Bioclues Newsletter July-September 2023

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Sep 29, 2023, 1:11:16 AM9/29/23
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Quarterly newsletter of Bioclues.org
July - September 2023 | Vol 14 | Issue 3
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BIOCLUES SPEAKS

“For good ideas and true innovation, you need human interaction, conflict, argument, debate”. 
                                                                                                                        Margaret Heffernan
 

Dear Biocluers,

Bioclues is a non-profit virtual organization for, by, and of the Indian Bioinformaticians. A largest bioinformatics societies in India. Bioclues was built on the foundation of connecting people. Bioclues aims to bring together the Indian bioinformaticians, foster a strong working mentor-mentee relationship, provide access to bioinformatics resources, organize conferences and workshops besides imparting information about research, training, education, employment, and current events and news from bioinformatics, genomics, and related fields.

Read on to know more about our latest events and members

Stay Safe and be healthy!
Editors: Indrani Biswas, Rajul Jain, Sandeep Kumar and Rashmi Sukumaran

With inputs from Prashanth N Suravajhala 

Bioclues mourns the passing away of   
M.S. Swaminathan, Father of the green revolution in India.  May his soul rest in eternal peace!

Art by Nabomita Paul

Entrepreneurship Chair: Madhurima Kahali, PhD

A senior publishing professional with experience working across business verticals, Madhurima currently leads the B2C Marketing team of Taylor and Francis group in South Asia and Sub-Saharan Africa, focused on Open Research content growth. She has experience in working with researchers, large academic societies, institutes, cross-cultural teams and key opinion leader besides being 

passionate about open science, digital products and innovations in publishing. Having built and grown high-value life science/ biomedical science books and journal programs, Madhurima has subject matter knowledge with an in-depth understanding of good research practices, publishing ethics, and India's higher education funding landscape. Taylor and Francis has published over 300 books including textbooks, major reference works, and professional books and is instrumental in data-driven book program development, new journal acquisition, journal takeovers, management, and strategic partnerships. Welcome, Madhurima and thank you for organising the Taylor and Francis webinar series with Bioclues. 

Student Representatives of Bioclues 

Nabomita Paul is a PhD Scholar in Biotechnology who offers sharp time management, organizational and assistance skills. She also bears a personable individual willing to work hard and take on any task. Over the last few years, she has pursued a full-time role involved in Bioinformatics data analysis besides participating in a wide number of training programs and conferences. 

Apart from scientific activities, she also participated as social media strategist and community leader. She bears exceptional skills in scientific writing, communication, handling with various sorts of instruments and photography. She also served as a research intern at Indian Institute of Technology, Kanpur and as teacher assistant at Sant Hirdaram Girls College, Bairagarh. She served as student volunteer at Sri Sathya Sai College for Women, where she worked in the field of medical biotechnology. Working as a tutor in UrbanPro, she has built and maintained rapport with students through active listening and clear communication. She helped students in defining and planning academic goals and milestones to support progress. She cooperated with students, teachers and parents to determine student needs and develop tutoring plans. She also used online learning platforms to develop lessons, post assignments and communicate with students. Further, she attended continuing education conferences to foster continuous awareness of industry trends and developments. Welcome, Nabomita!

🔬 Discover the Insights from 
Integrated Systems Bioinformatics Workshop 2023!

Dear Bioinformatics Enthusiast,

We are thrilled to take you on a retrospective journey through the remarkable Integrated Systems Bioinformatics Workshop 2023, hosted by BIOCLUES- BIOinformatics CLUb for Experimenting Scientists. The workshop, held from July 17th to July 29th, brought together experts, researchers, and enthusiasts from around the world to delve into the fascinating realm of bioinformatics and systems biology.

Let's rewind and recap the enriching sessions that unfolded during this insightful event:

📅 July 17, 2023 

Prash kicked off the workshop with an invigorating session on "Introduction to Bioinformatics and Systems Biology." Participants were encouraged to install Cytoscape with the CytoHubba app, while ensuring their Java software was up to date. This foundational session set the stage for the days to come. 

📅 July 18, 2023

Diving into the realm of machine learning, Jayaraman K Valadi guided attendees through "Methods in Machine Learning." Attendees were directed to download the LIBSVM software, paving the way for integrating cutting-edge machine learning techniques into bioinformatics research.

📅 July 19, 2023

The spotlight then shifted back to Prash as he unravelled the "Essentials of Next Generation Sequencing." Attendees were encouraged to create accounts on UseGalaxy.org, igniting a journey into the realm of bioinformatic analysis of the data generated by high-throughput sequencing technologies.

📅 July 20, 2023

VS Sundararajan brought data science to the forefront in the session titled "Data Science for Bioinformatics." Attendees were urged to download the Weka software, a powerful tool for data analysis and machine learning, from its official repository.

📅 July 21, 2023

Rohit Reja took the stage to demystify the intricacies of "Analysis of Epigenetics and Chromatin Data." Attendees were provided access to a treasure trove of datasets crucial for comprehending the complexities of epigenetic regulation.

📅 July 22, 2023

Gyaneshwer Chaubey introduced attendees to the captivating world of "Population Genomics." The session led participants to explore valuable resources stored in the shared Google Drive folder, uncovering insights into genetic variations within populations.

📅 July 24, 2023

Sandeep Kumar from Jain University provided a comprehensive exploration of tackling infectious diseases through a systems biology lens. Access additional resources related to this topic here and here.

📅 July 25, 2023

Renuka Suravajhala from Amrita University elucidated the principles and applications of molecular docking in bioinformatics. Access resources found here.

📅 July 26, 2023

K. Sri Manjari guided participants through hands-on exercises designed to refine their skills in systematic and meta-analysis review. The participants embarked on a journey of critical analysis and exploration, paving the way for new insights.

📅 July 27, 2023

Anil Kumar S shared an insightful primer on plant bioinformatics, uncovering the fascinating connections between plant biology and informatics.

📅 July 28, 2023

Pushpendra Singh in his insightful talk on molecular epidemiology, offering a perspective on how molecular data can be harnessed to understand and combat the spread of diseases. Discover more through the resources provided here.

📅 July 29, 2023

Indrani Biswas led the session with a focus on Meta-analysis II, providing participants with a comprehensive toolkit for impactful research and analysis.

But the journey doesn't end here.

As we reflect on the knowledge shared and connections made during these sessions, we invite you to be part of our thriving community. Don't miss out on future updates, workshops, and invaluable insights. 

Thank you for being a part of the Integrated Systems Bioinformatics Workshop 2023. Your commitment to learning and growth is what propels the bioinformatics community forward. Until next time, keep exploring, experimenting, and envisioning new frontiers in the world of bioinformatics.

                                                                                                                                Nabomita Paul (PhD)

ACHIEVEMENTS

Heartiest congratulations Rajul Jain and Renuka Suravajhala et al. for their 10.7 IF paper!

Bioclues is proud to be a part of this Grand challenges article!

OUR PAST EVENTS

In ‘Sci’versation with Prash:

KRS Sambasiva Rao, Ph.D.

VC Mangalayatan University, Jabalpur, India

on September 13, 2023.

View recording >>
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In ‘Sci’versation with Prash:

GPS Raghava, Ph.D

Prof. & Head, Computational Biology, IIT-Delhi

on August 23, 2023.

View recording >>
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How to make an effective LinkedIn profile

Prash N. Suravajhala, Ph.D., 

Principal Scientist. Amrita University, Kerala

View recording >>
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GCCI: Changing the face of recurrent pregnancy loss

Pulakes Purkait, Ph.D.

Director, Origin Life, Chandigarh.

View recording >>
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Journal Club

ReproducibiliTea and Bioclues Joint Journal Club Session was conducted on 01.09.2023, with an opening journal club talk delivered by Indrani Biswas on implications of drug repurposing in cancer biology and limitations faced across this dogma. It was a lively event, with several UG, PG and research scholars getting fascinated by the learning outcome.

Introducing IN-KIND Life Memberships

Dear Members,

Bioclues as a non-profit organization would like to introduce 100 "in-kind" Life Members (LM) of our society and accorded from all States and Union Territories of India. In the next one month, we want to have 100 "in-kind" LMs who are needy, facing financial problems, but love doing bioinformatics, and are eager to join this society. If you have any student who is deprived of taking services at the expense of not being able to pay the membership fee, please let us know! The members would be given a full fee waiver for Life Membership. We anticipate that these less-privileged members will bring one paid LM each in due course.

Contact our secretary, Dr. K. Sri Manjari, to express your interest at s...@bioclues.org

LIFE MEMBERSHIP

Welcome to our new Life Members!

  1. Bijayanta Sircar
  2. Praveen Ebenezer
  3. Arushi Tiwari
  4. Durga Dheeraj Tammana
  5. Pulakesh Purkait
  6. Tamanna
  7. Supriya Kumari
  8. Deepika Goyal
  9. Manav Jain
  10. Pooja Solanke
  11. Ankita Tiwari
  12. Srishti Singh
  13. Rakesh Tiwari 
  14. Malavika J
  15. Suresh Gopi
  16. Nihal Najeeb
  17. Suresh Kumar Mendem
  18. Rajarshi Mondal
  19. Harsh Choudhary
  20. Robandeep Kaur
  21. P Sandeep Mallya
  22. Pragasam Viswanathan
  23. S. Muthukumaran
  24. Pankaj Yadav
  25. Manoj VR
  26. Nitya Bundela
  27. Sanjeevi Deeksha
  28. Tuhin James Paul
  29. Shubhangi
Become a Life Member!
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Benefits enjoyed by a Life Member

Unlocking Young Minds: 

The BIXS Program's Impact on Shaping Future Scientists

In today's ever-changing world, nurturing young minds by imparting additional knowledge and skills is crucial for cultivating and enhancing critical thinking abilities. Bioclues recognizes the significance of empowering the next generation of scientists, which is why we have introduced the Bioinformatics for School children (BIXS) program. Tailored for students aged 12-18, this flagship initiative aims to provide them with a strong foundation in bioinformatics, setting them on a path towards a brighter scientific future.

The importance of introducing young minds to bioinformatics cannot be overstated. A study conducted by Ana Martins and colleagues in 2020 shed light on the transformative potential of bioinformatics education in high schools. This study focused on the effects of four bioinformatics laboratories, aptly named "Mining the Genome: Using Bioinformatics Tools in the Classroom to Support Student Discovery of Genes," on 387 high school students. One of the central findings of the study was that students who were exposed to bioinformatics tools exhibited improved literacy, interest, and attitudes towards the subject. By actively engaging with bioinformatics, students not only gained a better understanding of concepts such as genes, protein synthesis, nucleic acids (DNA, RNA), start and stop codons, genome, evolutionary relationships, and genomic/genomic comparative but also dispelled misconceptions that had previously hindered their scientific growth. The study revealed that introducing comparative genomics into the learning experience significantly enhanced students' comprehension of curricular content. They not only became proficient in identifying genes within genomic sequences but also developed the ability to make evolutionary assumptions—a skill set that is increasingly valuable in the field of modern biology. Perhaps the most encouraging outcome of the study was the students' positive attitude towards integrating bioinformatics-based approaches into their learning practices. They recognized the intuitive nature of many bioinformatics tools, especially for beginners, which greatly bolstered their confidence in tackling complex biological questions. The findings emphasized that students who participated in bioinformatics-based activities displayed an improved awareness of the real-world applications and potential of bioinformatics. This insight into the practical side of bioinformatics encourages them to envision how they can contribute to solving real-world scientific challenges.

The BIXS program by Bioclues aligns with the spirit of the study's conclusions. Our dedicated lectures encompass a wide range of bioinformatics topics, ranging from Introduction to Bioinformatics and Microbiology to Big Data and Linux programming, equipping students with the skills and knowledge they need to excel in the world of science. The program also includes 9-12 orientation sessions followed by 16-24 weeks of hands-on projects, ensuring that students not only grasp the theory but also gain practical experience.

This study by Ana Martins and colleagues underscores the need to reconsider high school education in light of the evolving scientific landscape. At Bioclues, we firmly believe that the BIXS program is a step in the right direction. It equips young minds with the tools and insights they need to thrive in the modern scientific world. As we continue to expand our efforts, we are committed to addressing the questions raised by the study, such as the influence of teachers on students' performance and the potential impact of bioinformatics-based activities at different school levels. We are dedicated to refining and enhancing our program to maximize its positive influence on students' scientific growth. The BIXS program is not just about imparting knowledge; it's about shaping the future. It is about preparing the next generation of scientists who will drive innovation, discover solutions to global challenges, and redefine the boundaries of what is possible. Together, let's unlock the potential of young minds through the power of bioinformatics.

Further reading

Martins, A., Fonseca, M. J., Lemos, M., Lencastre, L., & Tavares, F. (2020). Bioinformatics-based activities in high school: fostering students’ literacy, interest, and attitudes on gene regulation, genomics, and evolution. Frontiers in microbiology, 11, 578099.

Unveiling the Python Prodigy: 

Your Exclusive Python Workshop Chronicle!

Greetings, Trailblazing Coders!!
Prepare to embark on an extraordinary journey through the boundless realms of Python programming with our brand-new Python Workshop Chronicle.
As we dive into the heart of Python, we'll unlock its unparalleled potential and showcase its magic like never before. It's an immersive experience designed to ignite your passion for coding and unleash your inner Pythonista.
In each edition, prepare to be captivated by Python's enchanting syntax, its versatility, and its limitless possibilities. We'll be your companions on this journey, providing you with not just tutorials, but interactive adventures. You'll wield Python's power through hands-on exercises and explore the latest developments and trends in the Python ecosystem.
Be ready to unravel Python's secrets, no matter your coding aspirations – be it web development, automation, data analysis, or crafting cutting-edge AI solutions. Python's adaptability and vast library support make it the perfect partner on your coding odyssey. So, we conducted Python Module 2 workshop from 17th July 2023 till 7th August 2023 which included wide spectra of advanced Python courses taught by Dr. Prashanth N Suravajhala Founder of Bioclues and Principal Scientist, School of Biotechnology, Amritapuri.

 

Following topics were covered during the training program:

1. Basics of Python’s reinstantiation
2. Arrays
3. Data types in Python Dictionary
4. Libraries
5. Operators 
6. List and tuples 
7. Functions, Classes and methods
8. Numpy
9. Object and Variables
10. Biopython module
11. Matplotlib.
                                                                                                                                  Goldy and Malavika

OUR INDUSTRY PARTNERS

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TissueGnostics

A solution provider for Precision Medicine / Next-Generation Digital Pathology and provides fully integrated cutting-edge tissue cytometers

WOULD YOU LIKE TO CONTRIBUTE?

We would love to publish your research highlights, achievements, popular science articles, poems, drawing, cartoon or photographs. 

Write to us at indrani...@gmail.com, kc.sa...@jainuniversity.ac.in.

Newsletter Editors: Team Bioclues

BIOinformatics CLUb for Experimenting Scientists (BIOCLUES)
Mail: ad...@bioclues.org
 

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