NGSomics (Next-Generation Sequencing Genomics)

Project (2015-2016): http://ngsomics.com

Introduction: NGSomics is a mobile-optimized, cloud-based NGS pipeline that utilizes Docker containers for parallelization and automation of genomic analysis (from alignment to variant annotation).

Abstract: Personalized medicine achieved through individualized analysis of genetic data is the future that connects bioinformatics and biomedicine. This field posits solutions to previously incurable diseases and opens up pathways towards better treatment options. A hallmark of bioinformatics research is the massive amount of data collected and generated from raw sequences of DNA which the genomic analysis software seeks to efficiently analyze. Even though many different genomic analysis programs are currently used by professionals to find mutations within a sequence, most of these tools are inaccessible for public use. This issue is caused by both a lack of practical interpretation of the resulting data and an absence of a platform capable of running intense operations while also being convenient and easy-to-use. A full-scale, parallelized and automated genomic analysis pipeline, NGSomics, is a solution which offers not only accurate variant calls, efficient processing speeds, and easy-to-replace bioinformatics tools, but also directly connects the user with applicable information through its responsive platform. NGSomics is hosted on a public domain and offers digestible and applicable data interpretations. Built on Docker, NGSomics is primed for seamless updating of currently integrated tools, such as the BWA aligner and SAMtools variant caller, as well as for the implementation of newly-developed genomic analysis tools. With the standardized Human Genome 19 data set used in the comparative GCAT test, it is asserted that NGSomics is an equally suitable option for DNA variants-based studies, as it is able to yield reliable outputs when compared with other genomic analysis pipelines. Future improvements to NGSomics would include implementing the concepts of one discarded design, a prototype which added WGCNA for identifying gene modules across specific biological conditions. Nevertheless, current developments in personalized medicine reveal high demands for the feature set of NGSomics. Its ability to branch lengthy bioinformatics data with clinically relevant information for the public is vital, especially as personal DNA sequencing becomes more affordable and commonplace.

Video Explanation

Project Details:

  • Project Page (here)
  • Github repository (here)
  • Docker image / repository (here)
  • Bioplanet GCAT report / comparison test (here)

Improving Photosynthesis: Multi-gene Editing Techniques to Induce C3 Characteristics into C4 Plants

Project (2015-2016): http://nathanwong.io/exploravision/index.html

Introduction: A report on how multi-gene editing techniques with CRISPR and CAS9 can be used to solve a potential global food crisis.

Abstract: Productive societies are founded on the abundance of agricultural produce. However, not all communities have access to reliable sources of nutrients, such as rice. A global food crisis exists: 854 million people are malnourished and 25 thousand people die yearly from inadequate diets. Addressing this problem involves the improvement of crop yield by enhancing traditional agricultural methods, which are currently limited by inefficient energy outputs. Our solution entails the induction of efficacious C4 photosynthetic characteristics into C3 photosynthesisbased plants through the mass-application and advancement of gene-editing techniques. While multi-gene editing tools have not been developed to an extent which our solution can be implemented on a cost-effective and widespread level, the untapped capabilities of the highlyaccurate CRIPSR/Cas9 gene-editing tool along with recent headway in DNA replication techniques posits a future in which supercharged photosynthesis is more than a possibility, bringing to fruition the goal to feed millions of malnourished people.

Full Paper Embedded

Project Details:

Firefigher Mini: A virtually designed apparatus to help solve fire stove problems.

Project (2016): https://www.youtube.com/watch?v=hAlUYp8ZGMo

Music Analgesics (Next-Generation Sequencing Genomics)

Project (2014-2015): https://bit.ly/musicvsstress

Introduction: A mathematical equation was derived to analyze music and correlated those results with my participant’s EDA (indicator for stress) in order to identify “stress-relieving” music.

Abstract: 

Just as how no two people have the same genetic fingerprints, there are no two pieces of music that have the same mathematical measurements.  Regardless, music is said to have alleged benefits such as building valuable brain connections and reduce stress in youth. Imagine if we could harness the power of music in such a way that we could modify our own behaviors just by listening to music.  Medical music (Biofeedback) is already a growing field, but what if instead of just subjectively thinking about the different musical qualities of a music piece, we could actually mathematically define the music that helps ameliorate our medical conditions. It is definitely a hard goal to reach, but this study was intended to be a step into the right direction. Due to the positive correlation between stress and the Galvanic skin activity, also known as electrodermal activity, this study examined the correlation between the sound wave energies of music and the electrodermal activities of a randomized sample of the Monta Vista student body (ages 13-18). In conclusion, it was clear that music affects people in such different ways so that although I was unable to identify a consistent correlation between my analyzed music and electrodermal activity (EDA), I instead found that each person has different ideal levels of psychological arousal that govern their individual performance level and offer ways to implement music into individualized analgesics.

Video Explanation

Project Details:

  • Google Science Fair Project Page (here)