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
Interesting Talks to Attend during Symposium
Interesting Talks to Attend during Symposium
Submit SlidesSubmit Slides
June 16, 2025
BTD draftBTD draft
June 30, 2025
Printing, Creating Display for a final exhibitionPrinting, Creating Display for a final exhibition
May 1, 2025 → May 6, 2025
prepare dataprepare data
Working on the DesignWorking on the Design
May 16, 2025 → May 31, 2025
Speaking Presentation - BDC SymposiumSpeaking Presentation - BDC Symposium
June 11, 2025 → June 13, 2025
Test LAMP-PCR PrimersTest LAMP-PCR Primers
Order LAMP-PCR primersOrder LAMP-PCR primers
Run positive control GMO detectiveRun positive control GMO detective
order GMO detective kit and make sure that it worksorder GMO detective kit and make sure that it works
BTD submissionBTD submission
June 30, 2025
waiting
In progress
Biodesign Symposium Call for Papers 2026Biodesign Symposium Call for Papers 2026
May 8, 2025 → May 10, 2025
Paper submission - 9 mayPaper submission - 9 may
April 28, 2025
Consumables & Equipment
Consumables & Equipment
Done
Timeline planningTimeline planning
February 5, 2025 → February 6, 2025
PCR test 1PCR test 1
February 6, 2025 → February 28, 2025
PCR test 2PCR test 2
March 1, 2025 → March 16, 2025
Object Design 1Object Design 1
February 18, 2025 → March 31, 2025
Object Design 2Object Design 2
April 1, 2025 → April 30, 2025
Secure housingSecure housing
Follow the instructions from emailFollow the instructions from email
Device Prototype + Changing color dyesDevice Prototype + Changing color dyes
Fishing GameFishing Game
C
Caroline ChouPosterPoster
Karolina Sulich
Karolina SulichSubmissionSubmission
March 11, 2025
Lab meeting BrainstormLab meeting Brainstorm
March 10, 2025
Exhibit - Event dayExhibit - Event day
April 25, 2025
Boston - 2025 Bioremediation SymposiuBoston - 2025 Bioremediation Symposiu
June 23, 2025 → June 26, 2025
agreeing on a shape production/makingagreeing on a shape production/making
March 11, 2025 → March 24, 2025
Lab presentation progress dayLab presentation progress day
March 17, 2025
IDM ShowcaseIDM Showcase
May 7, 2025 → May 9, 2025
Gallery Exhibition setupGallery Exhibition setup
June 10, 2025 → June 11, 2025
Design LAMP-PCR primersDesign LAMP-PCR primers
Research on shapes and materialsResearch on shapes and materials
February 18, 2025 → March 10, 2025
Writing Methods sectionWriting Methods section
February 10, 2025 → February 14, 2025
positive controlspositive controls
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)
February 15, 2025 → February 17, 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
February 10, 2025 → February 17, 2025
Do PCR’sDo PCR’s
March 13, 2025 → March 15, 2025
Order Primers 3 Primer sets for 3 different genes Order Primers 3 Primer sets for 3 different genes
February 18, 2025 → February 21, 2025
adjusting presentation / project for BDCadjusting presentation / project for BDC
May 16, 2025 → May 28, 2025
ConclusionConclusion
April 4, 2025 → April 17, 2025
ResultsResults
March 25, 2025 → April 3, 2025
MethodsMethods
January 29, 2025 → March 24, 2025
Lit ReviewLit Review
February 6, 2025 → February 28, 2025
BDC (11-14 June) Bio Design ChallengeBDC (11-14 June) Bio Design Challenge
June 3, 2025