High-Level Project Summary
The GenomeBugs project to study the dynamics of insects biodiversity can be a solution to uncover and visualize distinctive patterns embedded in the intrinsic data organization of their whole genome sequencing. The goal is to detect, track and predict changes over time along the history of insects' life using, e.g., available resources from NCBI Genome Datasets. GenomeBugs is based on our recent Genomebits open source program to study characteristics of signals from genome sequences of viruses according to their progression along the nucleotide bases position. We aim to determine today's genetic information of insects at a single nucleotide level to pass it to future generations of humans.
Link to Project "Demo"
Link to Final Project
Detailed Project Description
Our planet Earth so far as we know is unique and it contains life depicted in millions of creatures of different species. Most classified species on Earth are insects, and our human life depends on their biodiversity, behavior and transformations. A small change in these variables, some species may face extinction and in turn it may affect our natural living environment. Therefore it becomes extremely urgent to combat any loss of life biodiversity for the well-being of all species.
To achieve this goal, we propose to consider quantifying and characterizing the dynamics of insects biodiversity in order to preserve and understand better their Nature.
We aim to "solve" this challenge by implementing GenomeBugs, a tool to study the dynamics of biodiversity by uncovering distinctive patterns embedded in the intrinsic data organization of the genome sequences of insects.
We have developed a open source Graphics User Interface (GUI) to the intrinsic data organization of any genome sequences according to its progression along the nucleotide bases position. This method is based on a finite alternating sum series having independently distributed terms associated with binary (0,1) indicators for the nucleotide bases A,C,T,G. From the view of statistics, such a sequence is equivalent to a discrete-valued time series for statistical identification and characterization of data sets as studied in financial series.
The GUI runs under Linux Ubuntu O.S., and it can be useful to study the dynamics of insects genome variants using available available resources, e.g., those from NCBI Genome Datasets.
This goal is important since allows to detect, track and predict changes over time along the history of insects life. If we determine historical genetic information at a single nucleotide level we can preserve it for the benefit of future generations.
Space Agency Data
We used open resources and links in our project as for example:
- The National Center for Biotechnology Information (NCBI) advances science and health by providing access to biomedical and genomic information. NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. You can find and download gene, transcript, protein and genome sequences, annotation and metadata: https://www.ncbi.nlm.nih.gov/datasets/
- The GISAID Initiative which promote the rapid sharing of data from all influenza viruses and the coronavirus causing COVID-19. This includes genetic sequence and related clinical and epidemiological data associated with human viruses, and geographical as well as species-specific data associated with avian and other animal viruses, to help researchers understand how viruses evolve and spread during epidemics and pandemics.
- We were also inspired by the video of the Nasa space apps challenge (Seeing the Unseeable - Viewing Bugs from Space)
- https://honeybeenet.gsfc.nasa.gov/
- Earth Science Data Systems (ESDS) Program for Genome Evolution in Polar Fishes.
Hackathon Journey
During the Space Apps experience we learn more about the real importance and impact in our lives of insects biodiversity. We also acknowledge the NASA Apps Challenge and the support Team for allowing us to share our ideas and thoughts.
References
MOLECULAR EVOLUTION AMONG SEVERAL ORDERS OF INSECTS BASED ON MITOCHONDRIAL DNA ANALYSIS
Hong L., PhD Thesis, Univ Simon Fraser (1993)
A database devoted to the insects of the cultural heritage
F. FOHRER, M. MARTINEZ, F. DORKELD, J. Entomological and Acarological Research 43 (2011) 95-98
THE GLOBAL TAXONOMY INITIATIVE 2020: A STEP-BY-STEP GUIDE FOR DNA BARCODING
CBD Technical Series No. 94
Insect genomic resources: Status, availability and future
Poonam Chilana, Anu Sharma and Anil Rai, CURRENT SCIENCE, VOL. 102, NO. 4, 25 FEBRUARY 2012
Uncovering signals from the Coronavirus Genome
E. Canessa, Genes (Basel) 2021 Jun 25;12(7):973. doi: 10.3390/genes12070973.
Best Practices in Insect Genome Sequencing: What Works and What Doesn’t
Stephen Richards and Shwetha C. Murali, Curr Opin Insect Sci. 2015 February 1; 7: 1–7. doi:10.1016/j.cois.2015.02.013
Insights into the genomic evolution of insects from cricket genomes
Guillem Ylla et al. COMMUNICATIONS BIOLOGY | (2021) 4:733 | https://doi.org/10.1038/s42003-021-02197-9 | www.nature.com/commsbio
Tags
#GenomeBugs, #genomebits, #DNA, #genome, #diversity, #Nature, #Planet, #software, #Insects, #Bugs, #NASASpaceApps2021, #signal ,#Linux, #creativity, #awareness, #Better-world
Global Judging
This project has been submitted for consideration during the Judging process.