Manubot - Manuscripts, open and automated

Manubot is a workflow and set of tools for the next generation of<br>scholarly publishing.<br>Write your manuscript in<br>markdown, track it with<br>git, automatically convert it to<br>.html, .pdf, or .docx, and deploy<br>it to your destination of choice.

Get Started

On GitHub

How It Works

input markdown

process w/ Manubot tools and<br>Pandoc

output .html, .pdf, .docx

test and deploy

The Best Parts

Open, collaborative, versioned

Author your manuscript the open-source way. Let anyone propose changes.<br>Iteratively<br>review, discuss, and refine with collaborators. Coordinate teams of<br>any size<br>with ease. Keep track of versions, to-dos, revisions, and who wrote what<br>and when. All in a<br>central location.

Automated and continuous

Never use a reference manager again. Provide a DOI, ISBN, PubMed ID,<br>URL, etc., and let Manubot generate and number citations for you. Choose<br>from thousands of existing<br>citation styles. See your manuscript update right away as you make changes. Test and<br>deploy automatically with<br>continuous integration.

Beautiful and interactive

Static is out, dynamic is in. The contemporary look and interactive<br>features people have come to love and expect from modern webpages, now<br>applied to scholarly articles: tooltips, public annotations, table of<br>contents, figure viewer, and more.

Free and open-source

There's no need to pay to produce brilliant manuscripts. Manubot is free<br>and open-source (aside from optional workflow integration with<br>GitHub and<br>Travis CI). Its tools are developed<br>and supported by a community of responsive and passionate software<br>developers and researchers.

Made With Manubot

The probability of edge existence due to node degree: a baseline for network-based predictions

From the retina to action: Dynamics of predictive processing in the visual system

Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager

Genotyping structural variants in pangenome graphs using the vg toolkit

The people of the 24ᵗʰ annual Pacific Symposium on Biocomputing in Hawaii

Two real use cases of FAIR maturity indicators in the life sciences

Bitcoin: A Peer-to-Peer Electronic Cash System

Introducing yt 4.0: Analysis and Visualization of Volumetric Data

Edit me to practice contributing to a collaborative Manubot manuscript

SARS-CoV-2 and COVID-19: An Evolving Review of Diagnostics and Therapeutics

Widespread redundancy in -omics profiles of cancer mutation states

Packaging research artefacts with RO-Crate

Towards a pragmatic definition of cell type

Des illusions visuelles aux hallucinations: une porte sur la perception

Incorporating biological structure into machine learning models in biomedicine

Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative

Sci-Hub provides access to nearly all scholarly literature

The LOTUS Initiative for Open Knowledge Management in Natural Products Research

Analysis of science journalism reveals gender and regional disparities in coverage

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

Integrative Analytical and Computational Strategies for Qualitative and Semi-quantitative Plant Metabolome Characterization

Opportunities and obstacles for deep learning in biology and medicine [update in progress]

Analysis of scientific society-awarded honors reveals disparities

ANN: A platform to annotate text with Wikidata IDs

treeheatr: an R package for interpretable decision tree visualizations

Comparative analyses of two primate species diverged by more than 60 million years show different rates but similar distribution of genome-wide UV repair events

Expanding polygenic risk scores to include automatic genotype encodings and gene-gene interactions

Scaling tree-based automated machine learning to biomedical big data with a feature set selector

Plasmids for independently tunable, low-noise expression of two genes

Formes & perception

Morphofunctional changes at the active zone during synaptic vesicle exocytosis

Expanding a Database-derived Biomedical Knowledge Graph via Multi-relation Extraction from Biomedical Abstracts

Automated segmentation and description of the internal morphology of human permanent teeth by means of micro-CT

Ten Quick Tips for Deep Learning in Biology

sPlotOpen – An environmentally-balanced, open-access, global dataset of vegetation plots

Extension of Roles in the ChEBI Ontology

Open collaborative writing with Manubot

Collaborative Writing with Manubot

Sci-Hub proporciona acceso a casi toda la literatura académica

Systematic integration of biomedical knowledge prioritizes drugs for repurposing

Catalog

Our Philosophy

Manuscripts are the primary basis of scholarly communication, yet the<br>process of creating them has not kept in step with the advancement of<br>technology or the evolving best-practices of science.

Traditionally, authoring of manuscripts takes place in a...