Research Uncovered—Accelerating the Diagnosis of Drug-Resistant Tuberculosis: using a Combined Genetic and Computational Approach

 stjo_0130cm-bwWhat: Accelerating the Diagnosis of Drug-Resistant Tuberculosis: using a Combined Genetic and Computational Approach

Who: Philip Fowler

When: 13.00—14.00, Tuesday 22 November 2016

Where: Weston Library Lecture Theatre (map)

Access: all are welcome

Admission: free

Booking: registration is required

The discovery of antibiotics in the middle of the 20th century helped reduce the number of deaths from infectious diseases globally. Unfortunately, the use of antibiotics has inevitably led to bacteria developing resistance. It is vital, therefore, that doctors know which antibiotics can (and which cannot) be used to treat a patient with a bacterial infection, such as Tuberculosis (TB).

At present, a sample taken from the patient is sent to a laboratory, usually in a hospital, where the bacteria are grown and then different antibiotics administered to see which ones are effective. For a slow-growing bacterium like TB this process can take around a month. The incredible rate at which gene sequencing has got faster and cheaper now means that researchers, including the world-leading Modernising Medical Microbiology (MMM) group here at the University of Oxford, are beginning to replace the lab-based method with a genetics-based method.

This talk will describe this shift from lab-based to genetics-based microbiology that is happening in our hospitals and look at new methods that aim to predict the effect of individual mutations in TB genes.

Philip Fowler is a Senior Researcher working in the Modernising Medical Microbiology group at the John Radcliffe Hospital which is part of the Nuffield Department of Medicine at the University of Oxford. He is a computational biophysicist and his research focusses on using computer simulation to understand and predict how proteins and small molecules, like antibiotics, move and interact with one another. Philip blogs and is active on Twitter, @philipwfowler.

Research Uncovered—Illuminating David Livingstone’s 1870 Field Diary with Spectral Imaging

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What: Illuminating David Livingstone’s 1870 Field Diary with Spectral Imaging

Who: Adrian S. Wisnicki, Megan Ward, Roger Easton, Keith Knox, James Cummings

When: 13:00—14:00, Wednesday 16 November 2016

Where: Centre for Digital Scholarship, Weston Library (map)

Access: all are welcome

Admission: free

Booking: registration is required

The Livingstone Spectral Imaging Project is an international digital humanities collaboration to apply advanced imaging technology to the study of the manuscript of Victorian explorer David Livingstone. Previously featured in a National Geographic documentary, the project has now concluded its second phase of research (2013–16) and members of the team including scholars and scientists will present on the results. The first phase (2010–13) confirmed that spectral imaging could be applied to recover “invisible” text in some of David Livingstone’s most damaged texts. In the new phase, the team takes the technology in a new direction—to study the material history of Livingstone’s 1870 Field Diary in order to understand its passage across space, time, and through many, many hands. The team will discuss the image processing techniques applied to the diary and how these techniques have helped uncover significant new information about the diary and the many environments through which it has circulated.

Dr Adrian S. Wisnicki is an assistant professor of English at the University of Nebraska-Lincoln and a faculty fellow of the university’s Center for Digital Research in the Humanities. His research focuses on the digital humanities, Victorian studies, and African studies. He directs Livingstone Online and the Livingstone Spectral Imaging Project and has received grants from the National Endowment for the Humanities, the British Academy, and the Modern Humanities Research Association.

Dr Megan Ward is an assistant professor of English at Oregon State University and Associate Director of Livingstone Online. She specializes in digital archives, material histories, technology studies, and Victorian realism, and is completing a book project titled Human Reproductions: Victorian Realist Character and Artificial Intelligence. She co-directs both Livingstone Online and the Livingstone Spectral Imaging Project.

Dr James Cummings is a Senior Academic Research Technology Specialist for IT Services at the University of Oxford. James is founding Director of the annual Digital Humanities at Oxford Summer School and previously chair of the TEI Consortium’s Technical Council. His PhD was in Medieval Studies from the University of Leeds and he was Director of Digital Medievalist (2009-2012).

Dr Roger Easton has been on the faculty of the Chester F. Carlson Center for Imaging Science of the Rochester Institute of Technology since 1986, where he teaches courses in imaging mathematics and optics. Since the mid 1990s, his research interests have focused on imaging tools for historical objects, primarily manuscripts. He was head of the imaging team for the Archimedes Palimpsest project and been a member of the teams for the David Livingstone Diaries, the Martellus World Map, and the palimpsests at St. Catherine’s Monastery.

Dr Keith Knox is an imaging scientist with the Early Manuscripts Electronic Library (EMEL). He has 40 years experience in conducting research in scanning, printing and astronomical image processing. Keith retired in 2015 to focus his efforts on the imaging and recovery of cultural heritage information from historical documents and artifacts.

Access: If you have a University or Bodleian Reader’s card, you can get to the Centre for Digital Scholarship through the Mackerras Reading Room on the first floor of the Weston Library, around the gallery. If you do not have access to the Weston Library you are more than welcome to attend the talk: please contact Pip Willcox before the event (pip.willcox@bodleian.ox.ac.uk).

You can download a flyer for this talk.

An invitation to hack sound

University-OeRC-logosThe Centre for Digital Scholarship and the University of Oxford e-Research Centre invite you to a day of sound hacking.

Image from Johns Hopkins University: http://hub.jhu.edu/2012/11/07/timbre-hearing-prosthetics/.

Image from Johns Hopkins University: http://hub.jhu.edu/2012/11/07/timbre-hearing-prosthetics/.

What: Hacking Sound

When: Thursday 20 October 2016

Where: University of Oxford e-Research Centre, 7 Keble Road, Oxford OX1 3QG (Directions)

Access: free and open to all, with places allocated by first come, first served

Registration: required

We welcome anyone with an interest in sound, its production, reception, and technologies, and people who want to play with hearing their data. There is no requirement for technological, musical, or coding experience.

Sounds surround us everywhere, and in our urban and industrial environments we are permanently immersed in music and noise—alarms, vending machines, phones have familiarized us with mechanical sound as signal. Sonifications, or audiograms, are beginning to attract attention (including from BBC News and Wolfram Research), yet this area of study continues to be less studied than, for example, visual analytics.

The celebrations of Ada Lovelace’s 200th birthday demonstrated a larger interest in the intersection of machinery, music, and culture, and pushed existing disciplinary boundaries. The hack day will build on this and we look forward to developing ideas and approaches together.

Our hack day will experiment with ways of representing data with sound or music and exploring the sonic world. We encourage you to bring data and existing projects to share, and to start on fresh ideas. The day will encourage networking and developing ideas and projects, ending with a showcase of what we’ve produced and future directions we might take. We hope many of us will find new collaborators and be inspired to pursue new projects.

For more information and to book tickets: http://hackingsound.org/.

Digital Methods— Peaches and lemons are foodstuffs. Trying to classify historical texts using the BBIH Thesaurus.

LimeAndLemonLowResWhat: Peaches and lemons are foodstuffs. Trying to classify historical texts using the BBIH Thesaurus.

Who: Simon Baker, Jonathan Blaney, Marty Steer

When: 13:00—14:00, Thursday 6 October 2016

Where: Centre for Digital Scholarship, Weston Library (map)

Access: all are welcome

Admission: free

Booking: registration is required

The Institute of Historical Research collates and classifies a large variety of material relating to History in UK Higher Education. With the rise of open access publishing and the proliferation of web resources, keeping up has become more and more difficult. Funding from the AHRC has allowed the IHR’s digital team to explore ways of automatically classifying works based on features such as book blurbs, article abstracts, titles and metadata.

This talk will cover the challenges the AHRC-funded TOBIAS project has met in classifying this material, using the Royal Historical Society’s fine-grained vocabulary of British and Irish history. Techniques the team is trying range from “bag of words” string matching to machine learning.

Simon Baker is the editor of the Bibliography of British and Irish History (BBIH).

Jonathan Blaney is the Project Editor for British History Online.

Marty Steer is the Website Manager at the Institute of Historical Research.

All three speakers are engaged with the TOBIAS project, funded under the  AHRC’s Follow-on Funding Impact & Engagement Scheme.

Access: If you have a University or Bodleian Reader’s card, you can get to the Centre for Digital Scholarship through the Mackerras Reading Room on the first floor of the Weston Library, around the gallery. If you do not have access to the Weston Library you are more than welcome to attend the talk: please contact Pip Willcox before the event (pip.willcox@bodleian.ox.ac.uk).

You can download a flyer for this series.

Research Uncovered—A corpus stylistics approach to the discourse of adoption in Picture Books: Social uses of multimodal creativity

CoralCalvaMaturanaWhat: A corpus stylistics approach to the discourse of adoption in Picture Books: Social uses of multimodal creativity

Who: Coral Calvo Maturana

When: 13.00—14.00, Wednesday 10 August 2016

Where: Centre for Digital Scholarship, Weston Library (map)

Access: all are welcome

Admission: free

Booking: registration is not required

This presentation explores the discourse of adoption through an analysis of how adoption is linguistically and visually delineated in a corpus of picture books. The aim is to understand how adoption is portrayed, and what the concerns and viewpoints of the three main participants are: child, adoptive parents, and birth parents, as well as those of the voices that surround them.

The study combines a quantitative and qualitative analysis, in which computer-based software is combined with the closer analysis of the individual texts.

The project lies under the umbrella of the major enterprise of understanding how adoption is conceived, the words and patterns used to talk about it, how it is visually represented, and in what ways these choices depict, challenge, and reshape society’s understanding of parenthood and families.

Dr Coral Calvo Maturana is English Lecturer at the University of Cádiz in Spain. Her research interests include stylistics, (critical) discourse analysis, corpus linguistics, and multimodality. Her doctoral thesis: ‘Motherhood and Poetic Voices in The Adoption Papers by Jackie Kay: a corpus stylistics study’, resulted in her special interest in the discourse of adoption, and its multimodal representation in both literary and non-literary texts.

Access: If you have a University or Bodleian Reader’s card, you can get to the Centre for Digital Scholarship through the Mackerras Reading Room on the first floor of the Weston Library, around the gallery. If you do not have access to the Weston Library you are more than welcome to attend the talk: please contact Pip Willcox before the event (pip.willcox@bodleian.ox.ac.uk).

You can download a flyer for this talk.

Research Uncovered— Digital Hermeneutics and Cross Platform Research: Walking to the Theatre in Shakespeare’s London

BOOK FREE TICKETS!

PLEASE NOTE THE CHANGE OF VENUE: WESTON LIBRARY LECTURE THEATRE.

ThomasDabbsWhat: Digital Hermeneutics and Cross Platform Research: Walking to the Theatre in Shakespeare’s London

Who: Thomas Dabbs

When: 13.00—14.00, Thursday 1 September 2016

Where: Centre for Digital Scholarship, Weston Library Lecture Theatre (map)

Access: all are welcome

Admission: free

Booking: registration is not required but is advisable to ensure your place

By exploring the cross-platform interoperability of new or relatively new digital projects in development, this talk will present a street view of theatre routes that London playgoers walked before and during the Shakespearean period. It will examine the physical environs experienced while ambling to the theatres inside and outside the city and also probe into another crucial walk, the stroll through the St Paul’s precinct.

The nave of St Paul’s, then called Paul’s Walk, and the bookshops of Paul’s Cross churchyard instantiated, by a type of cultural accident, a general centre for hearing the news and, for readers, the gateway to remaining au courant. Walking and browsing in this area was something of a prerequisite for playgoers and, for playwrights, a locale where one could hear what was on the buzz and also a reservoir from which to cull material for successful plays.

There have been a number of recent and fines studies connecting London city life with the early modern theatre. This talk will examine how digital initiatives may advance this field by offering more insights into theatre going and into how plays were fashioned for then current audiences by Shakespeare and other playwrights.

Thomas Dabbs is a professor of English at Aoyama Gakuin University in Tokyo, where he has taught Shakespeare and the English Bible since 2003. Prior to this Dabbs taught at Hiroshima University. He is the author of Reforming Marlowe: the Nineteenth-Century Canonization of a Renaissance Dramatist and Genesis in Japan: The Bible beyond Christianity. His recent research and publication focuses on the St Paul’s cathedral precinct in early modern London and the impact of this area on Shakespearean drama. He is a native of the state of South Carolina in the USA.

Access: If you have a University or Bodleian Reader’s card, you can get to the Centre for Digital Scholarship through the Mackerras Reading Room on the first floor of the Weston Library, around the gallery. If you do not have access to the Weston Library you are more than welcome to attend the talk: please contact Pip Willcox before the event (pip.willcox@bodleian.ox.ac.uk).

You can download a flyer for this talk.

Software Sustainability Institute Research Data Visualization Workshop

Our colleagues at the Software Sustainability Institute announce…

Research Data Visualization Workshop

University of Manchester
28 July 2016

There will be some presentations on data visualization in different domains (social science, medical informatics, geographic information system) during the morning. There will be time for networking during breaks, and hands-on sessions in the afternoon. In the hands-on session attendees will have the opportunity to create their own visualizations using their own data on a platform of their choice (Python, R, MATLAB and Javascript).

Find out more and book a place: http://software.ac.uk/rdvw.

Digital Methods—Visual Analytics Series

We are delighted to welcome Margaret Varga, chair of the NATO Exploratory Visual Analytics Research Task Group and visiting fellow at the University of Oxford’s Department of Oncology, to present a major series on Visual Analytics at the Centre for Digital Scholarship. Each lecture will stand alone, and attending more of them will build to give an overview of this increasingly vital and profoundly interdisciplinary work from a world expert in the field.

VisualAnalytics

MargaretVargaWhat: Visual Analytics Series

Who: Margaret Varga

When: 13:00—14:00, Thursdays, between 23 June and 8 December 2016

Where: Centre for Digital Scholarship, Weston Library (map)

Access: all are welcome

Admission: free

Booking: registration is not required but is recommended to assure you a place

Series: Visual analytics is the science of analytical reasoning facilitated by interactive visual interface.  This Visual Analytics lecture series aims to provide some basic understanding of visual analytics and it applications to a number of different real-world applications in: aviation safety, cyber security, maritime situation awareness, financial risk management, healthcare and social media analysis.  

23 June: Application of visual analytics to aviation safety

Bird strikes pose serious problems for both civil and military aircraft.  This seminar will discuss a Visual Analytics approach to working with and understanding the raw incident reporting data.

Book free tickets

30 June: Application of visual analytics to healthcare associated infection

Healthcare associated infections (HAI) are of important concern in patient care.  This seminar will describe Visual Analytics techniques which have been developed to help detect, monitor, analyse and understand trends, clusters and outbreaks of HAI.

Book free tickets

13 October: Application of visual analytics to maritime domain awareness

This seminar will discuss the application of visual analytics to the detection and analysis of security threats in the maritime domain.

Book free tickets

3 NovemberApplication of visual analytics to cyber security

This seminar will describe, compare and contrast user-centric and system-based approaches in the cyber security application domain.

Book free tickets

17 November: Application of visual analytics to financial stability monitoring

This seminar will consider the application of Visual Analytics to address challenges in financial stability monitoring.

Book free tickets

24 November: Application of visual analytics to social media analysis

This seminar discusses the application of Visual Analytics in the exploration of trends, patterns and anomalies in social media data.

Book free tickets

8 December: What is Visual Analytics?

This seminar introduces how Visual Analytics integrates technologies to support all facets of the human analysis and reasoning processes.

Book free tickets

Margaret Varga received her PhD in statistical pattern recognition from the University of Cambridge. She is a director at Seetru Ltd. and is the chairman of the NATO Exploratory Visual Analytics Research Task Group, as well as a visiting fellow at the University of Oxford. Her research interests are in visual analytics, visualisation, uncertainty analysis, network analysis, evidential reasoning, provenance analysis and visualisation, Bayesian reasoning, pattern processing, financial systemic risk and stability monitoring, image processing. Dr. Varga led the team that developed the world’s first automated breast cancer histopathology diagnosis systems, and she holds seven patents for this system.  She has over a hundred publications.

You can download a flyer for this series.

Research Uncovered—Digital Humanities: Ferment in the Field

DavidBerryWhat: Digital Humanities: Ferment in the Field

Who: David Berry

When: 13.00—14.00, Thursday 2 June 2016

Where: Centre for Digital Scholarship, Weston Library (map)

Access: all are welcome

Admission: free

Booking: registration is required 

As Digital Humanities continues to grow and develop as a discipline, both in terms of its interdisciplinary work and the development of research questions specific to itself, there has emerged a number of controversies about its supposed nature. These critical voices have been articulated from a number of disciplinary traditions, but tend to be mostly from the humanities.

This talk will look at the developing field of digital humanities, and examine these sites of controversy in terms of the the changing nature of humanities research, partly due to the undoubted expansion of digital resources and digital scholarship more generally, but also in terms of the history and development of the field of digital humanities understood as somehow contrary to the humanistic pursuits of the university. This talk will look at a number of ways in which digital humanities does indeed suggest new ways of working for the humanities, but also how these can augment existing approaches, rather than necessarily being in opposition to them, but also why they raise such anxieties around the future of the humanities and the university in a digital age.

David M. Berry is Professor of Digital Humanities in the School of Media, Film and Music at the University of Sussex. He writes widely on computation and the digital and is the author of Critical Theory and the Digital, The Philosophy of Software: Code and Mediation in the Digital Age, Copy, Rip, Burn: The Politics of Copyleft and Open Source, the editor of Understanding Digital Humanities and co-editor of Postdigital Aesthetics: Art, Computation and Design (with Michael Dieter). His forthcoming book in 2016 is Digital Humanities (with Anders Fagerjord).

Access: If you have a University or Bodleian Reader’s card, you can get to the Centre for Digital Scholarship through the Mackerras Reading Room on the first floor of the Weston Library, around the gallery. If you do not have access to the Weston Library you are more than welcome to attend the talk: please contact Pip Willcox before the event (pip.willcox@bodleian.ox.ac.uk).

You can download a flyer for this talk.

Making the most of digitized books and manuscripts: a free IIIF workshop

Mirador workspace

Notes and slides for this talk are now available.

What: Making the most of digitized books and manuscripts: a free IIIF workshop

Who: Emma Stanford, on behalf of Bodleian Digital Library Systems and Services and the Centre for Digital Scholarship

When: 10.00 – 12.00, Friday 27 May 2016

Where: Centre for Digital Scholarship, Weston Library (map)

Access: all are welcome

Admission: free

Booking: This event is now fully booked. If you do not have a ticket but would still like to attend, please contact emma.stanford@bodleian.ox.ac.uk.

Learn about new digital tools for humanities research and build your own virtual workspace for viewing books and manuscripts from libraries around the world in this short talk and workshop presented by BDLSS and the Centre for Digital Scholarship.

Since 2012, the International Image Interoperability Framework (IIIF) has been enabling scholars to view, annotate and remix digitized images. The Bodleian has been in the vanguard of these developments, first with Digital.Bodleian, our IIIF-compatible digitized special collections website, and now with the Digital Manuscripts Toolkit, which will open up IIIF technology to humanities researchers with a set of easy-to-use tools. In this workshop, you will learn about the basic principles of IIIF, see the technology in action at the Bodleian and other institutions, and find out how to use free tools such as Mirador and the Universal Viewer in your own research. You will also have the opportunity to get involved in the development and testing of the Digital Manuscripts Toolkit.

Refreshments will be provided. Please bring your own laptops for the hands-on portion of this event.

Access: If you have a University or Bodleian Reader’s card, you can get to the Centre for Digital Scholarship through the Mackerras Reading Room on the first floor of the Weston Library, around the gallery. If you do not have access to the Weston Library you are more than welcome to attend the talk: please contact Emma Stanford before the event (emma.stanford@bodleian.ox.ac.uk).