diff --git a/README.md b/README.md new file mode 100644 index 0000000..9f691f0 --- /dev/null +++ b/README.md @@ -0,0 +1,46 @@ +# ModelBricks WebApp + +A web-based platform to explore and visualize public biological models. +This application enables researchers and developers to interact with computational biology models through a simple and intuitive interface. + +--- + +## 🚀 Features + +- 🔍 Explore publicly available biological models +- 📊 Visualize model data and relationships +- ⚡ Fast and responsive web interface +- 🌐 Integration with external APIs for model data + +--- + +## 🛠️ Tech Stack + +- **Frontend:** Handlebars, HTML, CSS +- **Backend:** Node.js, Express.js +- **Data Handling:** JSON-based model storage +- **Deployment:** Docker support + +--- + +## ⚙️ Installation & Setup + +### Prerequisites +- Node.js (v14 or above) +- npm (Node Package Manager) +- Docker (optional) + +### Steps + +```bash +# Clone the repository +git clone https://github.com/your-username/modelbricks-webapp.git + +# Navigate to project directory +cd modelbricks-webapp + +# Install dependencies +npm install + +# Start the application +npm start diff --git a/views/index.hbs b/views/index.hbs index f76c4c6..139c367 100644 --- a/views/index.hbs +++ b/views/index.hbs @@ -2,23 +2,41 @@
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Welcome to the ModelBricks project

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Welcome to the ModelBricks Project

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+Biological computational models are often created for single-use purposes. +Their assumptions and descriptions are usually found only in research papers. +

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+Reusing or extending these models is difficult and often requires repeating work, +such as searching for kinetic parameters, initial conditions, and modeling details. +

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+ModelBricks provides a solution by offering +well-annotated, reusable biological components that can be assembled into +fully annotated mathematical models for cell biology. +

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Browse ModelBricks →

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Many computational models in biology are built and intended for "single-use"; the modeling assumptions and -descriptions of model elements must be found in the corresponding paper. Expanding models to new and more complex situations is non-trivial. -As a result, new models are almost always created anew, repeating literature searches for kinetic parameters, initial conditions and modeling specifics. It is akin to building a brick house starting with a pile of clay. Here we present a database of ModelBricks - well-annotated, reusable component mechanisms that can be assembled into - fully annotated mathematical models for cell biology. -
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Browse ModelBricks

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Each ModelBrick contains

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-1. Sets of molecules (species) uniquely identified with universal identifiers, their initial concentrations and transport properties. +1. Molecules (species) uniquely identified with universal identifiers, including their initial concentrations and transport properties.

-2. Reaction(s) (changes in state) identified by known biochemical mechanisms and defined by a flux reaction with parameters for -forward and reverse rates (kf and kr). -Flux terms can be simple mass action kinetics or complex functions. +2. Reactions (state changes) defined by known biochemical mechanisms, with forward (kf) and reverse (kr) rate parameters. +Flux terms may follow simple mass action kinetics or complex functions.

-3. An identified cellular Compartment(s) where the reaction occurs and the species reside. +3. Cellular compartments where reactions occur and species are located.

-4. A Publication ID or other identifier of the author and peer-review status for the original model from which a ModelBrick is derived +4. Publication ID or author reference indicating the origin and validation of the model.


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ModelBricks can be

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-1. Downloaded in mulltiple formats, such as SBML or VCML formats +1. Downloaded in multiple formats such as SBML or VCML.

-2. Inserted into an existing SBML compatible model including all annotations and defined parameters. +2. Inserted into existing SBML-compatible models with all annotations and parameters included.

-3.Created from existing models and submitted for inclusion in the repository. +3. Created from existing models and submitted to the repository.

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Browse ModelBricks

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Browse ModelBricks →

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