/Data/ccdB">Celldeath (ccdB)</a>
<a href="http://2008.igem.org/Team:KULeuven/Data/HybridProm">Hybrid Promotor</a>
</div>
</span>
<span>
<a>Components</a>
<div>
<a href="http://2008.igem.org/Team:KULeuven/Data/Input">Input</a>
<a href="http://2008.igem.org/Team:KULeuven/Data/Output">Output</a>
<a href="http://2008.igem.org/Team:KULeuven/Data/Filter">Filter</a>
<a href="http://2008.igem.org/Team:KULeuven/Data/Inverter">Invertimer</a>
<a href="http://2008.igem.org/Team:KULeuven/Data/Reset">Reset</a>
<a href="http://2008.igem.org/Team:KULeuven/Data/CellDeath">Cell Death</a>
<a href="http://2008.igem.org/Team:KULeuven/Data/Memory">Memory</a>
</div>
</span>
<a href="http://2008.igem.org/Team:KULeuven/Data/FullModel">Full Model</a>
</div>
</li>
<li>
<a>Software</a>
<div>
<a href="http://2008.igem.org/Team:KULeuven/Software/MultiCell">Multi-cell Toolbox</a>
<a href="http://2008.igem.org/Team:KULeuven/Software/Simbiology2LaTeX">Simbiology2LaTeX Toolbox</a>
</div>
</li>
<li>
<a>Notebook</a>
<div>
<a href="http://2008.igem.org/Team:KULeuven/Meeting_Calendar">Calendar</a>
<a href="http://2008.igem.org/Team:KULeuven/SummerHolidays">Summer Holidays</a>
<span>
<a>Reports</a>
<div>
<a href="http://2008.igem.org/Team:KULeuven/Meeting Reports">Daily</a>
<a href="http://2008.igem.org/Team:KULeuven/Weekly Meetings">Weekly</a>
</div>
</span>
<span>
<a>Lab Data</a>
<div>
<a href="http://2008.igem.org/Team:KULeuven/Freezer">Freezer</a>
<a href="http://2008.igem.org/Team:KULeuven/Primers">Primers</a>
<a href="http://2008.igem.org/Team:KULeuven/Ligation">Ligation</a>
</div>
</span>
<a href="http://2008.igem.org/Team:KULeuven/Tools">Tools</a>
<a href="http://2008.igem.org/Team:KULeuven/Press">Press</a>
<a href="http://2008.igem.org/Team:KULeuven/Guestbook">Guestbook</a>
</div>
</li>
</ul>
</div>
</div>
</html>
Contents |
Modeling
CellDesigner
Output
| Name | Value | Reference |
|---|---|---|
| Degradation | ||
| CFP (protein) | 1.05E-4 /s | link |
| CFP (mRNA) | 0.0023 /s | link |
| Transcription Rate | ||
| CFP | OmpF dependent | |
| Translation Rate | ||
| CFP | 0.167 /s | Based on effenciency RBS |
Cell Death
| Name | Value | Reference |
|---|---|---|
| Degradation | ||
| LuxR (protein) | 0.0010 /s | |
| LuxR (mRNA) | 0.00227 /s | link |
| CcdB (protein) | 7.7E-5 /s | link |
| CcdB (mRNA) | 0.00231 /s | link |
| HSL | 1.02E-6/s | link |
| Dissociation Rate | ||
| ka (HSL+LuxR) | 1E6 /s | chosen to be relatively (to the other rate constants) high and such that Kd equals 1E-6 |
| kd (HSL+LuxR) | 1 /s | |
| Dissociation Constant | ||
| HSL-LuxR | 1E-6 M/L | link |
| Binding LuxR on LuxPromotor | 1E-9 M/L | link |
| Transcription Rate | ||
| LuxR (constitutive promotor) | 0.025 mRNA/s | see sections on Constitutive Promotors & E. coli transcription Rates |
| CcdB (LuxR repressor) | k_1*K_m^n/(K_m^n + [LuxR]^n) = 0.025*1E-9/(1E-9^1+[LuxR]) |
Inverter
| Name | Value | Reference |
|---|---|---|
| Degradation | ||
| LuxI (protein) | 0.00231 /s | |
| LuxI (mRNA) | 0.0025 /s | link |
| LuxI (complex) | 0.00125 /s | |
| LacI (protein) | 0.00231 /s | |
| LacI (gesloten mRNA) | 0.0046209812 /s | |
| LacI (open mRNA) | 0.0023104906 /s | |
| open mRNA LacI complex | 0.0023104906 /s | |
| HSL | 1.02E-6 /s | link |
| Dissociation Rate | ||
| Transcription Rate | ||
| LacI | 0.0011 /s | |
| LuxI | 0.0025 /s | |
| K_m | 1.0E-10 /s | |
| Translation Rate | ||
| LuxI (RBS B0034) | 0.5 /s | |
| LacI (RBS ?) | 0.16667 /s | |
| Equilibrium Constant | ||
| closed and open mRNA LacI | 0.015 | |
| closed and complex mRNA LacI | 0.0212 /M | |
| Hill coëfficiënt | ||
| n | 2 | |
| Others | ||
| LuxI --> HSL | 0.16 | |
| LuxI (mRNA) + anti sense <-> complex LuxI | 4.22E14 | |
Memory
| Name | Value | Reference |
|---|---|---|
| Degradation | ||
| P2ogr (protein) | 0.002265 /s | |
| P2ogr (mRNA) | 0.002265 /s | link |
| P22CII (protein) | 0.002311 /s | |
| P22CII (mRNA) | 0,0022651 /s | link |
| antimRNA_luxI | 0.0045303/s | |
| Transcription rate | ||
| P2ogr | 0.0125 | |
| P22CII | 0.0125 | |
| AntimRNA | 0.0094 | |
| Dissociation Constant | ||
| P2-ogr | 4.2156 M | link |
| R0053-P22CII | 0.1099 M | |
| Hill coëfficiënt | ||
| n | 2 |
Filter
| Name | Value | Reference |
|---|---|---|
| Degradation | ||
| pT7_tag(protein) | 0.00155/s | |
| mRNA_RIBOKEY (RNA) | 0.00462 /s | link |
| gesloten_mRNA_T7 (RNA) | 0.00462 /s | link |
| open_mRNA_T7 (RNA) | 0.00231 / s | link |
| open_mRNA_T7_complex (RNA) | 0.00231 /s | link |
| Equilibrium Constant | ||
| closed and open mRNA | 0,015 | |
| closed and key complex mRNA | 0.0212 /M | |
| Transcription Rate | ||
| mRNA_RIBOKEY | Input dependent | |
| mRNA_T7 | 0,0011 mRNA/s |
Pulse Generator
Constant Lactonase production
Partial Model
Kinetic Constants
ETHZ list of parameters
mRNA decay
T7 RNAP
- Initiation of Transcription by T7 RNA Polymerase at Its Natural Promoters
- Kinetic and Thermodynamic Basis of Promoter Strength: Multiple Steps of Transcription Initiation by T7 RNA Polymerase Are Modulated by the Promoter Sequence
- data T7 team Tsinghua 2007
- Transient State Kinetics of Transcription Elongation by T7 RNA Polymerase
LacI - LuxI
LuxI, LuxR, mRNALuxI, mRNALuxR decay
HSL stuff
- Rapid Acyl-Homoserine Lactone Quorum Signal Biodegradation in Diverse Soils Fig 6: half-life 185 h ==> decay rate 1.02 * 10^-6 s^-1 ==> 0.00889 nM/h
OmpR, OmpF
- A simulation model of Escherichia coli osmoregulatory switch using E-CELL system (Relevance: High), bekijk pg.11/13
- Transcription Regulation of ompF and ompC by a Single Transcription Factor, OmpR (Relevance: Medium)
- Transmembrane Signal Transduction and Osmoregulation in Escherichia coli: Functional Importance of the Transmembrane Regions of Membrane-Located Protein Kinase, EnvZ (Relevance:?), geen toegang tenzij account
- DNA-Binding Properties of the Transcription Activator (OmpR) for the Upstream Sequences of ompF in Escherichia coli Are Altered by envZ Mutations and Medium Osmolarity (Relevance: Low)
- A Distant Upstream Site Involved in the Negative Regulation of the Escherichia coli ompF Gene (Relevance: ?), voor repressor regulatie van OmpF door OmpR
- micF Antisense RNA Has a Major Role in Osmoregulation of OmpF in Escherichia coli (Relevance: Low), invloed 'Antisense RNA' op OmpF regulatie, hmm...
Psid met P2ogr promotor
Constitutive promoters
- Estimated transcription rate for J23105:[1]
- Scale other transcription rate with table in parts registry.
- Estimate the rate of transcription from a constitutive promotor family member.
E. coli transcription rates
Paper about the calculated transcription rates for every E.coli ORF
Tables with the calculated transcription rates for every E.coli ORF
