{"id":58541,"date":"2023-05-15T12:00:00","date_gmt":"2023-05-15T10:00:00","guid":{"rendered":"https:\/\/www.embl.org\/news\/?post_type=embletc&p=58541"},"modified":"2023-05-16T09:58:53","modified_gmt":"2023-05-16T07:58:53","slug":"visualising-biology-new-tools-of-the-trade","status":"publish","type":"embletc","link":"https:\/\/www.embl.org\/news\/embletc\/issue-100\/visualising-biology-new-tools-of-the-trade\/","title":{"rendered":"Visualising biology: new tools of the trade"},"content":{"rendered":"\n

Biological imaging reveals to us the wonderful inner worlds of living organisms, bringing into sharp focus all their quirks, oddities, and moving pieces. EMBL has long been a world leader in this field, spearheading advances in imaging technology at the same time as making imaging services accessible to the wider scientific community.<\/p>\n\n\n\n

With progress in imaging technology, however, comes the problem of handling the huge datasets that such methods inevitably produce. Researchers across EMBL have been collaborating to find a solution to this 21st-century problem, and the tools they are developing will help researchers across the world share, analyse, and collaborate on imaging data for years to come. <\/p>\n\n\n\n

The problem of big data in microscopy<\/strong><\/h2>\n\n\n\n

In addition to letting us peek inside organisms, bioimaging helps us understand how they function. They also let us track the way these functions change in response to disease states or environmental challenges. From the 16th-century compound microscopes created by Dutch spectacle-makers to today\u2019s state-of-the-art cryo-electron microscopy facilities, bioimaging technologies share a common purpose: to allow us to see deeper into the fundamental mechanisms of living systems. <\/p>\n\n\n\n

The last few decades have seen explosive growth in the capabilities of such technology systems. In recent years, EMBL researchers have pioneered techniques that, among other applications, let us decrypt molecular structures inside cells<\/a>, combine imaging with next-generation sequencing<\/a> methods, and measure the mechanical properties of developing embryos<\/a>. In addition to increasing the resolution<\/a> of optical microscopy beyond what was once thought possible, scientists worldwide have made significant advances in combining different modalities of bioimaging in the form of correlative microscopy. <\/p>\n\n\n\n

Correlative microscopy allows researchers to place layers of information on top of each other. While one technique, e.g. electron microscopy, might show us cellular ultrastructures, another, like fluorescence microscopy, might help us pinpoint the location of various proteins. By combining such information, researchers can gain significant insight into biological functions.<\/p>\n\n\n\n

However, the ever-increasing resolution and scope of imaging technologies result in ever-expanding datasets, with file sizes ranging into the order of terabytes. This, unfortunately, makes it impossible to open and view such files on an ordinary computer, requiring the use of extensive computing resources. Additionally, extracting biological meaning out of such colossal datasets can be a time-consuming as well as error-prone endeavour. <\/p>\n\n\n\n

Mobilising MoBIE<\/strong><\/h2>\n\n\n\n
\"A
Scientists can explore cell types and tissues using the MoBIE interface. The image above shows a scatter plot depicting single cells based on their morphological properties and a section of electron microscopy volume of a Platynereis<\/em> larvae, with different colours representing automatically determined animal tissues. Credit: Valentyna Zinchenko\/EMBL<\/figcaption><\/figure>\n\n\n\n

In order to deal with this challenge, EMBL scientists Christian Tischer, Yannick Schwab, Anna Kreshuk, and Detlev Arendt, began a collaboration in 2018 to build a tool that would allow researchers across the world to share and view such multifaceted datasets on simple computing systems.<\/p>\n\n\n\n

The result of their efforts was MoBIE \u2013 a software tool that allows scientists to handle large imaging datasets, as well as share and analyse them collaboratively. It can help scientists visualise data in multiple dimensions (e.g. in 2D, 3D, and 4D) and integrate data from many different domains of biology. <\/p>\n\n\n\n

\u201cMoBIE enables the exploration and sharing of really big correlative image datasets,\u201d said Tischer. \u201cIt builds on existing technologies, such as BigDataViewer<\/a> and next-generation image file formats<\/a>, and adds features for combining large heterogeneous images and corresponding segmentations into easily browseable projects.\u201d <\/p>\n\n\n\n

First described in a publication in Nature Methods<\/em><\/a> earlier this year, MoBIE allows users to seamlessly stream data from a remote server, and share \u201cviews\u201d of imaging datasets with each other. It is also free to download for researchers worldwide. In addition to electron microscopy data, MoBIE can be used to integrate data from fields ranging from gene expression to X-ray imaging<\/a>. <\/p>\n\n\n\n

According to Schwab, this development is also significant for imaging services. \u201cA tool like MoBIE can enable smooth communication with users. By using MoBIE, data producers and users can interact with the datasets after and even during the production process,\u201d he said. <\/p>\n\n\n\n

Machine learning to decode cellular signatures<\/strong><\/h2>\n\n\n\n

One of the early adopters of this tool was Detlev Arendt, whose group studies the evolution of the nervous system by using the worm Platynereis <\/em>as a model system. In 2021, the researchers created the first multimodal cellular atlas<\/a> combining electron microscopy and expression data for an entire animal, which was made available to the global research community via the MoBIE technology.<\/a><\/p>\n\n\n\n

The creation of this atlas was enabled by volume electron microscopy, which is a method wherein electron microscopy techniques are applied to \u2018large\u2019 volumes to generate a three dimensional view of a cell, tissue \u2013 or an entire organism, in the case of Platynereis<\/em>.<\/p>\n\n\n\n

\u201cThis approach exemplified this important transition to go from serial sections into visualising the entire volume of an animal\u201d, said Arendt. \u201cYou can almost think of it now as a virtual reality space \u2013 using your cursor, you can travel through this volume, and find things that have never been seen before.\u201d<\/p>\n\n\n\n

However, with such a huge dataspace full of so many unknowns, correctly annotating cells or tissues can be an important challenge \u2013 one that can take hours of painstaking manual labour. <\/p>\n\n\n\n

To solve this problem, in another new study, published in eLife<\/em><\/a>, <\/em>Arendt and Kreshuk describe a novel approach to analysing this dataset and extracting meaningful biological information from it. By using a neural network-based deep learning approach, the team automated the process of identification of cells, cell types, and tissues at organism-scale by identifying distinct morphological features. The method, aptly named \u2018MorphoFeatures\u2019, could group similar cells and cell types \u2013 classifications that could be verified by using gene expression data. <\/p>\n\n\n\n

During the whole life-cycle of the MorphoFeatures development, MoBIE was used to explore the data and visually validate the method, as well as discover and study morphological points of interest. Now, researchers in the world can now take a look at the data and apply the MorphoFeatures method themselves. <\/p>\n\n\n\n

\u201cThis is a pioneering study for this kind of analysis in volume electron microscopy, and we want to generate many more such analyses,\u201d said Arendt. \u201cThis is a new field that is just starting and visualisation tools such as MoBIE are critical to do the same for many more organisms in many different ways.\u201d<\/p>\n\n\n\n

\n
\n

\n Volume electron microscopy at EMBL <\/h3>\n

Volume EM (vEM) was first introduced at EMBL around 10 years ago by the Electron Microscopy Core Facility<\/a> and the Schwab team<\/a>. In recent years, this versatile technique has seen widespread use in many life science fields. In 2022, EMBL researchers contributed to a primer on vEM<\/a> published in Nature Review Methods<\/em>. They are also helping organise the first Gordon Research Conference on vEM<\/a>, to be held in July 2023. In addition to pioneering the use of vEM for answering fundamental biological questions, EMBL has also been a leader in integrating vEM with other imaging technologies, especially 3D fluorescence microscopy and X-ray imaging.<\/p>\n <\/div>\n<\/article>\n\n\n\n\n

Looking ahead<\/strong><\/h2>\n\n\n\n
\"Outdoor
Caption: The four collaborators in 2018. From left to right: Christian Tischer, Yannick Schwab, Detlev Arendt, Anna Kreshuk. Credit: Yannick Schwab\/EMBL<\/figcaption><\/figure>\n\n\n\n

According to Arendt, this approach will also be crucial for the types of comparative studies his group is currently doing, in which they compare the nervous systems of many different animals to figure out what the brains of our distant ancestors looked like. For this purpose, the team will also be collecting organisms during the ongoing TREC expedition<\/a>, to be analysed with volume electron microscopy and the new tools the scientists are developing. <\/p>\n\n\n\n

And this is just the beginning for such applications. \u201dWe used MoBIE to share a large number of tomograms of the SARS-CoV-2 virus, which COVID-19 researchers across the world have access to now,\u201d said Schwab. The teams continue to collaborate with each other and across EMBL, making the dual tasks of knowledge-extraction and sharing from biological imaging data easier for the entire scientific community. <\/p>\n\n\n\n

\n
\n

\n Funding <\/h3>\n

This research received additional support from various grants from the European Union\u2019s Horizon 2020 research and innovation programme, the Chan Zuckerberg Initiative, and the European Research Council.<\/p>\n <\/div>\n<\/article>\n\n","protected":false},"excerpt":{"rendered":"

EMBL researchers are pushing the frontiers of big data analysis in biological imaging, allowing scientists to gain a many-layered and multidimensional view of organisms, tissues, and cells in action.<\/p>\n","protected":false},"author":124,"featured_media":58965,"parent":0,"menu_order":0,"template":"","tags":[14301,417,136,43,602,604,79,410,14303],"class_list":["post-58541","embletc","type-embletc","status-publish","has-post-thumbnail","hentry","tag-analysis","tag-arendt","tag-electron-microscopy","tag-heidelberg","tag-kreshuk","tag-machine-learning","tag-microscopy","tag-schwab","tag-tischer"],"acf":{"featured":true,"show_featured_image":false,"field_target_display":"embl","field_article_language":{"value":"english","label":"English"},"article_intro":"

EMBL researchers are pushing the frontiers of big data analysis in biological imaging, allowing scientists to gain a many-layered and multidimensional view of organisms, tissues, and cells in action.<\/p>\n","related_links":[{"link_description":"Arendt Group\r\n","link_url":"https:\/\/www.embl.org\/groups\/arendt\/"},{"link_description":"Kreshuk Group","link_url":"https:\/\/www.embl.org\/groups\/kreshuk\/"},{"link_description":"Schwab Team\r\n","link_url":"https:\/\/www.embl.org\/groups\/schwab\/"},{"link_description":"Advanced Light Microscopy Facility\r\n","link_url":"https:\/\/www.embl.org\/groups\/advanced-light-microscopy-core-facility\/"}],"source_article":[{"publication_title":"MoBIE: a Fiji plugin for sharing and exploration of multi-modal cloud-hosted big image data","publication_link":{"title":"","url":"https:\/\/doi.org\/10.1038\/s41592-023-01776-4","target":""},"publication_authors":"Pape, C., Meechan, K. et al","publication_source":"Nature Methods","publication_date":"10 February 2023","publication_doi":"10.1038\/s41592-023-01776-4"},{"publication_title":"MorphoFeatures for unsupervised exploration of cell types, tissues, and organs in volume electron microscopy","publication_link":{"title":"","url":"https:\/\/doi.org\/10.7554\/eLife.80918","target":""},"publication_authors":"Zinchenko V., Hugger J. et al","publication_source":"eLife","publication_date":"16 February 2023","publication_doi":"10.7554\/eLife.80918"}],"in_this_article":false,"press_contact":"None","article_translations":false,"languages":"","embletc_issue":[{"ID":58531,"post_author":"124","post_date":"2023-05-15 12:00:00","post_date_gmt":"2023-05-15 10:00:00","post_content":"","post_title":"Issue 100","post_excerpt":"","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"issue-100","to_ping":"","pinged":"","post_modified":"2023-05-15 13:01:59","post_modified_gmt":"2023-05-15 11:01:59","post_content_filtered":"","post_parent":0,"guid":"https:\/\/www.embl.org\/news\/?post_type=embletc-issue&p=58531","menu_order":0,"post_type":"embletc-issue","post_mime_type":"","comment_count":"0","filter":"raw"}],"embletc_in_this_issue":[{"ID":58543,"post_author":"124","post_date":"2023-05-15 12:00:00","post_date_gmt":"2023-05-15 10:00:00","post_content":"\n

With the ambitious aim of examining life along European coasts, EMBL\u2019s planetary biology flagship project Traversing European Coastlines (TREC) launched officially in March this year. A press conference in Paris on 8 March 2023 introduced the project to audiences in Europe, along with its aim of studying coastal ecosystems and their response to the environment, on scales from molecules to communities. <\/p>\n\n\n\n

\"Collage
EMBL DG and colleagues during the official launch of TREC in Paris, France. Credit: Mylene Andre\/EMBL<\/figcaption><\/figure>\n\n\n\n

The expedition has been several years in the making. The launch of EMBL\u2019s 2022-26 programme unveiled the organisation\u2019s visionary new plan to study \u2018life in context\u2019. To help achieve this, EMBL initiated several transversal themes which support the multidisciplinary science necessary to realise projects like these. One of these themes is Planetary Biology, which aims to study, from the molecular to the population level, how microbes, plants, and animals respond to each other and to their environment.<\/p>\n\n\n\n

TREC is the Planetary Biology transversal theme\u2019s flagship project, and it aims to explore the interactions within and between the two major ecosystems on our planet: ocean and land. It will bring molecular sciences to environmental research in a Europe-wide project at an unprecedented scale, to better understand how organisms \u2013 from viruses to animals \u2013 respond to natural and human-made environmental changes.<\/p>\n\n\n\n

\"Map
Map of proposed TREC sampling sites along the coast of Europe. Credit: Tara Europa.<\/figcaption><\/figure>\n\n\n\n

The expedition began in Roscoff, France in April 2023 and will conclude in Malta in mid-2024. During this period, researchers from EMBL, the Tara Oceans consortium, together with the Tara Ocean Foundation, and numerous European collaborating institutes and organisations will work at 120 sampling sites along the European coastline.<\/p>\n\n\n\n

TREC will combine the scientific expertise of many partners as well as existing knowledge of local ecosystems and processes, with EMBL\u2019s latest technology developments and expertise in examining life at the smallest scales.<\/p>\n\n\n\n

The sampling kicked off in Roscoff in April 2023, with researchers from EMBL and Tara, as well as partner institutions including the Station Biologique de Roscoff, heading off to collect soil, water, and sediment samples that will help move forward the expedition\u2019s constituent scientific projects<\/a> and provide a snapshot of the health of these ecosystems. <\/p>\n\n\n\n

\"Collage
Researchers collecting samples at Roscoff, France during April 2023. Credit: Kinga Lubowiecka\/EMBL<\/figcaption><\/figure>\n\n\n\n

A recurring challenge for molecular biology field expeditions is the lack of ready access to sophisticated lab facilities, which are often needed for sample preparation for advanced applications like electron microscopy. The TREC expedition provides a unique and innovative solution to this \u2013 to bring the labs to the samples rather than the samples to the labs.<\/p>\n\n\n\n

It will achieve this with the help of mobile laboratories, which will travel to specific stops and include cutting-edge light microscopy, sample preparation for (cryo)-electron microscopy, and single-cell pheno-genomics. Additionally, advanced tools for environmental measurements from soil, air, sediment, and water samples will be part of the standard equipment. By providing these technologies across Europe throughout the expedition, EMBL Advanced Mobile Services will support the interdisciplinary approaches that underpin TREC. <\/p>\n\n\n\n

\"Collage
EMBL\u2019s Advanced Mobile Services, including this Sample Processing Lab, will enable scientists to perform leading subcellular research in direct proximity to the field. Credit: Kinga Lubowiecka\/EMBL<\/figcaption><\/figure>\n\n\n\n

Engaging with the public in our member states<\/strong><\/h2>\n\n\n\n

However, TREC\u2019s aims and scope are not limited to answering scientific questions and bringing state-of-the-art mobile services to European coasts. We live in an interconnected world, and coastal regions are key functional ecosystems on which humans depend for their livelihoods and well-being. Two of the aims of this expedition are also to engage the general public in debate and discussion to raise awareness of the role of science in society and to inspire the next generation of scientists by raising awareness of the importance of understanding life on this planet among pupils and teachers. <\/p>\n\n\n\n

To this end, EMBL\u2019s office of Science Education and Public Engagement (SEPE) is travelling alongside TREC to various coastal sites and conducting public engagement activities aimed at engaging, informing, educating, and entertaining non-expert audiences and spreading awareness regarding the importance of coastal ecosystems. <\/p>\n\n\n\n

\"Collage
Caption: Public engagement activities by SEPE at Roscoff, France. Credit: Kinga Lubowiecka\/EMBL<\/figcaption><\/figure>\n\n\n\n

The Road to Roscoff<\/strong><\/h2>\n\n\n\n

While TREC officially began in 2023, its organisers have been working tirelessly behind the scenes for many years to plan a successful expedition and smooth out any wrinkles. Three separate pilot expeditions were conducted between 2019 and 2022, helping the researchers optimise the sample collection procedures and associated processes that would serve them in the field during the main expedition, among other things. <\/p>\n\n\n\n

The first pilot was conducted in Naples<\/a> and the nearby island of Ischia, where scientists collected samples of microbes and marine organisms at several spots along Ischia\u2019s coast, in collaboration with the Stazione Zoologica Anton Dohrn di Napoli (SZN), a marine research institute in Naples, which also runs a research station on Ischia.<\/p>\n\n\n\n

\"Collage
Glimpses of sample collection from the coast of Naples during a TREC pilot project in 2019. Credit: Patrick Mueller\/EMBL<\/figcaption><\/figure>\n\n\n\n

A second pilot took place in Villefranche-sur-Mer, France in 2021. EMBRC hosted this expedition that enabled unprecedented high-definition ultrastructure images from fresh samples, such as this plankton which was frozen under high pressure on the beach. Soil and sediments were also sampled along the Villefranche sea-land transects and the river Var estuary.<\/p>\n\n\n\n

\"\"
Researchers collecting samples during the TREC pilot expedition in Villefranche-sur-Mer, France in 2021. Credit: Paola Bertucci\/EMBL<\/figcaption><\/figure>\n\n\n\n

The third and final TREC pilot expedition<\/a> was held in Iceland during August, 2022. EMBL researchers and their collaborators visited three different locations in Iceland \u2013 Reykjavik, Westfjords, and Akureyri \u2013 with unique climatic and environmental conditions. They collected marine organisms, soil, seawater, and sediments, and tested out experimental protocols that would become critical for the core TREC expedition in 2023 and 2024.<\/p>\n\n\n\n

\"Collage
EMBL researchers conducted a pilot project in Iceland as the final preparatory step before commencing their journey traversing European coastlines. The visit coincided with a volcanic eruption located 60 Km from the first sampling site. Credits: Niko Leisch\/EMBL, Hiral Shah\/EMBL, Richard Jacoby\/EMBL, \u00a9Kristinn Ingvarsson\/University of Iceland<\/figcaption><\/figure>\n\n\n\n

Forging ahead<\/strong><\/h2>\n\n\n\n

The TREC expedition is the first time researchers from across Europe will study life at all biological scales, from molecules to communities, along the entire European coast, to provide a richer and deeper understanding of how ecosystems respond to natural and human-made challenges. This will produce new knowledge and discoveries that will help to provide our societies, governments, and regulatory agencies with the ability to best predict the possible effects of environmental changes and impacts. It is an ambitious \u2013 and essential \u2013 project, given the environmental challenges that our planet faces. <\/p>\n\n\n","post_title":"In pictures: the story of TREC","post_excerpt":"EMBL\u2019s newest expedition attempts to answer some of the biggest questions in planetary biology, and will help scientists find solutions to pressing global concerns. ","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"in-pictures-the-story-of-trec","to_ping":"","pinged":"","post_modified":"2023-05-25 10:25:24","post_modified_gmt":"2023-05-25 08:25:24","post_content_filtered":"","post_parent":0,"guid":"https:\/\/www.embl.org\/news\/?post_type=embletc&p=58543","menu_order":0,"post_type":"embletc","post_mime_type":"","comment_count":"0","filter":"raw"},{"ID":58547,"post_author":"77","post_date":"2023-05-15 12:00:00","post_date_gmt":"2023-05-15 10:00:00","post_content":"\n

Professor Dame Janet Thornton is one of the world's pioneers in structural bioinformatics. Her incredible career and active voice on many topics, including science in Europe, open data, and women in science, have inspired scientists the world over. <\/p>\n\n\n\n

As the Director of EMBL\u2019s European Bioinformatics Institute (EMBL-EBI) between 2001 and 2015, Thornton led the growth of the institute from 160 to over 600 people. She currently leads a research group at EMBL-EBI, studying the biology of proteins and ageing, and is a leading voice in the scientific community, having undertaken leadership and governance roles in the Royal Society, European Research Council, ELIXIR, and many other organisations.  <\/p>\n\n\n\n

\"Cake
Thornton's celebration cake for her stepping down as Director of EMBL-EBI. Credit: Robert Slowley\/EMBL<\/figcaption><\/figure>\n\n\n\n

In recognition of Thornton\u2019s upcoming retirement in summer 2023, we reflect on some of her highlights and achievements during her time at EMBL. <\/p>\n\n\n\n

Structural biology and bioinformatics<\/strong><\/h2>\n\n\n\n

Thornton has seen the field of structural biology change completely. When she started her career, there were only about 20 known protein structures, and now there are over 200,000 structures in the Protein Data Bank (PDB), and over 200 million predictions by AlphaFold. Her work at EMBL has been highly interdisciplinary, interfacing with the fields of structural biology, bioinformatics, biological chemistry and chemoinformatics. <\/p>\n\n\n\n

\"Female
Thornton giving a speech at the EMBL-EBI 20th anniversary celebration. Credit: Robert Slowley\/EMBL<\/figcaption><\/figure>\n\n\n\n

Thornton started her career by trying to predict protein structures from their sequences. She spent years characterising and analysing the new protein structures as they were determined and stored in the PDB. She is also well known for developing, with Roman Laskowski, the widely used ProCheck software<\/a> for checking the quality of protein structures. Together with her colleague Christine Orengo, Thornton also introduced the CATH classification of protein structures, which provides information on the evolutionary relationships of protein domains. CATH<\/a> now exists as an open-access database and is part of the ELIXIR infrastructure. <\/p>\n\n\n\n

The recent structure predictions by AlphaFold by DeepMind, based on deep learning approaches, have delighted Thornton, together with the fact that more than 200 million predicted structures are now openly available at EMBL-EBI in the AlphaFold Database<\/a>. <\/p>\n\n\n\n

Investigating Enzymes<\/strong><\/h2>\n\n\n\n

Thornton's research group<\/a> at EMBL-EBI is developing robust search, comparison, and annotation tools for enzymes,  which are available as open-access algorithms and web tools for quantitative similarity searches between enzyme reactions. Recent work from the group has led to several exciting new knowledge-based approaches for investigating the evolution of enzymes, most recently at a mechanistic level<\/a>.<\/p>\n\n\n\n

\u201cI\u2019m very lucky to work with such brilliant minds every day,\u201d said Thornton. \u201cMy team at EMBL-EBI is truly an outstanding group of scientists. They\u2019re passionate, driven, and never fail to inspire and surprise me.\u201d <\/p>\n\n\n\n

Data sharing across Europe<\/strong><\/h2>\n\n\n\n

Thornton led the establishment of ELIXIR<\/a>, an intergovernmental organisation that brings together life science data resources from across Europe. Its goal is to ensure sustainable funding and harmonise data resources within the bioinformatics ecosystem, making it easier for scientists to find and share data, exchange expertise, and agree on best practices.<\/p>\n\n\n\n

\u201cThe launch of ELIXIR was the first step towards building a distributed infrastructure for biological information throughout Europe,\u201d said Thornton. \u201cBy providing public access to the wealth of knowledge generated by the global research community, ELIXIR empowers researchers in academia and industry to solve some of society\u2019s most pressing problems.\u201d<\/p>\n\n\n\n

\"Two
Janet Thornton and then UK Minister for Universities and Science David Willetts at the opening of the EMBL-EBI South Building and ELIXIR Hub. Credit: Robert Slowley\/EMBL<\/figcaption><\/figure>\n\n\n\n

Inspiring the next generation<\/strong><\/h2>\n\n\n\n

As an advocate for women in science, Thornton has spoken openly about what can be done to support all scientists throughout their careers. One impact of this includes the establishment of the Janet Thornton Fellowship<\/a>, which funds researchers who have taken a career break. Throughout her career, Thornton has also supervised a large number of PhD and postdoctoral researchers including Sarah Teichmann<\/a>, Head of Cellular Genetics and Senior Group Leader at the Wellcome Sanger Institute, and David Jones<\/a>, Professor of Bioinformatics at University College London.<\/p>\n\n\n\n

\"Female
Janet Thornton holding her medal after she was appointed Dame Commander of the Order of the British Empire (DBE) in the 2012 Birthday Honours for services to bioinformatics. Credit: EMBL<\/figcaption><\/figure>\n\n\n\n

\u201cI think every scientist, but perhaps especially women, needs to decide how they will deal with their work\u2013life balance. There is no \u201cright\u201d way to do this \u2013 different solutions suit different people,\u201d said Thornton. \u201cA scientist has about 50 years to do their research; taking a short time out of that time to be at home for whatever reason should certainly be possible.\u201d<\/p>\n\n\n\n

 During her career, Thornton also stood out as an exemplary public speaker and science communicator. Her regular appearances in the press, explaining complex concepts in an accessible and engaging way, shared her wonder for the molecular world beyond the many colleagues, collaborators and mentees who have had the privilege to meet and work with Thornton in person.<\/p>\n\n\n\n

\u201cI have much enjoyed my career as a scientist and would advocate it as one of the best jobs I can imagine,\u201d said Thornton. \u201cI have met and worked with brilliant people at Oxford, Birkbeck, UCL and EMBL and enjoyed being part of a joint endeavour to discover the fabulous world of protein structures.\u201d<\/p>\n\n\n\n\n","post_title":"Janet Thornton retires: a pioneer in structural bioinformatics","post_excerpt":"In recognition of Janet Thornton\u2019s retirement, we look back at some of her biggest accomplishments in shaping the field of bioinformatics.","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"janet-thornton-retires-a-pioneer-in-structural-bioinformatics","to_ping":"","pinged":"","post_modified":"2023-05-15 12:24:36","post_modified_gmt":"2023-05-15 10:24:36","post_content_filtered":"","post_parent":0,"guid":"https:\/\/www.embl.org\/news\/?post_type=embletc&p=58547","menu_order":0,"post_type":"embletc","post_mime_type":"","comment_count":"0","filter":"raw"}]},"yoast_head":"\nVisualising biology: new tools of the trade | EMBL<\/title>\n<meta name=\"description\" content=\"EMBL researchers are pushing the frontiers of big data analysis in bioimaging, allowing a multidimensional view of living systems.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.embl.org\/news\/embletc\/issue-100\/visualising-biology-new-tools-of-the-trade\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Visualising biology: new tools of the trade | EMBL\" \/>\n<meta property=\"og:description\" content=\"EMBL researchers are pushing the frontiers of big data analysis in bioimaging, allowing a multidimensional view of living systems.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.embl.org\/news\/embletc\/issue-100\/visualising-biology-new-tools-of-the-trade\/\" \/>\n<meta property=\"og:site_name\" content=\"EMBL\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/embl.org\/\" \/>\n<meta property=\"article:modified_time\" content=\"2023-05-16T07:58:53+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/05\/MoBIE_platy-e1683203825910.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"1000\" \/>\n\t<meta property=\"og:image:height\" content=\"600\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:site\" content=\"@embl\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"6 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/www.embl.org\/news\/embletc\/issue-100\/visualising-biology-new-tools-of-the-trade\/\",\"url\":\"https:\/\/www.embl.org\/news\/embletc\/issue-100\/visualising-biology-new-tools-of-the-trade\/\",\"name\":\"Visualising biology: new tools of the trade | EMBL\",\"isPartOf\":{\"@id\":\"https:\/\/www.embl.org\/news\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\/\/www.embl.org\/news\/embletc\/issue-100\/visualising-biology-new-tools-of-the-trade\/#primaryimage\"},\"image\":{\"@id\":\"https:\/\/www.embl.org\/news\/embletc\/issue-100\/visualising-biology-new-tools-of-the-trade\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/05\/MoBIE_platy-e1683203825910.jpg\",\"datePublished\":\"2023-05-15T10:00:00+00:00\",\"dateModified\":\"2023-05-16T07:58:53+00:00\",\"description\":\"EMBL researchers are pushing the frontiers of big data analysis in bioimaging, allowing a multidimensional view of living systems.\",\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/www.embl.org\/news\/embletc\/issue-100\/visualising-biology-new-tools-of-the-trade\/\"]}]},{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/www.embl.org\/news\/embletc\/issue-100\/visualising-biology-new-tools-of-the-trade\/#primaryimage\",\"url\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/05\/MoBIE_platy-e1683203825910.jpg\",\"contentUrl\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/05\/MoBIE_platy-e1683203825910.jpg\",\"width\":1000,\"height\":600,\"caption\":\"A section of electron microscopy volume of a Platynereis larvae. 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