This document outlines the steps of implementation of Chemesis-3.
Chemesis is a library of biochemical reaction objects for modeling calcium concentration, originally contributed by Avrama Blackwell (firstname.lastname@example.org) to G-2. The G-3 implementation of Chemesis, called Chemesis-3, is based on the G-2 functionality, the code is mostly rewritten from scratch, with small snippets copied pasted over.
The global outline of adding new functionality to G-3 is defined as:
The core of this process is in the first step. A software developer can be fully focussed on the new mathematics and algorithms without being distracted or feeling restricted by overhead of G-3 maintenance. The other these steps are semi-automatic. It is possible but not required to start with step 2 and 3 before finishing step 1.
The steps required for the creation and the implementation of the Chemesis-3 library are (1) implementation of the independent solver objects, (2) definition in the DeveloperPackage, (3) initial creation of the workspace under version control, (4) configuration of the model-container for the new Chemesis-3 tokens, (5) connecting the model-container’s Chemesis-3 tokens with the solver objects via the model-container API, (6) connecting the solvers with the scriptable software components of G-3 such as SSPy, SSP and the gshell, and (7) implementation of documentation for the new functionality.
The order key defines the build order of the Chemesis-3 library. The Chemesis-3 library is built after Heccer (build order 2) and before SSP (build order 3). The command
reveals the details of the software component build order.
neurospaces_new_component --package-name chemesis-3
This command creates a new workspace under control of the DeveloperPackage and populates it with configuration scripts and makefiles. After the creation of the workspace, it can be populated with the source code that was created in the first step and the makefiles can be updated with compilation and installation targets as necessary.
description: a reaction between different molecule concentration pools
FORWARD_RATE: forward reaction rate, from substrate(s) to product.
BACKWARD_RATE: backward reaction rate, from product to substrate(s).
Setting up a repository server is what is required to make Chemesis-3 available for others. To initialize the server repository, implement steps (2) and (3) explained in the previous section on the server PC. Then use the neurospaces_serve command to start the server. For an explanation of permissions and other security aspects, see Installation Debian Server 5.0.3.
To incorporate the new software component in existing and new installations, the following configuration snippet in the file /etc/neurospaces/developer/build.yml defines the Chemesis-3 library for the DeveloperPackage. Note that this configuration snippet is now builtin in the developer package. This snipped should not be created in your filesystem.
Then the neurospaces_upgrade command can be used to automate the process of importation and installation of the new component.