BioInfoSummer 2019

With half my home state on fire and the lead up to Christmas, this post has been in the works for a few weeks. But here it is – better late than never! My brief recap of my recent adventure to BioInfoSummer 2019.

Conference details

Title: BioInfoSummer 2019

Date: December 2nd – 6th 2019

Location: University of Sydney, Australia

Overview:

BioInfoSummer brings together advanced undergraduate and postgraduate students, researchers and professionals from the mathematics, statistics, medical sciences and information technology disciplines. Attendees develop bioinformatics skills, national networks and employability. The central themes of the 2019 conference were Epigenetics/genomics, Single cell omics, Mass spec analytics and BioCAsia/precision medicine.

Overall thoughts and impressions

Of all the conference travel I have done this year, BioInfoSummer was the closest to home and the furthest from a normal conference. The wide applicability of omics techniques meant a broad spectrum of research topics presented by a diverse collection of researchers with a common love for data analysis. In addition, being targeted at students and early-career researchers meant the dynamic of the seminar sessions was quite different – an atmosphere in which students were comfortable asking questions and driving the discussion around world-leading best practices in the field of bioinformatics. This was supported by plentiful and generous travel scholarships boosting the participation of interstate early-career researchers.

Even though my research has been edging into bioinformatics for a little while, this was my first formal foray into the community. While I was a little anxious about being immersed in a new group of people, luckily bioinformaticians are a friendly bunch! This meant that the workshops had a welcoming feel, creating a safe space to actively try out the techniques presented during the morning symposium sessions.

Last but not least, the location and timing of BioInfoSummer meant that they were able to share sessions and speakers with BioC Asia, and were followed directly by ABACBS Annual Conference. This enriched the sessions and provided even greater diversity and networking opportunities. This truly was a fantastic blend representative of the bioinformatics scene in Australia. I cannot recommend enough for new PhD students or post-doctoral researchers new to bioinformatics in it’s many incarnations.

Lessions learnt

1. Bioinformatic techniques for proteomic analyses lags behind the trail blazed by genomics – this was evident in the distribution of the program, but also attendees. However, I also think that…

2. The distinction between proteomics and genomics is sometimes unhelpful – similar underlying data structures make some methods applicable to both, and leveraging the substantial ground that has been covered in genomics will assist in the rapid progression and development of proteomics methods.

3. Single cells are the future, but not the complete story – innovations in single-cell proteomics and ongoing developments in single-cell RNAseq will continue to push the boundaries of our understanding of biology on the smallest scales. However, one of my favourite talks of the conference was on the value of bulk methods in an era of single-cell capabilities. And I agree – these methods should be applied as appropriate and often one and inform the other.

4. Seeing is believing – two-dimensional imaging mass spec and spatial transcriptomics are the next frontier. With these techniques, we are starting to understand the spatial distribution and cooperation of cells in health and disease.

5. The future is now – the big data buzzword – everyone will have heard the term big data. This is becoming more the norm than the exception, even in biological research. This has meant that method development and bioinformaticians are in high demand, and become recognised as an integral part to any research project. This was exemplified by one of the conference keynotes, in which the speaker discussed the essential skills for a bioinformatician in the next five years; many of these included the ability to wrangle, access and store large amounts of data, as well as being able to leverage this data for biological insight.

6. Unexpected acquaintances – I travelled to Sydney expecting to know no-one. In a classic small-science-world moment, within five minutes of arriving I ran into a post-doc from another research group in my building! While we had met and talked a little previously, the chance to spend a week nerding out over data analysis and coding methods was the perfect way to get to know each other better. In fact, this was one of the best parts of the conference. As well as this, I met a handful of people from my alma mata who grew up in a similar corner of the world as I did.

Take home resources

There were too many great resources to share them all, but if you’re looking for tutorial style activities then the Material for each of the BioCAsia workshops is a great place to start. Other than this, below are a few of the packages, tutorials or databases that I am keen to check out after hearing about them during the conference:

• RNAseq workshop
• AnVIL project‘s featured workspaces demonstrate common genomic analysis pipelines deployed using data and tools available on AnVIL.
• STEMFORMATICS is a portal to a series of public experiments describing mouse and human stem cells and how they differentiate to become mature cells, tissues and organs.
• Pyteomics is a collection of lightweight and handy tools for Python that help to handle various sorts of proteomics data.
• PaDuA: A Python Library for High-Throughput (Phospho)proteomics Data Analysis
• The PythonProteomics repository contains a list of open source Python tools for Proteomics analysis. The list is very likely incomplete and we are happy to take pull request with new tools.
• The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language.
• CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets

These will hopefully give you a flavour of the overall themes covered at the conference, but if you are new to the world of bioinformatics I thoroughly encourage you to get involved next year. The conference is slated to be held next December in Canberra, so keep an eye out for the official announcement!

Overall, BioInfoSummer was a great opportunity to connect and build community with like-minded people. I was so lucky to be supported by an AMSI ChooseMaths travel award – without their support, I could not have travelled to attend the conference and I cannot thank them enough for their support of Women in STEM. If you are new to or interested in the world of bioinformatics I whole-heartedly recommend checking it out next year!