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Team:IIT Roorkee/Notebook

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Project
Months Work Done
January
  1. After exploring different ideas for the competition independently, first official team meet was organised
  2. Prof Naveen K. Navani took hold as faculty advisor to the team to support administrative and research activities
  3. Discussion on pyocins and phage therapy to treat bacterial infections
  4. Analysis of TAU Israel Project 2019
February
  1. Discussions with department professors about iGEM Competition
  2. Presented road map to Head of Department (HoD), Department of Biotechnology, for iGEM 2020
  3. Attended Antibiotic Resistance - One Health Perspective conference, IIT Roorkee
  4. Prof Ranjana Pathania agreed to host our Team under her lab and provided assistance in understanding A. baumannii
  5. Designed pyocin fusion through the assistance of researchers, Siva and Somok
  6. Drafted proposal for institute committees, TIDES incubation and sponsorship support
  7. Preliminary experiments were performed 
  8. Team recruitments were opened for undergraduate and masters’ students across disciplines 
  9. Curated human practices and fund raising strategies for March-April
March

*Due to CoVID-19, all the team activities came to a halt and plans were suspended

Attended Ambassador Calls to share the challenges faced by the team and seek guidance 

April
  1. Established new format for working remotely and had a complete team meeting
  2. Launched our Official Social Media Pages on Instagram, Facebook, and LinkedIn
  3. Prepared pitch deck for the funding support at the university 
  4. Participated in the iBEC Competition
May
  1. Completed Registration and Jamboree Fee payment 
  2. Attended the iGEM 2020 Opening Weekend Festival 
  3. Re-designed project strategy and explored new areas to cover
  4. Research on Machine Learning and biophysical modeling
  5. Attended Webinar: Introduction to the Benchling Platform
June
  1. Focussed on human practices activities through multiple brainstorming sessions
  2. Researched on educational tools to curate relevant & impactful content
  3. Software team presented the design and framework for TailScout 
  4. Received mentorship from Computer Science students to understand the pipeline and resources required for our software TailScout
  5. Collaborated with Design Studio, IIT Roorkee for assistance in team branding and designing 
  6. Attended Measurement Webinars Week 3: Modeling and DNA Assembly

COVID impacted our project journey and roadmap significantly, as accessing funding, labs, experiments and Team Work became difficult to realise. Settling in the new format took us some time and by June 15 we had finalised the core team members. With brief plans to proceed in 5 main directions - Research Design, Software, Human Practices, Public Engagement, and Machine Learning, we formalised our subsystems and worked on the team constitution. The iGEM IIT Roorkee Constitution was drafted to lay down the team structure and guidelines for future teams from IIT Roorkee. We maintained a new lab notebook to track our progress and fulfillment of project goals in different categories.

Wet Lab

  • Researched on microbiomes and thought of possible application of Pyocin in gut microbiome research
  • Worked on design of alternate pyocins with tail fibers of other A. baumannii phages
  • Considered the possibility to use iron in the formulation which prevents Ab infection
  • Researched Urinary tract infection and wound infections as a possible target

Dry Lab

  • Chartered pipeline for gene detection
  • Coded for multiple sequences alignment.
  • Computed a gene detection algorithm using python which works as the first process of the TailScout
  • Read papers in machine learning for protein-protein interaction

Human Practices

  • Applied for Official iGEM Mentor
  • Mentorship meeting with IISER Bhopal to understand project planning
  • Attended German iGEM Meetup
  • Interviewed Dr. Anand Ratan Tiwari
  • Worked out on the Webinar Brochure and mails
  • Initiated AMR awareness campaign for the college students

Wet Lab

  • Engineered plasmid using gibson assembly 
  • Faced issues with sequence complexities that required expert opinion and guidance 
  • Decided to target pneumonia under all possible Ab infections
  • Devised the possibility of aerosol based delivery of our drugs directly to the site if infection 
  • Researched and conceptualised inhaled protein therapeutics

Dry Lab

  • Debugged errors in the gene detection algorithm and saw research about Biopython library
  • Scouted deep models in Machine learning
  • Identified the possibility  for including games on AMR in the wiki

Human Practices

  • Compiled the School database for the Webinar 
  • Outlined the Presentation for School Webinars 
  • Rolled out  mails to school
  • Formulated the resource booklets (according to different learning standards)
  • Collaboration meeting with team iGEM Montpellier 

Wet Lab

  • Opted for DNA Synthesis instead of cloning
  • Plasmid sent for verification
  • Validated gene fragments
  • Communicated with IDT Customer service for optimizing sequences for synthesis

Dry Lab

  • Orchestrated the software development workflow
  •  Catalogued various machine learning based approaches in AMR 
  • Formulated modelling methodologies for the fusion protein
  • Decided on bioinformatics modeling due to lack of lab access in COVID 

Human Practices

  • Hosted a webinar in St. Anne's Convent School, Chandigarh.
  • Collaborated with National Service Scheme IIT Roorkee
  • Hosted a webinar in ‘Srijan - Ek Soch’  NGO
  • Interviewed Dr. NandKishore Joshi
  • Released AMR Mythbusters and Team Introduction on social media handles

Wet Lab

  • Read papers on HAI’s and Ventilator-Associated Pneumonia caused mainly by A. baumannii

Dry Lab

  • Prepared the phage tail fibers database of their protein sequence. I.e, phage library
  • Started with structural modeling, energy minimization, and docking studies for proof of concept

Human Practices

  • Hosted a Webinar at Delhi Public School, Ghaziabad Vasundhara
  • Stimulated All India iGEM Meet 2020
  • Formulated content for ML workshop in All India iGEM Meet 

Wet Lab

  • Studied VAP for Proposed Implementation 
  • Meeting with Dr. Kulkarni helped set the points and made us focus on VAP.

Dry Lab

  • Searched for the Clustal Omega MSA and Jpred Secondary Structure Prediction REST Api’s
  • Decided to try all the three modeling methods and compare results

Human Practices

  • Fabricated our Presentation and Poster for AIIM
  • Consulted Dr. Rajesh Kulkarni to understand VAP infections
  • Conducted All India iGEM Meet

Wet Lab

  • Conducted in depth research and analysis Ventilator Associated Pneumonia  
  • Designed the delivery system based on nebuliser based-therapeutics

Dry Lab

  • Read papers for using Clustal Omega on the web server-based application
  • Founded error in first run for the models due to large size of model protein

Human Practices

  • Initiated collaboration activities for other iGEM teams
  • Project discussion with IISER Tirupati 
  • Created Team Spirit Poster for Global iGEM Meetup

Wet Lab

  • Switched from nebuliser system to Bolus delivery system

Dry Lab

  • Tested the individual codes on the system with different phages fibres
  • DId literature review for the model and found out that N-truncated fragment was sufficient for modeling

Human Practices

  • Prepared and rolled out emails to stakeholders (Clemedi, APT) 
  • Attended Global iGEM Meet

Wet Lab

  • Worked on Final Plasmid assembly with the help of Twist Biosciences

Dry Lab

  • ML approach discussions with Keerat and Harkirat
  • Added a more bacteriophages in the library
  • Identified the fusion protein sequence by crossing over AP22 bacteriophage with R2-NTF pyocin tail fiber instead of the complete R2 pyocin tail fiber 

Human Practices

  • First phase meeting with Clemedi
  • Proctored patient Interview
  • Received inputs from the iGEM judging committee that guided our further work 

Wet Lab

Dry Lab

  • Preliminary ML Analysis
  • Made Github repo for the WebServer and committed initial codes
  • Constructed the new sequence for the fusion protein - for 3 modeling methods

Human Practices

  • Second Phase meeting with Clemedi
  • Finalised our Team Merchandise 

Wet Lab

  • Worked on safety forms

Dry Lab

  • Tried to integrate the python code and REST Api’s but failed
  • Once the models were built, identified parameters that would help in comparing these models
  • Decided to compare alignment RMSD values for alignment with R2-NTF pyocin and AP22 phage 

Human Practices

  • Dispatched Learning material to Anushruti Academy for the Deaf via NSS
  • Participated in the survey Collaboration by IISER Berhampur and CCU iGEM 

Wet Lab

  • Submitted Safety forms

Dry Lab

  • Discussion with Mentor to finalize ML approach
  • For the next iteration for integration, learnt through videos on youtube of Django
  • Meetings with Institute Seniors for software integration

Human Practices

  • Project Discussion Meeting with Mentor
  • Designed survey for gauging the problem of HAI through medical staff
  • Conducted Medical Staff Survey

Wet Lab

Dry Lab

  • Discussion with institute administration for providing high computing PC
  • Made a presentation for running all the codes locally on an individual system
  • Decided to compare the Ramachandran plots of the models as well 

Human Practices

  • Built storyline script with Subtitles for Project promotion video 

Wet Lab

Dry Lab

  • Collection of the dataset for ML
  • Meeting with the mentor for discussion on the integration part and sent out a document explaining our problems and issues to relevant contacts
  • Discarded all the models obtained via threading from consideration because of their monomeric structure

Human Practices

  • Organised Awareness Quiz in AAD in collaboration with NSS
  • Wrapped up the production of Project Promotional Video

Wet Lab

Dry Lab

  • Preprocessed the dataset collected 
  • Django integration completely (i.e. Backend)
  • Set weightages for the comparison parameters andgave Ramachandran plot data the highest weightage

Human Practices

  • Collaborated with AUC Egypt - “Thank You Mentor”
  • Launched our Project Logo on Social Media platforms

Wet Lab

Dry Lab

  • Machine learning experiments completed
  • Carried out energy minimization for the best chosen model using Yasara energy minimisation toolkit

Human Practices

  • SDG Collaboration with iGEM UPCH Peru
  • Participated in the Collaboration “Envirospeaks” by iGEM RUM

Wet Lab

  • Developed Protocols
  • Collected the data of preliminary experiments for the wiki

Dry Lab

  • Working on the deployment of the web server 
  • Studied protein-protein interaction through docking
  • Searched the structure of the LPS receptor and the fusion protein but it wasn’t available in existing databases so, couldn’t perform docking

Human Practices

  • Co-produced Policy Review Report on AMR (with NSS IITR)
  • Ideation on hosting webinars in collaboration with NSS for underprivileged students of Roorkee schools

Wet Lab

Dry Lab

  • Collected available results of all the modeling
  • Sorted the Machine learning experiment results

Human Practices

  • Finalised all collaborations
  • Started our iGEM⤬SDG Collaboration - “SMILE”