Hi everyone,

The fifth session of 2021 will be on May 19th, join us from 5.30pm online! As usual, the meeting will be open for all to attend, and newcomers / beginners are very welcome.

Our online meetings are kindly being enabled by Red Hat. In order to join us you need to register with MeetUp.

Our speakers are Flic Anderson and Isabella Deutsch.

• Flic Anderson is a Research Assistant in Bioinformatics in the Wallace Lab (within the Institute for Cell Biology) at the University of Edinburgh. The Wallace Lab works to understand how translation works within cells (particularly of fungi) and what factors control and regulate protein synthesis. Flic is part of the development team for the ‘riboviz’ open source software package for processing and analysis of ribosome profiling data, working with colleagues from EPCC (University of Edinburgh) to make the codebase more robust & sustainable. With a background in Ecology and Botany (previously a Research Assistant at the Royal Botanic Garden Edinburgh), Flic has worked with a wide range of types of biological data using different software tools and programming languages (particularly R) for the last 8 years, and found herself drawn towards bioinformatics and research software engineering. Flic is a member of the Edinburgh Carpentries and a certified Carpentries instructor in foundational coding and data science skills for researchers.

• Isabella Deutsch is a PhD Student at the University of Edinburgh at the School of Mathematics focusing on Bayesian statistics. She gained degrees from the University of Vienna and the University of Oxford and collected ample work experience, from marketing to museum pedagogy. She co-founded of the Piscopia Initiative to encourage women and non-binary students to consider a PhD in mathematics and currently serves as a student trustee on the board of directors of Edinburgh University Students’ Association.

Putting the ‘viz’ back into ‘riboviz’: connecting Rmarkdown, Shiny and Nextflow

Flic Anderson

‘riboviz’ is an open source software package for processing and analysing ribosome profiling (RNA sequence) data. This talk will briefly cover the implementation of an Rmarkdown HTML output report and Shiny app for data visualisation of ribosome profiling datasets, added as part of development efforts to make riboviz more user-friendly and effective. Flic will describe the initial approach and pitfalls encountered while developing the new visualisation features, and discuss integrating the visualisation side of riboviz with the recently implemented workflow management system (Nextflow) riboviz has moved to. Including a short primer on what Workflow Management Systems such as Nextflow ‘do’ and why they’re useful for complex data pipelines, and details on how to get Rmarkdown HTML reports to play nicely as part of a Nextflow workflow.

The ABC of ABC: a handy guide to Approximate Bayesian Computation

Isabella Deutsch

The Guardian called Bayes’ Theorem “obscure”, but I find it rather neat! In this talk I will gently introduce you to Bayesian statistics, with its advantages and criticisms, and guide you towards the first steps in Bayesian data analysis using Approximate Bayesian Computation: what it is, how you program it from scratch in R, and how you can utilise it for your own work.

May 2021 meeting: the ABC of ABC + connecting Rmarkdown, Shiny and Nextflow

Our speakers are Flic Anderson and Isabella Deutsch.

See you there!

Federico Andreis