Blog · Stencila

A web-native approach to open source scientific publishing

The open access eLife journal introduces Executable Research Articles, enabling authors to publish more transparent, interactive, and reproducible research.

Opensource.com, Giuliano Maciocci, Nokome Bentley · Nov 7, 2020
Contribute to Stencila during Hacktoberfest 2020

We welcome you to contribute to Stencila's multiple open-source projects, and in return get a limited edition T-shirt or plant a tree.

Colette Doughty · Sep 27, 2020
Extensions to Schema.org for structured, semantic & executable research documents

As we near a v1.0 release, Nokome Bentley presented and asked for feedback on, the current state of Stencila Schema. View the recording hosted on Thursday 24 September.

Colette Doughty · Sep 20, 2020
The new age of preprints: enhanced, reproducible, and reusable

In the era of Covid-19, life science and medical preprint submission has been rapidly rising. At the same time, more preprint sites and related services are appearing that could help preprints quickly evolve to be the dynamic, evolving story of research that journal articles have failed to realize.

Stratos - Strategies for Open Science · Sep 9, 2020
SORSE event - Executable Research Article: Enrich a research paper with code and data

View the recording of Dr. Emmy Tang & Alex Ketchakmadze contributing to the International Series of Online Research Software Events (SORSE) on Wed 9 Sept 2020.

Dr. Emmy Tang (eLife UK) and Alex Ketchakmadze (Stencila) · Sep 9, 2020
Welcome to a new ERA of reproducible publishing

New open-source technology lets eLife authors publish Executable Research Articles that treat live code and data as first-class citizens.

Emmy Tsang and Giuliano Maciocci from eLife · Aug 27, 2020
Creating an Executable Research Article

Enjoy the webinar recording to find out how you could enhance your paper published with eLife.

Emmy Tsang (eLife) & Alex Ketchakmadze (Stencila) · Aug 24, 2020
Launch of the Executable Research Article project

In partnership with eLife, we are excited to announce the launch of the Executable Research Article (ERA) project. ERA allows authors to publish interactive, reproducible and semantic research articles from existing formats such as R Markdown and Jupyter Notebooks.

Nokome Bentley, Alexander Ketchakmadze, Colette Doughty · Aug 24, 2020
Stencila Community Call, 4 September 2019

Read a recap of our September community call.

Jacqueline Wijaya · Sep 4, 2019
Stencila Community Call, 4 July 2019

Join the Stencila community call on July 4th (or 3rd for most time zones!) at 6am NZST (see the blog post to find out the exact time for your time zone). During the call Stencila team members will present some of their recent work, and will be happy to answer any questions you may have.

Jacqueline Wijaya · Jul 1, 2019
From blobs to trees: semantic code analysis

We do semantic analysis of code for cell dependency analysis and package requirement analysis. In this post, I take Github's Semantic, a cross-language tool for semantic analysis of code, for a test drive.

Nokome Bentley · Jun 19, 2019
Stencila Community Call, 4 June 2019

We would like to invite you to our Stencila community call on June 4th (or 3rd for most time zones!) at 8am NZST (see the blog post to find out the exact time for your time zone). During the call Stencila team members will present some of their recent work, and will be happy to answer any questions you may have.

Jacqueline Wijaya · May 28, 2019
Stencila Design Updates and csv,conf,v4

Learn about our recent UX explorations on Stencila Hub. Also, Jacqueline was at csv,conf,v4!

Jacqueline Wijaya · May 17, 2019
Stencila Community Call, 7 May 2019

We would like to invite you to Stencila Community Call on 7th May (or 6th for most time zones!) at 8am NZT (see the blog post to find out the exact time for your time zone). During the call Stencila team members will present some of their recent work and we are happy to answer any questions that you may have.

Aleksandra Pawlik · May 4, 2019
Stencila Hub Enhancements for April 2019

We're always working to improve the user experience on the Stencila Hub, with enhancements and new features driven by user engagement. The April 2019 update contains fixes to reliabilty and tweaked styles.

Ben Shaw · Apr 30, 2019
Stencila Team Meet

2 weeks, 1.3 kg of coffee beans, 1 bag of pineapple lumps and dozens of dusky dolphins. This is a short summary of the first Stencila Team Meet which took place in Aotearoa - New Zealand at the end of March and early April.

Aleksandra Pawlik · Apr 25, 2019
Consistent Versioning and Deployment of Django and Express

As Stencila grows, we need to make sure our release processes scale along with it. This post discusses how we implemented a consistent versioning and tagging interface for both Django and Express, to simplify the release process for developers.

Ben Shaw · Apr 17, 2019
Alex Ketchakmadze joins Stencila

We are happy to introduce Alex Ketchakmadze who joined Stencila in March 2019 as a Designer and a Software Engineer. Alex is determined to help make Stencila accessible and delightful for researchers of all technical backgrounds.

Aleksandra Pawlik · Apr 10, 2019
Jacqueline Wijaya joins Stencila

We are happy to introduce Jacqueline Wijaya who joined Stencila in March 2019 as a Product Designer. At Stencila Jacqueline is specifically interested in the task of developing open-source tools and growing a community around them.

Aleksandra Pawlik · Mar 12, 2019
Introducing Ben Shaw

We are happy to introduce Ben Shaw, Stencila's Senior Software Engineer. Ben has started working with Stencila first as a contractor and then he moved to the full time role. Ben's technical skills range across a number of topics from web development and design to low level programming and system design. He also brings in experience in team leading, mentorship and project management.

Aleksandra Pawlik · Mar 7, 2019
Learning Docker through Dockter

"A short summary of my, somewhat painful, route to discovering that what I thought I knew about Docker was in fact just the tip of the iceberg. Fortunately, I was able to upgrade my understanding through testing and using a new tool we have been developing: Dockter, a container image builder for researchers."

Aleksandra Pawlik · Mar 5, 2019
Stencila Hub Enhancements for February 2019

We're always working to improve the user experience on the Stencila Hub, with enhancements and new features driven by user engagement. The February 2019 update contains details on changes to linked sources, project archiving and the permissions system.

Ben Shaw · Feb 25, 2019
Stencila contributes to eLife’s first computationally reproducible article

We are very excited to be a part of the Reproducible Document Stack (RDS) project led by eLife Innovation. This open-source technology enables researchers to publish reproducible manuscripts through online journals.

Giuliano Maciocci, Michael Aufreiter and Nokome Bentley · Feb 20, 2019
Using JSON Schema for developing and validating executable documents

We're representing executable documents as a tree of JSON data and using [JSON Schema](https://json-schema.org/) to specify and validate their structure. In this post I introduce some of the development tools and techniques we are using based on JSON Schema and some of the other benefits that flow from this approach.

Nokome Bentley · Feb 18, 2019
Stencila at Linux Conf AU 2019

The end of January 2019 has been really busy for us. We attended the 2019 linux.conf.au conference which took place in Christchurch, Aotearoa - New Zealand. This year's theme was Linux of Things and we run a Stencila tutorial on one of our recently developed components called Dockter for easing the process of building Dockter images for reproducible research.

Aleksandra Pawlik, Nokome Bentley · Feb 1, 2019
Integrating Binder and Stencila

Binder has now first class Stencila support. You can launch any Stencila project directly in Binder. This blog post tells the whole story.

Daniel Nüst, Institute for Geoinformatics at the University of Münster, Germany · Nov 20, 2018
Further funding from the Alfred P. Sloan Foundation!

We are pleased to announce that Stencila has received further funding from the Alfred P. Sloan Foundation. The Foundation funded initial development of Stencila in 2017 and their ongoing support has enabled us to develop the underlying architecture, implement and user test initial versions, engage with research communities, and develop strategies for long-term sustainability.

Aleksandra Pawlik, Nokome Bentley and Danielle Robinson · Nov 7, 2018
What we've been up to

It's been a quiet few weeks on our blog but very busy time at Stencila. We have been working on further development of Stencila Hub which allows for easy collaboration and sharing of Stencila projects.

Aleksandra Pawlik · Sep 21, 2018
Bringing it together - summarising feedback from recent user workshops

Between end of June and beginning of August 2018 we ran 4 hands-on workshops to collect feedback from researchers trying out Stencila on real life tasks. In this blog post we present the summary of the feedback we received and the lessons learned.

Aleksandra Pawlik & Nokome Bentley · Aug 13, 2018
Stencila workshop at SIGNAL ITC Grad School

After runnning 3 workshops focusing on introduction to R with Stencila we switched to Python. On 6th August we run a hands-on workshop at SIGNAL ICT Grad School at Christchurch, New Zealand.

Aleksandra Pawlik · Aug 11, 2018
Stencila workshop at the University of Canterbury

The series of our user workshops continued with the event organised at the University of Canterbury in New Zealand. Thanks to the support from the University Library Services we taught some basics of data manipulation with R on 24th July.

Aleksandra Pawlik · Aug 10, 2018
Stencila workshop at the Bioluminescent Superbugs Lab

On 12th and 13th July we run our second workshop "Introduction to R using Stencila". The participants were researchers from the the Bioluminescent Superbugs Lab at the University of Auckland.

Aleksandra Pawlik · Jul 25, 2018
eLife Stencila – an office suite for reproducible research

eLife Sciences published our article introducing Stencila. We are reposting it on our blog.

Michael Aufreiter, Aleksandra Pawlik, Nokome Bentley · Jul 3, 2018
Stencila workshop at the University of Otago Medical School

Last week, on 28th and 29th June, we run the first "Introduction to R using Stencila" workshop. The event was attended by the researchers from the University of Otago Medical School at Christchurch, New Zealand. We used Stencila Hub so that the participants did not have to install anything on their machines. Guided by the Data Carpentry materials we taught filtering and visualising data with the tidyverse R package.

Aleksandra Pawlik · Jun 2, 2018
Stencila at Open Neuroscience

Nokome Bentley joined the Open Neuroscience meeting hosted at Sainsbury Wellcome Centre in London to discuss open science workflows.

Aleksandra Pawlik · May 27, 2018
Custom functions in Stencila

This post describes a solution to allow for custom user functions.

Oliver Buchtala · May 17, 2018
Stencila in Binder

At the recent eLife sprint in Cambridge Daniel Nüst and Min Ragan-Kelley had chosen to do a project involving Stencila. Nokome Bentley joined them remotely and as a result you can now run Stencila projects on Binder connecting to a Jupyter kernel.

Aleksandra Pawlik · May 11, 2018
Stickers!

Stencila stickers have arrived! Yes to sticker madness!

Aleksandra Pawlik · May 2, 2018
Aleksandra Pawlik joins Stencila Team

We have a new addition to our team! Aleksandra Pawlik joined Stencila in April 2018 as the Community Advocate. Her role will focus on understanding users’ needs to direct Stencila further development, building open source developer community and keeping you all updated on what goes on with Stencila.

Aleksandra Pawlik · Apr 12, 2018
Reproducible Document Stack: development update community call

Get a demo of the latest developments with Stencila from Michael and Oliver during today's Reproducible Document Stack community call!

Nokome Bentley · Jan 25, 2018
Roadtrip Roundup! What we learned from 5 weeks on the Roadtrip

After five weeks of travel, including multiple user workshops, conferences and meetups we’ve been synthesizing all the ideas and feedback generated by the community. We held six workshops on features for Stencila Sheets. Here is the summary of the outcomes.

Danielle Robinson · Dec 1, 2017
Stencila at UC Berkeley

The University of California Berkeley (UCB) was the setting for the fourth workshop on Stencila Sheets. A big thank you to Amy Neeser and John Chodaki for helping us organise the event. We had a great group come along including people from Berkeley Initiative for Transparency in the Social Sciences, California Digital Library, D-lab, University of California Press and Open Humans.

Nokome Bentley · Nov 16, 2017
Stencila in Portland, Oregon

Stencila's visit to Portland, Oregon began with a day at the Oregon Health and Science University (OHSU) Data Science Institute. We hosted out third workshop on this Roadshow at the very cool looking OHSU Collaborative Life Sciences Building. We also had a chance to see the beautiful Japanese Gardens.

Nokome Bentley · Nov 14, 2017
Stencila at the University of Oregon

Stencila visited the University of Oregon. We met up with the Data Services staff and had a peek look into the Research Library. Our workshop brought us a lot of useful feedback, with particular focus on Stencila Sheets.

Danielle Robinson · Nov 8, 2017
Stencila in the Big Apple

Last week Stencila had some busy time in New York City. Alfred P. Sloan Foundation hosted our first user feedback sessions. We visited ProPublica and had a number of fruitful discussions. Here are the details.

Danielle Robinson · Nov 7, 2017
Stencila world tour at Mozfest, eLife and Cambridge

Stencila started its 2017 roadtrip by attending several events and meetings in the U.K. We joined open source, knowledge and science communities at MozFest in London. Nokome Bentley presented Stencila to the eLife Open Science Soapbox group. We met with eLife in Cambridge. Here are all the details.

Danielle Robinson · Nov 2, 2017
Toads in Vancouver - using Stencila to teach SQL and R at UBC

Earlier this year, we connected with Giulio Valentino Dalla Riva, a data scientist based at the Master of Data Science programme at the University of British Columbia. Giulio was interested in piloting Stencila in one of his fall courses on Data Management for Business Analytics, a course for Master’s level business students at the UBC’s Sauder School of Business.

Danielle Robinson · Oct 3, 2017
A feature list for Stencila Sheets

Stencila Sheets development is under way and we need you to tell us which features are the most important and useful for you. We have listed 8 of those that already been suggested to us and would like to hear from a wider forum about your opinions and preferences. Have your say!

Nokome Bentley · Aug 20, 2017
Shrinking Stencila’s Docker images with strace

Docker containers are a useful way to manage dependencies - especially when your application has a lot of them. However, the down side is that those comprehensive images can get quite large. We used the strace tool to shrink Stencila images and make them easier and faster to deploy.

Finlay Thompson · Jul 28, 2017
We’re sponsoring C4RR!

Stencila is proud to be sponsoring the Docker Containers for Reproducible Research Workshop1 (C4RR)! C4RR is organised by the Software Sustainability Institute in the UK. The event brings together researchers, developers and educators to explore best practices when using containers, not only Docker, and the future of research software with containers.

Nokome Bentley · Jul 1, 2017
Funding from the Alfred P. Sloan Foundation to develop Stencila Sheets

Stencila has received funding from the Alfred P. Sloan Foundation to develop Stencila Sheets as an open and reproducible alternative to existing spreadsheet software in research.

Nokome Bentley · Apr 28, 2017
Thanks Coko!

A big thank you to our friends at the Collaborative Knowledge Foundation.

Nokome Bentley · Apr 2, 2017
Development update: a fresh start for Stencila Documents

A quick preview of the new editor for Stencila Documents

Michael Aufreiter, Nokome Bentley, Oliver Buchtala · Mar 6, 2017
Development update: Javascript execution contexts and Markdown extensions for interactive documents

On Node.js-like Javascript execution within documents, Markdown extensions for inputting and outputting document variables, and a little demo of how they can all be put together in a reactive document.

Nokome Bentley · Jan 13, 2017
On chunks, cells, beakers and functions: models for data driven content

In this post, I'm going to look at the models for data driven content used in popular tools for reproducible documents, RMarkdown and Jupyter. We'll then look at how to extend those models to documents that generate content in more than one execution context. I'll then wrap up with an explanation of the model that I've arrived at as being the best fit for Stencila.

Nokome Bentley · Dec 20, 2016
Diverse peers

How Stencila packages act as a network of diverse peers with differing capabilities and calling on each other to provide resources.

Nokome Bentley · Dec 5, 2016
Monolithic island to connected archipelago

Development update. How and why we decoupled Stencila's architecture to take it from a monolithic island to a connected archipelago.

Nokome Bentley · Nov 30, 2016
Easy ain't easy but it's getting easier.

How do we make it easy for researchers to use tools for reproducible research?

Nokome Bentley · Nov 24, 2016
Stencila blog reincarnated

Your own dog food can be hard to swallow sometimes. Particularly when you have just finished the strenuous task of pulling yourself up by your own boot straps. Our new blog uses Markdown and is published on Github pages. We're still eating our own dog food by using our Node.js package and by using our new document editor to author posts. But we're hoping that with this new approach there will be less friction in getting posts written and on to the web.

Nokome Bentley · Nov 21, 2016
A spreadsheet file format for humans

Spreadsheets are reactive programming environments that are usually only interacted with via a visual grid interface. For most other programming environments, the primary interface is a text file format specifically designed for humans. In contrast, spreadsheet file formats have been designed for machines, not humans. This post proposes a human friendly format for spreadsheets that can be used as an alternative interface for viewing and editing spreadsheets.

Nokome Bentley · Apr 24, 2016
Getting under Stencila sheets

A follow up post to the [introduction to Stencila sheets](https://blog.stenci.la/introducing-sheets). More technical details on how they work and why they are different from traditional spreadsheets.

Nokome Bentley · Mar 17, 2016
Spreadsheets are dead, long live reactive programming environments!

In 1979, Dan Bricklin and Bob Frankston created VisiCalc the world's first spreadsheet software. VisiCalc was an immediate success, became the Apple II's "killer app" and was credited by Steve Jobs with propelling the first explosion in personal computing. Ted Nelson, an internet pioneer, described the paradigm shift that the spreadsheet interface created...

Nokome Bentley in collaboration with Oliver Buchtala and Micheal Aufreiter · Mar 15, 2016

A web-native approach to open source scientific publishing

Contribute to Stencila during Hacktoberfest 2020

Extensions to Schema.org for structured, semantic & executable research documents

The new age of preprints: enhanced, reproducible, and reusable

SORSE event - Executable Research Article: Enrich a research paper with code and data

Welcome to a new ERA of reproducible publishing

Creating an Executable Research Article

Launch of the Executable Research Article project

Stencila Community Call, 4 September 2019

Stencila Community Call, 4 July 2019

From blobs to trees: semantic code analysis

Stencila Community Call, 4 June 2019

Stencila Design Updates and csv,conf,v4

Stencila Community Call, 7 May 2019

Stencila Hub Enhancements for April 2019

Stencila Team Meet

Consistent Versioning and Deployment of Django and Express

Alex Ketchakmadze joins Stencila

Jacqueline Wijaya joins Stencila

Introducing Ben Shaw

Learning Docker through Dockter

Stencila Hub Enhancements for February 2019

Stencila contributes to eLife’s first computationally reproducible article

Using JSON Schema for developing and validating executable documents

Stencila at Linux Conf AU 2019

Integrating Binder and Stencila

Further funding from the Alfred P. Sloan Foundation!

What we've been up to

Bringing it together - summarising feedback from recent user workshops

Stencila workshop at SIGNAL ITC Grad School

Stencila workshop at the University of Canterbury

Stencila workshop at the Bioluminescent Superbugs Lab

eLife Stencila – an office suite for reproducible research

Stencila workshop at the University of Otago Medical School

Stencila at Open Neuroscience

Custom functions in Stencila

Stencila in Binder

Stickers!

Aleksandra Pawlik joins Stencila Team

Reproducible Document Stack: development update community call

Roadtrip Roundup! What we learned from 5 weeks on the Roadtrip

Stencila at UC Berkeley

Stencila in Portland, Oregon

Stencila at the University of Oregon

Stencila in the Big Apple

Stencila world tour at Mozfest, eLife and Cambridge

Toads in Vancouver - using Stencila to teach SQL and R at UBC

A feature list for Stencila Sheets

Shrinking Stencila’s Docker images with strace

We’re sponsoring C4RR!

Funding from the Alfred P. Sloan Foundation to develop Stencila Sheets

Thanks Coko!

Development update: a fresh start for Stencila Documents

Development update: Javascript execution contexts and Markdown extensions for interactive documents

On chunks, cells, beakers and functions: models for data driven content

Diverse peers

Monolithic island to connected archipelago

Easy ain't easy but it's getting easier.

Stencila blog reincarnated

A spreadsheet file format for humans

Getting under Stencila sheets

Spreadsheets are dead, long live reactive programming environments!