Swedlow Lab

Jason Swedlow earned a BA in Chemistry from Brandeis University in 1982. He performed his PhD in Biophysics with Profs D. A. Agard and J. W. Sedat, finishing in 1994. Dr Swedlow was a postdoctoral fellow at UCSF and then Harvard Medical School from 1994 and 1998, supported by a Damon Runyon Walter Winchell Cancer Research Fund Fellowship from 1995 to 1997. In 1998, Dr Swedlow established his own laboratory at the Wellcome Trust Biocentre, University of Dundee, Scotland as a Principal Investigator and Wellcome Trust Career Development Fellow. He was awarded a Wellcome Trust Senior Fellowship in 2002, and named Professor of Quantitative Cell Biology in 2007. His lab focuses on studies of mitotic and interphase chromosome structure and dynamics. He is Co-Director of the Analytical and Quantitative Microscopy Course. He is co-founder of OME (along with Peter Sorger and Ilya Goldberg).

Sebastien Besson joined the OME team as a developer in March 2012. Originally trained as a physicist, he received his PhD from the Unversite Pierre at Marie Curie in Paris. He then carried out postdoctoral research at the interface between physics and biology at Harvard University. In 2011, Sebastien joined the Danuser lab to convert in-house image analysis into turn-key software packages for the cell biology community. He became part of the main Dundee team in 2015.

Jean-Marie Burel joined the staff of the Swedlow lab in 2003. Since then, he's been contributing to the development of OME, and spends most of his time working on the OMERO.insight project. He received is PhD in mathematics from the University of Brest in 2000. His research interests lie in the area of harmonic maps, harmonic morphisms and geometric structure. After his PhD, he worked in a private company as developer then moved (September 2001) to Lund University, Sweden, where he held a post-doctoral research position. Jean-Marie now enjoys the muddy rugby pitches of Scotland.

Mark Carroll joined the OME team in October 2012 as a software developer. Since graduating in computer science he has mostly worked in scientific and research computing as a software developer, system administrator, principal investigator, and technical writer. Past projects have included artificial intelligence (especially inference and planning), numerical simulation of physical systems (including sonar propagation, ligand-protein docking, and communications networks), using various programming languages (C, Perl, Java, Lisp, Haskell, and others), funded through academic institutions and the US military. At home he mostly eats, sleeps, watches television, and herds children, but hopes someday to make time for pursuits such as music, swimming, and cookery.

Helen Flynn joined the OME team in September 2012 as a technical writer. She received her PhD in Soil Science from the University of Aberdeen in 2003 and then spent 9 years as a post-doctoral researcher in the Environmental Modelling group, working on soil nutrient cycling, land management and climate change. Writing epic reviews for the likes of the International Fertilizer Industry Association has prepared her for this move into a more communication-based role. In her spare time, Helen enjoys getting out and about in the countryside, and playing sci-fi & fantasy roleplaying games.

David Gault joined the OME team in August 2015 as a software developer. David lives and works from Belfast N.Ireland where he graduated with a Masters in Computer Science from Queens University Belfast. Since then he has worked as a developer across many different industries including the Office team at Microsoft, investment banking, scientific image acquisition and cloud based streaming for TV and media. In his spare time he likes to research and tinker with projects in areas such as augmented reality and natural human interfaces.

Kenny Gillen joined the OME team in November 2012 as system administrator. He graduated from the University of Glasgow and initially worked with Strathclyde Fire & Rescue's management and incident information systems. From there he moved into the University of Glasgow's Robertson Centre for Biostatistics, part of the Glasgow Clinical Trials Unit, where he developed web and server applications for clinical research, alongside developing and maintaining the server, networking, storage and power systems in their dedicated clinical research data centre. When he's not configuring servers he is happiest in the the hills cycling, winter mountaineering, rock climbing, ice climbing, paragliding, and hill running. Kenny relaxes by playing the piano, learning the Celtic lap harp and perfecting the ultimate risotto.

Roger Leigh joined the OME team in March 2012 as a software developer. He received his PhD in Biology from the University of York in 2012 where he worked in the Centre of Immunology and Infection investigating the vascularisation of lymphoid organs during embryonic development using epifluorescence, confocal and multi-photon microscopy, of both live and fixed tissues in addition to utilising in vitro models of angiogenesis and vasculogenesis with ex vivo tissue explants. He also has interests in high-throughput high-content screening and image analysis, and worked on this while on placement at AstraZeneca during his Masters degree. Roger is also a developer of the Debian GNU/Linux distribution, having interests in lightweight virtualisation, object storage, build intrastructure and general systems programming using C, C++ and Perl. In his free time, Roger is a keen mountaineer, climber and cyclist, in addition to spending far too much time hacking on Debian and Free Software.

Simon Li joined the OME as a software developer in October 2012, and is working on visual image search and automated image annotation/labelling for OMERO. He has an interdisciplinary PhD in a mix of biological image analysis, machine learning and cell biology, and has previously worked on a wide variety of projects including developing an automated subtitling system, analysing homing pigeon navigation strategies, and working on a robot sheep dog simulator. In his spare time he enjoys walking and cycling in the hills, and is considering starting a bike polo group in Dundee, or learning the bagpipes.

Dominik Lindner joined the team in Dundee as a Software Developer in February 2014. After studying Bioinformatics at the University of Applied Sciences Weihenstephan, Freising, he worked at different places as Java Software Developer with a bit of Linux system administration. His projects mostly had a bioinformatics background (analysis of multiple sequence alignments, DNA sequence optimization) with a short side trip into the world of logistics/warehousing. In his spare time he enjoys exploring Scotland's countryside on foot, on the bicycle or on the motorbike; respectively when the days are short and the weather's bad, trying to set up the ultimate Linux system.

June Matthew joined the OME team at Dundee University in November 2013 as the project administrator.

Josh Moore is an American developer living in Walluf, Germany, with his wife and two kids. With a background in machine learning and distributed computing, Josh began work on the OMERO Java server in the Spring of 2005 as part of the Swedlow Lab, after evaluating use of the OME Perl server for the Mitocheck project while in the iBios group at the DKFZ, Heidelberg, Germany. Before that he was a German-language pre-school teacher at a Montessori school in Alabama, of all things. He's a lisp-loving, Aikido-practicing, vegan with interests in RDF, HDF, and various other three letter acronyms.

Will Moore came to Dundee as a cell biologist to do his PhD and then joined Jason's lab as a post-doc in 2003. Having got interested in the OME project from a user's point of view, he decided on a change of scene and left the lab to do an MSc in Applied Computing at Dundee University's School of Computing. He returned to the Swedlow lab for his MSc project. His goal was to make it easier for biologists to record their experimental metadata in a digital form. This was the start of the OMERO.editor development, which continued when he joined the lab as a developer in October 2007. His other interests include mountaineering, sailing and motorbiking.

Balaji Ramalingam joined the OME team at Dundee University in January 2014 as a software developer. He studied Biotechnology at Anna University, India. He is enthusiastic about working on the integration of computation, instrumentation and automation in biology. His field of expertise is in high throughput biology and automation management. He is a Matlab junkie, cricket fanatic and a hardcore fan of CSK. Conducting grass-roots cricket training programs for kids, and running behind them, was one of his favourite pastimes back in India.

Gabriella Rustici became part of the OME team in 2015 working on the IDR project. She earned her PhD in Genetics from the University of Cambridge in 2004, and first got involved in bioinformatics training while working at EMBL-EBI, with a particular focus on developing training solutions in the functional genomics domain. Gabriella's activities focus on training and educating the life science and biomedical communities to use bioinformatics resources for the analysis and interpretation of biological and biomedical data. She is a member of the ELIXIR Training Platform, helping to develop standards and best-practice guidelines for the assessment of training quality and impact. She is also an active contributor to the Global Organisation for Bioinformatics Learning, Education and Training (GOBLET) and the ISCB Education Committee.

Simone Leo joined the Dundee team in 2015 after being a satellite developer for OME based at CRS4 in Italy. He received an M.Sc. degree in Electronic Engineering from the University of Cagliari, Italy, in 2002 and a PhD in Biomedical Engineering from the same university in 2015. Before joining CRS4 in 2006, he worked in the private sector as a system administrator. His research interests are mainly focused on distributed computing models and applications, with an emphasis on their applicability to computational biology.

Aleksandra Tarkowska joined the OME project in 2007 as a software developer. She studied at the Technical University of Lodz where she received her engineering Master of Science degree in Computer Science and the Universite d'Artois in France as UE Socrates-Erasmus student. She specialises in web/internet technologies. She is enthusiastic and hardworking software developer and engineer, full of passion and commitment. Her software background includes object-oriented programming within cross-platform environments, as well as system integration in conjunction with IBM WebSphere product family. In a free time she relaxes her body and mind: riding a bike, windsurfing, skiing and mountaineering.

Petr Walczysko joined the OME project in October 2012 as a software specialist for testing and quality assurance. He studied at Charles University of Prague where he received Master of Science degree in Physics and the University of Freiburg in Germany where he received PhD in Biology. Throughout his PhD studies and his further career as a researcher he was intensively using conventional, confocal and multiphoton fluorescence microscopy applications on biological systems. He was adapting these optical microscopy techniques for particular biological problems, and also worked on the subsequent image analysis of microscopic images in a range of image analysis programmes. He enjoys yoga, reading and chess.

Harald Waxenegger joined the OME team in December 2015 to help implement new design ideas for viewing image data within OMERO.web. Previously he was working on an orthogonal volume viewer and GIS related projects. Altogether he has been developing applications for 15+ years now, both inside the scientific domain and outside. When he isn't working he is busy with his children and vice versa which means there is little time left for his favorite hobbies: 'Fussball' & Tennis - but then again he's getting too old and injury-prone anyhow so that watching them on TV is the healthier option.

Eleanor Williams joined the OME team in 2015 to work as a data annotator on the Image Data Repository project. She has a PhD in insect chemical ecology. After a few of years of research into crop pests she shifted to bioinformatics, working as a computer biologist at the Fred Hutchinson Cancer Research Center. She then moved to EMBL-EBI where she curated functional genomics data for the ArrayExpress and Expression Atlas databases. Outside of work she likes hanging out with her family, growing veg and is starting to really like running.

Wilma Woudenberg joined the OME team at Dundee University in April 2012 as Jason's PA. She also provides support for his work with Glencoe.

Funding

Development of OME technology in the Swedlow Lab is funded by the a Wellcome Trust Strategic Award (Ref: 095931) and awards from the BBSRC (Refs: BB/I000755/1 and BB/G022585/1).

Past awards to the OME Consortium through Jason Swedlow have been provided by the Wellcome Trust (Refs: 068046 and 077128) and the BRRSC (Refs: BB/D006589/1 and BB/D00151X/1)

Past members of the OME team in Dundee

Chris Allan — Chris has moved to work on OMERO for Glencoe Software.

Gus Ferguson joined the OME team in March 2012. His focus is human factors engineering, user interface design, usability and user experience. He trained in Medicine in Cape Town and did an MSc in HCi at Heriot-Watt University in Edinburgh. Most of his work has involved drawing on his experience in clinical and research medicine for system developments in the areas of Biomedical Informatics and Bioinformatics. Previous areas of computing research have included cancer genetic risk analysis, modelling of cancer genetic screening, evolutionary computing and augmented virtual reality. He lives in Fife and most of his leisure time is spent swimming, walking or just geeking out with his son. He is also involved in promoting wildlife conservation in farming, which somehow always seems to involve lots of mud.

Colin Blackburn joined the OME project in late 2007 as a Python developer. Originally graduating in physics, and then computational physics, he has worked in psychology, physiology and astronomy as a developer of scientific software. When he finds the time he balances the sedentary nature of his obsession with cryptic crosswords with orienteering, fell running and the occasional mountain marathon.

Kelli Griffis joined the OME team in January 2014 as social media assistant. She studied philosophy at Swarthmore College and received her MA in English from Georgia State University. Previously she taught high school English in Atlanta and the San Francisco Bay area. When not tweeting or chasing after her children, she may often be found at Carnoustie Theatre Club rehearsals preparing for the next season’s panto.

Andrew Patterson joined the OME project in 2007 to manage the data model and project documentation. As a software developer he has worked on games, e-learning and personal development applications. In his spare time his interests include historic reenactment and costuming. He has typeset and published an illustrated book on armour making. He would like a computer controlled sewing machine but has managed, so far, to resist temptation. He studied at the University of Dundee and the University of St Andrews and has lived in Fife since 1989. Update: In April 2012 he bought a Elna 8300 Embroidery Machine.

Blazej Pindelski joined the OME project in April 2012 as a software developer. He studied at the Technical University of Opole and the University of Abertay Dundee as an Erasmus programme student. He holds a MSc in Computer Science and BSc in Computing and networks. His field of expertise are client-server systems and web-based applications. He is devoted to best-practice and pattern-based approach to solving computational problems. His hobbies include network and software security research and open-source technologies. He likes spending time outdoors during nice weather and interesting literature.

Joyce Walsh joined the OME team at Dundee University in February 2013.

Scott Littlewood joined the OME team in August 2011 as a software developer. He received a BSc in Compuer Science from The University of Nottingham in 2004 and continued his research on protein structure prediction for a further 2 years. Since then he has worked at several small telecommunications companies as a software developer gaining experience in agile software development and test driven design. His interests range from scalable system architectures and security to web based applications and their integration. When not in the office he can be seen running between Dundee and Carnoustie in preparation for his next marathon or alternative running event.

Emma Hill received her PhD from the University of Cambridge, where she completed her research at the MRC-LMB. She then carried out post-doctoral research at The University of California, Berkeley. In 2005, Emma moved into scientific publishing as an Associate Editor for PLoS Biology. She joined the Journal of Cell Biology as Executive Editor in 2007. During her three years there Emma worked closely with OME to help develop and implement the JCB DataViewer. After moving to Dundee in 2010, Emma worked as administrator for the Dundee Cancer Centre for a year before joining the OME team in 2011.

Scott Loynton became involved in the OME project through his doctoral work in the Usable Image team. His research work investigated the integration of user-centered design (UCD) with scientific software and the specific contextual constraints of academic scientific software development. The research work investigated these challenges from within the OMERO project to understand more about scientific software development in order to and include access to and strategic use of user knowledge, funding environment, complexity and range of stakeholders. To address this, the research proposed a new framework for developing academic SSD that responds to these problems. His research interests are in UCD, design theory and methodologies, user interfaces, CSCW, e-Science, and scientific software development. Scott graduated with an BSc(Hons) in Computer Science from the University of Hertfordshire and the University of Wales Swansea with an MSc in Computing and Software Technology. Outside of work Scott enjoys cycling, traveling and is attempting to learn French.

Simon Wells joined the OME project in 2011 as a software developer. Simon is a computer scientist whose doctoral research used argument-based dialogue protocols to guide communication between huge numbers of intelligent software entities. His interests lie generally in answering the question of how we can build the large-scale, heterogeneous, distributed, robust, and intelligent computational systems of the future. A particular interest is in how we can build such systems from individual components which act rationally, using justifiable strategic behaviours, to satisfy both their individual and wider societal goals. Away from work Simon can be found walking his rescued Collie in North-East Fife and hanging around in dusty bookshops.

Brian Loranger joined the Dundee team in early 2006 and is currently developing the various import tools used by OME. Originally an aeronautical engineering student, he migrated to software development in the early 90s, and has been programming ever since. He spent most of his early programming days working in the private sector, primarily in the telecommunications industry. When not working on OME, he enjoys cycling, hiking, and (when he can find a snow-covered slope) snowboarding.

Donald MacDonald started work as a developer on the OME project in January 2006. He received his PhD in Computer Science from the University of Paisley. His research interests include Statistical Natural Language processing, Data Visualization and Image Classification specifically Remote Sensing images. Donald has worked as a developer for a number of companies and recently as lecturer in Computer Science before seeing the light and joining the OME group in early 2006.

Andrea Falconi joined the staff of the Swedlow lab in 2002. Since then, he's been contributing to the development of OME. Over the years, Andrea has consulted on large software projects and actively joined the development of several applications in different domains, ranging from earth-observation to medical and to business. Having had his brain irremediably damaged by mathematics, his main interests are now in formal software analysis and design as well as design patterns. Andrea now lives in South Africa, but keeps in touch, and may even read the CVS commits!

Stefan Frank has been doing software-development both in the academic and in the commercial field for nearly 10 years now. After graduating in Mathematics and Philosophy in the beautiful city of Bochum, he worked for companies like Springer, SAP, debis, DKFZ(German Cancer Research Center) and several dot-com ventures. His main interest lies in Software Architecture, where he tries to bring as much sound object-oriented principles into the application, as the current state of the J2EE-Specification allows. He is currently based in Heidelberg, Germany, where, if he is occasionally absent from his keyboard, the most probable place to find him is a basketball-court.