R Consortium talked to Bioconductor Asia co-organizer Matt Ritchie about the upcoming conference (BioC Asia 2021), how COVID has affected attendance at the conference, and how they deal with multilingualism at their meetings.
RC: What is the R community like for Bioconductor Asia?
In terms of other Bioconductor groups, such as Europe and America, Bioconductor Asia is quite small. We are building up, and are grateful to receive R Consortium support for our event. The first BioC Asia was held in 2015 as a satellite of the GIW/InCoB meeting in Japan. The program included a workshop day, followed by a mini-conference where people could learn about Bioconductor and present their research. Martin Morgan (project lead at the time) gave a talk and an introductory workshop on Bioconductor to around 30 participants. In the following years, we organized our meetings as satellite events to the larger ABACBS annual conference in Australia (Brisbane 2016, Adelaide 2017, Melbourne 2018 and Sydney 2019). In 2020, we were planning an in-person meeting in China hosted by Tsinghua University and were expecting a large audience of around 200 attendees. Oddly, after we went digital we ended up having 400 registrants. Thanks to the generous support of our sponsors, BioC Asia 2020 offered free registration and more people could participate in the workshops than ever before. In 2021, we will again run our event virtually, with lead organizer Kozo Nishida from RIKEN in Japan. We are also keen to have conferences in other countries. Last year we had several people from South Korea attend, so maybe future BioC Asia events can be hosted virtually (or in person) by South Korean researchers.
RC: How has COVID affected your ability to connect with members?
We canceled the in-person conference and went virtual. Zoom was the main tool that we use to communicate, and we set up a #biocasia2020 channel on the Bioconductor community slack for further discussion. Because of the virtual conference we were able to increase attendees in the workshops, where we had more people possible for virtual than in person (100 plus people online versus 30 or so for in person workshops, often limited due to physical restrictions of space). For the conference, we used the Orchestra platform that Sean Davis developed for running workshops in the cloud. We recently used this platform to run virtual training in Africa, so it’s been well tested now in different parts of the world and can scale up or down very easily. We are likely to keep a hybrid option in the future as it is more accessible for students and people without a travel budget. We want our meetings to be as accessible as possible. It’s also nice to have a meeting in your general time zone as opposed to one that is scheduled for when you were hoping to be asleep, which is often the case for meetings based around other time zones.
RC: Can you tell us about one recent presentation or speaker that was especially interesting and what was the topic and why was it so interesting?
I enjoyed the presentation by Koki Tsuyuzaki on tensor decomposition and the work that has gone into applying this approach to single-cell data analysis in the scTensor package (a video of this presentation is available from the Bioconductor YouTube channel). F1000Research, who also sponsored our meeting, hosted the slides from this presentation which were accessible before and after the talk so people could easily follow along at home. F1000Research also allows hosting of poster presentations, which is great for virtual poster sessions.
RC: What trends do you see in R language affecting your organization over the next year?
The growing influence that the tidyverse is having on the Bioconductor project, with software such as tidyBulk and plyranges applying these principles to genomic data analysis. Both packages have been developed by researchers based in our region, and it will be exciting to see further applications in the future.
RC: Do you know of any data journalism efforts by your members? If not, are there particular data journalism projects that you’ve seen in the last year that you feel had a positive impact on society?
Although not directly related to Bioconductor, the work led by Rafael Irizarry that I saw presented at an AMSI Bioinfosummer public lecture in 2019 on estimating the number of excess deaths in Puerto Rico in the aftermath of Hurricane Maria (bioRxiv preprint here and news story here) is very inspiring. They modeled data to look at excess deaths and found that the government reported figures grossly underestimated the real impact of the disaster, which lasted long after the Hurricane had ended.
RC: When is your next event? Please give details!
BioC Asia 2021 will be held Nov 1-4 as a virtual event. The lead organizer is Kozo Nishida from RIKEN, who represents our region on the Bioconductor Community Advisory Board. This is the second time the event is hosted in Japan, albeit virtually this time around.
RC: Of the Funded Projects by the R Consortium, do you have a favorite project? Why is it your favorite?
An early one funded in the 2016 round: ‘Software Carpentry R Instructor Training’ by Dr Laurent Gatto was a really valuable contribution for teaching countless people how to use R. Software carpentry is an amazing platform for onboarding new users, and Laurent and colleagues are currently planning a new curriculum that introduces the world of Bioconductor using this approach.
RC: Of the Active Working Groups, which is your favorite? Why is it your favorite?
R / Medicine, as a lot of Bioconductor tools are used in clinical research and there is a lot of interest in Bioconductor from that sector. R / Medicine has an annual conference that will be held virtually this year on August 24-27th.
RC: There are four projects that are R Consortium Top Level Projects. If you could add another project to this list for guaranteed funding for 3 years and a voting seat on the ISC, which project would you add?
More support for teaching R in other Languages would be great for our work. At BioC Asia 2020 we ran workshops in Mandarin which proved very popular. We have also published RNA-seq analysis workflows in English and Chinese. It would be great to see more multilingual vignettes and workflows so that people can learn about different packages in whatever language suits them best. We are looking at redeveloping the Bioconductor website and aim to have key landing pages and training material translated into different languages. Adding closed captioning in English to talks can also improve accessibility.
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