Progress report for Sheffield
Tania Allard and Michael Croucher
Reporting period from March 2017 to January 2018
Finance and administration
- Supported a number of lecturers in Sheffield to migrate to Jupyter and CoCalc (formerly SageMathCloud). Also, provided continued support to those that had already been using CoCalc and Jupyter notebooks for their courses. These included lecturers from Computer Science, Physics, Biomedical Science, Bioinformatics, and Materials Science. (D2.17, T2.6)
- The previously generated CoCalc tutorial was extended by adding tutorial sections for students having courses in CoCalc as well as with a hands-on tutorial for lecturers to get started. The material can be found as a website at https://tutorial.cocalc.com/ (The repository for this is located at:https://github.com/sagemathinc/cocalc_tutorial) (D2.17, T2.6).
- Developed a Jekyll template for use by academics and researchers using Jupyter notebooks for course materials and dissemination. This will allow them to easily produce course websites based on Jupyter notebooks connected to cloud computing resources such as Microsoft Azure Notebooks (D2.17, T2.6).
- Developed a Python package: nbjekyll that complements the Jekyll template developed . This package converts Jupyter notebooks into .md files that can be readily usable by Jekyll. It also uses nbval to perform notebook validation and add custom headers indicating the last update date, version and test status of the notebook (D2.17, T2.6).
Work in progress
- Involvement in the Sheffield Machine Learning Network: working with the Machine Learning group at Sheffield to leverage the use of Jupyter notebooks and related technologies (e.g. code cafe, coding dojos) (T2.3)
- Creation of an online journal based on Jupyter notebook submissions and with a content review performed in GitHub (the first volume will be generated from a sprint/hackathon) (D2.17, T2.6, T2.3)
- In collaboration with Code FirstGirls: Development of a data analytics course for women and individuals that identify themselves as women (D2.17, T2.5).
- Workshop on reproducible workflows using the Jupyter notebooks (PyCon 2018).
Workshops and dissemination activities
- Developed and delivered a workshop on using Jupyter notebooks for reproducible research for the 2nd international Research Software Engineering conference. The workshop was one of the most popular across the entire conference and, as such, we were asked to deliver it twice in order to meet demand. Workshop materials at https://github.com/trallard/JNB_reproducible and blog post at RSE Sheffield blog which was reposted in the Software Carpentries Blog (D2.17, T2.6).
- Developed and delivered Bioinformatics Awareness Days https://github.com/trallard/BAD_days in Collaboration with Prof. Luisa Cutillo of Parthenope University of Naples (D2.17, T2.6).
- Developed training materials and provided training for over 95 women in the last 12 months at Sheffield and Manchester in partnership with CodeFirstGirls (D2.17, T2.6,T2.5).
- Participation in the Diversity and Inclusion in Scientific Computing unconference by direct invite of NUMFOCUS (T2.5).