Team:Wageningen UR/Notebook/Riemer
Here you can find the notebooks from Riemer.
Software
- June
- July
- August
- September
- October
- November
- July 2021
- Augustus 2021
- September 2021
- October 2021
Started work on the Wikibase by following introductions into python programming. Started creating the architecture for the semantic web and made and finished the data structure for this. Installed The DIAMOND Protein Aligner on the SSB server.
Made the pipeline to download data from the iGEM registry, annotate this and save it to the Wikibase. Finished with the architecture for the semantic web. Started testing my program on the SSB server. Initial runtime proved too high therefore changes were made and one direct download from the iGEM registry was chosen.
Finished the pipeline to upload biobricks to the Wikibase. Started running test queries to verify mechanics worked. Mechanics proved not to work and started bugfixing specifically the PREFIXes from the SPARQL query system.
Uploaded all biobricks to the Wikibase and continued bug-fixing regarding the PREFIXes from the SPARQL query system. Started writing down my work and example queries.
Continued writing down thesis and testing example queries. Minor bug-fixes. All biobricks are uploaded by now (over 14 days of running).
Finished thesis and defended thesis in my colloquium. Awarded with a pass.
Restarted work on the Wikibase and The iGEM PIPE. Started cleaning up git repository and working on minor issues with the tutorials.
Sent The iGEM PIPE to Maastricht and Groningen iGEM teams. Asked them to get some aspect (initially just the dependencies) working. Waited for feedback.
Received feedback and started implementing this. For more information consult the collaborations page.
Finished packaging The iGEM PIPE and resent this to Maastricht and Groningen iGEM teams. Besides cleaning up git repository no further action taken.
Wetlab - July
- Week 1: 5th of July - 9th of July
- Week 2: 12th of July - 16th of July
- Week 3: 19th of July - 23th of July
- Week 4: 26th of July - 30th of July
Here I was introduced into the laboratory. Having no prior experience extra care was given to best lab practices and safety. Started with very simple lab tasks such as making media.
Started making glycerol stocks of newly arrived SEVA strains. Additionally I also made glycerol stocks of the newly arrived C1Saux SIJ488 strains. In this week I also designed my Gblocks for IDT and Twist.
In this week I confirmed the KnockOuts of the SIJ488 strains that arrived last week. I also continued designing my Gblocks for IDT and Twist. These GBlocks incorperated the sMMO genes and the M. capsulatus chaperones. (GROL and GROS)
Here I orderd my Gblocks from IDT and TWIST. I also designed an approach for the SEVA2610 and SEVA391 plasmids. I started with my PCRs to get the linear DNA to construct these new plasmids via Gibson assembly.
Wetlab - August
- Week 5: 2nd of August - 6th of August
- Week 6: 9th of August - 13th of August
- Week 7: 16th of August - 20th of August
- Week 8: 23th of August - 27th of August
- Week 9: 30th of August - 3th of September
In This week I Gibson assembled my SEVA plasmids. I transformed them in Dh5α strains and screened with cPCR. After confirmation I sent them in for sequencing and went on vacation.
Whole week on vacation. In Berlin with my friends.
Partially on vacation and afterwards returned to check sequencing. Both constructions appeared succesfull via cPCR yet SEVA2610
This week my Gblocks arrived and via PCR amplification I prepared my next Gibson assemblies. Additionally, I PCR amplified GroEL-2 and GroES from E. coli MG1655 in preparation for the following Gibson.
Gibson assembled SEVA2610_sMMO(1-2), SEVA2610_sMMO(3-4), SEVA2610_sMMO(3-5), SEVA391_chap(1-2) and SEVA391_chap3_MDH. Transformed into DH5α strain via heat shock.
Wetlab - September
- Week 10: 6th of September - 10th of September
- Week 11: 13th of September - 17th of September
- Week 12: 20th of September - 24th of September
- Week 13: 27th of September - 1st of October
Confirmed Gibsons via cPCR and gel electrophorese, no correct assemblies. Redone Gibson assembly PCR steps. Made sure to get more pure DNA and incubate longer.
This we I have redone me Gibsons trying to assemble all interim plasmids I transformed again in DH5α via heatshock.
Via cPCR I confirmed the assembly of SEVA2610_sMMO(1-2), SEVA2610_sMMO(3-4), SEVA_2610_sMMO(3-5), SEVA391_chap(1-2). Grew and miniprepped cultures and send in for sequencing. Transformed C1Saux strain with bsMDH plasmid via electro competence.
Sequencing confirmed correct assembly of SEVA2610_sMMO(1-2), SEVA2610_sMMO(3-5) and SEVA391_chap(1-2), but other plasmids incorrectly assembled. Started working on SM1 and C1Saux growth experiments. Also worked on pMMO in vitro assay and prepared for in vivo assay.
Wetlab - October
- Week 14: 4th of October - 8th of October
This week I have redone the assembly of SEVA2610_sMMO(3-4) and SEVA391_chap3_MDH, confirmed SEVA_sMMO(3-4) via cPCR. Continued working on pMMO in vitro assays. Finished growth experiments with SM1 and C1Saux, with and without Mdh strains.