The Washington DC Walter E. Washington Convention Center was the venue for the recent Cell Bio 2022 Meeting that took place on 3-7 December 2022. Cell Bio 2022, the joint meeting of the American Society for Cell Biology (ASCB) and European Molecular Biology Organization (EMBO), is the largest yearly gathering for the Cell Biology community.

The fourth international Global Genome Biodiversity Network (GGBN) Conference took place in Aguascalientes, Mexico from October 17th to October 20th 2023 where it was hosted by the Universidad Autónoma de Aguascalientes.

The 12th international meeting on Visualizing Biological Data took place on March 16–18, 2022 (AKA VIZBI 2022). This conference is always a visual treat, and with its focus on transforming how Life Scientists view data from Molecular and Cellular Biology and Biomedical Science this year's event was no exception.

The increasingly multidisciplinary nature of scientific research necessitates a need for Open Data repositories that can archive data in support of publications in scientific journals. Recognising this need, even before GigaScience launched in 2012, GigaDB was already in place and taking data for a year before (making it 11 this year). Since GigaDB launched, there has been a consistent growth in this resource in terms of data volume, data discoverability and data re-use. In this commentary, we provide a retrospective of key changes over the last decade, and the role of Data Curation in enhancing the user experience. Furthermore we explore a much needed emphasis on enabling researchers to interact with and explore datasets prior to data download.

Background The spatio-temporal organisation of many biological processes such as gene-expression and neuronal activity is critical to understanding the overall biological behaviour, phenotype and disease. This is especially true during embryonic development. During development spatial patterns of gene expression are key to segmentation, tissue differentiation and organ development. In situ techniques can reveal the activity of genes and the presence of proteins to a very high sub-cellular resolution but typically at high resolution only a few probes can be used on any sample therefore to compare many such patterns requires mapping of image-based data to a standard spatial framework. Once mapped those data can be collated, queried and analysed in purely spatial terms to reveal unknown combinatorial gene-activity that could not be discovered any other way. Mapping spatial data to image domains with systematic variation in shape and pose, such as embryos or elongated organs, presents special problems. Automated techniques available for more constrained systems can not deliver the mapping fidelity required to analyse these data therefore we have developed a manual editing tool, WlzWarp, for mapping 3D image data using the constrained distance transform (CDT) which uniquely can deliver the complex transforms required. Results We have implemented a fully open-source tool (available on GitHub), WlzWarp to provide interactive complex spatial mapping of 3D image data. We have applied WlzWarp to map a set of gene-expression patterns in the developing mouse embryo that could not be mapped by any other technique. The transform procedure was tested by using multiple images of the same gene from independent samples and thereby testing the full end-to-end mapping process. WlzWarp is implemented in C++ using open-source packages Qt, Coin and SIMVoleon for cross-architecture compatibility. It has been developed under Linux but also tested on Mac OSX and MS Windows. Conclusions WlzWarp is a freely available software tool for non-linear registration and alignment of complex 2D & 3D spatial patterns from one image to another or to an atlas model. It has been tested in the context of embryo data but can be used for any 3D or 2D image registration problem.

The International Neuroinformatics Coordinating Facility (INCF) had its annual Neuroinformatics Assembly from 12 th -16 th September 2022.

Wnt signalling controls patterning and differentiation across many tissues and organs of the developing embryo through temporally and spatially restricted expression of multi-gene families encoding ligands, receptors, pathway modulators and intracellular components. Here, we report an integrated analysis of key genes in the 3D space of the mouse embryo across multiple stages of development. We applied a method for 3D/3D image transformation to map all gene expression patterns to a single reference embryo for each stage, providing both visual analysis and volumetric mapping allowing computational methods to interrogate the combined expression patterns. We identify territories where multiple Wnt and Fzd genes are co-expressed and cross-compare all patterns, including all seven Wnt paralogous gene pairs. The comprehensive analysis revealed regions in the embryo where no Wnt or Fzd gene expression is detected, and where single Wnt genes are uniquely expressed. This work provides insight into a previously unappreciated level of organisation of expression patterns, as well as presenting a resource that can be utilised further by the research community for whole-system analysis.

Cell Bio 2020 Virtual – the online ASCB|EMBO Meeting – took place on 2-16 December 2020 and offered many invaluable insights on the structural and evolutionary basis of biological systems.

Congenital abnormalities of the kidney and urinary tract are among the most common birth defects, affecting 3% of newborns. The human kidney forms around a million nephrons from a pool of nephron progenitors over a 30-week period of development. To establish a framework for human nephrogenesis, we spatially resolved a stereotypical process by which equipotent nephron progenitors generate a nephron anlage, then applied data-driven approaches to construct three-dimensional protein maps on anatomical models of the nephrogenic program. Single-cell RNA sequencing identified progenitor states, which were spatially mapped to the nephron anatomy, enabling the generation of functional gene networks predicting interactions within and between nephron cell types. Network mining identified known developmental disease genes and predicted targets of interest. The spatially resolved nephrogenic program made available through the Human Nephrogenesis Atlas (https://sckidney.flatironinstitute.org/) will facilitate an understanding of kidney development and disease and enhance efforts to generate new kidney structures.

Advanced 3D imaging modalities, such as micro-computed tomography (micro-CT), have been incorporated into the high-throughput embryo pipeline of the International Mouse Phenotyping Consortium (IMPC). This project generates large volumes of raw data that cannot be immediately exploited without significant resources of personnel and expertise. Thus, rapid automated annotation is crucial to ensure that 3D imaging data can be integrated with other multi-dimensional phenotyping data. We present an automated computational mouse embryo phenotyping pipeline that harnesses the large amount of wild-type control data available in the IMPC embryo pipeline in order to address issues of low mutant sample number as well as incomplete penetrance and variable expressivity. We also investigate the effect of developmental substage on automated phenotyping results. Designed primarily for developmental biologists, our software performs image pre-processing, registration, statistical analysis and segmentation of embryo images. We also present a novel anatomical E14.5 embryo atlas average and, using it with LAMA, show that we can uncover known and novel dysmorphology from two IMPC knockout lines.

The dizzying complexity of biological systems necessitates an abundance of tools that allow researchers to understand the deluge of sequence, structural, and systems-level data that is being generated in cell, molecular, and developmental biology.

The National Academies of Sciences, Engineering, and Medicine (NASEM) hosted the two-day virtual workshop “Changing the Culture of Data Management and Sharing” on 28th-29th April 2021 to discuss the challenges and opportunities for establishing effective data management and sharing practices and exploring the question of universal availability of scientific data.

Intelligent Systems for Molecular Biology (ISMB) conference is an annual gathering for scientists from bioinformatics, molecular biology, and data science and provides a multidisciplinary environment for disseminating recent research and development in computational biology.

The International Neuroinformatics Coordinating Facility (INCF) hosted their Neuroinformatics Assembly on 19 th -23 rd April 2021. This conference aims to highlight open innovation in neuroscience, and additionally to showcase recently developed software tools and data infrastructures.

The view from the Marie Sklodowska Curie Museum, where Marie lived as a child. This year’s Neuroinformatics 2019 meeting took place in the beautiful and historic city of Warszawa (Warsaw). Warszawa remains a pilgrimage city for scientists, with arguably its most famous resident Marie Sklodowska Curie being the first woman to win a Nobel Prize, and the only person ever to win the Nobel Prize twice in two different scientific fields.

The 10th anniversary of the EMBO Workshop: Visualising Biological Data (VIZBI 2019) took place in EMBL in Heidelberg last week. GigaScience Data Scientist Chris Armit was there and was astonished at the cinematic quality of the visualisations that were showcased over this 3-day meeting.

With a large increase in the volume and type of data archived in GigaScience Database (GigaDB) since its launch in 2011, we have studied the metrics and user patterns to assess the important aspects needed to best suit current and future use. This has led to new front-end developments and enhanced interactivity and functionality that greatly improve user experience. In this article, we present an overview of the current practices including the Biocurational role of the GigaDB staff, the broad usage metrics of GigaDB datasets and an update on how the GigaDB platform has been overhauled and enhanced to improve the stability and functionality of the codebase. Finally, we report on future directions for the GigaDB resource.

The Walter E. Washington Convention Center in Washington DC was the venue for this year’s ASCB|EMBO 2019 Meeting that took place on 7-11 December 2019. The American Society of Cell Biology conference, now merged with the EMBO meeting, is the largest yearly gathering for the cell imaging community, and GigaScience has attended in the past.

EMBL Heidelberg was the venue for the EMBL Symposium: Seeing is Believing – Imaging the Molecular Processes of Life that took place on 9-12 October 2019. This was the second EMBL meeting on imaging data we attending this year after VIZBI (see the write-up here), GigaScience Data Scientist Chris Armit was there and was astonished at how recent breakthroughs in imaging technology are enlightening our understanding of the Life Sciences.