{"id":58547,"date":"2023-05-15T12:00:00","date_gmt":"2023-05-15T10:00:00","guid":{"rendered":"https:\/\/www.embl.org\/news\/?post_type=embletc&p=58547"},"modified":"2023-05-15T12:24:36","modified_gmt":"2023-05-15T10:24:36","slug":"janet-thornton-retires-a-pioneer-in-structural-bioinformatics","status":"publish","type":"embletc","link":"https:\/\/www.embl.org\/news\/embletc\/issue-100\/janet-thornton-retires-a-pioneer-in-structural-bioinformatics\/","title":{"rendered":"Janet Thornton retires: a pioneer in structural bioinformatics"},"content":{"rendered":"\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\n\n\n
\n\"\"
\n

\n \n Celebrating 100 issues of EMBLetc. \n <\/path>\n <\/svg>\n <\/a>\n <\/h3>\n

This snippet from EMBLetc. issue 8 (August 2001) discusses Janet Thornton taking up the mantle of EMBL-EBI leadership.<\/p>\n <\/div>\n<\/article>\n\n","protected":false},"excerpt":{"rendered":"

In recognition of Janet Thornton\u2019s retirement, we look back at some of her biggest accomplishments in shaping the field of bioinformatics.<\/p>\n","protected":false},"author":77,"featured_media":58735,"parent":0,"menu_order":0,"template":"","tags":[28,36,369,493],"class_list":["post-58547","embletc","type-embletc","status-publish","has-post-thumbnail","hentry","tag-bioinformatics","tag-embl-ebi","tag-thornton","tag-women-in-science"],"acf":{"featured":true,"show_featured_image":false,"field_target_display":"embl","field_article_language":{"value":"english","label":"English"},"article_intro":"

In recognition of Janet Thornton\u2019s retirement, we look back at some of her biggest accomplishments in shaping the field of bioinformatics.<\/p>\n","related_links":[{"link_description":"Thornton Group","link_url":"https:\/\/www.ebi.ac.uk\/research\/thornton\/"},{"link_description":"Allyship and support: an interview with Janet Thornton\r\n","link_url":"https:\/\/www.embl.org\/news\/lab-matters\/allyship-interview-janet-thornton\/"},{"link_description":"Organisations should embrace open science faster \u2013 interview with Prof. Dame Janet Thornton\r\n","link_url":"https:\/\/www.embl.org\/news\/lab-matters\/organisations-should-embrace-open-science-faster\/"}],"source_article":false,"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":58541,"post_author":"124","post_date":"2023-05-15 12:00:00","post_date_gmt":"2023-05-15 10:00:00","post_content":"\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

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","post_title":"Visualising biology: new tools of the trade","post_excerpt":"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.","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"visualising-biology-new-tools-of-the-trade","to_ping":"","pinged":"","post_modified":"2023-05-16 09:58:53","post_modified_gmt":"2023-05-16 07:58:53","post_content_filtered":"","post_parent":0,"guid":"https:\/\/www.embl.org\/news\/?post_type=embletc&p=58541","menu_order":0,"post_type":"embletc","post_mime_type":"","comment_count":"0","filter":"raw"},{"ID":58545,"post_author":"124","post_date":"2023-05-15 12:00:00","post_date_gmt":"2023-05-15 10:00:00","post_content":"\n

Science, technology, and ethics have always been closely intertwined concepts.  Science<\/em> allows systematic investigation of nature. Technology<\/em> applies the knowledge so gained for human benefit. And ethics<\/em> provides governing principles for moral conduct. Advances in science and technology often demand a reexamination of the associated ethical standards, while changes in our collective ethical consciousness can affect our approach towards scientific research and its applications. <\/p>\n\n\n\n

The ethics surrounding scientific research, therefore, form part of the bedrock of modern research endeavours and ensure that the highest standards are maintained as we extend the frontiers of human knowledge.<\/p>\n\n\n\n

Recognising the importance of this field, particularly in the context of current global concerns and challenges, EMBL\u2019s next Science & Society conference<\/a> will examine the breadth of ethical issues in the life sciences through the lens of molecular biology research. The conference, titled \u2018Terra Incognita\u2019, will be held virtually on 19 and 20 June 2023 and will feature a dazzling array of speakers from a wide range of backgrounds.<\/p>\n\n\n\n

\"The Science & Society Programme helps create a platform for dialogue and debate,\u201d said Lucia von Bredow, EMBL Bioethics Manager and Science & Society Lead. \u201cIt\u2019s a collaborative initiative, within which we try to facilitate an exploration of the societal context in which scientific research operates.\u201d<\/p>\n\n\n\n

As one of the previous attendees, Chris Dye from the University of Oxford, stated: \u201cThe excellent EMBL Science & Society conferences are a terrific opportunity for scientists at all career stages, and from anywhere in the world, to join wide-ranging debates on the practical, ethical, and social implications of today\u2019s research.\u201d<\/p>\n\n\n\n

Bioethics and beyond<\/strong><\/h2>\n\n\n\n

EMBL\u2019s Bioethics Office provides the organisation with guidance on ethical issues arising in research, coordinates training via the Ethics Academy, and delivers an external engagement programme on the ethical, legal, and social implications of EMBL\u2019s research via Science & Society.<\/p>\n\n\n\n

There are many ways to approach ethics in scientific research. For example, the Ethics Academy at EMBL categorises ethics-related training into three major areas. The first is bioethics \u2013 standards that apply to the usage of biological material, involving environmental, biosafety, and biosecurity aspects, among others. Second, there is data ethics, which deals with the ethics of emerging technologies, data protection, and records management. And finally, there\u2019s workplace ethics, which deals with institutional culture; equality, diversity, and inclusion; and research integrity. <\/p>\n\n\n\n

In order to navigate this vast field, the Terra Incognita conference takes an innovative approach, by distilling these concepts down using two specific case studies. The first case study deals with technology ethics, and will be kicked off with a keynote address by Sandra Wachter, Professor of Technology and Regulation at the Oxford Internet Institute at the University of Oxford. Wachter\u2019s research deals with the legal and ethical implications of AI, Big Data, and robotics as well as Internet and platform regulation. <\/p>\n\n\n\n

With the recent popularity and rise in the use of generative AI like ChatGPT, this session will come at an opportune time to reexamine the ethical concerns related to the usage of such technology. This session also includes talks by science historian Mathew Cobb from the University of Manchester, EMBL group leader Jan Korbel, and Nikola Biller-Andorno, Professor and Director of the Institute of Biomedical Ethics of the University of Zurich, Switzerland.<\/p>\n\n\n\n

The second case study will deal with the ethics surrounding the use of organoid systems to aid research in molecular biology. EMBL is a leader in this field, particularly with several groups based in EMBL Barcelona pushing the boundaries of organ-on-chip and microphysiological system research. The session will present different perspectives on organoid use ethics, beginning with a keynote address from Insoo Hyun, Director of Research Ethics at the Harvard Medical School, USA. It will also feature talks by EMBL Barcelona group leader Talya Dayton, Fruzsina Moln\u00e1r-G\u00e1bor from the BioQuant Zentrum, Germany, and Madeline Lancaster from the MRC Laboratory of Molecular Biology, UK.<\/p>\n\n\n\n

\u201cOrganoid and embryo modelling research represent two rapidly moving areas of science, where the ethical and policy issues are unfolding in real-time alongside the science. It is therefore crucial that conversations among policymakers and ethicists occur proactively with researchers who are at the cutting edge of such work,\u201d said Insoo Hyun. <\/p>\n\n\n\n

Leading ethics discussions<\/h2>\n\n\n\n

In addition to the case studies, the conference will feature discussions on ways to involve the public in discussions about ethics and science. This session will be led by a keynote address from Richard Milne, Deputy Director of the Kavli Centre for Ethics, Science, and the Public, University of Cambridge, UK, and will feature a roundtable on scientists\u2019 role in ethics-related discussions, as well as a debate on better involvement of underrepresented groups in the discussion of ethics. <\/p>\n\n\n\n

\"The ethics of research in genomics and the life sciences is hugely important \u2013 it affects not only how we do science, but why and for whom,\" said Milne. \"It\u2019s also important that this isn\u2019t just left to ethicists and social scientists alone, but that we all work together as part of a multidisciplinary community.\"<\/p>\n\n\n\n

\"As Europe\u2019s unique intergovernmental life sciences research organisation, a consideration of ethical issues in scientific research is of key importance,\u201d said EMBL Director General Edith Heard. \u201cIt is also essential for our mission to integrate and support the life sciences across Europe.\u201d<\/p>\n\n\n\n

Lucia von Bredow agrees. \u201cIt is not only essential for EMBL to play a leading role in discussions around ethics, but it is also important for us to set the bar high, and strive to meet the standards for the highest quality ethical research. It is our aim that EMBL serves as a model of best practice for research ethics in a European context, and this conference is one of many steps in our road towards achieving that goal.\u201d<\/p>\n\n\n\n

The conference is free to attend and open to everyone. Registrations are now open until 16 June 2023. Find more information here<\/a>.<\/p>\n","post_title":"Terra Incognita: exploring new horizons in scientific ethics","post_excerpt":"EMBL\u2019s upcoming Science & Society conference takes a deep dive into the ethical considerations surrounding the use of technology and organoids in life science research. 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