Team:Amsterdam/project/diary/

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__NOTOC__
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<h1>Diary</h1>
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<!-- LAB JOURNAL -->
<!-- LAB JOURNAL -->
<center><h2>Lab</h2></center>
<center><h2>Lab</h2></center>
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<center><h4>26/04/2012</h4></center>
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<center>'''26/04/2012'''</center>
We arrive at the lab to get started! First items on the agenda are getting settled at the lab and acquiring our needed equipment. As a bonus we do a transformation need tot test the Gibson method we will be using throughout these months.
We arrive at the lab to get started! First items on the agenda are getting settled at the lab and acquiring our needed equipment. As a bonus we do a transformation need tot test the Gibson method we will be using throughout these months.
We will do this by cloning a GFP into a pET28 vector using our transformation protocol.
We will do this by cloning a GFP into a pET28 vector using our transformation protocol.
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<center><h4>27/04/2012</h4></center>
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<center>'''27/04/2012'''</center>
Succesfully transformed the plasmids. Ordered the primers for our gibson assembly and started to prepare things. Aliquoting our phusion and gisbon master mix.
Succesfully transformed the plasmids. Ordered the primers for our gibson assembly and started to prepare things. Aliquoting our phusion and gisbon master mix.
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<center><h4>07/05/2012</h4></center>
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<center>'''07/05/2012'''</center>
Preparing O/N cultures which can be taken out of 37C in the weekend by a friend
Preparing O/N cultures which can be taken out of 37C in the weekend by a friend
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<center><h4>08/05/2012</h4></center>
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<center>'''08/05/2012'''</center>
Our friend former igem member Yuri of 2011 will take out our O/N cultures.
Our friend former igem member Yuri of 2011 will take out our O/N cultures.
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<center><h4>09/05/2012</h4></center>
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<center>'''09/05/2012'''</center>
Yuri forgot... Start again. Note; rely on ourselves
Yuri forgot... Start again. Note; rely on ourselves
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<center><h4>10/05/2012</h4></center>
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<center>'''10/05/2012'''</center>
The primers arrived. we reconstituded them and tried them on the plasmids after mini-prepping our O/N culture.
The primers arrived. we reconstituded them and tried them on the plasmids after mini-prepping our O/N culture.
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<h2>Modelling</h2>
<h2>Modelling</h2>
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<h4>08/23/12 - pBAD as an alternative to pLac</h4>
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'''08/23/12 - pBAD as an alternative to pLac'''
It has been some time since I have updated this diary, but we haven't been idle!
It has been some time since I have updated this diary, but we haven't been idle!
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Now on to modelling pBAD operon and the systems functioning when we let it control our fusion protein and let's see if we achieve desirable results <i>in silico</i>!
Now on to modelling pBAD operon and the systems functioning when we let it control our fusion protein and let's see if we achieve desirable results <i>in silico</i>!
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<h4>08/14/12 - Automatically convert Stochpy input to LaTeX</h4>
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'''08/14/12 - Automatically convert Stochpy input to LaTeX'''
Wouldn't it be nice if you could convert your model description files to LaTeX automatically, so when you want to update your Wiki or report with your latest models they can be published right away?
Wouldn't it be nice if you could convert your model description files to LaTeX automatically, so when you want to update your Wiki or report with your latest models they can be published right away?
In case you've been using the nice python program [http://stompy.sourceforge.net/ Stochpy] to do your simulations you no longer have to be left craving: we've created a tool that parses model description files in MDL format that Stochpy uses and spits out a nicely formatted latex document.
In case you've been using the nice python program [http://stompy.sourceforge.net/ Stochpy] to do your simulations you no longer have to be left craving: we've created a tool that parses model description files in MDL format that Stochpy uses and spits out a nicely formatted latex document.
You can find it on [https://github.com/slagtermaarten/MDL2Latex github].
You can find it on [https://github.com/slagtermaarten/MDL2Latex github].
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<h4>08/02/12 - Fusion protein activity</h4>
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'''08/02/12 - Fusion protein activity'''
There are no \(k_{cat}\) values available for the methyltransferase that we use, M.ScaI. We will have to do a parameter scan of plausible \(k_{cat}\) values. Comparing the rates of other methyltransferases will hopefully yield sensible upper and lower boundaries for this parm scan.
There are no \(k_{cat}\) values available for the methyltransferase that we use, M.ScaI. We will have to do a parameter scan of plausible \(k_{cat}\) values. Comparing the rates of other methyltransferases will hopefully yield sensible upper and lower boundaries for this parm scan.
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<h4>07/31/12 - Stochastic model of the Lac operon</h4>
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'''07/31/12 - Stochastic model of the Lac operon'''
We are using a glucose-insensitive lac operon to control the expression of our Zinc-Finger-methyltransferase fusion protein (FP), by replacing the three naturally controlled genes (LacY, LacZ and LacA) with our fusion protein.
We are using a glucose-insensitive lac operon to control the expression of our Zinc-Finger-methyltransferase fusion protein (FP), by replacing the three naturally controlled genes (LacY, LacZ and LacA) with our fusion protein.
The signal to be registered in our proof of principle, lactose, controls the expression this operon.
The signal to be registered in our proof of principle, lactose, controls the expression this operon.
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<!-- TOOL JOURNAL -->
<!-- TOOL JOURNAL -->
<h2>Celullar Logbook Construct Designer</h2>
<h2>Celullar Logbook Construct Designer</h2>
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<h4>01-09-2012</h4>
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'''01-09-2012'''
*The tool is online and working. During the next meeting it will be discussed with the advisors and the team members to see if any (minor) adjustments are required.
*The tool is online and working. During the next meeting it will be discussed with the advisors and the team members to see if any (minor) adjustments are required.
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<h4>07-08-2012</h4>
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'''07-08-2012'''
*The tool now also has the minor things that were not yet added but essential in store.
*The tool now also has the minor things that were not yet added but essential in store.
*Creates a seperate memory plasmid gb file and a restriction site plasmid gb file.
*Creates a seperate memory plasmid gb file and a restriction site plasmid gb file.
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*Next week we can start with dressing up the tool for extra features such as primer generation / cloning steps
*Next week we can start with dressing up the tool for extra features such as primer generation / cloning steps
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<h4>29-07-2012</h4>
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'''29-07-2012'''
*We have a working tool that generates a genbank file given a backbone plasmid. The next few days will have to be spent to automatically and correctly insert the features that are to go with our memory plasmid.
*We have a working tool that generates a genbank file given a backbone plasmid. The next few days will have to be spent to automatically and correctly insert the features that are to go with our memory plasmid.
*Adjusted the tool so it correctly makes all the objects and it's sub objects / functions
*Adjusted the tool so it correctly makes all the objects and it's sub objects / functions
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<h4>25-07-2012</h4>
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'''25-07-2012'''
*Had a meeting for our plasmid design tool establishing the rules for the plasmid generation
*Had a meeting for our plasmid design tool establishing the rules for the plasmid generation
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<!-- WIKI JOURNAL -->
<!-- WIKI JOURNAL -->
<h2>Wiki</h2>
<h2>Wiki</h2>
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<h4>05-09-2012</h4>
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'''05-09-2012'''
*Filling the glossary with data
*Filling the glossary with data
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<h4>07-08-2012</h4>
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'''07-08-2012'''
*To catch up on what should have already been done the following will be worked on tomorrow:
*To catch up on what should have already been done the following will be worked on tomorrow:
**Easier navigation
**Easier navigation
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**Adding medal requirements and a link to the respective data that fullfills these requirements
**Adding medal requirements and a link to the respective data that fullfills these requirements
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<h4>31-07-2012</h4>
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'''31-07-2012'''
*Put the following stuff on the wiki:
*Put the following stuff on the wiki:
**Protocols, Applications, Safety - questions, Safety - components, Frequently Asked Questions
**Protocols, Applications, Safety - questions, Safety - components, Frequently Asked Questions
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<h4>29-06-2012</h4>
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'''29-06-2012'''
*Project Description:
*Project Description:
**Spent some time the past few days to write (read: Mostly put together already existing parts) a project description to put on the wiki. Somewhere in the coming days we will review it with the group and put it online afterwards.
**Spent some time the past few days to write (read: Mostly put together already existing parts) a project description to put on the wiki. Somewhere in the coming days we will review it with the group and put it online afterwards.
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<h4>25-07-2012</h4>
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'''25-07-2012'''
*Had a meeting for our wiki
*Had a meeting for our wiki
*We are going to add the following stuff in the coming weeks:  
*We are going to add the following stuff in the coming weeks:  
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Latest revision as of 01:46, 26 September 2012