Left column: Webtool Notebook
Right column: Lab notebook
We divided the team into an experimental subgroup and a programming subgroup. At this stage there was a third subgroup that was a hybrid group that later was dissolved.
We in the programming group had our first meeting where we set up a GANTT chart and a WBS for our project. In addition to that, we discussed modeling criterias, which was yet to be known, and read up on disease models.
Decided focusing on asthma
We had a meeting with our supervisor to discuss the project and to get us started on using GitHub.
Planned for the work that will be performed during summer. Some research on the components of inflammation and touched up on basic knowledge about immunology was also done.
During this week, we all installed the MODifieR package to our computers since it is necessary for our project. We also started working in groups with smaller projects for the webtool in preparation for the real project.
Literature study on inflammation and immunology.
We had a workshop with our supervisor in preparation of the project and continued with the smaller projects. A new design from the design team was also applied to the webtool.
Started researching asthma, different types and what proteins are involved
We all had this week off since it was exam period.
We read articles about MODifieR this week and finished the smaller projects.
Literature study of asthma.
This week was the official start for the project and we were all very excited! We started to implement inference modules and PPI networks to the webtool.
Literature study, aiming to find 3 good asthma biomarkers each.
We started implementing ClusterProfiler and maintaining the main page and continued implementing inference methods and PPI networks. We had also got some feedback from potential users which we discussed how we could implement the webtool and a new potential named for it.
Deciding on creating a biosensor, which will help in asthma diagnostic
We continued to implement ClusterProfiler and maintain the main page during this week.
Literature search regarding biosensors.
We had a half time evaluation about the project so far and continued with the work from the former week.
Compiling a list of asthma biomarkers and choosing 3 ones that is the best fit for our project.
Started preparing for beta testing and it was the last week working on ClusterProfiler and maintaining main page.
Educational week, project advisors were showing how to work in Benchling.
This week some of us started working on GWAS along with some from the experimental group while the others continued with maintaining the webtool. We also held a beta testing for potential users.
Designing chosen biomarkers in Benchling
We continued working on GWAS and updating the webtool from feedback we received from the beta testing
Literature search to find protocols regarding protein expression, purification and labeling for lab work.
This week we started filming for the promotional video which was a lot of fun, especially since we got to meet each other for the first time in all summer. We also worked on improving the mainpage and making the webtool more user friendly. We even got some data to run with MODifieR.
This week we worked on how implement our biosensor theoretically together with biomarkers.
We are still implementing improvements from the beta testing feedback and preparing data to run on the cluster.
Ordering earlier constructed plasmid in Benchling from IDT and continue looking for protocols.
We continued to update the webtool from the beta testing and started preparing us to finish up the summer part of the project.
Educational week, during which the lab advisor and PIs teached experimental team members some basis of lab work with the bacteria. We also had safety laboratory instruction.
There are only three issues left on GitHub meaning the webtool is almost done! We had meetings about how we will proceed with the project during the fall and fixed some bugs in the webtool.
Successfully expressed EDN and ECP in E.coli BL21 strain and purified it.
The webtool is finished! Just in time before school starts again. We worked on joining the experimental and programming parts of the project. We decided a new date for another beta testing.
Dialysis and nanoDFS was performed on ECP in order to ensure protein fold.
We decided on a name for the webtool - Clustersy, and added some new functions to the webtool and planned for some enrichment analysis.
This week dialysis and nanoDFS was still performed on ECP in order to ensure protein fold.
The enrichment analysis is done and we started to study the results. We also found a way to validate the biomarkers. The v-NIC also happened this week which was great.
Data was analyzed from the dialysis and nanoDFS and samples were run on MALDI - TOF.
We started to prepare for the next beta testing.
The data from MALDI - TOF was analyzed.
