BDB-Lab March 2025 Updates
Extremely open science
Focus of the Quarter: #ExtremelyOpenScience
Our lab prioritises reproducible, high-quality open research. Thus, we embarked on a project called Extremely Open Science (EOS), where we openly work on a project.
What is Extremely Open Science?
Open science is about making the underlying data and analysis code that supports claims made in a published paper (ideally, an open access paper). Extremely open science (EOS) takes this a step further and is sharing the whole research process in real-time as it is being carried out rather than simply once the results are finished
The EOS project aims to allow anyone to observe, discuss, and learn about the science as it unfolds. We discuss and solve the problem entirely online in live streaming. We discuss results in a public mailing list that anyone can join or the public Discord channel. All code is on GitHub and all data will be publicly accessible. This includes code that gets abandoned, draft versions, buggy versions, everything…
Why #ExtremelyOpenScience?
There are multiple motivations behind this project. First, Luis wanted to keep some hands-on involvement in research to keep PI-disease at bay. Another reason is to demo the entire process of what we usually do from the root level. This is because often junior researchers only see the final polished products from established groups and may struggle with minor issues, not realising everyone must go through these challenges. So, we stream even when it means spending time fighting with Python versioning issues. Finally, we are really trying to solve some scientific problems related to how quality control of metagenome-assembled genomes, which is a long-time concern of ours.
Project Progress
In season 1, we discussed whether antibiotic resistance genes co-occur in genomes or metagenomes, and if it matters and what could be the implications of these.However, we did not reach a conclusion and a paper came out doing a lot of what we were thinking about, which everyone should read: Horvath et al., 2024.1
In season 2, we are investigating whether we can estimate the quality of an assembled genomes based on the number of apparent pseudogenes. You can watch recaps of season 2 here or explore more on GitHub.
Updates
People
Catarina Loureiro got a postdoc fellowship to join us and work on subspecies variation.
Talks and Conferences
Brett (Co-supervised by Luis with Ben Woodcroft) presented at Mobile Genetic Element Symposium (MGEAUS) 2025 held at La Trobe University Melbourne Campus.
An abstract by Alexandre and Luis was accepted for the International Conference on Environmental Applications of Advanced Oxidation Processes (EAAOP7)
Award and recognition
Vedanth’s microtalk on argNorm at mVIF won the award for Best MicroTalk.
Brett was awarded Best Student Speaker award for his talk at MGEAUS.
Kruthi got selected as Finance Manager for OneTRI Student Committee.
Luis has joined the ABABCS Executive Committee.
Software
argNorm received an update from version 0.6.0 (August 2024) to version 0.7.0 (March 2025) which includes numerous improvements such as support for both AMRFinderPlus v4.0.19 and v3.10.30, enhanced manual curation for many genes, and updated argNorm mappings for CARD and ARO v4.0.0.
SemiBin v2.2.0 released! Generally speaking, SemiBin v2.2.0 is more robust, will fail in fewer corner cases and will give you better error messages when it does.
Other
Xing-Ming Zhao visited us from Fudan University (Shanghai) in February.
We are looking for PhD students!
You can still watch the streams or the recap of season 1 here. All materials are stored on GitHub and are publicly available.