notebook.html

{% extends "layout.html" %} {% block title %}Notebook{% endblock %} {% block
lead %}{% endblock %} {% block page_content %}

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    background-image: url("https://static.igem.wiki/teams/5346/doodle/journalling.png");
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  <p>
    Our iGEM journey has been an exciting blend of ideation, problem-solving,
    and consistent progress. From the initial stages in June to our current
    strides in September, we've worked hard to bring our vision of IMPROViSeD to
    life. Below is a detailed reflection on the key moments from March through
    September, where we highlight the pivotal tasks, decisions, and milestones
    that shaped our project.
  </p>

  <h1>March — June</h1>
  <p>
    <b>Ideation and Exploration.</b>
    The early months were all about brainstorming and exploring different
    directions. From March to June, we rigorously debated potential projects,
    experimenting with ideas like predicting metal-binding proteins and
    genome-wide miRNA prediction. These discussions gave us critical insight
    into various possibilities, but it wasn't until late June that we began to
    narrow our focus toward protein complexes and integrated modelling platforms,
    an area that would soon give rise to IMPROViSeD.
  </p>

  <h1>July</h1>

  <p>
    <b>Settling on IMPROViSeD and Laying the Groundwork.</b>
    With July, came a burst of momentum. Our team finalized the IMPROViSeD
    platform, which centered on using experimental cross-linking data for
    modelling protein complexes. We now had a solid direction, and the task ahead
    was to bring this platform to life.
  </p>

  <h2>Week of 14th July</h2>
  <p>
    The first week after our decision was focused on ensuring the
    <b>responsiveness of our web page</b> to make it user-friendly and
    accessible, and this is where we started laying the foundations of our wiki.
    Meanwhile, we also worked on the <b>team logo</b> design, a crucial part of
    our identity, and made strides in planning an
    <b>educational app for computational biology</b> to engage with younger
    audiences. While the designs were still being refined, the core framework of
    the project was coming together, and our <b>registration code</b> for
    modelling went through its initial phase of implementation.
  </p>

  <h2>Week of 21st July</h2>
  <p>
    Alongside technical progress, we were actively engaging in outreach. Our
    <b>school visits</b> were postponed this week, but we kept busy with
    presentations on <b>GPCRs</b> (we were yet to finalize the wet lab aspects
    of the project), adding to our educational efforts and refining our
    storytelling abilities for future workshops. These talks were intended to help us
    present our scientific ideas in a more accessible format.
  </p>

  <h2>Week of 28th July</h2>
  <p>
    The final week of July saw us diving into full-scale <b>workshops</b>. We
    also participated in the <b>AIIM judging session</b> (we presented our
    project to a panel of judges comprising field experts and iGEM ambassadors
    and also a poster to the congregation) while mapping out a detailed plan for
    our upcoming experimental procedures. Additionally, we began a
    <b>literature review</b> focused on AI-based functional prediction of
    proteins and expanded our documentation efforts for future use. This was
    also the week when our coding team refined
    <b>EDMC (Eucledian Distance Matrix Completion)</b> methods and focused on
    <b>geometric refinement</b> for the protein models.
  </p>

  <h1>August</h1>
  <p>
    <b>Refining the Platform and Expanding Our Reach.</b> August was a month of
    refining our technical workflows and enhancing outreach efforts.
  </p>

  <h2>Week of 4th August</h2>
  <p>
    We began the creation of our <b>Project Promotion Video</b>, a crucial step
    in communicating our vision to the broader iGEM audience. This week also
    included a visit to <b>NPS Rajajinagar School</b>, where we connected with
    students, sparking interest in synthetic biology. On the technical front,
    the team continued refining the <b>EDMC methods</b>, overcoming some initial
    challenges and progressing with <b>geometric refinement</b>, ensuring the
    stability of our model.
  </p>

  <h2>Week of 11th August</h2>
  <p>
    The middle of August was marked by the organization of a <b>hackathon</b>,
    where we brainstormed contact lists, platforms, and problem statements. This
    gave our project a fresh burst of energy. Concurrently, we focused on
    completing important forms, like the <b>safety forms</b> and
    <b>team page updates</b>. In terms of coding, we made strides with
    <b>refinement II</b> for our modelling methods, making the system more
    robust.
  </p>

  <h2>Week of 18th August</h2>
  <p>
    By the third week of August, we had successfully completed the second round
    of <b>CLI refinement</b> (the BEPT tool). Meanwhile, we tackled the final
    stages of the hackathon, making sure everything was in place for a smooth
    experience. Documentation was also underway, with updates on the safety and
    attribution forms.
  </p>

  <h2>Week of 25th August</h2>
  <p>
    The last week of August was a productive one. We integrated a
    <b>SDP (Semi-Definite Program) Solver</b> into the platform, further
    enhancing its functionality. This week also involved refining our
    <b>safety form submission</b>, ensuring that all necessary precautions were
    meticulously documented and in line with iGEM requirements. This is also
    where we had finalized on our wet lab aspects and discussed with
    <b>Dr. Manjula Das</b> regarding protein availability.
  </p>

  <h1>September</h1>
  <p>
    <b>The Final Push.</b> September marked the final stretch, where everything
    started coming together.
  </p>

  <h2>Week of 1st September</h2>
  <p>
    The first week of the month was marked by the submission of our
    <b>final safety form</b> and the <b>Project Promotion Video</b>. This was a
    significant milestone, as it marked the completion of key deliverables for
    the competition. We focused heavily on getting the video ready, making sure
    that it visually captured our journey and the core ideas behind IMPROViSeD.
  </p>

  <h2>Week of 8th September</h2>
  <p>
    With the video submitted, we turned our attention toward the
    <b>team roster</b> and polishing the final theme design. The homepage design
    was crafted with care, bringing to life the essence of our project.
    Simultaneously, the <b>attribution and documentation process</b> began,
    making sure that every contribution was properly acknowledged and recorded
    for the final submission. We received the <b>LCN2 Protein</b> this week and
    began standardizing the in-gel digestion protocol. The software team was
    focusing on post-processing steps.
  </p>

  <h2>Week of 15th September</h2>
  <p>
    Mid-September was all about field visits and visual presentation. We
    organized an <b>industry and clinic visit</b>, aimed at bridging the gap
    between our theoretical work and real-world applications. A
    <b>team photo</b> was also taken, which would be used on our website.
  </p>

  <h2>Week of 22nd September</h2>
  <p>
    As the month drew to a close, we entered the final phase of preparations.
    <b>Attribution forms, judging forms, and software submissions</b> were all
    tackled with care and precision, ensuring that nothing was left incomplete.
    The documentation effort also intensified, with every element being
    thoroughly reviewed and refined. The post-processing steps for the software
    were nearing completion. The <b>mass spectrometry data</b> for the in-gel
    digested peptide was available from the mass spectrometry facility at IISc.
    We also received <b>MMP9</b> this week and began standardizing the
    cross-linking experiments.
  </p>

  <h2>Week of 29th September</h2>
  <p>
    The final week was all about polishing and validating our work. We focused
    on optimising the results, making sure that our platform was ready for the
    judges. The last push toward submission involved wrapping up documentation,
    preparing final validation results, and ensuring that all loose ends were
    tied up.
  </p>

  <h1>October</h1>
  <p>
    <b>Conclusion.</b> From ideation to execution, each phase of our project has
    been crucial in shaping IMPROViSeD into a powerful tool for understanding
    protein complexes. Our journey through these months reflects the hard work,
    collaboration, and dedication of each team member. As we enter the final
    stages of the competition, we're excited to present our work and demonstrate
    the impact of our platform.
  </p>
  <figure>
    <img
      src="https://static.igem.wiki/teams/5346/cfa93407-1b04-416b-ac66-38e42eb6530d.jpg"
      alt="Fuelling up for the final push! Midnight pizza party as we review and put the finishing touches on our wiki, just hours before the submission deadline."
    />
    <figcaption>Fuelling up for the final push! Midnight pizza party as we review and put the finishing touches on our wiki, just hours before the submission deadline.</figcaption>
  </figure>
</div>

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