DISCOVER: Pave Your Own Path with Discovery and Research
Join our open-source movement focused on digital resources, skills, and community for democratized research in high-demand fields. Dr. Feltus invites you to discover at the Praxis Academy Global Research Lab.
Praxis Academy Model
The shortest path to learning a useful skill is practice, practice, practice. When it comes to the complex skills required for 21st century data mining and discovery, it can be challenging to know how to begin a skilling journey. What question does one ask? Who can train me? Where do I find data? Can I train myself? If I need to use computers, how do I gain access to practice? Help!
Built from decades of experience training professional BioScientists, we have opened a training and research environment called the Praxis Academy. In the Praxis Academy, learning is always experiential and modern, so skills are translatable to the workforce. At the core of the academy are BioHackathon events where learners work on teams to solve open ended but specific problems. Skilling begins before the hackathon and continues until skills have been practiced and used for real world discovery. Proof of skills include digital badges and research products – like software repositories and technical publications.
Here is the BioHackathon process*:
- Start with a motivated human. A passionate BioHackathon VIP is identified. They bring the core question, sustained interest in the results, and motivation for all participants.
- Start the skilling process. Praxis AI facilitates the pre-training activities (theory data access, prerequisite skills, compute environment), logistics, adapting the problem to the scientific method (i.e. hypothesis generation and testing) and follow-up.
- Initiate the research. Phase 1 research occurs in a three ½ day synchronous team-based hacking event.
- Deep dive research. Follow up Phase 2 research leading to more skilling and results for the VIP, training for the hackers (even if they are citizen scientists), and products (papers, github, etc).
- Create product and proof of the skilling process. Phase 3: Publications, GitLab Repositories, and Digital Badges
*Note: multiple BioHackathon event threads can occur in parallel.
As often happens in the discovery process, serendipity introduced scientists at Praxis AI with Dr. Shivani Gupta who is a passionate explorer and practitioner of the Ayurvedic medicine and the medicinal properties of Turmeric and Curcumin. You can enjoy our conversation in the BioHackers Podcast.
Soon it became clear that a BioHackathon would be great way to discover the molecular mechanisms underlying turmeric anti-inflammatory properties and teach hackers some very modern computational biology research skills desperately sought by biotech companies and academic research institutions.
Phase 1: The BioHackaton Event
Everything that enters our body is made of atoms. These atoms are arranged into molecules with specific shape and surface chemistry. It is this molecular structure that can interact with other biochemical molecules that make up our cells, tissues, and organs. If a molecule that originated outside of our body from food, air, or drug administration bounces into and interacts (sticks) with a biochemical gene product in or near a cell, that molecule has the potential to affect the (up or down) activity of the gene. This change in the gene’s purpose could propagate into a macro-effect that we appreciate (not-hungry, fever gone) or one that we want to avoid (allergic reaction, cellular death).
Ayurvedic medicine is a holistic approach to physical and mental health. Ayurvedic medicine is one of the world’s oldest medical systems where treatment combines natural products, diet, exercise, and lifestyle to improve health. For example, when you eat turmeric, a wonderful spice and Ayurvedic medicinal tool, you are ingesting a lot of molecules with different concentrations and structures. Turmeric powder is primarily carbohydrate but also contains water, protein, fat, dietary minerals, essential oils, dietary fiber, and curcuminoids of which curcumin is of high interest due to its bioactive structure.
Curcumin has many beneficial effects on health including profound anti-inflammatory activity. Curcumin interacts (aka sticks) to about 1000 human proteins encoded in least 981 genes indicating high potential for affecting many biochemical pathways that that are induced by these genes. Thus, it may be that genetic subsystems including inflammation pathways are modulated through biochemical interactions of human proteins with the curcumin molecule (see below).
Curcumin actions in the body are mediated through dozens of interactions with human proteins that are associated with multiple pathways. In this three, half-day BioHackathon, hackers learned how to understand and address this hypothesis via:
- Lectures and discussions of the holistic Ayurvedic medicine approach, the known effects of curcumin on the human body, and systems biology approaches to uncovering enough comprehensive biochemistry from small molecule interactions with all human gene product to begin to identify the biochemical mechanisms of one facet of Ayurvedic medicine.
- Initialize data mining with pretraining tutorials in the Praxis LXP with real Linux VMs for computation. Preskilling included content on Comparative Toxicogenomics Database (ctdbase.org), PharmGKB (www.pharmgkb.org), and Protein Data Bank (www.rcsb.org).
- Collaborate with other creative people to identify how curcumin works holistically at the biochemical and genetic levels using bioinformatic and systems biology approaches.
At the end of the event, teams presented their research and decided if they wanted to continue the training process.
Phase 2: Deep-Dive Research
After the hackathon event ended, three research threads remained, project leads were identified, and hackers were assigned tasks. Essentially, dynamic research teams were formed without the need for a closed research environment often found in professional research settings. Democratized research now!
Research Thread A: Mechanisms of curcumin action in osteoarthritis
Research Question: Identity osteoarthritis bioactive gene targets of curcumin and interacting compounds.
- Task_A001: Write Python that will obtain all gene products that interact with bioactive compounds in turmeric, ginger, and black pepper, and first neighbor protein:protein interactions (PPIs).
- Task_A002: Build a high-quality chemical-gene interaction network of target and first neighbors. Modularize the network and perform pathway profiling.
- Task_A003: Assign tissue-specific gene expression attributes to the network from Task_A002.
- Task_A004: Analyze curcumin-treated osteoarthritic chondrocytes gene expression profiles from this study: https://www.frontiersin.org/articles/10.3389/fphar.2022.931914/full
Research Thread B: Mechanisms of curcumin action in neurodzegenerative disease
Research Question: What are the molecular mechanisms of curcumin and other derivatives in counteracting neurodegenerative diseases?
- Task_A001: Investigate the gene and protein targets of curcumin and other spice derivatives
- Task_A002: Investigate if curcumin and derivatives counteract neurodegenerative gene expression profiles
Project Lead: Shrikant Pawar
Research Thread C: Mechanisms of curcumin action in hypercholesterolemia
- Task_C001: Investigate if curcumin and derivatives influence hypercholesterolemia gene expression
Phase 3: Proof of Skilling and Research Products
This Academy event is in progress and will yield digital badges and research products for those who continue to participate.