follow key-paths through nested objects
Cache of biochemical pathway interactions
Self-host the Pathway Extreme font in a neatly bundled NPM package.
Olive learning pathway component - gamification
Pathway Design System tokens — CSS custom properties, JS export, and DTCG JSON
Self-host the Pathway Extreme font in a neatly bundled NPM package.
Self-host the Pathway Gothic One font in a neatly bundled NPM package.
Cache of biochemical pathway interactions
Pathway platform design system — Chakra theme, tokens, and shared UI (Netfusion-aligned brand layer)
Clinical pathway decision engine for EBM-based clinical decision support systems
Cache of biochemical pathway interactions
Shared constants and types for Pathway
Bluegenes Pathway Visualizer is a tool made for [BlueGenes](http://bluegenes.apps.intermine.org) following BlueGenes Tool API. Add more description of your tool here! :)
Library to facilitate access to the Pathway Commons web service
Explore roles, generate agent profiles, and surface career expectations so progression and team configuration are visible, not guessed.
Pathway Gothic One typeface
Biological pathway diagram viewer for WikiPathways.org
Use the Pathway Extreme font family from Google Fonts in your Expo app
Pathway Gothic One latin typeface
Use the Pathway Gothic One font family from Google Fonts in your Expo app
Gulp plugin to compile javascript source directories into Pathway modules
Pathway SDK
[**Read the docs →**](https://components.ai/docs/typefaces/pathway-gothic-one)
Reactome biological pathway database
a library for Rust
First-party deterministic pathway routing engine for Jacquard
Loaders for gapseq's reference data tables (SEED, MNXref, biomass JSON, pathway tables).
Pathway/reaction finder for gapsmith: selects pathways, orchestrates alignment, classifies hits, scores completeness.
A framework for saving and loading application state in Bevy.
A framework for saving and loading application state in Bevy.
High-performance CRDT library with dual pathways: JSON-native for web APIs and Cap'n Proto zero-copy for binary transport
Alignment abstraction for gapsmith: blast/diamond/mmseqs2 runners + precomputed TSV ingestion.
Command-line interface for gapsmith.
Core types for gapsmith: Model, Reaction, Metabolite, StoichMatrix, GPR.
Draft model construction for gapsmith (port of src/generate_GSdraft.R + helpers).
FBA / pFBA / gap-filling via good_lp + HiGHS for gapseq
Define your business logic in simple steps.
Helps your track the pathways in your app so that you can pave the cowpaths. Uses MongoDB to traverse the paths looking for little nuggets.
# DECC 2050 CALCULATOR TOOL A C version and ruby wrapper for the www.decc.gov.uk 2050 energy and climate change excel calculator Further detail on the project: http://www.decc.gov.uk/2050 Canonical source: http://github.com/decc/decc_2050_model ## DEPENDENCIES 1. ruby 1.9.2 (including development headers) 2. basic c development headers This has ONLY been tested on OSX and on Ubuntu 64 bit EC2 ami. Grateful for reports from other platforms. In the util folder there is an example script that creates a new EC2 EMI, installs all the dependencies and then compiles the gem. It may be useful if you are trying to figure out the complete set of dependencies. ## INSTALLATION Note that this compiles the underlying c code, which might take 10-20 minutes or so gem install decc_2050_model ## UPDATING TO NEWER VERSIONS OF EXCEL MODEL First of all, you need to be working on the github version of the code, not the rubygem: git clone http://github.com/decc/decc_2050_model Then put the new spreadsheet in spreadsheet/model.xlsx Then, from the top directory of the gem: bundle bundle exec rake The next step is to check whether Rakefile, lib/model/_model_result.rb and lib/model/model_structure.rb need to be altered so that they pick up the correct places in the underlying excel. The final stage is to build and install the new gem: gem build model.gemspec gem install decc_2050_model-<version>.gem ... where <version> is the version number of the gem file that was created in the folder. Now follow the instructions in the twenty-fifty server directory in order to ensure that it is using this new version of the gem.
# BELGIAN 2050 CALCULATOR TOOL A C version and ruby wrapper for the Belgian 2050 calcualtor ## GOTCHAS Some versions have a special formula in 2050!B2 that the translator doesn't recognise. Just write 2050 in that cell and recompile. Some tests fail for columns AN and AM on OUTPUT. I think this is due to rounding differences between excel and C. ## DEPENDENCIES 1. ruby 1.9.2 (including development headers) 2. basic c development headers This has ONLY been tested on OSX and on Ubuntu 64 bit EC2 ami. Grateful for reports from other platforms. In the util folder there is an example script that creates a new EC2 EMI, installs all the dependencies and then compiles the gem. It may be useful if you are trying to figure out the complete set of dependencies. ## INSTALLATION Note that this compiles the underlying c code, which might take 10-20 minutes or so gem install belgium_2050_model ## UPDATING TO NEWER VERSIONS OF EXCEL MODEL First of all, you need to be working on the github version of the code, not the rubygem: git clone http://github.com/decc/belgium_2050_model Then put the new spreadsheet in spreadsheet/2050Model.xlsx Then, from the top directory of the gem: bundle bundle exec rake The next step is to check whether lib/belgium_2050_model/belgium_2050_model_result.rb and lib/belgium_2050_model/model_structure.rb need to be altered so that they pick up the correct places in the underlying excel. The final stage is to build and install the new gem: gem build belgium_2050_model.gemspec gem install belgium_2050_model-<version>.gem ... where <version> is the version number of the gem file that was created in the folder. Now follow the instructions in the twenty-fifty server directory in order to ensure that it is using this new version of the gem.
# DECC 2050 CALCULATOR TOOL A C version and ruby wrapper for the www.decc.gov.uk 2050 energy and climate change excel calculator Further detail on the project: http://www.decc.gov.uk/2050 Canonical source: http://github.com/decc/decc_2050_model ## DEPENDENCIES 1. ruby 1.9.2 (including development headers) 2. basic c development headers This has ONLY been tested on OSX and on Ubuntu 64 bit EC2 ami. Grateful for reports from other platforms. In the util folder are two example scripts than can be helpful: 1. start-high-memory-instance.sh - is the script we use to setup an aws server to compile the model. You can't use it directly, because you won't have the right keys and certificates, but it can give clues. 2. setup-2050-model-builder-script.sh - is the script we use to get all the dependencies on that aws server correct, download this code, and then compile the model. Again, it may not be quite right for you but can server as inspiration ## INSTALLATION Note that this compiles the underlying c code, which might take 10-20 minutes or so gem install decc_2050_model ## UPDATING TO NEWER VERSIONS OF EXCEL MODEL First of all, you need to be working on the github version of the code, not the rubygem: git clone http://github.com/decc/decc_2050_model Then put the new spreadsheet in spreadsheet/2050Model.xlsx Then, from the top directory of the gem: bundle bundle exec rake The next step is to check whether lib/decc_2050_model/decc_2050_model_result.rb and lib/decc_2050_model/model_structure.rb need to be altered so that they pick up the correct places in the underlying excel. The final stage is to build and install the new gem: gem build decc_2050_model.gemspec gem install decc_2050_model-<version>.gem ... where <version> is the version number of the gem file that was created in the folder. Now follow the instructions in the twenty-fifty server directory in order to ensure that it is using this new version of the gem.
Ruby Neural Network implementation using backpropagation and gradient descent for training
hati-command offers a clear, minimal abstraction for implementing composable service objects and command-pattern interactors. By enforcing explicit Success and Failure result pathways, it aligns well with autonomous system pipelines, decision-chain architectures, and AI-driven orchestration flows.
Models synaptic plasticity with critical periods, pathway strengthening, and pruning
Neuromodulatory system modeling dopamine, serotonin, norepinephrine, and acetylcholine pathways for brain-modeled agentic AI
= Webservice Client Library for InterMine Data-Warehouses This library provides an interface to the InterMine webservices API. It makes construction and execution of queries more straightforward, safe and convenient, and allows for results to be used directly in Ruby code. As well as traditional row based access, the library provides an object-orientated record result format (similar to ActiveRecords), and allows for fast, memory efficient iteration of result sets. == Example Get all protein domains associated with a set of genes and print their names: require "intermine/service" Service.new("www.flymine.org/query"). new_query("Pathway") select(:name). where("genes.symbol" => ["zen", "hox", "h", "bib"]). each_row { |row| puts row[:name]} == Who is this for? InterMine data warehouses are typically constructed to hold Biological data, and as this library facilitates programmatic access to these data, this install is primarily aimed at bioinformaticians. In particular, users of the following services may find it especially useful: * FlyMine (http://www.flymine.org/query) * YeastMine (http://yeastmine.yeastgenome.org/yeastmine) * RatMine (http://ratmine.mcw.edu/ratmine) * modMine (http://intermine.modencode.org/release-23) * metabolicMine (http://www.metabolicmine.org/beta) == How to use this library: We have tried to construct an interface to this library that does not require you to learn an entirely new set of concepts. As such, as well as the underlying methods that are common to all libraries, there is an additional set of aliases and sugar methods that emulate the DSL style of SQL: === SQL style service = Service.new("www.flymine.org/query") service.model. table("Gene"). select("*", "pathways.*"). where(:symbol => "zen"). order_by(:symbol). outerjoin(:pathways). each_row do |r| puts r end === Common InterMine interface service = Service.new("www.flymine.org/query") query = service.new_query("Gene") query.add_views("*", "pathways.*") query.add_constraint("symbol", "=", "zen") query.add_sort_order(:symbol) query.add_join(:pathways) query.each_row do |r| puts r end For more details, see the accompanying documentation and the unit tests for interface examples. Further documentation is available at www.intermine.org. == Support Support is available on our development mailing list: dev@intermine.org == License This code is Open Source under the LGPL. Source code for this gem can be checked out from https://github.com/intermine/intermine-ws-ruby
Cognitive reserve for LegionIO — resilience through redundant pathways, compensatory mechanisms, and graceful degradation under damage
An MCP server that provides access to BioRuby KEGG functionality, allowing AI assistants to query KEGG databases for biological pathways, compounds, and other molecular information.
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