Notebook

Spring 2022



220130 - 220205:

  • First meeting: discussed basic tenets and principles of synthetic biology
  • Discussed past iGEM projects that included wetlab and modeling

220206 - 220212:

  • Read hisat manual
  • Looked into previous iGEM projects
  • Prepared for lab safety check

220213 - 220219:

  • Ran hisat program using DH5a genome
  • Read papers on synthetic biology fiedability and B. subtilis engineering
  • Brainstormed 2022 project ideas
  • Had a team meeting

220227 - 220305:

  • Looked into igem projects and papers about synthetic biology and fieldability
  • Brainstormed project ideas
  • prepared for an education event
  • Meeting: discussed synbio fieldability

220306 - 220312:

  • Review igem projects and papers about synthetic biology and fieldability, papers on synthetic biology chassis
  • Brainstormed project ideas
  • Meeting: discussed synbio fieldability

220313 - 220319:

  • Spring Break

220320 - 220326

  • Read papers and igem projects on synthetic biology bioremediation, soil contamination, biosensors
  • Brainstormed project ideas
  • Meeting: discussed papers and igem projects on synthetic biology bioremediation soil contamination, biosensors

220327 - 220402

  • Looked into papers and igem projects on synthetic biology bioremediation, contamination in the environment
  • Brainstormed project ideas
  • Worked on team member introduction, photos, and science puns to introduce our team to people that pass the lab
  • Meeting: discussed team member intro and synthetic biology bioremediation and environment pollution

220403 - 220409

  • Did autoclave training for new members
  • Did wet lab training
  • Brainstormed project ideas
  • Read synthetic biology in the environment
  • Prepared for education event for William & Mary students(making kahoot games, cookie activity, advertising bioengineering minor program)

220410 - 220416

  • Read papers on potential chassis, soil erosion, biofilm, environment pollution, bioremediation
  • Held education event for students at W&M
  • Brainstormed project ideas
  • Meeting: talked about bioremediation, IHP, biosensing, and soil pollution

220417 - 220423

  • Viewed papers on biodegradation, bioremediation, modeling on pollutants, soil bioengineering, pollutants in soil, chassis, circuit, and biofilm
  • Downloaded files from galaxy
  • Did safety training
  • Viewed soil bioengineering papers
  • Looked into modeling bacterial diffusion in soil
  • Reviewed papers on chassis selection
  • Had a team meeting

220424 - 220430

  • Reviewed papers on soil bioengineering and synthetic biology circuits
  • Miniprep practice for new members
  • Meeting:
    • Talked about output measurement in soil
    • Discussed soil bioengineering

220501 - 220507

  • Looked for biofilm producing circuits, bacterial genomes, chassis
  • Did online safety training
  • Meeting:
    • Talked about potential chassis
    • Discussed soil bioengineering

220508 - 220514

  • Viewed circuit parts on different chassis, output measurements
  • Did online safety training
  • Meeting:
    • Talked about output measurement
    • Discussed soil bioengineering

220515 - 220521

  • Reviewed chassis, biofilm, erosion, biodegradation, circuits, bacterial survival in the soil, bacterial readout, safety, and modeling
  • Wet lab: minipreping and making glycerol stock for plasmid pZS1, pET-GFP, pDawn-Ag43
  • IHP: conducted interview with Randolph Chambers

220522 - 220528

  • Looked for sfgfp sequence in putida, putida plasmids, gene assembly technologies
  • Reviewed articles about P. putida, E. coli, chassis selection, bacterial survival in the soil, bacterial readout, safety, and modeling
  • Worked on IBC protocol and M. smegmatis transformation protocol
  • Meeting:
    • Discussed plans for summer

Summer 2022



220529 - 220604

  • Worked on IBC protocol revision
  • Reviewed materials on gene assembly technologies
  • Sought IHP people
  • Looked for primers for GFP in P. putida
  • Looked into PAH degradation circuits
  • Viewed PCR assaying methods
  • Sought primers specific to bacterial genus, species, and strains
  • Did safety training
  • Wet lab: confirmed PCHERRY plasmid by inoculation, plate making, miniprep, PCR, making glycerol stock, made LB
  • Conducted literature review on chassis selection, bacterial survival in the soil, bacterial readout, safety, and model
  • Searched on rewriting biom-format to_tsv()
  • Wrote a script to determine stats about EMP dataset
  • Worked on EMP data analysis
  • Collaboration: picked up trash and took pictures
  • Had a team meeting

220605 - 220611

  • Reviewed articles on qRT PCR, soil experiments, soil kits, primers specific to bacterial genus, species, and strains, M. Smegmatis transformation, sfGFP primers
  • Seek out local soil organizations and IHP people
  • Designed primers for mcherry
  • Wet lab: confirmed pTD-C_sfYFPTwinStrep, pTDpelB-C_sfYFPTwinstrep, pDCAF3-IS5 and pBAM1 by making glycerol stock and miniprep, inoculation, restriction digest; transformed pCHERRY into DH5a
  • Reviewed requirements for impact grant
  • Worked on M. Smegmatis transformation protocol
  • Looked into growth model, models designed for food safety, and spatial models
  • Worked on tensorflow program
  • Assembled data into tables
  • Looked at supplementing missing sample metadata with GIS information
  • Tried to filter and export rebiom data
  • Built coalesced spreadsheet of parameters to pull from QIITA metadata
  • Worked on assembling QIITA data and augmenting with GIS
  • Identified soil type parameters for chassis model
  • Did CITI training:
    • Biomedical Research - Area III: Biomedical Research Investigators - PHSC (ID 42412)
    • AREA III Disciplines - Research Ethics (ID 68963)
  • Had a team meeting

220612 - 220618

  • Reviewed biosensors, paper strip testing, circuit design, bioremediation circuits,genome integration, chassis, primers
  • Worked on M. Smegmatis transformation protocol
  • Wetlab: made LB, midiprep PTDpelB-C_sfYFPtwinStrep, ran a gel for the midiprep done this week
  • Drafted IHP emails
  • Made impact grant powerpoint
  • Filled out the safety form
  • Worked on finding GIS data sources
  • Extracted qiita data
  • Figured out modeling output
  • Analyzed data
  • Incorporated biotic factor
  • Worked on metadata resolver
  • IHP: conducted interview with Dan Schwartz and John Marken, joined Virginia Soil Health Coalition Quarterly Meeting
  • Had a team meeting

220619 - 220625

  • Conducted literature review on bioremediation circuits, paper strip, bacteria growth state, P. putida primers, P. putida circuit, bacteria growth model
  • Drafted autoclave protocol, Taqman probe+primer protocol, and soil experiment protocol
  • Wetlab: did restriction digest and gel analysis for pBAM-1,pTD-C, pDCAF, and pTDpelB-C, making 7h9 media, made plates, inoculated and minipreped PTD-C and pBAM-1, and measured OD for PTD-C and pBAM-1
  • Wrote impact grant
  • Did circuit analysis
  • Analyzed midiprep results
  • Revised M. Smegmatis transformation protocol
  • Filled out the safety form
  • Participated in the interlab study
  • Tried to design paper strips experiment
  • Wrote wiki page for project description
  • Worked on getting WISE dataset integrated into datastream
  • Tried to refetch samples from redbiom
  • Figured out how to do non-linear regression in R
  • Made the regression more accurate
  • Analyzed regression results
  • Exported data from bg7
  • Added GIS sources
  • Computed model
  • Tried to visualize ML model on bg7
  • Worked on a small GIS-based interface for interacting with the model
  • IHP: conducted interview with Peter Savelyev, Alan Franzluebbers, Jessica Stephens
  • Collaboration: Gaston Day School
  • Had a team meeting

220626 - 220702

  • Reviewed bacteria circuits, P. putida backbones, removing the insert from the backbone in pTD-C, bioremediation circuits
  • Worked on impact grant
  • Drafted 7H10 plate protocol, soil testing protocol, and 16S PCR protocols
  • Searched the literature 16S primers
  • Designed paper strip experiments
  • Sought bacteria specific primers
  • Attended Github igem session
  • Ordered primers for mcherry and sfgfp
  • Wet lab: midiprep pBAM-1 and pDCAF, making glycerol stocks of M. Smegmatis, making 7H10 plates, restriction digest, measuring OD of M. Smegmatis, miniprep on sfgfp e coli, wm21-014, inoculating M. Smegmatis, pTD-C, pTDpelB, restriction digest and gel analysis for pDCAF, pBAM-1, interlab study, soil collection, soil fluorescence testing
  • Retrieved parameters from bg7
  • Generated data subset
  • Processed raw data
  • Downloaded datasets
  • Tried to process data for all BIOM files
  • Figured out how to add a model response endpoint to the Flask chassis visualization server
  • Worked on web visualization with GIS
  • Collaboration: Biocrew and Hopkins
  • Had a team meeting

220703 - 220709

  • Reviewed paper strip testing, band pass, primer resuspension protocol, bioremediation circuits, metabolism circuits
  • Worked on developing the 16s protocols and fluorescence testing protocol
  • Wetlab: minipreped and running digest on WM21_016 pDCAF3 and PTD-C_sfYFPTwinStrep circuits, autoclaved soil, did interlab study, made 7H10 media and Electrocompetent M. Smegmatis cells, made PBS, transformed M. Smegmatis, made LB, resuspended mCherry primer, performed PCR to confirm efficacy of mCHerry Primers, did restriction digest and gel analysis on the PCR products, inoculated M. Smegmatis
  • Tried to collected data analyzed by underscore+endswith script
  • Worked on QIITA dedupe
  • Implemented a micro-scale model of our bacterial system in soil
  • Developed a micro-scale model using python
  • Fixed data issues
  • Built new macro model
  • Had a team meeting

220710 - 220716

  • Reviewed metabolism circuits, bioremediation circuits, paper strip, distribution kit, previous software projects, 16S, previous igem projects and medal requirements, papers and databases on metagenomic data in water, air, soil, and gut microbiome, ihp contacts
  • Sought 16S data in gut microbiome, water, air, and soil
  • Wet lab: did colony PCR on M. Smegmatis pCHERRY3, gel electrophoresis and analysis on the PCR, inoculated M. Smegmatis, interlab study, made 7H9, made LB plates
  • Built on the genome-scale metabolic model
  • Worked on gut microbiome model of the relative abundance models
  • Reanalyzed QIITA data on HPC
  • Implemented parameter resolver
  • Revamped raw data processing
  • Collaboration: Baltimore Biocrew and John Hopkins, VIT project
  • Had a team meeting

220717 - 220723

  • Reviewed plate reader operation, papers and databases on metagenomic data in water, air, soil, and gut microbiome, IHP contacts, isolating DNA for M. Smegmatis, 16S, circuits
  • Worked on video script
  • Sought 16S data in gut microbiome, water, air, and soil
  • Drafted 16s PCR protocol
  • Took team photos
  • Made a calendar for upcoming tasks
  • Wet lab: minipreped M. Smegmatis, tested out different PCR protocols, did gel electrophoresis and gel analysis for PCR products, minipreped pCHERRY3, made glycerol stocks of untransformed DH5a cells, made LB agar plates without antibiotics to have untransformed cells , resuspended 16S primers, did interlab study
  • Built on microbiome analysis program
  • Tried to understand genome-scale metabolic model concepts
  • Attempted to solve the poetry error generated by HPC
  • Established the concept of a "source data block" in the microbiome data processor
  • Worked on growth and relative abundance and environment selection model
  • Collaboration: Baltimore BioCrew education meeting
  • Had a team meeting

220724 - 220730

  • Sought 16S data in gut microbiome, water, air, and soil
  • Worked on promotional video script
  • Participated in the interlab study
  • Reviewed papers on 16s sequencing and phage growth rate in relation to bacterial growth rate models
  • Wet lab: tried out for the best PCR method, did gel analysis and PCR purification on the products
  • Developed presentation to talk to funders of the university about our research
  • Continued to work on microbiome analysis program
  • Installed MPI in WSL to test concurrent dataset processing
  • Built on relative abundance and growth rate model for soil, air, and water
  • Worked on resolving genome-scale metabolic analysis of cinnamaldehyde system issues
  • Solved a circular import issue related to units interacting with DataVal. Python-specific
  • Created local venv to run cobra simulations
  • Started on the system for more effectively implicitly assuming units
  • IHP: conducted interview with Joseph Wood
  • Had a team meeting

220731 - 220806

  • Looked into mCherry codon optimization, incorporating plasmids into GEMS, phage growth rate in relation to bacterial growth rate, IHP contacts, interactions between inserted circuits and their chassis cell
  • Worked on promotional video script
  • Recorded and integrated interlab calibration data
  • Wet lab: collected soil for 16s experiments, performed soil DNA extraction and purification, PCR, did restriction digest and gel analysis on the products
  • Worked on software interface
  • Looked into microbiome analysis program
  • Generated data subset from individual studies
  • Searched for Genome-scale metabolic models
  • Collaboration: John Hopkins/Biocrew meeting, reach out to VIT Vellore, Gaston Day School
  • Education: Terraforming Mars game expansion pack
  • IHP: conducted interview with Ms Bouchra Ezzamouri, Dr. Bryn Adams, Dr. Salerno
  • Had a team meeting

220807 - 220813

  • Wrote Review of Chassis Selection
  • Tried to incorporate genome-scale metabolic model
  • Rebuilt software package for new platform
  • Performed testing with multiple designs for sliders with explicit values + units
  • Worked on promotional video
  • Performed 16s PCR
  • Coded and wrote for wiki
  • Education: Booklet for children about chassis selection/associated games, terraforming Mars expansion pack, Re-Terraforming Earth Game
  • Collaboration: Participated in Mid Atlantic Meetup with other iGEM teams
  • IHP: conducted interview with Dr. Kunjapur
  • Had a team meeting

220814 - 220820

  • Worked on Terraforming Mars expansion pack
  • Coded for wiki meet the team page
  • Designed Re-terraforming Earth cards
  • Recorded video sound track
  • Ordered the updated primer set
  • Conducted 16S sequencing experiments to test out our model
  • Developed circuits to improve a part
  • Created chassis selection software package
  • Generated unfiltered water parameters set
  • Collaboration: Hopkins/BioCrew, mid-Atlantic meetup, Gaston Day School
  • Had a team meeting

220821 - 220827

  • Translated video script into Chinese, Spanish, and portuguese
  • Wrote notebook page for wiki
  • Processed 16S data
  • Worked on Terraforming Mars Expansion Pack
  • Conducted 16S sequencing experiments
  • Designed Re-Terraforming Earth Game
  • Developed Promotional Vide
  • Continued with developing circuits to improve a part
  • Worked on genome-scale metabolic model
  • Collaboration follow-up: Gaston Day School iGEM, UMaryland iGEM, PuiChing_Macau iGEM
  • Had a team meeting

Fall 2022




220828 - 220903

  • Looked into papers on validating our projects
  • Worked on wiki pages writing & coding
  • Sent out IHP emails
  • Continued Writing chassis literature review
  • Designed cards for Terraforming Mars expansion pack
  • Developed the booklet
  • Worked on the Re-Terraforming Earth game
  • Filled out safety form and judging forms
  • Continued with developing circuits to improve a part
  • Drafted soil-drying protocols
  • Wet lab: did DNA purification for 16s PCR gene from soil, imaged gel for the 16s purified PCR products Performed an analysis of the generic top bacteria in our datasets
  • Implemented moisture level GIS from OpenLandMap and lembrechts temperature GIS
  • Worked on a unified raster system
  • Extracted regression info from R data snapshot to feed into gradient descent optimization
  • Tried SGD optimization in tensorflow with regression equation
  • Collaboration: Gaston Day School Model, VIT Vellore Model, John's Hopkins University Video, University of Maryland Storybook, PuiChing Macau Meetup, UNSW iGEM, GEMS Taiwan iGEM, NTHU Taiwan iGEM
  • Had team meetings

220904 - 220910

  • Looked into papers on validating our projects
  • Worked on wiki pages writing & coding
  • Sent out IHP emails
  • Continued Writing chassis literature review
  • Designed cards for Terraforming Mars expansion pack
  • Developed the booklet
  • Worked on the Re-Terraforming Earth game
  • Filled out safety form and judging forms
  • Determined which species to transform our improved part intp
  • Crafted soil-drying protocols
  • Wet lab: DNA purification for 16s PCR gene from soil, conducting PCRs/PCR purification, sfgfp circuits, mcherry circuit, and sent samples for sequencing
  • Added scrollbox support
  • Added a filter to the output list that selects Genus, Species, or both
  • Added explicit value tags to parameters that are returned by the API on the JS-end
  • Collaboration: Gaston Day School Model, VIT Vellore Model, John's Hopkins University Video, University of Maryland Storybook, PuiChing Macau Meetup, UNSW iGEM, GEMS Taiwan iGEM, NTHU Taiwan iGEM
  • Had team meetings

220925 - 221001

  • Worked on finalizing software
  • Designed Expansion Pack Cards
  • Assembled and tested our improving a part constructs
  • Filmed and edited chassis selection video
  • Worked on developing wiki
  • Automated regression
  • Gathered images for wiki
  • Had team meetings

221002 - 221008

  • Finalized software
  • Developed wiki
  • Tested our improving a part constructs
  • Analyzed improve a part data
  • Tested our Re-terraforming Earth game
  • Designed Expansion Pack Cards
  • Developed parts pages
  • Had team meetings

221002 - 221008

  • Developed wiki
  • Had team meetings