Notebook
Project log

FRET-EryK Benchling Notebook

AtPCS Benchling Notebook

ECFP cloning and device calibration Benchling Notebook

Hardware Timeline

📍 February

February 28, 2023

  • First meeting with the 'iGem-NeoTech' group and consolidation of the Hardware team.

📍 March

March 10, 2023

  • First internal meeting of the 'hardware team', background research and brainstorming for the generation of a device.

March 21, 2023

  • Introduction to the laboratory, the team learns in more detail about the objectives and progress of the laboratory work, and makes a first approach to a concept for the development of a device.

March 25, 2023

  • First concept generation in CAD (including geometry, manufacturing and material selection) using SolidWorks.

📍 April

April 5, 2023

  • 3D printing of the first model using PLA.

April 6, 2023

  • First test of the assembled model, improvements and corrections are proposed.

April 7, 2023

  • The hardware team collaborates and it is introduced as a section on the Wiki.

April 10, 2023

  • Weekly 'hardware team' meeting; areas are created to distribute assignments (CAD design, circuits-instrumentation, wiki and finance).

April 15, 2023

  • Modifications and improvements in the CAD design for the first prototype (LED-LDR) and re-printing.

April 28, 2023

  • Instrumentation of the model using different excitation sources (LEDs).

📍 May

May 17, 2023

  • Tests in the biotech lab with the fluorescent protein 'mCherry' on the first prototype.

May 23, 2023

  • Weekly team meeting, model reassessment (introduction of TCS320 RGB color sensor module).

📍 June

June 8, 2023

  • CAD model redesign, validation and approval of model dimensions.

June 15, 2023

  • Printing and device assembly tests.

June 26, 2023

  • Final print of the second prototype, assembly and electrical instrumentation.

📍 July

July 10, 2023

  • 3D model assembly in the laboratory. Tests were performed with various materials to test and characterize the system. Finally we tested with 'mCherry' protein in different concentrations, the reading of the samples was performed in order to evaluate fluorescence.

July 23, 2023

  • Initiates development of software for intensity scaling.
  • Transilluminator tests for evaluation of mCherry excitation.
  • New dilutions of mCherry and mCherry induced in E.Coli were tested.
  • An adjustment is made to the model, and two UV light LEDs are introduced to the design.

July 24, 2023

  • The model is adjusted in the CAD software, and re-printed, generating the third prototype.

July 25, 2023

  • Implementation of UV excitation source (UV led 390-400 nm) in the device and tests with pure mCherry.
  • Prototype redesign, the geometry of the model is restructured and the sensor is repositioned. The sensor model is changed and a sketch of the new model is generated. More UV LEDs are added to the model.
  • New CAD model is generated and 3D printed (fourth prototype). Assembly tests are performed and the model is electronically instrumented.
  • Implementation of a new color sensor TCS34725 (Color Light-to-Digital Converter with IR Filter TCS34725, TAOS™).
  • Laboratory tests with the new color sensor and mCherry.

July 26, 2023

  • Dataset development started.
  • Tests and measurements with EGFP, RFP and YFP (donated by Mexico's City Monterrey Institute of Technology and Higher Education).

📍 August

August 2, 2023

  • Compilation of photos from results and advances.
  • Started Wiki formatting.

August 9, 2023

  • Laboratory tests and collecting data from four different proteins (EGFP, RFP, YFP, and ECFP).

August 11, 2023

  • Laboratory tests and collecting data from four different proteins (EGFP, RFP, YFP, and ECFP).

August 23, 2023

  • Continue to describe more in depth prototypes revisions in Wiki.

📍 September

September 3, 2023

  • Welding of electronic components.

September 5, 2023

  • Started development of an interface.
  • Implementation of a bluetooth module.
  • New CAD model is designed.

September 15, 2023

  • Due to time constraints, bluetooth and interface development were suspended.
  • The 3D model is printed.
  • Device assembly and testing.
  • Device completed.

September 22, 2023

  • Laboratory tests and collecting data from EGFP, RFP, YFP, and ECFP.

📍 October

October 5, 2023

  • Laboratory tests and collecting data from EGFP, RFP, YFP, and ECFP.

October 6, 2023

  • Laboratory tests and collecting data from EGFP, RFP, YFP, and ECFP.

October 9, 2023

  • Laboratory tests and collecting data from EGFP, RFP, YFP, and ECFP.

October 10, 2023

  • Cleaned and shaped the database.
  • Development of machine learning algorithm K-Nearest Neighbors.
  • Training the algorithm.
  • Testing, tuning and evaluation of the machine learning model.
  • Wiki corrections and concluding.

Human Timeline

📍 January

January 07, 2023

  • First meeting with the human practices team.

📍 February

February 14, 2023

  • Project planning session with the advisor.

February 19, 2023

  • Conference and feedback day with Dr. Pablo Nikel.

February 23, 2023

  • Meeting with the communication leader to plan work resources via Zoom.

February 28, 2023

  • First meeting with the 'iGem-NeoTech' group.

📍 March

March 1, 2023

  • Meeting with Ernesto, contact to do workshops for blind children.

March 6, 2023

  • Meeting with the team to create the questions for the interviews and the surveys in the town "El Salto".

March 16, 2023

  • Meeting with the group "Women for the future" to organize a collaboration for Women in STEM.

March 19, 2023

  • Second meeting with the group "Women for the future" to organize the event.

March 23, 2023

  • Sensing day to the community "El Salto" with the entire team.

March 29, 2023

  • First meeting with the "wiki" team.

📍 April

April 17, 2023

  • Scientific lottery design

April 24, 2023

  • Organization of the "Women in STEM" round table and conference.

📍 May

May 17, 2023

  • We sent emails to experts requesting interviews via Zoom for feedback on the project.
  • The round table “Women in STEM” was carried out.

May 17, 2023

  • The round table “Women in STEM” was carried out.

May 20, 2023

  • The association SINGREM was contacted via email.

May 23, 2023

  • Weekly team meeting.

May 25, 2023

  • The coordinator of SINGREM OCCIDENTE replied to the email.

May 30, 2023

  • The coordinator of SINGREM OCCIDENTE was contacted through a cell phone call so that the project could be proposed.

May 31, 2023

  • Interview with expert Dr. Luis Figueroa for feedback via zoom.
  • The coordinator of SINGREM OCCIDENTE sent the archives for the collaboration.

📍 June

June 8, 2023

  • Interview with expert Dr. Jorge Rodriguez for feedback via zoom.

June 12, 2023

  • Meeting with entrepreneurship specialist.

June 15, 2023

  • We had the first meeting to start with the entrepreneurship part of the project.

June 21, 2023

  • The academic advisor, Carlos Domenzain, helped us to send the archives of SINGREM to all the areas of the campus that were involved in the installation of the containers.

📍 July

July 10, 2023

  • Weekly team meeting.

July 29, 2023

  • The project of the installation of the containers was proposed to “Planta física” and approved by them.

📍 August

August 2, 2023

  • Compilation of photos from results and advances.
  • Started Wiki formatting.

August 7, 2023

  • First check up entrepreneurship information for Wiki.

August 9, 2023

  • Weekly team meeting.

August 16, 2023

  • The legal leader Western Region . GDA Campus, Guillermo Solorio, was contacted via email.

August 22, 2023

  • The Urban Forest Agency of the Guadalajara Metropolitan Area was contacted via whatsapp.

August 23, 2023

  • Revisions in Wiki.

August 24, 2023

  • Reunion with The Urban Forest Agency of the Guadalajara Metropolitan Area to propose the idea of the workshops.

📍 September

September 9, 2023

  • The document where the project is presented in detail is sent to The Urban Forest Agency of the Guadalajara Metropolitan Area through email.

September 6, 2023

  • The legal leader Western Region validates with different areas of the campus, the installment of the containers.

September 8, 2023

  • The Urban Forest Agency of the Guadalajara Metropolitan Area through email approved the project of imparting workshops in the Bosque Urbano Tlaquepaque.

September 14, 2023

  • The legal leader asked for more details about the containers and the legal documentation of SINGREM i.
  • The itinerary for the workshops with the collaboration of The Urban Forest Agency of the Guadalajara Metropolitan Area was approved i.

September 20, 2023

  • Via email the details and the legal documentation of SINGREM were asked for.

September 21, 2023

  • The coordinator of SINGREM OCCIDENTE sent the documents that were asked for.

September 23, 2023

  • Workshops in “Bosque urbano Tlaquepaque”.

September 25, 2023

  • The School for Blind Children A.C. was contacted.

September 27, 2023

  • The legal documentation of SINGREM was sent to the legal leader as well as a document with the specifications he asked for.
  • The nursing home Residencia Guadalupe was contacted via email.

September 28, 2023

  • The coordinator of Residencia Guadalupe responded and established a date for the visit.

September 29, 2023

  • The School for Blind Children A.C deliberated if the collaboration could be made.

📍 October

October 2, 2023

  • The collaboration with the School for Blind Children A.C was approved.

October 4, 2023

  • Visit to the School for Blind Children A.C.

October 5, 2023

  • Visit to the nursing home “Casa Guadalupe”.

October 6, 2023

  • Meeting with the team for wiki corrections.
  • Specialists entrepreneurship meeting.
  • The green light is given to the signing of the agreement between our university and the association SINGREM to proceed with the containers installation.

October 7, 2023

  • Team member, Sofia Méndez, at the Latin American Congress of Engineers in Medicine and Biology.

October 9, 2023

  • Meeting with the team for wiki corrections.

October 10, 2023

  • Wiki corrections and concluding.
  • Meeting with the team for wiki corrections.

October 11, 2023

  • Entrepreneurship Wiki corrections and concluding.