tyson-swetnam / circos-binder

Run Circos software in a Jupyter environment served by MyBinder.org.

circos-binder

tl;dr:
Click any launch Circos on Jupyter badge on this page to run Circos inside your browser.

Alternatively, use Cyverse with the launch vice badge under Running Circos on CyVerse/VICE below.

---

Circos is a software package for visualizing data and information that was created by Martin Krzywinski.

This repository enables running Circos software in a Jupyter notebook envrionment served to your broswer via the Binder system deployed at MyBinder.org.

Launch and run the notebooks via Binder by clicking any badge anywhere on this page.
Alternatively, use Cyverse with the launch vice badge under Running Circos on CyVerse/VICE below.
An active notebook session will be spun up just for you in a process that generally only takes a few seconds. Subsequently, you can follow the steps detailed in the included notebooks to run Circos. Tutorials paralleling those at the main site are included as Jupyter notebooks that can be run actively in the launched session. (The Circos tutorial-associated archive is already included in the launched environment.)

Resources

• See 'Getting Started with Circos' from the official Circos source and documentation site.

• A nice introduction to Circos, entitled 'Making genomic data come alive with circos plots'

• Introduction to Circos with details/examples and terminology explanations for genomics use

• My collection of Circos-related utility scripts (Python)

  • UCSC_chrom_sizes_2_circos_karyotype.py UCSC chrom.sizes files --> karyotype.tab file for use in Circos

Attribution

This repository was set up to take advantage of the Binder system to offer a resource to run Martin Krzywinski's Circos software without the user needing to download, install, or maintain any software. See here for documentation about Binder as deployed at MyBinder.org.

Remember, if you are using Circos, Martin Krzywinski and colleagues request you please cite:
Krzywinski, M. et al. Circos: an Information Aesthetic for Comparative Genomics. Genome Res (2009) 19:1639-1645. Download the citation here.

Running Circos on CyVerse/VICE

The VICE (Visual Interactive Computing Environment) in the CyVerse Discovery Environment enables users to run Jupyter Lab in a more powerful and more persistent environment. To use VICE, sign up for a free NSF-supported CyVerse account.

The VICE environment supports large-scale analyses. Users can upload and download files, and save and share results of their analyses in their user accounts.

Follow these steps to run Jupyter Lab on VICE

Location of tutorial notebooks

If you are interested in the accompanying tutorial-like notebooks that you see in the sessions launched from here, the code for them is available outside of the active Jupyter session at this repository here. In an effort to streamline development, they have been moved there. Importantly, that allows the version of the Circos software to remain 'locked' in the Cyverse app, yet allow me to improve the accompanying material. This also has the effect that the MyBinder-served core image doesn't need building often.

---

Click the badge below to get started (or see the Cyverse section if you prefer to use it there):