Arsenal
This is my favorite resources’ page
TABLE OF CONTENTS
- Metabolic modeling
- Genomics and Metagenomics
- Databases
- Statistics for microbiome analysis
- Visualizations
- My dictionary
- Cool bioinfo
Metabolic modeling
You may have a look at this 
e-book I’ve been working on.
Genomics and Metagenomics
| Tool | Description | Documentation | Architecture | Repo | DOI | |
|---|---|---|---|---|---|---|
| skani | determining average nucleotide identity (ANI) via sparse approximate alignments | wiki | stand-alone | GitHub | OA | |
| LocalHGT | ultrafast horizontal gene transfer detection from large microbial communities | - | stand-alone | GitHub | OA | |
| gRodon | estimates maximal growth rates of prokaryotes and microbial eukaryotes from genome-wide codon usage statistics | site | R package | GitHub | original | v2 @ biorxiv |
| gcplyr | microbial growth curve data analysis | pages | R package | GitHub | OA | |
| drep | https://drep.readthedocs.io/en/latest/choosing_parameters.html |
Hierarchical Modelling of Species Communities (Hmsc) is a flexible framework for Joint Species Distribution Modelling (JSDMs). relate species occurrences or abundances to environmental covariates, species traits and phylogenetic relationships. JSDMs are a special case of species distribution models (SDMs) that take into account the multivariate nature of communities which allows us to estimate community level responses as well capture biotic interactions and the influence of missing covariates in residual species associations. GitHub
Kinbiont – an ecosystem of numerical methods integrating advanced ordinary differential equation solvers, non-linear optimization, signal processing, and interpretable machine learning algorithms. https://pinheirogroup.github.io/Kinbiont.jl/ https://www.biorxiv.org/content/10.1101/2024.09.09.611847v1.full
Databases
| Resource | Description | Link | DOI |
|---|---|---|---|
| eggo | estimated growth rates from gRodon online | GitHub | OA |
Statistics for microbiome analysis
My dictionary
In the following table I describe some terms I usually read/write about.
| Term | Description |
|---|---|
| richness | number of different taxa in a community |
| evenness | the commonness or rarity of a species |
| mucin | a family of high molecular weight, heavily glycosylated proteins (glycoconjugates) produced by epithelial tissues in most animals |
| effective number | refers to the number of equally abundant species needed to obtain the same mean proportional species abundance as that observed in the dataset of interest (where all species may not be equally abundant) |
| copiotrophs | taxa living in environments rich in nutrients |
| succession | changes in the presence, relative abundance or absolute abundance of one or more organisms within a microbial community. Its processes can be deterministic or stochastic. Factors that drive deterministic succession fall into three categories: abiotic factors (pH, redox potential), environmental factors (cross-feeding, diet or travel) and biological factors (innate and adaptive immunity). Stochastic succession is defined as microbial community changes that are not the consequence of environmentally determined fitness (ecological drift). Whether microbial succession is more deterministic or stochastic is driven by several factors in the formation of the community, including birth mode, travel, diet (for example, human breast milk) and antibiotics. |
Cool bioinfo
https://www.dbvis.com/thetable/
where we gather together to learn about and simplify the complexity of working with database technologies.
for example, here is how to combine mysql with docker https://www.dbvis.com/thetable/containerizing-mysql-with-docker-and-dbvisualizer/
creating beautiful command line interfaces in a composable way with as little code as necessary. https://click.palletsprojects.com/en/stable/
part of the Pallets community : https://palletsprojects.com
panGPT and panPrompt: Generative Pre-Trained Transformer for Large Pangenome Models (LPMs) from scratch. https://github.com/mol-evol/panGPT
