Update website (#10)

* removed description on readme description was outdated and not needed so it has been removed from the readme. Can be added later if needed * Update index.md * updated description * using GitHub icon * made CRIPT Scripts logo into a link * using bigger CRIPT Scripts logo on front page using logo in full ratio instead of a width of 250 * changed width of the front page logo * Update index.md improved the UI on landing page * added Excel icon to CRIPT Sheets index.md * Update index.md added graph logo to graph/index.md * Create index.md * added badges to front page * updated readme.md badge style * updated readme.md to comment out the badges * updated .gitignore * updated spacing between word * created CRIPT JSON section * updated Calabrese Rubber * CRIPT Graph * Excel file * JSON file * updated .gitignore * reordered current graphs * added Cao Protein JSON to CRIPT Graph JSON section * added Cao Protein Excel * added Xia Brush polymer research * added code icon to CRIPT Scripts Page * added Olsen Rod-Coil Block Copolymers graph * removed incorrect description within `Files` section * updated research paper link in Olsen_rcbc.md * updated file name for graphs/cao_protein.md * updated file name for graphs/Olsen_rcbc.md * added Olsen_rcbc.md JSON * updated wording for Olsen_rcbc.md CRIPT Graph * removing Olsen_rcbc.json because not ready yet * added link for landing page for CRIPT Graph JSON * updated working in home page * updated wording from CRIPT to the CRIPT platform * added resources section to CRIPT Scripts landing page * made headings more uniform * trying to exclude readme, but not working * organizing Scripts scripts/python scripts/typescript * parent and grandparent working * parent and grandparent working with TypeScript * renamed Polymer Experiment.csv renamed from Polymer Experiment.csv to Sample Polymer Experiment.csv * added AFRL Script to Python CRIPT Script sections * updated CRIPT_Data_Structure_Template.pptx * updated color to match research paper * Added TypeScript AFRL Script * updated CRIPT Graph powerpoint color to match research paper * removed materia_uploader.py and polymer mixture experiment.md because it was just the AFRL script that I accidentally uploaded multiple times * added link to TypeScript to home page * updated TypeScript Scripts wording on Home page * renamed typescript/AFRL/README.md to instructions.md this rename was needed because otherwise Jekyll kept grabbing it and showing it in the navigation, which was wrong * renamed typescript/AFRL/README.md back * updated wording on scripts page * updated CRIPT Scripts icon and TypeScript Scripts * updated h2 from `File` to `Excel File`
C-Accel-CRIPT · Apr 13, 2023 · 36a1411 · 36a1411
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diff --git a/.idea/.gitignore b/.idea/.gitignore
diff --git a/README.md b/README.md
@@ -1,7 +1,13 @@
 <div>
- <img width="250" src="/assets/images/criptscripts-logo.svg" alt="CRIPT Scripts logo">
+ <img src="./assets/images/criptscripts-logo.svg" alt="CRIPT Scripts logo">
 </div>
 
-> A curated list of scripts and tools for interacting with [CRIPT](https://criptapp.org).
-
+<!--
+![Markdown](https://img.shields.io/badge/Language-Markdown-lightgrey?style=for-the-badge&logo=markdown)
+![Ruby](https://img.shields.io/badge/Language-Ruby-red?style=for-the-badge&logo=ruby)
+![Ruby Package Jekyll](https://img.shields.io/badge/Ruby%20Gem-Jekyll-red?style=for-the-badge&logo=jekyll)
+![HTML](https://img.shields.io/badge/Language-HTML5-red?style=for-the-badge&logo=html5)
+![CSS](https://img.shields.io/badge/Language-CSS-blue?style=for-the-badge&logo=css3)
+![Fontawesome](https://img.shields.io/badge/Icons-Fontawesome-blueviolet?style=for-the-badge&logo=fontawesome)
 
+-->
diff --git a/cript_graph/Olsen_rcbc.md b/cript_graph/Olsen_rcbc.md
@@ -0,0 +1,18 @@
+---
+layout: default
+title: Olsen Rod-Coil Block Copolymers CRIPT Graph
+parent: CRIPT Graphs
+---
+
+# Structure and Thermodynamics of Weakly Segregated Rod-Coil Block Copolymers
+
+[Research paper](https://pubs.acs.org/doi/10.1021/ma051468v) 
+written by Bradley D. Olsen and Rachel A. Segalman*.
+
+The CRIPT graph has been expertly made by
+[Professor Olsen of MIT](https://cheme.mit.edu/profile/bradley-d-olsen/) to serve as an example for 
+the [CRIPT platform](https://criptapp.org).
+
+## Files
+
+- [Olsen_RCBC.pptx](./graph_ppt/Olsen_RCBC.pptx)
diff --git a/cript_graph/calabrese_rubber.md b/cript_graph/calabrese_rubber.md
@@ -1,21 +1,18 @@
 ---
 layout: default
-title: Calabrese Rubber
+title: Calabrese Rubber CRIPT Graph
 parent: CRIPT Graphs
 ---
 
 # Development of a Rubber Recycling Process Based on a Single-Component Interfacial Adhesive
 
-Research paper written by Michelle A. Calabrese, Wui Yarn Chan, Sarah H. M. Av-Ron, and Bradley D. Olsen
+[Research paper](https://pubs.acs.org/doi/abs/10.1021/acsapm.0c01343) written by 
+Michelle A. Calabrese, Wui Yarn Chan, Sarah H. M. Av-Ron, and Bradley D. Olsen
 
 The CRIPT graph has been expertly made by
-[Professor Olsen of MIT](https://cheme.mit.edu/profile/bradley-d-olsen/) to serve as an example for CRIPT.
+[Professor Olsen of MIT](https://cheme.mit.edu/profile/bradley-d-olsen/) 
+to serve as an example for the [CRIPT platform](https://criptapp.org).
 
-## Files
+## File
 
-The following includes the original research paper, representation of the research paper in CRIPT data graph, Excel file, and JSON
-
-- [Calabrese Rubber **Research Paper**](./calabrese_rubber/calabrese_rubber_recycling_paper.pdf)
-- [Calabrese Rubber **CRIPT Graph**](./calabrese_rubber/calabrese_ruber_recycling_data_graph.pptx)
-- [Calabrese Rubber **CRIPT Excel File**](./calabrese_rubber/calabrese_ruber_recycling_data_graph.pptx)
-- [Calabrese Rubber **CRIPT JSON**](./calabrese_rubber/calaberese_rubber.json)
+* [calabrese_ruber_recycling_data_graph.pptx](./graph_ppt/Calabrese_ruber_recycling_data_graph.pptx)
diff --git a/cript_graph/calabrese_rubber/Calabrese_rubber_recycling_paper.pdf b/cript_graph/calabrese_rubber/Calabrese_rubber_recycling_paper.pdf
diff --git a/cript_graph/cao_protein.md b/cript_graph/cao_protein.md
@@ -6,16 +6,12 @@ parent: CRIPT Graphs
 
 # Strengthening and Toughening of Protein-Based Thermosets via Intermolecular Self-Assembly
 
-Research paper written by Yiping Cao and Bradley D. Olsen.
+[Research paper](https://pubs.acs.org/doi/10.1021/acs.biomac.2c00372) written by Yiping Cao and Bradley D. Olsen.
 
 The CRIPT graph has been expertly made by
-[Professor Olsen of MIT](https://cheme.mit.edu/profile/bradley-d-olsen/) to serve as an example for CRIPT.
+[Professor Olsen of MIT](https://cheme.mit.edu/profile/bradley-d-olsen/) to serve as an example for 
+the [CRIPT platform](https://criptapp.org).
 
 ## Files
 
-The following includes the original research paper, representation of the research paper in CRIPT data graph, Excel file, and JSON
-
-- [Cao Protein **Research Paper**](./cao_protein/Cao_protein_materials_paper.pdf)
-- [Cao Protein **CRIPT Graph**](./cao_protein/Cao_protein_materials_data_graph.pptx)
-- [Cao Protein **CRIPT Excel File**](./cao_protein/Cao_CRIPT_template.xlsx)
-- [Cao Protein **CRIPT JSON**](./cao_protein/cao_protein.json)
+- [Cao_protein_materials_data_graph.pptx](graph_ppt/Cao_protein_materials_data_graph.pptx)
diff --git a/cript_graph/cao_protein/Cao_protein_materials_paper.pdf b/cript_graph/cao_protein/Cao_protein_materials_paper.pdf
diff --git a/cript_graph/graph_ppt/CRIPT_Data_Structure_Template.pptx b/cript_graph/graph_ppt/CRIPT_Data_Structure_Template.pptx
diff --git a/...Calabrese_ruber_recycling_data_graph.pptx → ...Calabrese_ruber_recycling_data_graph.pptx b/...Calabrese_ruber_recycling_data_graph.pptx → ...Calabrese_ruber_recycling_data_graph.pptx
diff --git a/...ein/Cao_protein_materials_data_graph.pptx → ...ppt/Cao_protein_materials_data_graph.pptx b/...ein/Cao_protein_materials_data_graph.pptx → ...ppt/Cao_protein_materials_data_graph.pptx
diff --git a/cript_graph/graph_ppt/Olsen_RCBC.pptx b/cript_graph/graph_ppt/Olsen_RCBC.pptx
diff --git a/cript_graph/graph_ppt/Xia_data_graphs.pptx b/cript_graph/graph_ppt/Xia_data_graphs.pptx
diff --git a/cript_graph/index.md b/cript_graph/index.md
@@ -4,8 +4,11 @@ title: CRIPT Graphs
 has_children: true
 ---
 
-# CRIPT Graphs
+<!-- import fontawesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.0/css/all.min.css" integrity="sha512-iecdLmaskl7CVkqkXNQ/ZH/XLlvWZOJyj7Yy7tcenmpD1ypASozpmT/E0iPtmFIB46ZmdtAc9eNBvH0H/ZpiBw==" crossorigin="anonymous" referrerpolicy="no-referrer" />
 
-CRIPT Graphs are a series of diagrams depicting the relationship of CRIPT nodes and how they interact with each other.
-They are also great examples that show translation of research to paper to
+
+# <i class="fa-solid fa-circle-nodes"></i> CRIPT Graphs
+
+CRIPT Graphs are a series of diagrams depicting the relationship of CRIPT nodes and how they interact with each other. They are also great examples that show translation of research to paper to
 [CRIPT Data model](https://pubs.acs.org/doi/suppl/10.1021/acscentsci.3c00011/suppl_file/oc3c00011_si_001.pdf).
diff --git a/cript_graph/xia_brush_polymers.md b/cript_graph/xia_brush_polymers.md
@@ -0,0 +1,18 @@
+---
+layout: default
+title: Xia Brush Polymer CRIPT Graph
+parent: CRIPT Graphs
+---
+
+# Efficient Synthesis of Narrowly Dispersed Brush Copolymers and Study of Their Assemblies: The Importance of Side Chain Arrangement
+
+[Research paper](https://pubs.acs.org/doi/full/10.1021/ja908379q) written by 
+Yan Xia, Bradley D. Olsen, Julia A. Kornfield,* and Robert H. Grubbs*
+
+The CRIPT graph has been expertly made by
+[Professor Olsen of MIT](https://cheme.mit.edu/profile/bradley-d-olsen/) to serve as an example for 
+the [CRIPT platform](https://criptapp.org).
+
+## File
+
+* [Xia_data_graphs.pptx](./graph_ppt/Xia_data_graphs.pptx)
diff --git a/...h/calabrese_rubber/calaberese_rubber.json → cript_graph_json/JSON/calaberese_rubber.json b/...h/calabrese_rubber/calaberese_rubber.json → cript_graph_json/JSON/calaberese_rubber.json
diff --git a/cript_graph/cao_protein/cao_protein.json → cript_graph_json/JSON/cao_protein.json b/cript_graph/cao_protein/cao_protein.json → cript_graph_json/JSON/cao_protein.json
diff --git a/cript_graph_json/calabrese_rubber.md b/cript_graph_json/calabrese_rubber.md
@@ -0,0 +1,17 @@
+---
+layout: default
+title: Calabrese Rubber CRIPT JSON
+parent: CRIPT JSON
+---
+
+# Development of a Rubber Recycling Process Based on a Single-Component Interfacial Adhesive
+
+[Research paper](https://pubs.acs.org/doi/abs/10.1021/acsapm.0c01343) written by 
+Michelle A. Calabrese, Wui Yarn Chan, Sarah H. M. Av-Ron, and Bradley D. Olsen
+
+The CRIPT JSON has been expertly made by one of the members of the [CRIPT platform](https://criptapp.org/) 
+to serve as an example for the [CRIPT platform](https://criptapp.org).
+
+## File
+
+* [calaberese_rubber.json](./JSON/calaberese_rubber.json) 
diff --git a/cript_graph_json/cao_protein.md b/cript_graph_json/cao_protein.md
@@ -0,0 +1,16 @@
+---
+layout: default
+title: Cao Protein CRIPT JSON
+parent: CRIPT JSON
+---
+
+# Strengthening and Toughening of Protein-Based Thermosets via Intermolecular Self-Assembly
+
+[Research paper](https://pubs.acs.org/doi/10.1021/acs.biomac.2c00372) written by Yiping Cao and Bradley D. Olsen.
+
+The CRIPT JSON has been expertly made by one of the members of the [CRIPT team](https://criptapp.org/) 
+to serve as an example for the [CRIPT platform](https://criptapp.org).
+
+## File
+
+* [cao_protein.json](./JSON/cao_protein.json) 
diff --git a/cript_graph_json/index.md b/cript_graph_json/index.md
@@ -0,0 +1,13 @@
+---
+layout: default
+title: CRIPT JSON
+has_children: true
+---
+
+<!-- import fontawesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.0/css/all.min.css" integrity="sha512-iecdLmaskl7CVkqkXNQ/ZH/XLlvWZOJyj7Yy7tcenmpD1ypASozpmT/E0iPtmFIB46ZmdtAc9eNBvH0H/ZpiBw==" crossorigin="anonymous" referrerpolicy="no-referrer" />
+
+
+# <i class="fa-solid fa-file-code"></i> CRIPT JSON
+
+Examples of the CRIPT JSON file is a representation of the CRIPT [CRIPT Data Model](https://pubs.acs.org/doi/10.1021/acscentsci.3c00011) in a JSON format.
diff --git a/cript_sheets/calabrese_rubber.md b/cript_sheets/calabrese_rubber.md
@@ -0,0 +1,16 @@
+---
+layout: default
+title: Calabrese Rubber CRIPT Sheet
+parent: Excel files
+---
+
+# Development of a Rubber Recycling Process Based on a Single-Component Interfacial Adhesive
+
+[Research paper](https://pubs.acs.org/doi/abs/10.1021/acsapm.0c01343) written by 
+Michelle A. Calabrese, Wui Yarn Chan, Sarah H. M. Av-Ron, and Bradley D. Olsen
+
+The CRIPT Sheet has been expertly made by one of the members of the [MIT Olson lab](https://olsenlab.mit.edu/) to serve as an example for the [CRIPT platform](https://criptapp.org).
+
+## Excel File
+
+* [calabrese_CRIPT_updated_template.xlsx](./example_excel_files/calabrese_CRIPT_updated_template.xlsx)
diff --git a/cript_sheets/cao_protein.md b/cript_sheets/cao_protein.md
@@ -0,0 +1,15 @@
+---
+layout: default
+title: Cao Protein CRIPT Sheet
+parent: Excel files
+---
+
+# Development of a Rubber Recycling Process Based on a Single-Component Interfacial Adhesive
+
+[Research paper](https://pubs.acs.org/doi/10.1021/acs.biomac.2c00372) written by Yiping Cao and Bradley D. Olsen.
+
+The CRIPT Sheet has been expertly made by one of the members of the [MIT Olson lab](https://olsenlab.mit.edu/) to serve as an example for the [CRIPT platform](https://criptapp.org).
+
+## Excel File
+
+* [Cao_CRIPT_template.xlsx](./example_excel_files/Cao_CRIPT_template.xlsx)
diff --git a/...graph/cao_protein/Cao_CRIPT_template.xlsx → ...ample_excel_files/Cao_CRIPT_template.xlsx b/...graph/cao_protein/Cao_CRIPT_template.xlsx → ...ample_excel_files/Cao_CRIPT_template.xlsx
diff --git a/...ber/Calabrese_CRIPT_updated_template.xlsx → ...les/calabrese_CRIPT_updated_template.xlsx b/...ber/Calabrese_CRIPT_updated_template.xlsx → ...les/calabrese_CRIPT_updated_template.xlsx
diff --git a/cript_sheets/index.md b/cript_sheets/index.md
@@ -4,6 +4,10 @@ title: Excel files
 has_children: true
 ---
 
-# CRIPT Sheets
+<!-- import fontawesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.0/css/all.min.css" integrity="sha512-iecdLmaskl7CVkqkXNQ/ZH/XLlvWZOJyj7Yy7tcenmpD1ypASozpmT/E0iPtmFIB46ZmdtAc9eNBvH0H/ZpiBw==" crossorigin="anonymous" referrerpolicy="no-referrer" />
+
+
+# <i class="fa-solid fa-file-excel"></i> CRIPT Sheets
 
 CRIPT Excel files of all different types that have been used to upload polymer data to [CRIPT](https://criptapp.org) using either the [CRIPT Python SDK](https://c-accel-cript.github.io/cript/) or the [CRIPT Excel Uploader](https://c-accel-cript.github.io/cript-excel-uploader/) tool.
diff --git a/index.md b/index.md
@@ -5,12 +5,42 @@ nav_order: 1
 has_children: false
 ---
 
+<!-- import fontawesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.0/css/all.min.css" integrity="sha512-iecdLmaskl7CVkqkXNQ/ZH/XLlvWZOJyj7Yy7tcenmpD1ypASozpmT/E0iPtmFIB46ZmdtAc9eNBvH0H/ZpiBw==" crossorigin="anonymous" referrerpolicy="no-referrer" />
+
 <div>
- <img width="250" src="/assets/images/criptscripts-logo.svg" alt="CRIPT Scripts logo">
+ <a href="https://criptscripts.org/">
+ <img width="550" src="/assets/images/criptscripts-logo.svg" alt="CRIPT Scripts logo">
+ </a>
 </div>
 
-CRIPT Scripts is a curated list of scripts and tools for interacting with [CRIPT](https://criptapp.org).
+CRIPT Scripts is a curated list of examples and tools for interacting with the [CRIPT](https://criptapp.org) platform.
+
+## [CRIPT](https://criptapp.org) Examples:
+* <i class="fa-brands fa-python"></i> [Python Scripts](scripts/python/index.md) 
+created with the [CRIPT Python SDK](https://pypi.org/project/cript/)
+
+* <i class="fa-solid fa-code"></i> [TypeScript Scripts](scripts/typescript/index.md)
+
+* <i class="fa-solid fa-file-excel"></i> [Excel files](./cript_sheets/index.md) 
+used with the [CRIPT Excel Uploader](https://c-accel-cript.github.io/cript-excel-uploader/)
+
+* <i class="fa-solid fa-circle-nodes"></i> [CRIPT Graphs](./cript_graph/index.md) 
+that translates research into the [CRIPT Data Model](https://pubs.acs.org/doi/10.1021/acscentsci.3c00011)
+
+* <i class="fa-solid fa-file-code"></i> [CRIPT Graph JSON](./cript_graph_json/index.md) 
+the shows the CRIPT graph in JSON format
 
-[CRIPT Scripts](https://criptscripts.org) gives you many examples to interact with [CRIPT](https://criptapp.org). The examples include [Python Scripts](./scripts/index.md) created with [CRIPT SDK](https://pypi.org/project/cript/), [Excel files](./cript_sheets/index.md) used with [CRIPT Excel Uploader](https://c-accel-cript.github.io/cript-excel-uploader/), and [CRIPT Graphs](./cript_graph/index.md) that translates research into the [CRIPT Data Model](https://pubs.acs.org/doi/suppl/10.1021/acscentsci.3c00011/suppl_file/oc3c00011_si_001.pdf).
 
-For more information please visit the [CRIPT Scripts GitHub page](https://github.com/C-Accel-CRIPT/criptscripts)
+## [CRIPT](https://criptapp.org) Resources:
+* <i class="fa-solid fa-file"></i> [CRIPT research paper](https://pubs.acs.org/doi/10.1021/acscentsci.3c00011)
+
+* <i class="fa-solid fa-file-lines"></i> [CRIPT data model](https://pubs.acs.org/doi/suppl/10.1021/acscentsci.3c00011/suppl_file/oc3c00011_si_001.pdf)
+
+* <i class="fa-solid fa-file-powerpoint"></i> [CRIPT graph template](./cript_graph/graph_ppt/CRIPT_Data_Structure_Template.pptx)
+
+
+---
+
+For more information please visit the 
+<i class="fa-brands fa-github"></i> [CRIPT Scripts GitHub page](https://github.com/C-Accel-CRIPT/criptscripts)
diff --git a/scripts/create_materials.md b/scripts/create_materials.md
diff --git a/scripts/full_experiment.md b/scripts/full_experiment.md
diff --git a/scripts/index.md b/scripts/index.md
@@ -1,9 +1,13 @@
 ---
 layout: default
-title: Scripts
+title: CRIPT Scripts
 has_children: true
 ---
 
-# CRIPT Scripts
+<!-- import fontawesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.0/css/all.min.css" integrity="sha512-iecdLmaskl7CVkqkXNQ/ZH/XLlvWZOJyj7Yy7tcenmpD1ypASozpmT/E0iPtmFIB46ZmdtAc9eNBvH0H/ZpiBw==" crossorigin="anonymous" referrerpolicy="no-referrer" />
 
-Example Python Script built with the [CRIPT Python SDK](https://c-accel-cript.github.io/cript/) to upload polymer data to [CRIPT](https://criptapp.org/)
+
+# <i class="fa-solid fa-file-code"></i> CRIPT Scripts
+
+Example script used to upload polymer data to the [CRIPT platform](https://criptapp.org/)
diff --git a/scripts/material_uploader.md b/scripts/material_uploader.md
diff --git a/scripts/polymer mixture experiment.md b/scripts/polymer mixture experiment.md
diff --git a/scripts/python/AFRL.md b/scripts/python/AFRL.md
@@ -0,0 +1,22 @@
+---
+layout: default
+title: Air Force Research Lab Python Script
+parent: Python Scripts
+grand_parent: CRIPT Scripts
+---
+
+# Air Force Research Lab Python Script
+
+The Air Force Research Lab (AFRL) Python script is a way to programmatically upload data from a
+CSV file to the [CRIPT platform](https://criptapp.org). This script is written using the
+[CRIPT Python SDK](https://github.com/C-Accel-CRIPT/cript), and it works by taking a row of data,
+converting it to a CRIPT node, and uploading it to CRIPT one node at a time.
+
+## Python Script
+
+* [upload.py](./python_sdk_scripts/AFRL/upload.py)
+
+## Supplemental File
+
+* [requirements.txt](./python_sdk_scripts/AFRL/requirements.txt)
+* [config.yaml](./python_sdk_scripts/AFRL/config.yaml)