A Year of progress, success and new ideas
2019 was an eventful year for Pine Biotech: new course launches, resource upgrades, collaborations – overall, a tremendous growth of the bioinformatics community we support. It was also a year of growth for our team as new faces join the effort to make bioinformatics available and accessible to everyone across the globe.
Developing Resources for Bioinformatics Training
This year, our team worked hard to revise the curriculum for virtual and on-campus programs we support, develop new training materials, projects examples and expand the online training portal.
|New Courses||Regional Programs||Projects||Online Training|
|Introduction to Genomics, Metagenomics and Epigenomics||Louisiana Biomedical Research Network, Amity University, Kolkata, ScienceCoach||SF9 Rhabdovirus, Ebola, Early Detection…||Transcrpitomics, Bioinformatics for Precision Oncology, Data Science for Biomedical Data|
A Growing Library of Online Resources
Students, faculty and researchers around the world need access to cutting edge bioinformatics resources, and high quality learning materials to learn and apply bioinformatics. That’s why we spent considerable time updating and expanding our free online courses on edu.t-bio.info. These offer various levels of bioinformatics hands-on learning leveraging the powerful t-bio.info platform to analyze big datasets with no coding prerequisites.
All of the introductory courses offer a comprehensive view of omics technologies, including Introduction to Bioinformatics, Introduction to Genomics, Transcriptomics 1, Introduction to Metagenomics, and Epigenetics 1. For those that are interested in more advanced topics, we provide collections of courses that cover main -omics data types in thorough detail. Recently, we published several courses on metagenomics, including Introduction to Metagenomics and Metagenomics 2. This course is dedicated to the applications of bioinformatics in the study of microbial communities affecting human health, environment and agriculture. In this course, we provide a guide on using metagenomics to compare microbial composition in different conditions, learning about 16s amplicon sequencing, and use the DADA2 analysis pipeline on server.t-bio.info specifically designed for metagenomic amplicon sequencing.
In 2019, we were excited to forge new collaborations with universities from around the world. From the United States to India, we collaborated with some of the top universities and had the opportunity to work alongside some of the best students and faculties who are contributing to bioinformatics in a variety of domains. Some of our newest collaborators include Georgetown University Program for Systems Medicine, Louisiana Biomedical Research Network, Loyola University, Tulane University, Amity University Kolkata, Sister Nivedita University and the Institute of Genetic Engineering.
Machine Learning II Workshop on March 22, 2019 at 10:00 am CST – In March, we had several workshops at LSU. On March 22, we organized a workshop on Machine Learning that provided an overview of useful techniques based on unsupervised and supervised approaches in data mining and machine learning. Oncology examples were used to speak about the methods, their tuning and their application in combination with standard regression-based and hypothesis testing techniques to get the most out of data.
We are especially excited about our continuous and close collaboration with the Louisiana Biomedical Research Network.
Louisiana Biomedical Research Network (LBRN) has already conducted several pilots using our OmicsLogic training materials and will now start offering individual modules to graduate and undergraduate students after obtaining a license to offer the materials at LBRN-member universities across the state. Louisiana State University in Baton Rouge will be the primary host of this program, offering a Spring Session Graduate Course on Transcriptomic Data Analysis: Applied Bioinformatics Concepts for Life Science Research.
The course is taught by Dr. Gus Kousoulas (LSU BioMMED) along with Dr. Ramesh Subramanian, Dr. Lyndon Coghill, Dr. Chris Taylor (LSUHSC), and Dr. Urska Svek (LSU Shreveport). In this course, participants will learn how gene expression can be studied using high throughput sequencing data, leveraging principles of bioinformatics. The course will cover essential steps of processing, analysis and interpretation of such data using commercial solutions for high performance computing (T-BioInfo) and open source applications (R). Similar courses are now being offered for credit at Grambling University and Southern University of Baton Rouge.
We also launched a collaboration with Science Coach, a program for gifted students in Missouri that learn about cutting edge research and are now learning about bioinformatics to compete at top STEM competitions across the country.
Over the course of the year, we have been working with Tulane University to provide bioinformatics learning opportunities and internships to their biology and biostatistics students. Recently, our team was invited to conduct a workshop by Dr. Ian Townley, a teaching professor at Tulane University in the Department of Cell and Molecular Biology. The program at Tulane will offer the Introduction to Bioinformatics Course from Pine Biotech where students can learn about the recent developments in bioinformatics and the application to various challenges like biomedical research, healthcare and agriculture.
The success of our bioinformatics training and research projects also reflects the hard work our partners at the Tauber Bioinformatics Research Center have been doing to continue and expand the T-BioInfo analytical platform. Several of the TBRC members recently joined the Annual Bioinformatics Conference at the Center for Computation and Technology at LSU. They were invited to share their experience in bioinformatics and present the newest sections added to their analytical platform.
In 2019, we expanded into countries outside of the US. In India, we are now closely collaborating with the nation-wide Bioclues organization. We are also working closely with a number of universities, like Amity University Kolkata, Sister Nivedita University, Kolkata, Institute of Genetic Engineering,Kolkata and University of Engineering and Management, (UEM) Kolkata. Our collaborations have led to establishing a bioinformatics community in these universities. With UEM our joint effort is to organize a BioOlympiad for students in the schools and colleges in Spring 2020.
In 2019, there were a lot of requests from participants in Africa to expand our Big Data Bioinformatics Training in Africa. Therefore, one of our Spring Programs in 2020 will be organized in Nigeria under the guidance of Dr. Voke Toye, a graduate of our past OmicsLogic training programs.
A Growing Global Community of Bioinformaticians in the Making
As our online community expands, our team regularly reviews the online community members, selecting top participants who perform exceptionally well. These profiles are featured on our blog and social media. In October, we highlighted Dr. Sara C. Zapico, an Instructor of Forensic Chemistry at Florida International University, Dr. Melyssa Bratton of Xavier University in New Orleans, Vamshi Venkat, a data scientist from Hyderabad, India, and Ayushman Kumar Banerjee, a BTech Biotechnology Student from Amity University in Kolkata, India.
This year, we started a “leaderboard” where you can see the most active participants of the bioinformatics training programs:
We are excited about this community growing rapidly. We see this as a confirmation for our mission to make bioinformatics more accessible and exciting for the millions of biologists, clinicians and researchers around the world. We plan to continue in 2020 to make bioinformatics easy to use and make it more engaging. We are already working with companies, universities, research labs and local networks to significantly expand their reach and start offering high quality bioinformatics training and infrastructure to the next generation of life scientists!