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.
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.
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.
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.
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.
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.
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.
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.
"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."
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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!
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.
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.
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.
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.
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.
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...