Results for pathways

Scenario-level LCA of energy systems and transition pathways

First-party deterministic pathway routing engine for Jacquard

a library for Rust

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

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.

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.

Ruby Neural Network implementation using backpropagation and gradient descent for training

Models synaptic plasticity with critical periods, pathway strengthening, and pruning

Neuromodulatory system modeling dopamine, serotonin, norepinephrine, and acetylcholine pathways for brain-modeled agentic AI

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.

= 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" =&gt; ["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 =&gt; "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

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.

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