From 1bd1d236df285ac06a9c49a0dbd7e8765ba8caff Mon Sep 17 00:00:00 2001 From: Chavhan675 <149674931+Chavhan675@users.noreply.github.com> Date: Tue, 17 Mar 2026 10:29:23 +0530 Subject: [PATCH 1/2] Add initial README.md for ModelBricks WebApp Added README.md with project overview, features, tech stack, and installation instructions. --- README.md | 46 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 README.md 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 From a864ad2285bf7f0f1c4244721a0593d036cb5682 Mon Sep 17 00:00:00 2001 From: Chavhan675 <149674931+Chavhan675@users.noreply.github.com> Date: Tue, 17 Mar 2026 12:08:52 +0530 Subject: [PATCH 2/2] Revise text for ModelBricks project page This PR improves the ModelBricks homepage content for better clarity and readability. Changes include: - Rewrote long paragraphs into shorter sections - Improved wording and consistency - Fixed typos and formatting issues - Enhanced button UI for better user experience These updates make the page more user-friendly and easier to understand. --- views/index.hbs | 81 ++++++++++++++++++++++++++++++++++--------------- 1 file changed, 56 insertions(+), 25 deletions(-) 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 @@
-

Welcome to the ModelBricks project

+

Welcome to the ModelBricks Project

- + + +

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

+ +

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

+ +

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

+ +
+ +
+

Browse ModelBricks →

+
+ + +
+
-


+


-

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. -
-

-

Browse ModelBricks

-
-

Each ModelBrick contains

@@ -26,51 +44,64 @@ As a result, new models are almost always created anew, repeating literature sea + + +

-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.


-


-
+ +

+
+

+ +

ModelBricks can be

+ +

-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.

-
-

Browse ModelBricks

+ +
+

Browse ModelBricks →

+
+ +