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IDM | NYU TANDON SCHOOL OF ENGINEERING 370 Jay street, 3rd Floor Brooklyn, NY 11201

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Karolina Thesis

Karolina Thesis

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 02-24-25

In 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)
Papers

Project tasks

Not started
LAMP 2
LAMP 2
April 13, 2025 → April 30, 2025
Presentations
Presentations
June 15, 2025
Printing, Creating Display for a final exhibitionPrinting, Creating Display for a final exhibitionIDM ShowcaseIDM ShowcaseBDC (11-14 June) Bio Design ChallengeBDC (11-14 June) Bio Design Challenge
waiting
In progress
PCR test 2
PCR test 2
March 1, 2025 → March 16, 2025
Object Design 2
Object Design 2
April 1, 2025 → April 30, 2025
LAMP 1
LAMP 1
March 18, 2025 → April 5, 2025
order GMO detective kit and make sure that it worksorder GMO detective kit and make sure that it worksRun positive control GMO detectiveRun positive control GMO detectiveDesign LAMP-PCR primersDesign LAMP-PCR primersOrder LAMP-PCR primersOrder LAMP-PCR primersTest LAMP-PCR PrimersTest LAMP-PCR Primers
Paper
Paper
Lit ReviewLit ReviewMethodsMethodsResultsResultsConclusionConclusion
Boston - 2025 Bioremediation Symposiu
Boston - 2025 Bioremediation Symposiu
June 23, 2025 → June 26, 2025
Follow the instructions from emailFollow the instructions from emailSecure housingSecure housingSubmit SlidesSubmit SlidesInteresting Talks to Attend during SymposiumInteresting Talks to Attend during Symposium
BTD paper (Biotechnology Design)
BTD paper (Biotechnology Design)
July 1, 2025
BTD draftBTD draftBTD submissionBTD submission
submit IDM Thesis
submit IDM Thesis
April 25, 2025 → May 9, 2025
Lab presentation progress dayLab presentation progress dayPaper submission - 9 mayPaper submission - 9 may
Done
Timeline planning
Timeline planning
February 5, 2025 → February 6, 2025
PCR test 1
PCR test 1
February 6, 2025 → February 28, 2025
rerun in silico PCR - make table with gene name, number of hits, amplicon size 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)pick the primers for the most promising ones (1 mistake!) (what genes that would be)Order Primers 3 Primer sets for 3 different genes Order Primers 3 Primer sets for 3 different genes Do PCR’sDo PCR’sPrep for PCRPrep for PCRWriting Methods sectionWriting Methods section
Object Design 1
Object Design 1
February 18, 2025 → March 31, 2025
Research on shapes and materialsResearch on shapes and materialsagreeing on a shape production/makingagreeing on a shape production/making
Research Excellence Exhibit
🖤
Research Excellence Exhibit
April 25, 2025
ApplicationApplicationPrepartionPrepartionExhibit - Event dayExhibit - Event day