Team:Groningen/Notebook

Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9 Week 10 Week 11 Week 12 Week 13 Week 14 Week 15 Week 16 Week 17 Week 18 Week 19 Week 20 Week 21 Week 22 Week 23 Week 24 Week 25 Week 26 Week 27 Week 28 Week 29 Week 30 Week 31 Week 32 Week 33 Week 34 Week 35 Week 36 Week 37 Week 38

Week 1:

The first team meeting took place this week. All members of the team suggested ideas for our iGEM project.

Week 2:

We finalized on two ideas: Saving coffee beans from a pathogen or combating parasitic nematodes. Both of these ideas were further investigated and were pitched to the supervisors.

Week 3:

Amongst the two ideas - Combating cyst nematodes was picked for our iGEM 2020 project. The topic was divided amongst all the team members, who looked into the different research aspects of this topic.

Week 4:

A detailed plan, was presented to the supervisors. We received feedback on how to proceed further and information on what facilities are available for our proposed experiments.

Week 5:

In the beginning of March, we heard the news about the COVID-19 virus and the possibility of a lockdown. To continue our weekly meeting through the pandemic, the idea of weekly Zoom meetings was proposed. Along with that, we continued to work and further refine our project ideas.

Week 6:

The team was divided into groups to work on specific parts of the project. A sponsor team was also setup. They looked up possible companies for sponsoring our team. By this time, Coronavirus is started to be taken seriously by governments around the world.

Week 7:

A lockdown was announced in the Netherlands. To adapt to this situation, our project was significantly altered to account for the fact that we could not enter the lab this year. The team brainstormed about which experiments we could conduct in silico.

Week 8:

A COVID-19-proof project idea was pitched. Different modeling ideas were considered and team members were assigned to investigate each idea. For the outreach, we decided on making a Massive Open Online Course (MOOC).

Week 9:

The dry lab team refined the population model. Three smaller model ideas were also proposed, among which was the biofilm feasibility analysis that would later become a big part of the dry lab.

Week 10:

In this week, we ran into some problems. The idea to put DAPG in RootPatch is cast into doubt due to its possibility to harm the biofilm formation. Also, since the potato planting season commenced, we started looking into a field trip to a potato farm to learn more about the problem.

Week 11:

The team decided to discard the DAPG idea after consultation with the HLB lab. We brainstormed ideas for overcoming obstacles to making a functional kill switch.

Week 12:

The computational models were refined based on what questions we want them to answer and how they fit into the whole project. The kill switch was improved to also trigger when potatoes are harvested.

Week 13:

A new team member - Ronja joined the dry lab team to help with modeling. The outreach team planned to the MOOC with the help of Science LinX.

Week 14:

The wet lab team changed organism to B. mycoides in response to feedback from Oscar Kuipers. Meanwhile, we started planning for hosting the Benelux Meetup.

Week 15:

The Benelux Meetup plan was further refined. We also set up strategies for the social media page for our project. The outreach team partnered up with NEMO for the MOOC.

Week 16:

The dry lab team shifted the Biofilm model from a micro-level approach to a macro-level approach based on feedback from Jordi van Gestel. B. mycoides was definitively chosen as our organism by the wet lab team based on the feedback from Jan Spoelder.

Week 17:

Every team worked on their part of the project. No major changes to the project were made in this week.

Week 18:

The team made a lot of content for the Benelux Meetup. No other major developments were made this week.

Week 19:

Our team had an interview with the UKrant about our project. The dry lab team successfully finished the rate equations for the models. Meanwhile, the outreach team fixed on topics for the MOOC.

Week 20:

This week, the dry lab team continued with developing the equations for the models. Wet lab and outreach further worked on their parts of the project. Along with this, the team was also planning the BeNelux Meetup.

Week 21:

The outreach team worked on circumventing issues with video recording for the MOOC. Transcriptomics data was used to find genes dependent on solanine by the dry lab team.

Week 22:

As the lockdown starts being lifted, we made efforts to find a physical working/meeting space. The dry lab team shifted the research questions of the biofilm model from qualitative to quantitative-based on feedback from Sander van Doorn.

Week 23:

The outreach team downscaled the MOOC to two 45 minute lessons due to time considerations. The team had talks with iGEM BITS Pilani-Goa about a possible partnership; we gave them advice on modeling.

Week 24:

New team members (Arne, Alex and Job) joined as the art team and are responsible for visual design. We designed a 3D printed trophy for the Benelux Meetup.

Week 25:

The team started working on the 2-minute video for the jamboree. We also finalized the planning and successfully hosted the Benelux Meetup.

Week 26:

This week we visited the HLB lab which has expertise in the Globodera pallida. We started working on the storyboard of the 2 minute video. The wet lab team wrote protocols of the experiments and the sensitivity analysis of the biofilm model was started by the dry lab team.

Week 27:

Equations for the dry lab are finished, both models started sensitivity analysis. We started discussing the work for the collaboration with NOVA Lisbon. Protocols and the lesson series were still being developed.

Week 28:

The team started working on hosting a webinar for the Global Meetup with NOVA Lisbon. The rendering of the 2-minute video shots began in this week as well. Dry lab, wet lab and outreach continued to work on their projects without significant alterations.

Week 29:

A webinar was hosted at the Global Meetup and the team spirit poster was made. An experimental layout was made for the Wiki. We started working on the 20-minute presentation for the jamboree.

Week 30:

The dry lab team concluded the analysis of the biofilm model. We also established contact with RIVM about the safety implications of our project. The outreach team finalized a plan for the recording of videos for the lesson series.

Week 31:

All team members started writing their Wiki text. The dry lab team continued to do the final analysis of the population model in this week.

Week 32:

The outreach team finalized scripts for the lesson series. Dry lab results are in; writing conclusions for the graphs. The first version of the storyboard for the 20-minute video was written.

Week 33:

The storyboard for the 20-minute video was revised and recording space was set. The outreach team started recording videos for the lesson series. Also, a model for team NOVA was developed.

Week 34:

The voiceover and final touches were made to the 2-minute promotional video and submitted to the iGEM PeerTube portal. Track selection was finalised to “Food & Nutrition”. Team roster was completed

Week 35:

Jamboree registration was completed. New sub-teams like Review and Video team were made since most parts of the dry lab, wet lab and writing for the Wiki were done. A schedule was set up for the Video team for writing the script, shooting and editing the 20-min presentation video.

Week 36:

Project title and abstract was finalised. The Video team was busy writing the field scenes of the presentation video.

Week 37:

The field scenes were shot at the Agrico Research facility. The script for the studio scenes was written and finalised. Lesson 1 of the outreach program was uploaded online.

Week 38:

The studio scenes were shot at the Academie MInerva studios and are being edited. Lesson 2 of the outreach program was uploaded online.

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