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AdvanceSyn Toolkit

Modelling and simulation play an increasing role in Systems Science; including Systems Biology, Synthetic Biology, and Metabolic Engineering. However, there are 4 major hurdles for many experimental biologists:

1. Most modelling and simulation tools require the user to be experienced in the mathematical underpinnings, which is in the domain of mathematicians.
2. The implementation of the model requires knowledge of specific modelling language, which is in the domain of computer scientists.
3. Most tools are specific in the modelling language use, which limits inter-operability and cross-utilization of analytical tools. For example, a metabolic model written in MATLAB cannot be used by most tools in systems biology, which tends to use SBML (Systems Biology Markup Language).
4. It is generally difficult and tedious to merge various small models into an aggregate for further use.

AdvanceSyn Toolkit is a suite of open-sourced tools for model development and model analysis; with an emphasis on systems biology, synthetic biology, and metabolic engineering. There are 3 objectives of AdvanceSyn Toolkit:

1. It aims to flatten the learning curve in model development for experimental biologists by reducing the amount of mathematics to its minimum.
2. It aims to be a model converter between different modelling languages, and enables merger of small models into larger models.
3. It aims to be a platform in which other modelling and simulation tools can be linked and aggregated for inter-operability and workflow development.

Citation

If you use AdvanceSyn Toolkit in your work, please cite the following:

• Ling MHT. 2020. AdvanceSyn Toolkit: An Open-Source Suite for Model Development and Analysis in Biological Engineering. MOJ Proteomics & Bioinformatics 9(4):83‒86.

If you use GSM-to-ASM in your work, please cite the following:

• Amir-Hamzah, N, Kuan, ZJ, Ling, MHT. 2022. Kinetic Models with Default Enzyme Kinetics from Genome-scale Models. Acta Scientific Computer Sciences 4(1): 59-63.

License

AdvanceSyn Toolkit is licensed under the Apache License, Version 2.0 (the "License") for academic and not-for-profit use only; commercial and/or for profit use(s) is/are not licensed under the License and requires a separate commercial license from the copyright owner (AdvanceSyn Private Limited); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

Contents

1. Installing AdvanceSyn Toolkit
2. Overview of AdvanceSyn Toolkit
3. Tutorials
   1. Writing an AdvanceSyn Model Specification (Type 1)
   2. Simulating a Model
   3. Performing One-Factor-At-A-Time (OFAT) Sensitivity Analysis
   4. Merging Two Models into One Model
4. List of Models in Repository
5. List of Native Operations
   1. genMO: Read the AdvanceSyn model specification file(s) and generate an internal model objects (MO) file.
   2. genNetwork: Read the AdvanceSyn model specification file(s) and generate a network / reaction visualization file.
   3. genODE: Generates an executable ODE model from a given model specification file.
   4. GSM-to-ASM: Converts genome-scale model (GSM) to draft kinetic model (ASM format) with default enzyme kinetics by building Michaelis-Menten equations using the reactants and products of each reaction listed in the GSM.
   5. installdep: Install external tools and dependencies.
   6. LSA: Performs local sensitivity using One Factor at a Time (OFAT) method.
   7. mergeASM: Read multiple AdvanceSyn model specification files and merge them into a single AdvanceSyn model specification file.
   8. printASM: Reads a AdvanceSyn model specification file and print out its details after before processing (generally for diagnostic purposes).
   9. readmodel: Reads a model specification file and print out its details after internal processing (generally for diagnostic purposes).
   10. readflux: Reads a model specification file and print out the fluxes (productions and usages) by model objects (generally for diagnostic purposes).
   11. runODE: Runs / Executes a generated ODE model and write out the simulation results.
   12. senGen: Generates a series of AdvanceSyn models from a single AdvanceSyn model, in preparation for sensitivity analyses.
6. List of Non-Native Operations: Cameo
   1. cameo-fba: Simulate a model using Flux Balance Analysis.
   2. cameo-medium-cpds: List the medium components in a model.
   3. cameo-medium-fba: Simulate a model after medium change(s) using Flux Balance Analysis.
   4. cameo-medium-pfba: Simulate a model after medium change(s) using Parsimonious Flux Balance Analysis.
   5. cameo-mutant-fba: Simulate a model after mutation(s) using Flux Balance Analysis.
   6. cameo-mutant-pfba: Simulate a model after mutation(s) using Parsimonious Flux Balance Analysis.
   7. cameo-pfba: Simulate a model using Parsimonious Flux Balance Analysis.
   8. cameo-rxn-cpds: List out the reactants and products of each reaction in a model.
   9. cameo-rxn-names: List out the reaction names, with upper and lower bounds, in a model.
7. Studies using AdvanceSyn Toolkit
8. Developers and Contributors