Evolutionary algorithm framework and tutorial.
The official TypeScript library for the Mechanix API
A fast feature counting tool for prokaryotic RNA-seq analysis, compatible with featureCounts
skani is a fast tool for calculating ANI between metagenomic sequences, such as metagenome-assembled genomes (MAGs). It is extremely fast and is robust against incompleteness and fragmentation, giving accurate ANI estimates.
Facade crate for primitive RustUse biology vocabulary
Allen Lab QIIME2 pipeline
Group theory coset analog to threadsafe SPSC ring buffers
Build phylogenomic datasets in seconds.
An ultra-fast, low-memory footprint and accurate taxonomy classifier for all
Genome size estimation from long read overlaps
Genome size estimation from long read overlaps
Netview: mutual nearest neighbor graphs for genome-wide, fine-scale population structure determination and visualization
Command-line interface for Orphos, a tool for finding protein-coding genes in microbial genomes.
High-throughput, extensible SAM/BAM pileup generator
Eukaryotic cell cycle modelled at different levels of precision. Has two levels at the moment: Simple and Virginia Tech.
Zz structures are an interesting way of representing relations invented by Ted Nelson, whose domain model I provide in a gem Yzz. In this gem, YNelson, I combine Yzz with the universal Petri net provided by YPetri (another gem I wrote) to obtain a hybrid data structure that formalizes and generelizes a spreadsheet. Because let us note spreadsheets (as I have seen them) can be considered Petri nets of a kind, with cell functions acting as Petri net transitions. At the same time, spreadsheets are globally orthogonal structures with 3 typical dimensions (rows, columns and sheets). By using zz structures, the globally orthogonal spreadsheet is generalized as a locally orthogonal zz structure, with relations represented as zz dimensions, thus generalizing and formalizing a spreadsheet. The catch is that I have not yet finished the thinking process regarding what everything should be a zz object: Places (cells) and transitions definitely yes, but how about nets and dimensions? Should YNelson go as far as making namespaces into zz objects? The reason why these questions are hard to answer is because Ted Nelson himself, while providing interfaces guidelines (zz structure views, cursors...) did not comment on these questions. While being a (textual) DSL, YNelson aims to provide convenience on par with actual spreadsheet apps. Unlike YPetri, YNelson also aims to be able to specify more than one Petri net node per command, but this is still under development. See the user guide and the documentation for the details. YNelson documentation is available online, but due to formatting issues, you may prefer to generate the documentation on your own by running rdoc in the gem directory. For an example of how YPetri can be used to model complex dynamical systems, see the eukaryotic cell cycle model which I released as "cell_cycle" gem.
YPetri is a DSL (domain-specific language) for modelling of dynamical systems. It is biologically inspired, but concerns of biology and chemistry have been purposely separated away from it. YPetri caters solely to the two main concerns of modelling, model specification and simulation, and it excels in the first one. Dynamical systems are described under a Petri net paradigm. YPetri implements a universal Petri net abstraction that integrates discrete/continous, timed/timeless and stoichiometric/nonstoichiometric dichotomies of the extended Petri nets, and allows efficient specification of any kind of dynamical system. Like Petri nets themselves, YPetri was inspired by problems from the domain of chemistry (biochemical pathway modelling), but is not specific to it. Other gems, YChem and YCell are planned to cater to the concerns specific to chemistry and cell biochemistry. A lower-level extension of YPetri is currently under development under the name YNelson. Its usage is practically identical to YPetri, so any YPetri user can now consider using YNelson instead. YNelson covers additional concerns: it allows relations among nodes and parameters to be specified under a zz structure paradigm (developed by Ted Nelson) and it is also aimed towards providing a higher level of abstraction in Petri net specification by providing commands that create more than one Petri net node per command. YPetri documentation is avalable online, but due to formatting issues, you may prefer to generate the documentation on your own by running rdoc in the gem directory. As for the user manuals, there are currently 3 documents applicable for both YPetri and YNelson, whose master copies are stored in the YNelson source directory: 1. Introduction to YNelson and YPetri (hands-on tutorial), 2. Object model of YNelson and YPetri, 3. Introduction to Ruby for YNelson users. These manuals are written to allow beginners, including those unfamiliar with Ruby, to start working with YPetri and/or YNelson. For an example of how YPetri can be used to model complex dynamical systems, see the eukaryotic cell cycle model which I released as "cell_cycle" gem.