Team:IISER Berhampur/Notebook
February - March
Week1
Call for project idea submission for iGEM 2021 - recruitment 1.0
Week2
- Project submission for iGem 2021.
- Call for different field vacancies for iGEM 2021 - recruitment 2.0
Week3
- Top 3 project proposals were declared.
- Submission for recruitment drive 2.0
Week4
Presentation of top 3 selected project ideas to the Principal investigator and expert committee.
April
Week2
Friday, 9 April
- Final iGEM 2021 team announced.
- First iGEM meet with iGEM 2021 team.
- Brainstorming for the final project.
Saturday, 10 April
- iGEM meet with PI - Dr. Vinay Bulusu, other advisors and 2020 team.
- Overview and summary of the project; division of team-roles and responsibilities.
Sunday, 11 April
- iGEM student group meet-Planning for wet lab, HP and modelling teams
Week3
Monday, 12 April
- iGEM group meeting - brainstorming session.
Tuesday, 13 April
- iGEM student group meet 1 (HP) with last year’s HP team.
- iGEM 2020 team discussed their experiments, experience and ideas with 2021 team
- iGEM 2021 team also put forward their ideas
Wednesday, 14 April
- iGEM wet lab group meet 2.
- Cas14, detection techniques.and reporter systems
Thursday, 15 April
- iGEM group meet with advisors
- Wet lab and sponsorship discussion.
Week4
Wednesday, 21 April:
- iGEM group meeting - brainstorming session
- iGEM group meeting - brainstorming session
Friday, 23 April
- iGEM group meeting - brainstorming session
Sunday, 25 April
- iGEM group meeting - brainstorming session
Wednesday, 28 April
- iGEM registration complete
May
Week1
Tuesday, 4 May
Started campaigning on twitter for Genscript sponsorship (for the month of May)
Wednesday, 5 May
- HP student team meet-
- Discussed posters for team and funding, demarcation, logo and team introduction posts.
- Collaborations and discussions
Saturday, 8 May
- Team meeting with PI
Discussed :-- Team registration
- Promega project outline
- Fine tuning proposal
- Modelling data collection and wet lab literature review
Sunday, 9 May
- Posting of demarcation
- Student registration into iGEM website
- Wet lab - started project promega outline and literature survey about strain distribution.
- modelling - epidemiology model lit survey, data collection and presentation work.
Week2
Monday, 10 May
- Posting the first tile of the project logo and caption - instagram.
- HP - emails sent to DOSA, CSA and social cell regarding retweets for sponsorship.
- Design team - Team poster in the making.
Tuesday, 11 May
- HP student team meet -
- Final distribution of sub team tasks (collaboration, social media and interviews, designing, sponsorships, blogs) to team members.
- Collaboration sub team student meet- Timeline and events scheduled and planned, work divided among team members.
- Continuing the comic strip activity message sent to iGEM team Costa Rica
Wednesday, 12 May
- Emails sent to NGOs and private TB organizations for Genscript retweets campaign
- Wet lab student team meet -
- Literature review for finding the relevant MDR-TB strain, promega sponsorship write up, project outline.
- Tasks were divided among the team members
Thursday, 13 May
- 3rd and 4th tile of logo posted on instagram Modelling student team meet
- Distribution of disease in age, seasonal variation and proportion of MDR, XDR and normal TB in the population
- Presentation - math model and data collection.
Friday, 14 May
- iGEM student team meet
- Discussed overall on goings-designing and social media.
- Modelling team presentation.
- Design student team meet -
- Discussed ideas for intro and team poster layout and design.
Saturday, 15 May
- Logo posted on twitter, genscript crossed 400 retweets!
- iGEM team meet with PI, advisors and 2020 team :-
- Math modelling presentation (Om and Ritika)- Explained the SEIRD model, equations and graphs, refining of model - considering background mortality
- Sponsorships - Genscript twitter campaign, promega write up, snapgene license
- HP team updated PI with - School event, comic strip event, collaboration with the Moscow team, and ideas for interviews with doctors.
- Wetlab - ongoing literature review
Sunday, 16 May
- Wiki student team meet-
- Division of work among sub team members (CSS and HTML)
- Bar tab to be designed and kept
- Current log to be updated on the website
- Team page to be updated
- Design student team meet - Worked on and finalized intro design poster.
- HP student team meet-Worked on treasure hunt patterns and questions
- Sent the comic strip event email to iGEM HQ.
Week3
Monday, 17 May
- Tweet for Genscript 50$ gift card sponsorship tweeted.
- HP student short meet for outreach program - treasure hunt, discussed riddles and answers for the hunt
Tuesday, 18 May
- HP outreach event (treasure hunt) student team meet- Discussed 11th grade hunt rules and riddle questions.
- Project introduction on twitter - part 1
Wednesday, 19 May
- Wiki team short meet - discussed google site
- HP treasure hunt - 9th and 10th hunt riddles discussion
- Sponsorships meet with PI - Beckman Coulter grant and discussed some budgets
Thursday, 20 May
- Wiki student team meet - Notebook update and wiki design (template, theme colours, google site)
- Treasure hunt mock run
- iGEM student team meet with ambassador (Ms. Shruti Sridhar) -
- Technical and non technical collaborations
- How to increase sponsorships
- Contribution for future teams
- Interviews - more important than surveys.
- Social work
Saturday, 22 May
- Poster and form for scrofula (treasure hunt) posted on social media
- Poster for rise of the phoenix (comic strip) posted on twitter
- Awareness Program for School Students (treasure hunt) email sent to CSA who circulated among faculties
- iGEM team meet with PI and advisors
- Wet lab presentation - lit review on mutation patterns, future plans
- HP treasure hunt-outreach program presentation
- Drawbacks were discussed and it was suggested to conduct the events in regional languages.
- Sponsorships, interviews and collaborations -
- Promega, Beckman Coulter, Merck , Biocon sponsorships
- International NGOs partnership/collab to spread awareness about TB and get funds
- Interview with MKCG - Dr Taher
- International collaboration (comic strip) email to HQ.
- Design student team meet -
- Team poster design
- Brochure design and content for crowd funding and sponsorships.
- iGEM student team meet with Vilnius-Lithuania iGEM team -
- Vilnius team presented their project outline and human practices.
- Bpr team presented our project and HP activities
- Discussed collaborations - surveys and interviews with Indian NGOs or doctors working in amoebiasis
- Future collaborations involving- combined interviews, podcasts, software development using mobile phone (for us)
- Wiki team student meet
- Discussed main design, social media icon images, description for origin of the project proposal, logo description and design and team 2021 design.
Sunday, 23 May
- Modelling and wet lab student team meetings
- Discussed - interview questions, podcast
Week4
Monday, 24 May
- First Outreach program held - Treasure hunt (The Tale of Scrofula) and interactive presentations for spreading awareness about MDR-TB and TB.
- Certificates for participation and winners to be given by 27th
- Received license for snapgene
Tuesday, 25 May
- HP student team meet -
- Treasure hunt in regional language and targeting international students
- Fundraising - contacting NGOs, Colouring book edition 2 - get funding estimate
- Emails to international and local schools for funds and awareness.
- HP team meet with PI - discussed fundraising and sending emails to NGOs
- Team Poster posted on twitter
Wednesday, 26 May
- Team poster posted on instagram
- Genscript campaign (ongoing since announcement) - 4 days left
- iGEM student team meet with IISER Tirupati iGEM team
- Discussed- each other’s project, wet lab (presentations-both) and modelling.TPT - contraceptive method using bacteria to block sperm entry.
- suggestions from TPT team -
- Making a disposal system for waste from our experiments
- Contacting Doctors from Safdarjung hospital- huge TB facility
- IGIB Delhi - can contact profs for interview
- Ongoing Human Practises discussion (from our side mainly)
- General discussions and collaborations ideas with both teams
Thursday, 27 May
- iGEM student team meet-
- Giveaway for retweets
- Created sub team group for managing Interviews
- Selected All India iGEM Meet (AIIM) representatives Promotion video discussion
- HP (collaboration, social media & interviews sub team) student team meet -
- Discussed - collaborations, prepared team list
- promoted comic strip
- Villinus team requirement list.
Friday, 28 May
- Genscript twitter campaign
Saturday, 29 May
- iGEM student team meet with PI and mentors (Wet lab brainstorming) -
- A paper that used cas14a+guide RNA recombinant plasmids
- Ordering of relevant plasmids
- Different approaches by PI and students in using sgRNAs (multiple & WT/mutants) and fluorescence production (detection).
- Settled on specific mutants
- Promega sponsorship project outline - final draft
- Interview sub team meet
Sunday, 30 May
- Interview with Dr Shaik Taheruddin (microbiologist MKCG medical hospital) -
- Presentation of project idea - wet lab and modelling questions
- Documentation
- General discussions
- iGEM and project brochure done
June
Week1
Wednesday, 2 June
- iGEM HP student team meet -
- School event - Small skit
- Crowdfunding ideas
- Podcast and promotion video ideas
- Collaboration ideas
- Merchandise
- Personal email to carry out comic strip
Thursday, 3 June
- Biobrick student team meet with 2020 biobrick team -
- I Plasmid and Restriction enzymes selection - preferably from the registry.
Saturday, 5 June
- List of researchers made for the Vilnius team
Sunday, 6 June
- iGEM team meet with Rochester iGEM team -
- Exchanged each other’s project ideas
- Our suggestions - attaching it to a BP/heart monitor etc. device
- Discussed Modelling aspects
- Human practices ideas exchange - promoted our comic strip, and invited them to our podcast
- Interviewees from US and India
- Email sent to Vilnius team of interview contacts on people working with amoebiasis
- Received interview contacts from Lithuania on people working with TB
Week2
Monday, 7 June
- iGEM student team meet -
- Promotion video ideas
- Podcast ideas
- Nukkad natak
- Podcast team meet with Niraj -
- Platforms (for editing and recording) and distribution manuals
- RSS link for podcasters
- Mic tips
- Audio to text conversion
- Wet lab student team meet -
- Hardware and software - general working
- Fluorescence detector and report software (app)
- Main hardware device
- General working of our system - guide RNAs and target genes
- Hardware and software - general working
Tuesday, 8 June
- Podcast student team meet -
- First 4 episodes of podcast - overview and topics to talk about
- Ideas for name and background music
- MIT_MAHE’s instagram fun activity participation invitation
- List of possible interviewees (for all sub teams)
Wednesday, 9 June
- Vinay sir’s intro post posted on instagram
- iGEM HP student team meet
- Promotional video - animation, graphs etc, one voice
- Nukkad Natak - video to be made after NGO replies
Friday, 11 June
- Wet lab student team meet
Saturday, 12 June
- Submission of Beckman Coulter sponsorship
- iGEM student team meet - presentation of wet lab project
- iGEM podcast team meet - trailer
Monday, 14 June
- Promotional video meet
- First draft of story outline headings
- Writing content for each heading and subheading
- Podcast student team meet -
- Script for trailer
- Work on episode 1
- Project Brochure done
Week3
Wednesday, 16 June
- Trailer video done
- Modelling Team meet:
- Discussed about future modelling plans - DNA amplification optimum time, amount of cas14 required, software app
Friday, 18 June
- iGEM interview with MDR-TB survivor Radhika Jatpag -
- Discussed in detail the life of an MDR-TB patient - symptoms and diagnosis, cost of treatment, medication and daily routine, mental health, support groups, spreading awareness and outreach to society (giving out free protein rich food)
- iGEM student team meet - discussed progress of work in each sub team, wet lab and human practices
Saturday, 19 June
- iGEM team meet with PI and advisors -
- Wet lab work on goings
- Sponsorships, multipurpose outline, rpob strain
- Human Practices - doctors and professors to interview, future sponsorships, promotional video
- Biobricks team meet - safety form biobricks details
Monday, 21 June
- Podcast trailer poster done
Tuesday, 22 June
- Modelling team meet with Arun sir - discussed docking and dynamics, future prospects
- Podcast trailer poster posted and Trailer released on youtube and spotify.
Thursday, 24 June
- iGEM student team meet - Hardware and software (modelling)
- iGEM podcast team meet - voice overs for 3rd episode, script writing and panel discussions
Friday, 25 June
- Modelling team meet -
- Decided the official document structure
- Epidemiological model in more detail - updating equations and parameters
- Sending emails to epidemiologists for cross checking data
- Submission of preliminary safety form
Week4
Saturday, 26 June
- Promotional video meet - decided final script, discussed video design and pattern
Sunday, 27 June
- iGEM team meet with Korea_HS team -
- Each others project through presentations
- Human practices - outreach and human interaction
- Possible collaboration topics - Modelling (fluorescence), wet lab (cytotoxicity)
- Rice art collaboration sent to Manipal
- Made official project presentation
Monday, 28 June
- iGEM student team meet
- iGEM team meet with Sridhar sir - Contact microbiologists rather than doctors, BIRAC for possible funds, make project more viable - Indian project for worldwide application, hardware prototype, developing the prototype for commercial use
- iGEM modelling team meet - current SIRD model - graphs, equations and values, possible interviews, future model prospects
- iGEM design team meet- discussed comic strip
Tuesday, 29 June
- iGEM HP team meet - plans in motion, collaboration ideas for NGOs, mailing for data and epidemiologists
- iGEM Modelling team meet - future model
Wednesday, 30 June
- Submission of impact grant
- Human Practises - flyers, apps, donation, targeting younger TB affected generation, human transmission
July
Week1
Thursday, 1 July
- iGEM team meet with IISER Kolkata iGEM team - Both team presented their projects. The detailed discussions are as follows :-
- Wet lab -
- CRISPR cas system
- Colorimetry
- conducting joint webinars/tutorials on crispr
- Modelling
- Data collection
- Graphs and equations
- Mathematical modelling approaches
- Human Practices -
- Podcasts invitation, joint interviews, awareness programs
- Collaboration on awareness for a larger audience via brochures, pamphlets etc.
- Wet lab -
- Dry lab and modelling collaboration
Friday, 2 July
- iGEM student team meet with NGO head Amit Tuteja (Discussion and advice) -
- Human Practices- Awareness, ideas to assist people currently diagnosed with TB, direct assistance via kit
- Wet Lab- discussed LAMP and strains, cost reduction- market survey
- Modelling - Epidemiological survey.
- Release of first podcast episode
Saturday, 3 July
- Russian meet event - Presented our project, casual interactions with other teams.
- Modelling team meet- discussed the future diagnostic model
- Comic strip post by iGEM costa rica and iGEM Kcl
Sunday, 4 July
- Comic strip post by igem stony brook, iGEM MUANL, iGEM China
- Human Practices- Awareness, ideas to assist people currently diagnosed with TB, direct assistance via kit
- Wet Lab- discussed LAMP and strains, cost reduction- market survey
- Modelling - Epidemiological survey.
Week2
Monday, 5 July
- iGEM team meet with PI -
- Updates of all sub teams given
- Discussed possible funds and interviews
- Discussed wet lab strain and mtb genome safety
- iGEM team meet with iGEM team Athens -
- Podcast
- Offer to conduct our wet lab experiments and provide reagents
- They provided inputs on designing tools
- Rochester, Athens and Vilnius agreed for podcast - work started
Tuesday, 6 July
- Modelling team meet - Discussed early, late and no detection model, enzyme kinetics - collaboration with wet lab
- iGEM team meet - Discussed wet lab, modelling - collab with wet lab for protocols etc. for enzyme kinetics model
- iGEM Global collaboration team meet - Discussed global meet between teams working with CRISPR worldwide for better wet lab collaboration and ideas for wet lab, modelling and other sub teams
Thursday, 8 July
- iGEM meet with lafafa for merchandise - Detailed discussion on design
- iGEM project and synthetic biology Informative posts on social media
Friday, 9 July
- Modelling team meet- discussion on ideas for official documentation
Sunday, 11 July
- iGEM wet lab team meet - Discussed LAMP and interview questions
- iGEM team meet (human practices) - Discussed Global CRISPR meet, AIIM event - organizers and event, Promotional video final
Monday, 12 July
- iGEM interview with Professor Rajesh Sudhir Gokhale -
- Emphasis on cost and funding - phosphothiode cost
- Product management and marketing strategies
- Funding companies and assistance in getting us contact for funds
- Efficiency and specificity of our project
- iGEM modelling team meet
Tuesday, 13 July
- Interview with Dr Sutirth Dey -
- Modelling aspects of the project presentation and brief introduction to the project
- Detailed discussion on the model equations and output graphs
- Data collection
- Discussion on hardware device
Week3
Wednesday, 14 July
- iGEM team with PI and mentors -
- Wetlab,- multipurpose document, POC and LAMP, promotional video; suggestions were given, modelling main goal and literature review
- HP team meet
- Event planning - workshop, teaching synthetic Biology
- Interview consent forms
- IHP discussion
- Sponsorship emails
- Release of podcast episode 2
Thursday, 15 July
- Unboxing of iGEM 2021 distribution kit at IISER Berhampur.
Monday, 19 July
- CRISPR meet team emails and slot booking
Tuesday, 20 July
- Meet with HP team and PI - Discussed fundraising ideas
- Project Management team meet - Discussed objectives and approaches towards cost analysis
- Wet lab meet - Interview questions discussion
- Start of IHP wiki work
Wednesday, 21 July
- Wet lab team meet - Discussion for interview questions
- AIIM meet - Indian iGEM team meets with briefing about events and schedule
Thursday, 22 July
- Promotional video updated
- iGEM team meet - Editing of presentation for AIIM event
- Updates on fundraiser
- IHP wiki work
- WAO meet - Making and sending questions to teams
Friday, 23 July
- AIIM events - participation in other events and WAO hosted by IISER Berhampur
- Mock presentation meet
- IGCC email to iGEMHQ
Saturday, 24 July
- AIIM project presentation
- IGCC meet - Discussed event rules
Sunday, 25 July
- AIIM event participation
- Fundraiser website sent for verification
- Emails drafted for IGCC
- Promotional video uploaded on social media
Week4
Monday, 26 July
- iGEM meet with PI and advisors - Modelling presentation. strain analysis discussion with Arun sir
Tuesday, 27July
- Biobrick team meet - Parts construct design discussion
- IGCC team meet - Discussed event particulars, schedule etc.
Wednesday, 28 July
- Fundraiser website approved and live
Thursday, 29 July
- Wet lab team meet with PI - Discussed strains, LAMP primers and sgRNA design
- School event workshop meet - Discussed techniques to teach them
- IGCC meet - Discussed schedule
Saturday, 31 July
- iGEM team meet - Discussed fundraiser and campaigning
- Ignite Life Science foundation grant proposal written
August
Week1
Sunday, 1 August
- IHP website design discussion
Monday, 2 August
- IGCC -
- Presentations details email sent to teams
- Details and photos of speakers received
- Campaign poster done
- Modelling team meet with PI
Wednesday, 4 August
- Impact grant winners announced [IISER Berhampur won]
Thursday, 5 August
- Modelling team meet with PI - Discussed Probable future rise in strains model and Enzyme kinetics
Friday, 6 August
- Received iGEM Rochester collaboration request
Saturday, 7 August
- HP update to leader
- Mail sent to Dr. Basudev Maji and Sundaram Acharya to confirm timing.
- Planning for campaign
Week2
Monday, 9 August
- IGCC work - sending emails
Wednesday, 11 August
- IGCC wirk
Thursday, 12 August
- IGCC - Invite emails to institutions, Syn Bio Quiz invitation for registered teams and in All India igem group
Saturday, 14 August
- IGCC event day 1
- Team presentations
- Quiz - Fun with synbio
Sunday, 15 August
- IGCC event day 2
- Team presentations
- Talks by speakers - Dr Sundaram Acharya and Dr Basudev Mazhi
Week3
Wednesday, 18 August
- iGEM impact grant form mail received
Thursday, 19 August
- NEB reagents arrived
- iGEM team wet lab meet with PI - Wetlab planning
- Won genscript sponsorship
Friday, 20 August
- iGEM team meet - Discussed about merchandise
- Purchasing Video and audio recording software
- iGEM meet team meet with iGEM IISER Kolkata
- Discussed children’s story book
Saturday, 21 August
- iGEM team meet with PI -
- Genscript grant celebration and discussion
- Hardware meeting
- Merchandise with grant money
Sunday, 22 August
- Meeting with theracues -
- Discussed project - brief introduction and prototype including specifications
- Wiki team meet - Discussed web page design
Week4
Monday, 23 August
- iGEM team meet with PI and Professor Sridhar -
- Presentation for Theracues
- Inputs from Sridhar sir - focus on prototype, POC and cost analysis
- iGEM team meet with iGEM NTU -
- Project presentations by both teams
- Discussed points of collaboration - Exchanging cas12 sequence, help in Hardware
Friday, 27 August
- Wet lab - Growing competent cells in LB media, preparing LB broth
Monday, 30 August
- Safety protocol and authorization orientation
- Lecture on GLP and introduction to equipments to be used
- Fixed workstation
Tuesday, 31 August
- Issued pipettes, pipette tips, pipette stand, 2 markers from UG-PG lab
September
Week1
Wednesday, 1 September
- School event meet - Discussed tutorials
Thursday, 2 September
- Wet lab
- Autoclaving of equipment
- Preparation of SOB media
Friday, 3 September
- Wet lab
- Primary and secondary inoculation
- Inoue buffer preparation
Saturday, 4 September
- Wet lab
- Elution of competent cells
- Storage in liquid nitrogen
Sunday, 5 September
- Inoculation of BAC clones
Week2
Monday, 6 September
- Plasmid isolation of BAC clones
- Synverse roundtable with team Vilnius released - episode 4
Wednesday, 8 September
- Wet lab - Agarose gel run
- Human Practices -
- Invitation to participate in problem book collaboration by team Russia
- Confirmation of inventa collaboration
- iGEM team meet with PI -
- Wet lab updates and future plan
- Modelling update - phylogenetic analysis
- Fundraiser and merchandise
- Discussion about jamboree meet up
- Biobricks - plasmid design discussion
Thursday, 9 September
- Hardware team meet with Dr Satyaprasad P Senanayak -
- General hardware model and brief introduction to the experiment
- Availability of laser
Sunday, 12 September
- iGEM all India team meet with ambassadors - Discussion about Jamboree meetup at Goa
- Duke mini Jamboree - Project presentation
- Registration for Dual safety workshop
- iGEM team meet for Giant Jamboree meet discussion
Week3
Monday, 13 September
- Human Practices
- Merchandise planning
- Confirmation to send NTU contacts
Week4
Wednesday, 22 September
- Hardware team meet - Discussed new development in the hardware model
Thursday, 23 September
- Wet lab
- Media preparation - LB broth and LB agar
Friday, 24 September
- Inventa talk
- Media preparation
Tuesday, 27 September
- Wet lab - Poured agar plates
-
Meet with PI -
- Gold medal criteria
- Modelling - different models and phylogenetic analysis
- Protocol for transformation
- Wiki team meet - Content discussion
Wednesday, 28 September
- Wet lab -
- Absorbance and fluorescence measurements of serially diluted venus, molar concentration calculations
- Transformation of plasmids (rpoB and KatG) in E coli
- Modelling team meet - Phylogenetic analysis discussion
Wednesday, 29 September
- Wet lab -
- LB media and broth preparation
- Autoclaving media, broth pipette tips and plates
October
Week1
Saturday, 2 October
- iGEM team meet -
- Medal criteria discussion
- Assigning tasks to team members
Sunday, 3 October
- Hardware meet - Prototype discussion
- Team meet for wiki design - Individual wiki page design and layout
Week2
Monday, 11 October
- Wet lab - cas14 and Bac clones primary inoculate
- Parts improvement discussion with Dr Selvi Bharatavikru
- Modelling - Phylogenetic trees
Tuesday, 12 October
- Wet lab planning & inoculation of cas14a1 plasmid
- Modelling - phylogenetic analysis
Wednesday, 13 October
- Plasmid isolation
- Transformation of plasmid into BL21DE3
Week3
- Documentation
- Working on Wiki page
November
Week2
Saturday, 13 November
- We reached Resort Marinha Dourada,Goa for our Giant Jamboree Meet
Sunday, 14 November
- Result declared at Giant Jamboree and we secured the GOLD medal.
