Team:TU-Eindhoven/Notebook

• Background research

• Selection of topic
• Further research
• Selection of project

• Further research

• Regular team meeting
• Looking for sponsors
• Month planning

Wetlab

• Researching about the promoters
• Researching about the possible proteins for CEST imaging

Drylab

• Defining what needs to be modeled and what type of model is the most appropriate for it

• Regular team meeting
• Looking for sponsors

Wetlab

• Researching and defining the killing mechanism

Drylab

• Starting the Molecular Dynamics model for the proteins selection.

• Regular team meeting
• Looking for sponsors

Wetlab

• Defining the needed materials
• Defining the needed equipment

Drylab

• Continuing the Molecular Dynamics model for the proteins selection.

• Regular team meeting
• Looking for sponsors

Wetlab

• Locating, booking and learning how to use the necessary equipment

Drylab

• Analyzing the results from the Molecular Dynamics model for the proteins selection and identifying the most useful proteins for CEST imaging
• Researching and defining the needed parameters for the analysis of the decoy sites through a stochastic simulations model

Human Practices

• Selecting a main project

• Regular team meeting
• Looking for sponsors

Wetlab

• Locating, booking and learning how to use the necessary equipment

Drylab

• Starting the stochastic simulations for the analysis of the decoy sites

Human Practices

• Selecting a main project

• Regular team meeting
• Looking for sponsors
• Collaborating with Purdue iGEM team
• Planning month activities

Wetlab

• General construct design

Drylab

• Continuing the stochastic simulations for the analysis of the decoy sites

Human Practices

• Defining the structure of the fact checker project

• Regular team meeting
• Looking for sponsors

Wetlab

• Protein design

Drylab

• Continuing the stochastic simulations for the analysis of the decoy sites

Human Practices

• Redacting the preliminary description and survey for collaborators of the fact checker project

• Regular team meeting
• Looking for sponsors

Wetlab

• Final design of the constructs

Drylab

• Continuing the stochastic simulations for the analysis of the decoy sites

Human Practices

• Revising the preliminary description and survey for collaborators of the fact checker project

• Regular team meeting
• Looking for sponsors

Wetlab

• Ordering the constructs
• Working on the protocols

Drylab

• Analyzing the results from the stochastic simulations for the analysis of the decoy sites

Human Practices

• Researching for facts and myths related to Synthetic Biology to be checked

• Regular team meeting
• Looking for sponsors
• Planning month activities

Wetlab

• Finalizing the protocols
• Planning lab schedule

Drylab

• Starting the ODE model for the analysis of the FNR promoter

Human Practices

• Researching for facts and myths related to Synthetic Biology to be checked

• Regular team meeting
• Looking for sponsors
• Collaborating with Purdue iGEM team

Drylab

• Continuing the ODE model for the analysis of the FNR promoter

Human Practices

• Researching for facts and myths related to Synthetic Biology to be checked

• Regular team meetings
• Looking for sponsors
• Collaborating with Purdue iGEM team

Wetlab

• Creating agar plates
• Transforming DNA
• Plating bacteria
• Making LB medium
• Creating small cultures
• DNA retention from cultures
• Nano-drop tests

Drylab

• Analyzing the results from the ODE model for the analysis of the FNR promoter

Human Practices

• Researching for facts and myths related to Synthetic Biology to be checked
• Sending the survey to collaborators

• Regular team meetings
• Looking for sponsors

Wetlab

• Creating agar plates
• Transforming DNA
• Plating bacteria
• Making LB medium
• Creating small cultures
• DNA retention from cultures
• Nano-drop tests

Drylab

• Merging the stochastic simulations model for the decoy sites with the ODE model for the FNR promoter

Human Practices

• Researching for facts and myths related to Synthetic Biology to be checked

• Regular team meetings
• Looking for sponsors
• Working on outreach ideas

Wetlab

• Creating the Cultures
• Retaining the DNA
• Nanodrop Test

Drylab

• Merging the stochastic simulations model for the decoy sites with the ODE model for the FNR promoter
• Working on the pharmacokynetics model

Human Practices

• Researching for facts and myths related to Synthetic Biology to be checked
• Working on the fact checker web platform
• Redacting the first facts to be added on our fact checker platform

• Regular team meetings
• Looking for sponsors
• Working on outreach ideas

Wetlab

• Creating the Cultures
• Retaining the DNA
• Nanodrop Test

Drylab

• Improving the merged model
• Making an ODE model of the decoy sites
• Working on the pharmacokynetics model

Human Practices

• Working on the fact checker web platform
• Preparing the instructions and example files for collaborating teams

• Regular team meetings
• Looking for sponsors
• Working on outreach ideas
• Sharing our project with colleagues and faculty members

Wetlab

• Digestion
• Construct Digestion
• Vector Digestion
• PCR Purification for the Constructs
• PCR Puricfication for the Vectors
• Nanodrop Results
• Continuing with the Purification
• Vector Purification
• Construct Purification
• Ligation
• Preparing Agar Plates
• Transformation
• Plating
• Colony Picking and PCR
• Culturing the Ligation Products

Drylab

• Sensitivity analysis of the merged model
• Estimating promotor rates
• Working on the pharmacokynetics model

Human Practices

• Working on the fact checker web platform

• Regular team meetings
• Looking for sponsors
• Working on outreach ideas

Wetlab

• Colony Picking and PCR
• Small Cultures and Preparation for Protein Expression
• Miniprepping New Constructs
• Sequencing
• Trnasformation and Plating
• Expressing Samples
• Protein Purification
• Determining Protein Concentration
• SDS Analysis
• Performing the Protein Expression in an Anaerobic Environment
• MRI Experiments

Drylab

• Working on the pharmacokynetics model

Human Practices

• Fact checker platform is up and running

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