update docs

README.md

@@ -1,80 +1,21 @@
 # ePlant
-ePlant is a gene-centered visualization tool for plant genomes.
+ePlant is a gene-centric 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_. 
+Choose a gene of interest (GOI) using the search bar on the left. Currently we only support the _Arabidopsis thaliania_ genome.
 
-Use the navigation dropdown to discover more information about the expression of that gene from a phenotypic to a molecular level.
+Use the navigation dropdown to select different views. Each view displays information from the organism level to the molecular leve. Nanometer scale all the way to the kilometer scale.
 
-Currently available views:
+Available views:
 
-  [ℹ️ Gene information]()
+  ℹ️ Gene information. This view provides a brief description, location, gene model, DNA sequence, and protein sequence
 
-  [📑 Publications ]()
+  📑 Publications. This view displays publications and Gene RIFs related to your gene of interest.
 
-  [🌱 Plant]()
+  🌱 Plant eFP. This view displays expression levels for your gene of interest at the organism level.
 
-  [🔬 Tissue & Experiment]()
+  🔬 Tissue & Experiment eFP: This view displays expression levels for your gene of interest after experimental treatment.
 
- > 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
 
@@ -84,42 +25,46 @@ Read the [onboarding blueprint](https://github.com/BioAnalyticResource/ePlant/is
 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.
+1. [Make a fork of eplant](https://github.com/BioAnalyticResource/ePlant/fork).
+
+2. Go to the new fork. There is a big green button to clone
+   ```bash
+   git clone <fork_address>
+   ```
+
+3. 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^.
+
+4. 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.
+5. Download all dependencies.
     ```bash
     npm i
     ```
-1. Run your local version of ePlant.
+6. 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.
+7. Comment on a ticket to take it.
+8. Turn on notifications for that thread.
+9.  Complete the necessary fix.
+10. 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 
+11. 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.
+    Click that link to bring up a dropdown menu of ePlant forks.
+12. Choose your fork as the head repository and `https://github.com/BioAnalyticResource/ePlant/` as the base repository.
+13. 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
 
@@ -128,14 +73,14 @@ If you'd like to contribute, [pick an issue](https://github.com/BioAnalyticResou
 
 ## Glossary
 
-**AtGenExpress**: A multinational effort designed to uncover the transcriptome of the multicellular model organism _Arabidopsis thaliana_. 
+**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/. 
+**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).
+**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).