Merge pull request #35 from zkdan/main

init readme

README.md

@@ -1,2 +1,141 @@
 # ePlant
-ePlant
+ePlant is a gene-centered visualization tool for plant genomes.
+
+## Using ePlant
+Create a new tab or choose a gene of interest (GOI) using the search bar on the left. 
+> Currently the only plant genome available is that of _Arabidopsis thaliania_. 
+
+Use the navigation dropdown to discover more information about the expression of that gene from a phenotypic to a molecular level.
+
+Currently available views:
+
+  [ℹ️ Gene information]()
+
+  [📑 Publications ]()
+
+  [🌱 Plant]()
+
+  [🔬 Tissue & Experiment]()
+
+ > Coming views:
+  🌡️ Heat map
+  🌎 World
+  🧬 Chromosome 
+  Interactions 
+  Molecule
+  Sequence 
+🔄 Pathways 
+
+### Gene information
+Contains a list of gene information:
+- Which views are available for this gene
+- The gene name and aliases
+- Brief and computational descriptions
+- Curator summary
+- Location and gene model
+- DNA sequence
+- Protein sequence
+
+### Publication
+A list of relevant publications.
+- Author, year, journal, title, and links to publications associated with the GOI
+- Gene RIFs with annotations and links source to paper
+
+### Plant (cm scale)
+A visual map of where the gene is expressed in the body of the plant.
+  - Choose a data mode (relative/absolute)
+  - Select diagram origin: [AtGenExpress](https://www.arabidopsis.org/portals/expression/microarray/ATGenExpress.jsp) or Klepikova (for Anna Klepikova, author of [this paper](https://pubmed.ncbi.nlm.nih.gov/27549386/) on arabidopsis)
+  - Sort diagrams by name or expression level
+  - Hover over images for more information
+
+### Tissue & Experiment (mm scale)
+Expression patterns in different cells.
+
+<!-- 
+### Heat map
+Based on experiments done by the lab, the striated bars show [when?where?] a given gene is expressed.
+Yellow: weak, red: strong
+
+### World (km scale)
+Gene extression infomration plotted on a map.
+You can overlay climate information (precipitation, historical max temp, historical min temp).
+
+
+### Chromosome (micro-meter, sub-micrometer)
+Localization of the gene on the chromosomes. Can see local genes as well
+
+### Interaction level
+ Protein-protein and protein-DNA interactions for a given gene and geen product.
+
+### Molecule (nano meter) 
+Protein sequence
+
+### Sequence viewer
+JBrowser instance from Araport
+
+### Navigation
+See the relations of the gene to other plant genes. -->
+
+## Roadmap
+
+## How to contribute
+Read the [onboarding blueprint](https://github.com/BioAnalyticResource/ePlant/issues/29).
+
+If you'd like to contribute, [pick an issue](https://github.com/BioAnalyticResource/ePlant/issues). We use a forking workflow. For an in-depth look at what that means, [read this article](https://www.atlassian.com/git/tutorials/comparing-workflows/forking-workflow).
+
+### Quickstart
+1. Create a fork and download it to your local machine.
+    ```bash
+    git clone <your fork address>
+    ```
+1. Set up the main ePlant project as your upstream branch.
+    ```bash
+    git remote add upstream https://github.com/BioAnalyticResource/ePlant
+    ```
+1. Verify your node and npm versions. Most folks are working with Node v18.0.0^ and npm 9.8.0^.
+    ```bash
+      node -v
+      npm -v
+    ```
+    If that command doesn't return anything, [install the LTS version of Node](https://nodejs.org/en/download).
+
+1. Download all dependencies.
+    ```bash
+    npm i
+    ```
+1. Run your local version of ePlant.
+    ```bash
+    npm run dev
+    ```
+1. Comment on a ticket to take it.
+1. Turn on notifications for that thread.
+1. Complete the necessary fix.
+1. Push your changes to **your** fork.
+    ```bash
+    git push origin main
+    ```
+1. Create a pull request. 
+    > Underneath where it says **Compare changes**, there is a line that says 
+      > `Compare changes across branches, commits, tags, and more below. If you need to, you can also compare across forks.`
+    Click that link to bring up a dropdown menu of ePlant forks. 
+1. Choose your fork as the head repository and `https://github.com/BioAnalyticResource/ePlant/` as the base repository.
+1. Give the pull request a descriptive title so that someone who didn't work on it will know what you did. Link the issue if possible.
+
+### Reviewing a pull request
+
+
+
+
+## Glossary
+
+**AtGenExpress**: A multinational effort designed to uncover the transcriptome of the multicellular model organism _Arabidopsis thaliana_. 
+
+**BAR**: Bio-analytic resource; a group of bioinformatics tools created by the [lab of Dr. Nicholas Provart](http://provart.csb.utoronto.ca/the-lab/) at the University of Toronto.
+
+**BAR API**: An application programming interface of bio-analytic resources available at https://bar.utoronto.ca/api/. 
+
+**GOI**: Gene of interest; the gene displayed in ePlant.
+
+**eFP**: Electronic fluorescent pictographic
+
+**GeneRIF**: Gene reference into function; A [standard](https://www.ncbi.nlm.nih.gov/gene/about-generif) that provides a mechanism to allow scientists to add to the functional annotation of genes described in [Gene](https://www.ncbi.nlm.nih.gov/gene).