ePlant is a gene-centered visualization tool for plant genomes.
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:
Coming views: π‘οΈ Heat map π World 𧬠Chromosome Interactions Molecule Sequence π Pathways
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
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
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 or Klepikova (for Anna Klepikova, author of this paper on arabidopsis)
- Sort diagrams by name or expression level
- Hover over images for more information
Expression patterns in different cells.
Read the onboarding blueprint.
If you'd like to contribute, pick an issue. We use a forking workflow. For an in-depth look at what that means, read this article.
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Create a fork and download it to your local machine.
git clone <your fork address>
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Set up the main ePlant project as your upstream branch.
git remote add upstream https://github.com/BioAnalyticResource/ePlant
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Verify your node and npm versions. Most folks are working with Node v18.0.0^ and npm 9.8.0^.
node -v npm -v
If that command doesn't return anything, install the LTS version of Node.
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Download all dependencies.
npm i
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Run your local version of ePlant.
npm run dev
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Comment on a ticket to take it.
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Turn on notifications for that thread.
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Complete the necessary fix.
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Push your changes to your fork.
git push origin main
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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. -
Choose your fork as the head repository and
https://github.com/BioAnalyticResource/ePlant/
as the base repository. -
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.
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 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 that provides a mechanism to allow scientists to add to the functional annotation of genes described in Gene.