About CRISpy-pop


CRISpy-pop is a web application that generates and filters guide RNA sequences for CRISPR/Cas9 genome editing. This tool focuses on generating guide RNA sequences for Yeast and Bacterial species used in bioenergy research. This tool supports a 1011 genome Saccharomyces cerevisiae strain set as well as a 167 strain set of S. cerevisiae isolates


How to cite CRISpy-pop:

Stoneman HR, Wrobel RL, Place M, Graham M, Krause DJ, De Chiara M, Liti G, Schacherer J, Landick R, Gasch AP, Sato TK, Hittinger CT. CRISpy-Pop: A Web Tool for Designing CRISPR/Cas9-Driven Genetic Modifications in Diverse Populations. G3 (Bethesda). 2020 Nov 5;10(11):4287-4294. doi: 10.1534/g3.120.401498. PMID: 32963084; PMCID: PMC7642938.



CRISpy-pop utilizes the following open-source software tools:



Cas-OFFinder

Bae S., Park J. & Kim J.-S. Cas-OFFinder: A fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 30, 1473-1475 (2014).

sgRNA Scorer

Chari R, Yeo N, Chavez A, Church GM (2017). sgRNA Scorer 2.0 – a species independent model to predict CRISPR/Cas9 activity. ACS Synthetic Biology. Accepted.

CasFinder

Aach J, Mali P, Church GM (2014). CasFinder: Flexible algorithm for identifying specific Cas9 targets in genomes. BioRxiv.


[v0.9.3] - 2026-11-06

Changed (2 changes)

  • Upgraded Rails from 8.1.4 to 8.1.4.1.
  • Upgraded rails-html-sanitizer to 1.7.2, loofah to 2.25.3 and nokogiri to 1.19.7, which Rails 8.1.4.1 requires.

Security (1 changes)

  • Rails 8.1.4.1 fixes 21 security advisories, including a critical Active Storage file read and write bug (GHSA-f3w6-w445-fwh9). See https://rubyonrails.org/2026/11/4/Rails-8.0.5.2-and-8.1.4.1-have-been-released

[v0.9.2] - 2026-11-03

Changed (1 changes)

  • Upgraded Ruby from 4.0.7 to 4.0.9.

Security (1 changes)

  • Ruby 4.0.9 fixes the Onigmo regexp CVEs CVE-2026-89078, CVE-2026-93577, CVE-2026-97229 and CVE-2026-110264.

[v0.9.1] - 2026-10-23

Security (2 changes)

  • Honeybadger error reports no longer include OAuth refresh tokens, CSRF tokens, or authentication cookies (#186).
  • Honeybadger error reports now filter the session cookie, which uses the default _session_id name in production (#186).

[v0.9.0] - 2026-10-15

Added (1 changes)

  • The csv gem as an explicit dependency, since it’s no longer a Ruby default gem and was previously only pulled in by HTTParty.

Changed (3 changes)

  • Set RAILS_ENV=production in the Docker production build and use SECRET_KEY_BASE_DUMMY for asset precompilation
  • Replaced the tmp_es6_igv package with the igv.js package
  • Replaced Font Awesome with Lucide.

Removed (4 changes)

  • Unused code
  • The HTTParty gem since it wasn’t being used.
  • The unused node-sass and resolve-url-loader yarn packages (esbuild-sass-plugin handles Sass).
  • Turbolinks, which was installed but never loaded.

Fixed (2 changes)

  • Some deprecated code updates in the python pipeline
  • The JavaScript bundle being included twice on every page.

Security (4 changes)

  • Updated Ruby to 4.0.7
  • Updated Rails to 8.1.4
  • Updated bundler and various gems
  • Updated yarn packages

[v0.8.0] - 2026-07-13

Added (1 changes)

  • Added a “How to cite CRISpy-pop” section to the About page with the CRISpy-Pop G3 (2020) publication reference (Stoneman et al.).

Changed (2 changes)

  • Updated rspec to use the selenium-webdriver gem instead of the webdrivers gem.
  • Tests in CI support the selenium/standalone-chromium service instead of having to install chrome/firefox into the application container.

[v0.7.0] - 2026-07-08

Added (1 changes)

  • Add Skylight performance monitoring

Changed (1 changes)

  • Updated ruby, gems, yarn packages

Fixed (2 changes)

  • Offsite search feature restored
  • Feedback Send Message button action redirect

[v0.6.1] - 2026-03-13

Changed (2 changes)

  • Footer version number is now a link to /about page, opening in a new tab
  • Prevent form submission when fields are blank

Security (1 changes)

  • Updated honeybadger gem

[v0.6.0] - 2026-02-12

Added (3 changes)

  • Docker setup for local development
  • Docker production setup
  • Staging environment

Changed (2 changes)

  • Converted all Dockerfiles to one Dockerfile that uses multi-stage builds
  • Package updates

[v0.5.0] - 2024-10-14

Changed (1 changes)

  • Updated gems and yarn packages for y6q4

Fixed (1 changes)

  • Picking ZM4 as the genome in offsite search did not work, have to convert gene name for python scripts

Security (1 changes)

  • Performed Y17Q4 maintenance

[v0.4.0] - 2022-10-28

Fixed (1 changes)

  • Export feature

[v0.3.0] - 2022-09-17

Changed (1 changes)

  • ruby and rails versions updated

[v0.2.0] - 2022-03-28

Changed (4 changes)

  • updated feedback gem version to 0.1.3
  • Updated gems and yarn packages
  • upgraded rails to v 6.1.5
  • Use feedback gem with setting for manual user and email entry

[v0.1.11] - 2021-10-22

Changed (2 changes)

  • Updating ruby and gems, js packages

Added (1 changes)

  • Opt-out for Google FLoC

[v0.1.11] - 2021-05-04

Added

  • Form field validation for custom target sequence

[v0.1.10] - 2021-04-02

Added (1 changes)

  • Captcha to feedback form

Fixed (1 changes)

  • sanitized inputs on command line pipeline

Changed (1 changes)

  • updated gems and js libraries

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog

Versioning is loosely based on Semantic Versioning

  • Major - large feature changes
  • Minor - bi-weekly update
  • Patch - mid-week update

[0.2.0] - 2020-10-09

Added

  • Honeybadger Error Tracking

[0.1.9] - 2020-09-25

Fixed

  • Issue with custom target searches throwing error

[0.1.8] - 2020-08-03

Added

  • PAM options
  • Strain set identifier to strain listings

Removed

  • ZM4 from GLBRC strain set

Changed

  • clean up strain coverage listing

[0.1.7] - 2020-05-21

  • removed gene alias name
  • change “% Activity” to “Activity Score”

[0.1.6] - 2020-04-13

  • Updated logo
  • Updated site title

Changed

  • Changed name of application to CRISpy-pop
  • New logo

[0.1.5] - 2020-04-08

Changed

  • Changed name of application to CRISpy-pop
  • New logo

[0.1.0] - 2019-12-11

Added

  • Enable python pipeline
  • Rework UI in React.js

[0.0.1] - 2019-10-07

Added

  • /api/v1/status endpoint
  • basic layout

Initial Application Configuration

  • Lograge Logging Configuration
  • GLBRC Auth
  • ESLint
  • Rubocop
  • RSpec
  • Brakeman
  • Bundler-Audit
  • Webpacker
  • React
  • Foreman Configuration