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)
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
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
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