education.html

{% extends "layout.html" %} {% block title %}Education{% endblock %}
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<h1>AIIM</h1>
<h2>What is AIIM?</h2>
<p>
  The <b>All India iGEM Meet (AIIM)</b> is a premier annual event where iGEM
  teams from across India come together to exchange ideas, showcase innovations,
  and learn from each other. Hosted by a different team each year, AIIM fosters
  <b>collaboration</b> and knowledge-sharing, with the 2024 edition organized by
  the IISc Bangalore team. Alongside insightful talks by leading experts from
  <b>academia, industry, and entrepreneurship</b>, the meet offers an
  exceptional opportunity for teams to <b>connect</b> and grow. In 2024, the
  IISc-Software team led an exciting <b>workshop</b> on <b>"Computational Biology
    and Structural Visualization of Proteins,"</b> delving into specialized topics
  such as <b>protein electrostatics and statistical mechanics</b>. AIIM served
  as a dynamic platform for sparking new ideas, building networks, and deepening
  participants' understanding of these cutting-edge fields.
</p>

<h2>Workshop Summary</h2>
<p>
  The <b>primary goal</b> of this workshop was to share our knowledge on protein
  electrostatics and statistical mechanics—topics that are often unfamiliar to
  undergraduate students. Recognizing this gap, we aimed to provide a
  <b>comprehensive introduction</b> and offer valuable resources to help
  participants gain a deeper understanding of these advanced subjects. All the
  codes, and hands-on exercises were shared with the participants in the form of
  a github repository. The link to the website is
  <a
    href="https://github.com/IISc-Software-iGEM/Ion-Channel-NCC/tree/main/AIIM-Workshop"
    >here</a
  >.
</p>
<ol>
  <li>
    <b>Protein Structure Visualization with PyMol:</b>
    <p>
      We demonstrated some basics of <b>PyMol</b>, talked about commonly used
      file formats like <b>PDB</b> and <b>PQR</b>, alongside advanced features
      like alignment, morphing, and mutagenesis. The focus protein, NCC, was
      used to explain ion channels and their mutations, which cause the
      <b>Gitelman Syndrome</b>.
    </p>
  </li>
  <li>
    <b>Python Automation and APBS Electrostatics:</b>
    <p>
      We covered automating PyMol tasks using Python and introduced participants
      to the <b>APBS</b> command-line tools and web-server for calculating
      electrostatic potentials, making the topic more approachable.
    </p>
  </li>
  <li>
    <b>Statistical Mechanics for Molecular Dynamics:</b>
    <p>
      Here we shared an overview of molecular simulations, underlying
      algorithms, limitations in their biological applications, and best
      practices for conducting simulations. The goal of this presentation was to
      highlight the potential of these methods in <b>synthetic biology</b>.
    </p>
  </li>
</ol>

<figure>
  <img
    src="https://static.igem.wiki/teams/5346/aiim/aiim-collage.png"
    alt="AIIM Collage"
  />
  <figcaption>AIIM Workshop Conducted by IISc-Software Team.</figcaption>
</figure>

<h2>Reviews</h2>
<p>
  The workshop was well-received by a diverse audience, including students from
  other iGEM teams, IISc undergraduates, and MTech students from the CDS
  department. Participants praised the practical insights into APBS and
  molecular simulations, expressing interest in similar future sessions. iGEM
  teams from IISER TVM and IIT Bombay were particularly enthusiastic, with many
  eager to explore these advanced topics further.
</p>

<h2>Talk by Dr. Debnath Pal - Our Primary PI</h2>
<p>
  In the talk titled <b>"Snippets from Computing on COVID"</b>, Debnath sir delved into the critical role of computational biology in understanding the complexities of SARS-CoV-2, especially when experimental data and observations were conflicting during the pandemic. The central question addressed was, <b>"Why is SARS-CoV-2 so contagious?"</b> Drawing from previous experiments and ongoing research, sir explained how computational models have been essential in reconciling divergent findings from lab-based experiments. One key focus was the <b>infection initiation model</b>, which helps explain the virus's heightened transmissibility compared to other coronaviruses. Current results from computational studies have provided insights into the virus's mechanisms of infection, such as its efficient binding to host receptors, which underpins its contagiousness. The talk concluded by emphasizing how computational approaches continue to be <b>invaluable for filling gaps</b> where traditional experiments fall short, ultimately advancing our understanding of COVID-19.
</p>
<figure>
  <img
    src="https://static.igem.wiki/teams/5346/aiim/debnath-sir-talk.webp"
    alt="AIIM Talk by Dr. Debnath Pal."
  />
  <figcaption>AIIM Talk by Dr. Debnath Pal.</figcaption>
</figure>
<iframe
  src="https://static.igem.wiki/teams/5346/aiim/workshop-aiim-pdf.pdf"
  class="presentation"
></iframe>

<h1>School Visit to NPS Rajajinagar</h1>

<p>
  To teach high school students about synthetic and computational biology, we
  began by introducing DNA and proteins, giving them a solid foundational
  understanding. This was followed by a
  <b>hands-on DNA extraction experiment</b> using papaya, allowing students to
  reinforce their knowledge through practical experience. Next, we conducted a
  quiz on molecular biology concepts to deepen their comprehension of synthetic
  biology. Finally, we demonstrated how scientists use software like PyMOL to
  visualize protein structures and biomolecules, enhancing the students'
  understanding of computational biology.
</p>
<p>
  Our team <b>tailored</b> the explanations for the students at a 10th-grade
  level, ensuring that the material on key biomolecular segments and relevant
  biophysical concepts was understandable. We did this after consulting with
  <b>Mrs. Sushma Ravikiran</b>, a biology faculty member at
  <b>Carmel School</b>, to make sure the content was appropriate for their
  educational level.
</p>
<figure>
  <img
    src="https://static.igem.wiki/teams/5346/school-visit/school-visit-collage.png"
    alt="school visit collage"
  />
  <figcaption>
    Interaction with students at NPS Rajajinagar, Bengaluru.
  </figcaption>
</figure>

<h2>Demonstration of DNA</h2>
<p>
  The students were highly responsive, showing genuine curiosity and asking many
  insightful questions about how and why things work in biology. They were
  especially fascinated by the revolutionary potential of
  <b>synthetic biology</b>, which sparked their interest in exploring more about
  the field.
</p>

<h2>Demonstration of Proteins</h2>
<p>
  Next, we introduced the students to protein structures, focusing on
  <b>Keratin</b> and <b>Haemoglobin</b>, two proteins that are familiar to the students.
</p>
<ul>
  <li>
    <b>Keratin</b>
    <p>
      We explained keratin as a structural protein found in hair, nails, and
      skin. The focus was on the difference between <b>alpha-keratin</b> in hair
      and <b>beta-keratin</b> in nails, linking the vertical lines in nails to
      the arrangement of beta-keratin.
    </p>
  </li>
  <li>
    <b>Haemoglobin</b>
    <p>
      We explored Haemoglobin's role in <b>oxygen transport</b> and used the
      <b>1a3n.pdb</b>
      file to visualize its tetrameric structure. Through PyMOL, we demonstrated
      how iron binds to oxygen and the structural changes during oxygen binding
      and release, giving students a clear view of this essential process.
    </p>
  </li>
</ul>
<iframe
  src="https://static.igem.wiki/teams/5346/school-visit/school-visit-ppt.pdf"
  class="presentation"
></iframe>
<p>
  The students were highly responsive, showing genuine curiosity and asking many
  insightful questions about how and why things work in biology. They were
  especially fascinated by the revolutionary potential of synthetic biology,
  which sparked their interest in exploring more about the field.
</p>

<h1>BioComp-Bytes</h1>
<p>
  We organised BioComp-Bytes, a series of talks where professors from all over
  the world known for their works in Computational Biology, Bioinformatics and
  other aspects of Biological Sciences present and interact with the audience.
</p>
<p>
  These talks are aimed at providing a platform for the students and researchers
  to learn about the latest advancements in the field of <b>Computational Biology
    and Bioinformatics</b>. This series is also intended to spread awareness about the
  different computational tools and techniques that are being used in the field
  of Biological Sciences, for Protein Structure Prediction, Drug Discovery,
  Protein Analysis and more.
</p>
<figure>
  <img
    src="https://static.igem.wiki/teams/5346/biocomp-bytes/biocomp-bytes-sessions.png"
    alt="BioComp-Bytes sessions"
  />
  <figcaption>BioComp-Bytes Sessions</figcaption>
<h2>Speakers</h2>
<p>
  IISc-Software Team organised four talks in the BioComp-Bytes series. The
  speakers for the talks were:
</p>
<ol>
  <li>
    <b>"Solving 3D Biomolecular Puzzles by Integrative Modelling"</b> by
    Professor Dr. A.M.J.J. (Alexandre) Bonvin, Utrecht University, Netherlands.
  </li>
  <li>
    <b>"Structural Map of the Human Proteome Using AlphaFold"</b> given by
    Professor Arne Elofsson from Stockholm University, Sweden.
  </li>
  <li>
    <b>"Cellular consequences of genetic variation"</b> given by Professor Pedro
    Beltrao from ETH Zurich, Switzerland.
  </li>
  <li>
    <b>"RNA Structure and Prediction"</b> given by Professor Janusz M. Bujnicki,
    Laboratory of Bioinformatics and Protein Engineering, International
    Institute of Molecular and Cell Biology in Warsaw.
  </li>
</ol>
<figure>
  <img
    src="https://static.igem.wiki/teams/5346/biocomp-bytes/biocomp-bytes.png"
    alt="BioComp-Bytes Collage"
  />
  <figcaption>Posters for the BioComp-Bytes Series.</figcaption>
</figure>
<h2>Audience and Participation</h2>
<p>
  The talks were attended by students from IISc, and other institutions across
  India. A google form was sent across iGEM India community, iGEM Slack and
  other platforms to register for the event. We had multiple registrations with
  50+ registrations for each talk. We also had students from various other
  countries, like China and the UK. The talk was conducted via Google Meets with
  great audience participation and interaction with the speaker.
</p>

<h1>Command Line Interface - BEPT</h1>
<figure>
  <img
    src="https://static.igem.wiki/teams/5346/cli/bept-logo.png"
    alt="Bept Logo"
  />
  <figcaption>BEPT logo</figcaption>
</figure>
<p>
  BEPT (Beginner-friendly Electrostatics for Protein analysis Tool) is a
  command-line tool that integrates the functionalities of the
  <b>pdb2pqr</b> and <b>APBS</b>
  tools, streamlining their usage for beginners. With Bept, users can explore
  these powerful tools without the need to delve into complex documentation,
  making the learning process smoother and more accessible.
</p>
<p>
  Bept is developed by the IISc-Software Team, in collaboration with future
  undergraduate iGEMers at IISc Bengaluru, under the guidance of our Principal
  Investigator (PI).
</p>

<h2>Who is Bept created for?</h2>
<p>
  Bept is designed for anyone interested in studying protein electrostatics,
  especially APBS Electrostatics. It caters to a wide audience, including
  students, research professionals, and industrialists. The intuitive and
  interactive interface makes it accessible to all, regardless of their prior
  experience with command-line tools.
</p>
<p>
  With Bept, users can confidently pursue research in protein electrostatics,
  contributing to faster scientific development and discovery globally. For more
  information, visit our official
  <a href="https://github.com/IISc-Software-iGEM/bept">Github Page</a>.
</p>

<figure>
  <img
    src="https://static.igem.wiki/teams/5346/cli/cli-education-collage-2.png"
    alt="BEPT team working together."
  />
  <figcaption>BEPT team working together.</figcaption>
</figure>

<h1>Beyond The Microscope</h1>
<p>
  In September, our team, alongside volunteers from the foundations, conducted
  online and hybrid sessions for the <b>“Beyond The Microscope”</b> initiative
  for <b>grades 9th to 12th</b>. The hybrid session engaged students from
  <b>Madhya Pradesh</b> and <b>Ladakh</b>, with participants attending from
  their school computer labs during school hours. This included schools where
  access to cutting-edge educational resources is often limited. The online
  sessions took place in the evenings, allowing students to join from their
  laptops and phones.
</p>
<p>
  These sessions focused on key concepts related to the conversion of DNA to
  proteins and the visualization of common protein structures, such as keratin
  and Haemoglobin, using PyMOL. We incorporated hands-on activities to illustrate
  DNA-to-protein conversion through online web servers. The protein
  visualization provided students with a deeper understanding of how these
  structures function within the body.
</p>
<figure>
  <img
    src="https://static.igem.wiki/teams/5346/beyond-the-microscope/photo-2024-10-02-00-42-12.jpg"
    alt="Heamoglobin pymol pic"
  />
  <figcaption>Haemoglobin Pymol Visualisation</figcaption>
</figure>
<p>
  The interactions during the sessions were engaging, and the feedback from
  students was overwhelmingly positive. Many expressed a desire for additional
  sessions and resources to further explore the topics discussed, demonstrating
  the impact of our initiative in inspiring interest in the field of synthetic
  biology.
</p>
<iframe
  src="https://static.igem.wiki/teams/5346/beyond-the-microscope/beyond-the-microscope.pdf"
  class="presentation"
></iframe>

<h1>BIOMANIA</h1>
<p>
  We organized an engaging online session for students in
  <b>grades 5th to 8th</b>, in collaboration with the
  <b>STEAM Vision Foundation</b>. The students were from schools across the
  country. This interactive session introduced young participants to the
  fundamentals of molecular biology and illustrated how these concepts are
  applied in synthetic biology. To enhance their experience, we incorporated fun
  <b>art and craft</b> activities that encouraged creativity and hands-on
  learning.
</p>
<figure>
  <img
    src="https://static.igem.wiki/teams/5346/biomania/biomania-collage.png"
    alt="Biomania craft collage"
  />
  <figcaption>BioMania - Model of DNA.</figcaption>
</figure>
<p>
  In the sessions, we focussed on an introduction to the molecular biology of DNA and
  Proteins. This gave them a better understanding of the importance of DNA in
  heredity and Proteins in our body. Each participant received our made 
  <b>synthetic biology booklet and bookmarks</b> as a reward for their active
  involvement in the session. <b>Volunteers</b> from the <b>STEAM Vision Foundation</b>
  played a crucial role in facilitating the crafts and ensuring that all
  students were actively engaged throughout the event. The students actively
  participated in making the <b>DNA models</b> with pencils, colored sticks and
  tapes. This initiative sparked interest in science while fostering community
  and collaboration in exploring synthetic biology.
</p>

<iframe
  src="https://static.igem.wiki/teams/5346/biomania/biomania.pdf"
  class="presentation"
></iframe>
<iframe
  src="https://static.igem.wiki/teams/5346/biomania/biomania-booklet.pdf"
  class="presentation"
></iframe>
<figure>
  <img
    src="https://static.igem.wiki/teams/5346/biomania/bookmarks-biomania.jpg"
    alt="Biomania bookmarks"
  />
  <figcaption>BioMania Bookmarks</figcaption>
</figure>

<h1>TechBio Ideathon</h1>
<p>
  We organized a synthetic and computational biology ideathon aimed at fostering
  interest and engagement in synthetic biology among
  <b>undergraduate students</b>
  nationwide. The problem statements were carefully designed to reflect
  <b>real-life challenges</b>, encouraging participants to explore the practical
  applications of synthetic biology in addressing these issues. The panel of
  judges comprised experts from a diverse range of fields, including
  <b
    >healthcare, biosensing, materials science, entrepreneurship, environmental
    science</b
  >, and other relevant disciplines. Their broad expertise ensured a
  comprehensive evaluation of the participants' innovative solutions, providing
  valuable insights and feedback.
</p>
<figure>
  <img
    src="https://static.igem.wiki/teams/5346/ideathon/ideathon-judges-collage.png"
    alt="TechBio Ideathon judges"
  />
  <figcaption>TechBio Ideathon Judges</figcaption>
</figure>

<iframe
  src="https://static.igem.wiki/teams/5346/ideathon/techbio-ideathon-first-ppt.pdf"
  class="presentation"
></iframe>
<p>
  The problem statements were:
</p>
<ol>
  <li>
    <b>Sustainable Bio-Fabrication for Circular Textiles</b>
    <p>
      Develop biodegradable and sustainable textiles using engineered microbes
      to produce natural fibers, dyes, or binding agents, while utilizing
      synthetic biology and also promoting a circular economy in the textile
      industry.
    </p>
  </li>
  <li>
    <b>Bio-Sensors for Environmental Monitoring</b>
    <p>
      Design scalable, synthetic biology-based biosensors for continuous
      real-time monitoring of environmental pollutants coupled with advanced
      data analysis systems to provide actionable environmental insights for
      informed policy and research decisions.
    </p>
  </li>
  <li>
    <b>Precision Medicine through Synthetic Biology</b>
    <p>
      Design a synthetic biology platform that enables the creation of
      personalized therapies, including custom gene therapies, engineered
      probiotics, and targeted drug delivery systems, while utilizing patient
      data to continuously refine and adapt treatments for optimal effectiveness
      and responsiveness to the patient’s evolving health status.
    </p>
  </li>
  <li>
    <b>Synthetic Biology driven Vaccine Development</b>
    <p>
      Design a synthetic biology platform that enables the rapid synthesis of
      antigens and optimizes immune responses, facilitating quick adaptation to
      emerging pathogens and enhancing vaccine development speed and efficiency
      in response to global health threats.
    </p>
  </li>
</ol>
<iframe
  src="https://static.igem.wiki/teams/5346/ideathon/techbio-ideathon-rules.pdf"
  class="presentation"
></iframe>

<h2>Highlights of Ideathon Event</h2>
<iframe
  src="https://static.igem.wiki/teams/5346/ideathon/ideathon-event-slides.pdf"
  class="presentation"
></iframe>

<p>
  We had around <b>125 registrations</b> from participants across the country,
  who sent in their ideas for the problem statement they selected. After careful
  judging by experts, we had <b>5 finalists</b> out of them, 1-2 from each idea
  for the final round. The winner of this ideathon, the best solution award was
  won by <b>Riya Jain</b> from the <b>Team MedTech Coders</b>. Students
  presented innovative solutions, demonstrating their creativity and critical
  thinking skills. The judges were highly impressed by the quality of the ideas
  generated during the event, underscoring the potential of synthetic biology in
  solving contemporary problems. We made sure to offer them
  <b>post-ideathon support</b> regarding any of their ideas on how to make them
  ready for the real world and connected them to judges who were experts in this
  field.
</p>
<figure>
  <img
    src="https://static.igem.wiki/teams/5346/ideathon/blurred-certificate.jpg"
    alt="TechBio Ideathon Certificate."
  />
  <figcaption>
    TechBio Ideation Participation Certification(blurred for data privacy).
  </figcaption>
</figure>


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{% endblock %}