Testbed

Basic formatting

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

External link

Internal link

italic text

bold text

strike-through text

Text with extra blank lines above and below

• list item a
• list item b
• list item c

1. ordered list item 1
2. ordered list item 2
3. ordered list item 3

1. top level list item
   • nested list item
     1. even deeper nested list item

Plain image:

Heading 1

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Heading 2

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Heading 3

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Heading 4

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Heading 5

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Heading 6

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

It was the best of times it was the worst of times. It was the age of wisdom, it was the age of foolishness. It was the spring of hope, it was the winter of despair.

// some code with syntax highlighting
const popup = document.querySelector("#popup");
popup.style.width = "100%";
popup.innerText =
  "Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.";

This sentence has inline code, useful for making references to variables, packages, versions, etc. within a sentence.

Lorem ipsum dolor sit amet.

Consectetur adipiscing elit.

Sed do eiusmod tempor incididunt.

Jekyll Spaceship

$ a * b = c ^ b $

$ 2^{\frac{n-1}{3}} $

$ \int_a^b f(x)\,dx. $

Components

Section

Section, background

Section, dark=true

Section, background dark=true

Section, size=wide

Section, size=full w/ figure

Figure

Button

Icon

Lorem Ipsum Dolor

Feature

Title

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Title

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

List

List citations

2023

2022

2020

2019

2018

List projects

Cool Dataset a subtitle

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

resource

Cool Package a subtitle

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

resource

Cool Tutorial a subtitle

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

resource publication

Cool Web App a subtitle

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

software

Cool Web Server a subtitle

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

software

List team members

Jane Smith Principal Investigator University of Colorado

John Doe PhD Student

Sarah Johnson Lead Programmer

List blog posts

2023

Example post 3

John Doe PhD Student

February 23, 2023 November 13, 2024

biology medicine

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

2021

Example post 2

Jane Smith Principal Investigator University of Colorado

September 30, 2021 November 13, 2024

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

2019

Example post 1

Sarah Johnson Lead Programmer

January 07, 2019 November 13, 2024

biology medicine big-data

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Citation

Open collaborative writing with Manubot

Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter

PLOS Computational Biology  ·  04 Dec 2020  ·  doi:10.1371/journal.pcbi.1007128

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Manubot

Manuscript Source

Website

open-science collaboration

Card

A Large Card A cool card

A cool description

manual-tag

A Small Card A cool card

Lorem ipsum

manual-tag

Portrait

Jane Smith Principal Investigator University of Colorado

John Doe PhD Student

Manual name

Post Excerpt

Example post 1

Sarah Johnson Lead Programmer

January 07, 2019 November 13, 2024

biology medicine big-data

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Alert

Tags

Float

Figures

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

Code

const test = "Lorem ipsum dolor sit amet, consectetur adipiscing elit.";

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Nulla facilisi etiam dignissim diam quis. Id aliquet lectus proin nibh nisl condimentum id venenatis a. Tristique magna sit amet purus gravida quis blandit turpis cursus. Ultrices eros in cursus turpis massa tincidunt dui ut ornare. A cras semper auctor neque vitae tempus quam pellentesque nec. At tellus at urna condimentum mattis pellentesque. Ipsum consequat nisl vel pretium. Ultrices mi tempus imperdiet nulla malesuada pellentesque elit eget gravida. Integer vitae justo eget magna fermentum iaculis eu non diam. Mus mauris vitae ultricies leo integer malesuada nunc vel. Leo integer malesuada nunc vel risus. Ornare arcu odio ut sem nulla pharetra. Purus semper eget duis at tellus at urna condimentum. Enim neque volutpat ac tincidunt vitae semper quis lectus.

Grid

Regular

With Markdown images

Square

With figure components

Grid of citations

2023

The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species

Tim E Putman, Kevin Schaper, Nicolas Matentzoglu, Vincent P Rubinetti, Faisal S Alquaddoomi, …, Damian Smedley, Peter N Robinson, Christopher J Mungall, Melissa A Haendel, Monica C Munoz-Torres

Nucleic Acids Research  ·  24 Nov 2023  ·  doi:10.1093/nar/gkad1082

Integration of 168,000 samples reveals global patterns of the human gut microbiome

Richard J. Abdill, Samantha P. Graham, Vincent Rubinetti, Frank W. Albert, Casey S. Greene, Sean Davis, Ran Blekhman

Cold Spring Harbor Laboratory  ·  11 Oct 2023  ·  doi:10.1101/2023.10.11.560955

MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes

Ricardo Avila, Vincent Rubinetti, Xinghua Zhou, Dongbo Hu, Zhongchao Qian, Marco Alvarado Cano, Everaldo Rodolpho, Ginger Tsueng, Casey Greene, Chunlei Wu

Nucleic Acids Research  ·  18 Apr 2023  ·  doi:10.1093/nar/gkad289

Hetnet connectivity search provides rapid insights into how two biomedical entities are related

Daniel S. Himmelstein, Michael Zietz, Vincent Rubinetti, Kyle Kloster, Benjamin J. Heil, …, David N. Nicholson, Yun Hao, Blair D. Sullivan, Michael W. Nagle, Casey S. Greene

Cold Spring Harbor Laboratory  ·  07 Jan 2023  ·  doi:10.1101/2023.01.05.522941

2022

Hetnet connectivity search provides rapid insights into how biomedical entities are related

Daniel S Himmelstein, Michael Zietz, Vincent Rubinetti, Kyle Kloster, Benjamin J Heil, …, David N Nicholson, Yun Hao, Blair D Sullivan, Michael W Nagle, Casey S Greene

GigaScience  ·  28 Dec 2022  ·  doi:10.1093/gigascience/giad047

MolEvolvR: A web-app for characterizing proteins using molecular evolution and phylogeny

Jacob D Krol, Joseph T Burke, Samuel Z Chen, Lo M Sosinski, Faisal S Alquaddoomi, …, Vincent P Rubinetti, Shaddai Amolitos, Kellen M Reason, John B Johnston, Janani Ravi

Cold Spring Harbor Laboratory  ·  22 Feb 2022  ·  doi:10.1101/2022.02.18.461833

2020

Open collaborative writing with Manubot

Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter

PLOS Computational Biology  ·  04 Dec 2020  ·  doi:10.1371/journal.pcbi.1007128

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Manubot

Manuscript Source

Website

open-science collaboration

Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations

Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene

Genome Biology  ·  11 May 2020  ·  doi:10.1186/s13059-020-02021-3

Constructing knowledge graphs and their biomedical applications

David N. Nicholson, Casey S. Greene

Computational and Structural Biotechnology Journal  ·  01 Jan 2020  ·  doi:10.1016/j.csbj.2020.05.017

2019

Sequential compression of gene expression across dimensionalities and methods reveals no single best method or dimensionality

Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene

Cold Spring Harbor Laboratory  ·  11 Mar 2019  ·  doi:10.1101/573782

2018

Sci-Hub provides access to nearly all scholarly literature

Daniel S Himmelstein, Ariel Rodriguez Romero, Jacob G Levernier, Thomas Anthony Munro, Stephen Reid McLaughlin, Bastian Greshake Tzovaras, Casey S Greene

eLife  ·  01 Mar 2018  ·  doi:10.7554/eLife.32822

Grid of blog posts

2023

Example post 3

John Doe PhD Student

February 23, 2023 November 13, 2024

biology medicine

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

2021

Example post 2

Jane Smith Principal Investigator University of Colorado

September 30, 2021 November 13, 2024

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

2019

Example post 1

Sarah Johnson Lead Programmer

January 07, 2019 November 13, 2024

biology medicine big-data

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Cols

Text

Images

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Code

const test = "Lorem ipsum dolor sit amet";

const test = "Lorem ipsum dolor sit amet";

const test = "Lorem ipsum dolor sit amet";

Search

Site Search