About this project
- Karolina’s Thesis that will be
- IDM final Thesis
- Published paper co-authored with Elizabeth Henaff, PhD in BTD
Thesis link
Overall understanding of the Project also known as project website
Notes 02-24-25In file: PCRinSilico.py
Tweaks of pcr_in_silico
replace line number 205
existing:
# amp_df.to_csv(out_file + '.tsv', index=False, sep="\t")change to:
amp_df.to_csv(out_file + '.tsv', mode='a', index=False, sep="\t")comment out line 254:
existing:
with pd.ExcelWriter(out_file + '.xlsx', engine='xlsxwriter') as writer:
amp_df.to_excel(writer, sheet_name='amplicons', index=False)
dimers.to_excel(writer, sheet_name='dimers', index=False)
tm_df.to_excel(writer, sheet_name='interactions', index=False)change to:
#with pd.ExcelWriter(out_file + '.xlsx', engine='xlsxwriter') as writer:
# amp_df.to_excel(writer, sheet_name='amplicons', index=False)
# dimers.to_excel(writer, sheet_name='dimers', index=False)
# tm_df.to_excel(writer, sheet_name='interactions', index=False)Project tasks
Not started
LAMP 2
LAMP 2
April 13, 2025 → April 30, 2025
PresentationsPresentationsPrinting, Creating Display for a final exhibitionIDM ShowcaseBDC (11-14 June) Bio Design Challenge
June 15, 2025
Printing, Creating Display for a final exhibitionIDM ShowcaseBDC (11-14 June) Bio Design Challengewaiting
In progress
PCR test 2PCR test 2
March 1, 2025 → March 16, 2025
Object Design 2Object Design 2
April 1, 2025 → April 30, 2025
LAMP 1LAMP 1order GMO detective kit and make sure that it worksRun positive control GMO detectiveDesign LAMP-PCR primersOrder LAMP-PCR primersTest LAMP-PCR Primers
March 18, 2025 → April 5, 2025
order GMO detective kit and make sure that it worksRun positive control GMO detectiveDesign LAMP-PCR primersOrder LAMP-PCR primersTest LAMP-PCR PrimersPaperPaperLit ReviewMethodsResultsConclusion
Lit ReviewMethodsResultsConclusionBoston - 2025 Bioremediation SymposiuBoston - 2025 Bioremediation SymposiuFollow the instructions from emailSecure housingSubmit SlidesInteresting Talks to Attend during Symposium
June 23, 2025 → June 26, 2025
Follow the instructions from emailSecure housingSubmit SlidesInteresting Talks to Attend during SymposiumBTD paper (Biotechnology Design)BTD paper (Biotechnology Design)BTD draftBTD submission
July 1, 2025
BTD draftBTD submissionsubmit IDM Thesissubmit IDM ThesisLab presentation progress dayPaper submission - 9 may
April 25, 2025 → May 9, 2025
Lab presentation progress dayPaper submission - 9 mayDone
Timeline planningTimeline planning
February 5, 2025 → February 6, 2025
PCR test 1PCR test 1rerun in silico PCR - make table with gene name, number of hits, amplicon size pick the primers for the most promising ones (1 mistake!) (what genes that would be)Order Primers 3 Primer sets for 3 different genes Do PCR’sPrep for PCRWriting Methods section
February 6, 2025 → February 28, 2025
rerun in silico PCR - make table with gene name, number of hits, amplicon size pick the primers for the most promising ones (1 mistake!) (what genes that would be)Order Primers 3 Primer sets for 3 different genes Do PCR’sPrep for PCRWriting Methods sectionObject Design 1Object Design 1Research on shapes and materialsagreeing on a shape production/making
February 18, 2025 → March 31, 2025
Research on shapes and materialsagreeing on a shape production/makingResearch Excellence ExhibitApplicationPrepartionExhibit - Event day
Research Excellence Exhibit
April 25, 2025
ApplicationPrepartionExhibit - Event day