René's URL Explorer Experiment


Title: GitHub - GallowayLabMIT/tangles_model: Code for simulating user-defined gene circuits under the influence of supercoiling-mediated feedback

Open Graph Title: GitHub - GallowayLabMIT/tangles_model: Code for simulating user-defined gene circuits under the influence of supercoiling-mediated feedback

X Title: GitHub - GallowayLabMIT/tangles_model: Code for simulating user-defined gene circuits under the influence of supercoiling-mediated feedback

Description: Code for simulating user-defined gene circuits under the influence of supercoiling-mediated feedback - GallowayLabMIT/tangles_model

Open Graph Description: Code for simulating user-defined gene circuits under the influence of supercoiling-mediated feedback - GallowayLabMIT/tangles_model

X Description: Code for simulating user-defined gene circuits under the influence of supercoiling-mediated feedback - GallowayLabMIT/tangles_model

Opengraph URL: https://github.com/GallowayLabMIT/tangles_model

X: @github

direct link

Domain: patch-diff.githubusercontent.com

route-pattern/:user_id/:repository
route-controllerfiles
route-actiondisambiguate
fetch-noncev2:820005f7-2159-89df-8ea9-73df2ae45997
current-catalog-service-hashf3abb0cc802f3d7b95fc8762b94bdcb13bf39634c40c357301c4aa1d67a256fb
request-id8D4E:3930F2:E96BC1B:1300B909:69774291
html-safe-nonce29730826fbed1c5ea3ebf326352862a7a6d2e6b6eed87fa7ec9e3a8f8f26c268
visitor-payloadeyJyZWZlcnJlciI6IiIsInJlcXVlc3RfaWQiOiI4RDRFOjM5MzBGMjpFOTZCQzFCOjEzMDBCOTA5OjY5Nzc0MjkxIiwidmlzaXRvcl9pZCI6IjQ2MjE3MTI1MzU0NDk5Nzc0ODkiLCJyZWdpb25fZWRnZSI6ImlhZCIsInJlZ2lvbl9yZW5kZXIiOiJpYWQifQ==
visitor-hmacf2212bedcff1360bb4f15a05199342654ca146c91a06f509838943cffaa486c8
hovercard-subject-tagrepository:483370945
github-keyboard-shortcutsrepository,copilot
google-site-verificationApib7-x98H0j5cPqHWwSMm6dNU4GmODRoqxLiDzdx9I
octolytics-urlhttps://collector.github.com/github/collect
analytics-location//
fb:app_id1401488693436528
apple-itunes-appapp-id=1477376905, app-argument=https://github.com/GallowayLabMIT/tangles_model
twitter:imagehttps://repository-images.githubusercontent.com/483370945/a7cace8f-db61-4cb6-aa10-80bcddcfc694
twitter:cardsummary_large_image
og:imagehttps://repository-images.githubusercontent.com/483370945/a7cace8f-db61-4cb6-aa10-80bcddcfc694
og:image:altCode for simulating user-defined gene circuits under the influence of supercoiling-mediated feedback - GallowayLabMIT/tangles_model
og:site_nameGitHub
og:typeobject
hostnamegithub.com
expected-hostnamegithub.com
None01d198479908d09a841b2febe8eb105a81af2af7d81830960fe0971e1f4adc09
turbo-cache-controlno-preview
go-importgithub.com/GallowayLabMIT/tangles_model git https://github.com/GallowayLabMIT/tangles_model.git
octolytics-dimension-user_id61291003
octolytics-dimension-user_loginGallowayLabMIT
octolytics-dimension-repository_id483370945
octolytics-dimension-repository_nwoGallowayLabMIT/tangles_model
octolytics-dimension-repository_publictrue
octolytics-dimension-repository_is_forkfalse
octolytics-dimension-repository_network_root_id483370945
octolytics-dimension-repository_network_root_nwoGallowayLabMIT/tangles_model
turbo-body-classeslogged-out env-production page-responsive
disable-turbofalse
browser-stats-urlhttps://api.github.com/_private/browser/stats
browser-errors-urlhttps://api.github.com/_private/browser/errors
release8b4769605623191b876ce084a47e46d8431b205a
ui-targetfull
theme-color#1e2327
color-schemelight dark

Links:

Skip to contenthttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model#start-of-content
https://patch-diff.githubusercontent.com/
Sign in https://patch-diff.githubusercontent.com/login?return_to=https%3A%2F%2Fgithub.com%2FGallowayLabMIT%2Ftangles_model
GitHub CopilotWrite better code with AIhttps://github.com/features/copilot
GitHub SparkBuild and deploy intelligent appshttps://github.com/features/spark
GitHub ModelsManage and compare promptshttps://github.com/features/models
MCP RegistryNewIntegrate external toolshttps://github.com/mcp
ActionsAutomate any workflowhttps://github.com/features/actions
CodespacesInstant dev environmentshttps://github.com/features/codespaces
IssuesPlan and track workhttps://github.com/features/issues
Code ReviewManage code changeshttps://github.com/features/code-review
GitHub Advanced SecurityFind and fix vulnerabilitieshttps://github.com/security/advanced-security
Code securitySecure your code as you buildhttps://github.com/security/advanced-security/code-security
Secret protectionStop leaks before they starthttps://github.com/security/advanced-security/secret-protection
Why GitHubhttps://github.com/why-github
Documentationhttps://docs.github.com
Bloghttps://github.blog
Changeloghttps://github.blog/changelog
Marketplacehttps://github.com/marketplace
View all featureshttps://github.com/features
Enterpriseshttps://github.com/enterprise
Small and medium teamshttps://github.com/team
Startupshttps://github.com/enterprise/startups
Nonprofitshttps://github.com/solutions/industry/nonprofits
App Modernizationhttps://github.com/solutions/use-case/app-modernization
DevSecOpshttps://github.com/solutions/use-case/devsecops
DevOpshttps://github.com/solutions/use-case/devops
CI/CDhttps://github.com/solutions/use-case/ci-cd
View all use caseshttps://github.com/solutions/use-case
Healthcarehttps://github.com/solutions/industry/healthcare
Financial serviceshttps://github.com/solutions/industry/financial-services
Manufacturinghttps://github.com/solutions/industry/manufacturing
Governmenthttps://github.com/solutions/industry/government
View all industrieshttps://github.com/solutions/industry
View all solutionshttps://github.com/solutions
AIhttps://github.com/resources/articles?topic=ai
Software Developmenthttps://github.com/resources/articles?topic=software-development
DevOpshttps://github.com/resources/articles?topic=devops
Securityhttps://github.com/resources/articles?topic=security
View all topicshttps://github.com/resources/articles
Customer storieshttps://github.com/customer-stories
Events & webinarshttps://github.com/resources/events
Ebooks & reportshttps://github.com/resources/whitepapers
Business insightshttps://github.com/solutions/executive-insights
GitHub Skillshttps://skills.github.com
Documentationhttps://docs.github.com
Customer supporthttps://support.github.com
Community forumhttps://github.com/orgs/community/discussions
Trust centerhttps://github.com/trust-center
Partnershttps://github.com/partners
GitHub SponsorsFund open source developershttps://github.com/sponsors
Security Labhttps://securitylab.github.com
Maintainer Communityhttps://maintainers.github.com
Acceleratorhttps://github.com/accelerator
Archive Programhttps://archiveprogram.github.com
Topicshttps://github.com/topics
Trendinghttps://github.com/trending
Collectionshttps://github.com/collections
Enterprise platformAI-powered developer platformhttps://github.com/enterprise
GitHub Advanced SecurityEnterprise-grade security featureshttps://github.com/security/advanced-security
Copilot for BusinessEnterprise-grade AI featureshttps://github.com/features/copilot/copilot-business
Premium SupportEnterprise-grade 24/7 supporthttps://github.com/premium-support
Pricinghttps://github.com/pricing
Search syntax tipshttps://docs.github.com/search-github/github-code-search/understanding-github-code-search-syntax
documentationhttps://docs.github.com/search-github/github-code-search/understanding-github-code-search-syntax
Sign in https://patch-diff.githubusercontent.com/login?return_to=https%3A%2F%2Fgithub.com%2FGallowayLabMIT%2Ftangles_model
Sign up https://patch-diff.githubusercontent.com/signup?ref_cta=Sign+up&ref_loc=header+logged+out&ref_page=%2F%3Cuser-name%3E%2F%3Crepo-name%3E&source=header-repo&source_repo=GallowayLabMIT%2Ftangles_model
Reloadhttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model
Reloadhttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model
Reloadhttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model
GallowayLabMIT https://patch-diff.githubusercontent.com/GallowayLabMIT
tangles_modelhttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model
Notifications https://patch-diff.githubusercontent.com/login?return_to=%2FGallowayLabMIT%2Ftangles_model
Fork 0 https://patch-diff.githubusercontent.com/login?return_to=%2FGallowayLabMIT%2Ftangles_model
Star 1 https://patch-diff.githubusercontent.com/login?return_to=%2FGallowayLabMIT%2Ftangles_model
MIT license https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/blob/main/LICENSE
1 star https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/stargazers
0 forks https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/forks
Branches https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/branches
Tags https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/tags
Activity https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/activity
Star https://patch-diff.githubusercontent.com/login?return_to=%2FGallowayLabMIT%2Ftangles_model
Notifications https://patch-diff.githubusercontent.com/login?return_to=%2FGallowayLabMIT%2Ftangles_model
Code https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model
Issues 0 https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/issues
Pull requests 0 https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/pulls
Actions https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/actions
Security 0 https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/security
Insights https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/pulse
Code https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model
Issues https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/issues
Pull requests https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/pulls
Actions https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/actions
Security https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/security
Insights https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/pulse
Brancheshttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/branches
Tagshttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/tags
https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/branches
https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/tags
219 Commitshttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/commits/main/
https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/commits/main/
imghttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/tree/main/img
imghttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/tree/main/img
notebookshttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/tree/main/notebooks
notebookshttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/tree/main/notebooks
outputhttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/tree/main/output
outputhttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/tree/main/output
srchttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/tree/main/src
srchttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/tree/main/src
testhttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/tree/main/test
testhttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/tree/main/test
writeupshttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/tree/main/writeups
writeupshttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/tree/main/writeups
.gitignorehttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/blob/main/.gitignore
.gitignorehttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/blob/main/.gitignore
CITATION.cffhttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/blob/main/CITATION.cff
CITATION.cffhttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/blob/main/CITATION.cff
LICENSEhttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/blob/main/LICENSE
LICENSEhttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/blob/main/LICENSE
Manifest.tomlhttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/blob/main/Manifest.toml
Manifest.tomlhttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/blob/main/Manifest.toml
Project.tomlhttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/blob/main/Project.toml
Project.tomlhttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/blob/main/Project.toml
README.mdhttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/blob/main/README.md
README.mdhttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/blob/main/README.md
requirements.txthttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/blob/main/requirements.txt
requirements.txthttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/blob/main/requirements.txt
READMEhttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model
MIT licensehttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model
https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model#supercoiling-mediated-feedback-rapidly-couples-and-tunes-transcription
https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/blob/main/LICENSE
https://creativecommons.org/licenses/by/4.0/
https://doi.org/10.1101/2022.04.20.488937
https://doi.org/10.5281/zenodo.7054395
https://doi.org/10.5281/zenodo.7041641
Replicating paper resultshttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model#replicating-paper-results
downloadhttps://doi.org/10.5281/zenodo.7041641
https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model#simulating-your-own-gene-networks
TanglesModel.jlhttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/blob/main/src/TanglesModel.jl
https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model#install-and-code-check
https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model#running-a-simulation
https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model#specifying-simulation-parameters
https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model#specifying-rna-polymerase-binding-torque-response-or-topoisomerase-perturbations
https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model#boundary-conditions
https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model#specifying-genes
https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model#specifying-a-discrete-configuration
https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model#selecting-the-type-of-output
https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model#replicating-paper-results
Zenodohttps://doi.org/10.5281/zenodo.7041641
setting a data directoryhttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model#setting-a-data-directory
replicating figureshttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model#replicating-figures
code checkhttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model#install-and-code-check
https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model#simulating-raw-simulation-data
MIT Supercloudhttps://supercloud.mit.edu
https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model#sidebar-simulating-the-zinani-data
Zinani et al.https://www.nature.com/articles/s41586-020-03055-0
the authors' codehttps://github.com/ozbudak/zinani_genepairing
genepaired_scenario1.mhttps://github.com/ozbudak/zinani_genepairing/blob/main/genepaired_scenario1.m
geneunpaired_scenario1.mhttps://github.com/ozbudak/zinani_genepairing/blob/main/geneunpaired_scenario1.m
https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model#merging-datasets
https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model#setting-a-data-directory
rushdhttps://github.com/GallowayLabMIT/rushd
https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model#replicating-figures
https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model#license-and-reuse
CC-BY-4.0https://creativecommons.org/licenses/by/4.0/
MIT licensehttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/blob/main/LICENSE
https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model#why-is-it-called-tangles-model
Readme https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model#readme-ov-file
MIT license https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model#MIT-1-ov-file
Please reload this pagehttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model
Activityhttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/activity
Custom propertieshttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/custom-properties
1 starhttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/stargazers
1 watchinghttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/watchers
0 forkshttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/forks
Report repository https://patch-diff.githubusercontent.com/contact/report-content?content_url=https%3A%2F%2Fgithub.com%2FGallowayLabMIT%2Ftangles_model&report=GallowayLabMIT+%28user%29
Releases 2https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/releases
Pre-publication version Latest Sep 6, 2022 https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/releases/tag/pre_article_doi
+ 1 releasehttps://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/releases
Jupyter Notebook 47.1% https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/search?l=jupyter-notebook
TeX 25.2% https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/search?l=tex
Julia 16.6% https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/search?l=julia
Wolfram Language 9.7% https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/search?l=wolfram-language
Python 1.1% https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/search?l=python
Shell 0.3% https://patch-diff.githubusercontent.com/GallowayLabMIT/tangles_model/search?l=shell
https://github.com
Termshttps://docs.github.com/site-policy/github-terms/github-terms-of-service
Privacyhttps://docs.github.com/site-policy/privacy-policies/github-privacy-statement
Securityhttps://github.com/security
Statushttps://www.githubstatus.com/
Communityhttps://github.community/
Docshttps://docs.github.com/
Contacthttps://support.github.com?tags=dotcom-footer

Viewport: width=device-width


URLs of crawlers that visited me.