The document summarizes the UK's investments in e-infrastructure for research from 2011-2015. It discusses the major investments made in high performance computing (HPC), networking infrastructure, and big data projects. The investments totaled £160 million in 2011-2012, £189 million in 2012-2013, and £257 million in 2014-2015. It also summarizes the results of a survey of the UK's e-infrastructure, including details on the largest HPC systems and datasets. Finally, it mentions that the Research Councils UK (RCUK) developed a roadmap for the UK's e-infrastructure with a vision for an integrated infrastructure to support researchers.
Cloud for Research and Innovation - UK USA HPC workshop, Oxford, July 205Martin Hamilton
How can public cloud and technologies like Docker and OpenStack help to deliver next generation scientific computing infrastructure? My talk for the UK/USA HPC workshop in July 2015, organized by HPC-SIG (UK) and CASC (USA).
From Jisc's campus network engineering for data-intensive science workshop on 19 October 2016.
https://www.jisc.ac.uk/events/campus-network-engineering-for-data-intensive-science-workshop-19-oct-2016
The user -driven evolution of Janet - Jisc Digifest 2016Jisc
Janet is one of the world’s most advanced networks built to support research and education across the UK, and through participation in GÉANT provides global reach, supporting key activities such as transnational education and access to global research facilities.
The latest version of the network – Janet6 – came into operation in November 2013. This talk will take a look at user requirements and how these are shaping the continued evolution of Janet to ensure that a flexible, reliable and secure network service is provided.
Presentation given at Digital Humanities in Practice Seminar, Open University, UK. 24th January 2013.
More info at http://ww1.discovery.ac.uk/digital-humanities-and-the-first-world-war/
Cloud for Research and Innovation - UK USA HPC workshop, Oxford, July 205Martin Hamilton
How can public cloud and technologies like Docker and OpenStack help to deliver next generation scientific computing infrastructure? My talk for the UK/USA HPC workshop in July 2015, organized by HPC-SIG (UK) and CASC (USA).
From Jisc's campus network engineering for data-intensive science workshop on 19 October 2016.
https://www.jisc.ac.uk/events/campus-network-engineering-for-data-intensive-science-workshop-19-oct-2016
The user -driven evolution of Janet - Jisc Digifest 2016Jisc
Janet is one of the world’s most advanced networks built to support research and education across the UK, and through participation in GÉANT provides global reach, supporting key activities such as transnational education and access to global research facilities.
The latest version of the network – Janet6 – came into operation in November 2013. This talk will take a look at user requirements and how these are shaping the continued evolution of Janet to ensure that a flexible, reliable and secure network service is provided.
Presentation given at Digital Humanities in Practice Seminar, Open University, UK. 24th January 2013.
More info at http://ww1.discovery.ac.uk/digital-humanities-and-the-first-world-war/
Shared services - the future of HPC and big data facilities for UK researchMartin Hamilton
Slides from Jisc panel session at HPC & Big Data 2016 with contributions from the Francis Crick Institute, QMUL and King's College London covering their use of the Jisc shared data centre and the eMedLab project
The research data spring project "DataVault" slides for the third sandpit workshop. Project led by University of Manchester and University of Edinburgh.
Presentation at the Open Knowledge Festival: Open Research and Education Stream, 20 September 2012, Helsinki; also
Presentation at the DINI-Jahrestagung - Bausteine für Open Science, 24 September 2012, Karlsruhe;
also Belgian Open Access Week: Open Access to Excellence in Research, 22 October 2012, Brussels.
Jisc Support for Asset Sharing - Kit-Catalogue National User Group November 2014Martin Hamilton
My slides introducing Jisc's support for asset sharing, at the 2014 Kit-Catalogue national user group. I talk about the rationale for Jisc becoming involved in supporting equipment sharing and the Jisc Kit-Catalogue pilot, and present some feedback from user group delegates about their experiences of equipment sharing. For more information about this initiative, please see http://www.jisc.ac.uk/research/projects/equipment-sharing
Research data spring - Jisc Digital Festival 2015Jisc
This demonstration explored a few ideas and the collborative process implemented by Jisc R&D to select ideas and gather feedback for technical tools, software and service solutions to support the management of research data.
Liberating facts from the scientific literature - Jisc Digifest 2016Jisc
Text and data mining (TDM) techniques can be applied to a wide range of materials, from published research papers, books and theses, to cultural heritage materials, digitised collections, administrative and management reports and documentation, etc. Use cases include academic research, resource discovery and business intelligence.
This workshop will show the value and benefits of TDM techniques and demonstrate how ContentMine aims to liberate 100,000,000 facts from the scientific literature, and ContentMine will provide a hands on demo on a topical and accessible scientific/medical subject.
Reading lists as open data - Meeting the Reading List Challenge 2016Martin Hamilton
My session at MTRLC 2016 describes how Jisc has been working with Lancaster University, the Open Data Institute and Talis to explore the potential of reading lists as open data. The immediate goal of this work is to use open reading list data to power an app for students, BookMart, which will help them to find affordable textbooks. This talk also covers other potential uses of open reading list data such as national deals and identifying areas where effort might usefully be devoted to open educational resources.
This session is sponsored by Fortinet.
Chair: Frances Burton, security services group manager, Jisc.
Cybersecurity has long been an area of activity for those responsible for providing, protecting and supporting digital services in research and education, but recent events have focused public and media attention on the scale of the threat.
Our security thread at this year’s conference is picking up on some of these themes and we have sessions covering a number of cybersecurity areas. There will be presentations on organisation experiences of email phishing and the results of our RPZ trial. Accreditation of services is being requested more often by project funders and will have a case study presentation on experience of obtaining ISO27001.
Running order of talks:
11:30-11:55 - RPZ trial
Speaker: Peter Dorey, Spamhaus
11:55-12:20 - Addressing the skills shortage in cybersecurity
Speaker: Debbie Tunstall, Cyber Security Challenge.
12:20-12:45 - Institutional issues with Bitcoin
Speaker: Jethro Perkins, London School of Economics and Political Science (LSE).
Kit-Catalogue - Discovering the Value of Equipment Sharing - Universities UK ...Martin Hamilton
Universities UK (UUK) 4th Annual Efficiency in Higher Education Conference talk from me and UCL's Jacky Pallas on accelerating equipment sharing. This covers Jisc initiatives such as our shared data centre and VAT cost sharing group, and our pilot of the Kit-Catalogue equipment database software - with a case study from UCL showing how they have used Kit-Catalogue.
Stronger together: community initiatives in journal managementJisc
There has been a recent growth of initiatives to address common problems regarding current and long-term access to e-journal content. Jisc is at the forefront of many of these with the close participation and active input of educational institutions.
This session aims to summarise the current state of key themes with pointers to future directions of areas such as sustainability, the move towards e-only environments, and shared consortia approaches. It will provide an overview and panel discussion on developing the supporting infrastructure to meet the needs of users. The discussion will focus on how institutions, community bodies and service providers can best work together to ensure sustainable, long-term initiatives by seeking to introduce uniformity, standardisation and collaboration to an even greater extent.
The session will introduce two new Jisc-supported projects in this area, the Keepers Registry Extra and SafeNet initiatives, and discuss how these fit alongside existing Jisc services such as Knowledge Base+, UK LOCKSS Alliance, Journal Archives and JUSP (Journal Usage Statistics Portal). The panel will address how this catalogue of services contributes towards a coherent strategy in the management of e-journal content.
Collaboration through technology: moving from possibility to practice - Marti...Jisc
Led by Martin Hamilton, futurist, Jisc.
With contribution from Daniel Fairbairn, e-learning manager, Uxbridge College.
This session will explore the potential that technology can bring to all forms of collaboration, and consider the difference that it has made to some local organisations and their practices.
Connect more in London, 28 June 2016
Using jisc's JUSP and CCM services effectively to manage resources - Jisc Dig...Jisc
This session discussed the very real, practical benefits gained from using Jisc services (JUSP, Copac Collections Management/CCM) in enabling more effective and efficient collection management activity to take place in higher education institutions.
Closing plenary - John Wilkin and David MaguireJisc
Infrastructure for US research and scholarship
Speaker: John Wilkin, dean of libraries and university librarian at the University of Illinois, previous executive director, HathiTrust.
Efficient infrastructure for UK research
Speaker: David Maguire, vice-chancellor of the University of Greenwich and chair of Jisc.
Jisc and CNI conference, 6 July 2016
Implementing Open Access: Effective Management of Your Research DataMartin Hamilton
The slides from my session with the DCC's Martin Donnelly at the Understanding ModernGov "Implementing Open Access" event in June 2014. Our talk is all about the support available from Jisc and the DCC to help you manage your research data, and potential future initiatives that might help institutions to handle the move to "open science".
Shared services - the future of HPC and big data facilities for UK researchMartin Hamilton
Slides from Jisc panel session at HPC & Big Data 2016 with contributions from the Francis Crick Institute, QMUL and King's College London covering their use of the Jisc shared data centre and the eMedLab project
The research data spring project "DataVault" slides for the third sandpit workshop. Project led by University of Manchester and University of Edinburgh.
Presentation at the Open Knowledge Festival: Open Research and Education Stream, 20 September 2012, Helsinki; also
Presentation at the DINI-Jahrestagung - Bausteine für Open Science, 24 September 2012, Karlsruhe;
also Belgian Open Access Week: Open Access to Excellence in Research, 22 October 2012, Brussels.
Jisc Support for Asset Sharing - Kit-Catalogue National User Group November 2014Martin Hamilton
My slides introducing Jisc's support for asset sharing, at the 2014 Kit-Catalogue national user group. I talk about the rationale for Jisc becoming involved in supporting equipment sharing and the Jisc Kit-Catalogue pilot, and present some feedback from user group delegates about their experiences of equipment sharing. For more information about this initiative, please see http://www.jisc.ac.uk/research/projects/equipment-sharing
Research data spring - Jisc Digital Festival 2015Jisc
This demonstration explored a few ideas and the collborative process implemented by Jisc R&D to select ideas and gather feedback for technical tools, software and service solutions to support the management of research data.
Liberating facts from the scientific literature - Jisc Digifest 2016Jisc
Text and data mining (TDM) techniques can be applied to a wide range of materials, from published research papers, books and theses, to cultural heritage materials, digitised collections, administrative and management reports and documentation, etc. Use cases include academic research, resource discovery and business intelligence.
This workshop will show the value and benefits of TDM techniques and demonstrate how ContentMine aims to liberate 100,000,000 facts from the scientific literature, and ContentMine will provide a hands on demo on a topical and accessible scientific/medical subject.
Reading lists as open data - Meeting the Reading List Challenge 2016Martin Hamilton
My session at MTRLC 2016 describes how Jisc has been working with Lancaster University, the Open Data Institute and Talis to explore the potential of reading lists as open data. The immediate goal of this work is to use open reading list data to power an app for students, BookMart, which will help them to find affordable textbooks. This talk also covers other potential uses of open reading list data such as national deals and identifying areas where effort might usefully be devoted to open educational resources.
This session is sponsored by Fortinet.
Chair: Frances Burton, security services group manager, Jisc.
Cybersecurity has long been an area of activity for those responsible for providing, protecting and supporting digital services in research and education, but recent events have focused public and media attention on the scale of the threat.
Our security thread at this year’s conference is picking up on some of these themes and we have sessions covering a number of cybersecurity areas. There will be presentations on organisation experiences of email phishing and the results of our RPZ trial. Accreditation of services is being requested more often by project funders and will have a case study presentation on experience of obtaining ISO27001.
Running order of talks:
11:30-11:55 - RPZ trial
Speaker: Peter Dorey, Spamhaus
11:55-12:20 - Addressing the skills shortage in cybersecurity
Speaker: Debbie Tunstall, Cyber Security Challenge.
12:20-12:45 - Institutional issues with Bitcoin
Speaker: Jethro Perkins, London School of Economics and Political Science (LSE).
Kit-Catalogue - Discovering the Value of Equipment Sharing - Universities UK ...Martin Hamilton
Universities UK (UUK) 4th Annual Efficiency in Higher Education Conference talk from me and UCL's Jacky Pallas on accelerating equipment sharing. This covers Jisc initiatives such as our shared data centre and VAT cost sharing group, and our pilot of the Kit-Catalogue equipment database software - with a case study from UCL showing how they have used Kit-Catalogue.
Stronger together: community initiatives in journal managementJisc
There has been a recent growth of initiatives to address common problems regarding current and long-term access to e-journal content. Jisc is at the forefront of many of these with the close participation and active input of educational institutions.
This session aims to summarise the current state of key themes with pointers to future directions of areas such as sustainability, the move towards e-only environments, and shared consortia approaches. It will provide an overview and panel discussion on developing the supporting infrastructure to meet the needs of users. The discussion will focus on how institutions, community bodies and service providers can best work together to ensure sustainable, long-term initiatives by seeking to introduce uniformity, standardisation and collaboration to an even greater extent.
The session will introduce two new Jisc-supported projects in this area, the Keepers Registry Extra and SafeNet initiatives, and discuss how these fit alongside existing Jisc services such as Knowledge Base+, UK LOCKSS Alliance, Journal Archives and JUSP (Journal Usage Statistics Portal). The panel will address how this catalogue of services contributes towards a coherent strategy in the management of e-journal content.
Collaboration through technology: moving from possibility to practice - Marti...Jisc
Led by Martin Hamilton, futurist, Jisc.
With contribution from Daniel Fairbairn, e-learning manager, Uxbridge College.
This session will explore the potential that technology can bring to all forms of collaboration, and consider the difference that it has made to some local organisations and their practices.
Connect more in London, 28 June 2016
Using jisc's JUSP and CCM services effectively to manage resources - Jisc Dig...Jisc
This session discussed the very real, practical benefits gained from using Jisc services (JUSP, Copac Collections Management/CCM) in enabling more effective and efficient collection management activity to take place in higher education institutions.
Closing plenary - John Wilkin and David MaguireJisc
Infrastructure for US research and scholarship
Speaker: John Wilkin, dean of libraries and university librarian at the University of Illinois, previous executive director, HathiTrust.
Efficient infrastructure for UK research
Speaker: David Maguire, vice-chancellor of the University of Greenwich and chair of Jisc.
Jisc and CNI conference, 6 July 2016
Implementing Open Access: Effective Management of Your Research DataMartin Hamilton
The slides from my session with the DCC's Martin Donnelly at the Understanding ModernGov "Implementing Open Access" event in June 2014. Our talk is all about the support available from Jisc and the DCC to help you manage your research data, and potential future initiatives that might help institutions to handle the move to "open science".
Software Sustainability: preserving the future of research softwareNeil Chue Hong
Talk given at the National Science Foundation on the UK e-Science programme, the UK Software Sustainability Institute, and some of the challenges faced in ensuring long term development and maintenance of scientific software
A High-Performance Campus-Scale Cyberinfrastructure: The Technical, Political...Larry Smarr
10.10.11
Presentation by Larry Smarr to the NSF Campus Bridging Workshop
Title: A High-Performance Campus-Scale Cyberinfrastructure: The Technical, Political, and Economic
Anaheim, CA
¿Es posible construir el Airbus de la Supercomputación en Europa?AMETIC
Presentación a cargo de Mateo Valero, Director del Barcelona Supercomputing Center, en el marco de la 30ª edición de los Encuentros de Telecomunicaciones y Economía Digital.
National scale research computing and beyond pearc panel 2017Gregory Newby
Panel at the PEARC 2017 event in New Orleans, July 11-13. Panelists were: Gregory Newby, Chief Technology Officer, Compute Canada; Florian Berberich, Member of the Board of Directors PRACE aisbl; Gergely Sipos, Customer and Technical Outreach Manager, EGI Foundation; and John Towns, Director of Collaborative eScience Programs, National Center for Supercomputing Applications.
Panel abstract: How might the international community of research computing users and stakeholders benefit from knowledge sharing among national- or international-scale research computing organizations and providers? It is common for large-scale investments in research computing systems, services and support to be guided and funded with government oversight and centralized planning. There are many commonalities, including stakeholder relations, outcomes reporting, long-range strategic planning, and governance. What trends exist currently, and how might information sharing and collaboration among resource providers be beneficial? Is there desire to form a partnership, or to build upon existing relationships? Participants in this panel will include personnel involved in US, Canadian and European research computing jurisdictions.
UK e-Infrastructure: Widening Access, Increasing ParticipationNeil Chue Hong
A talk given at the ICHEC Annual Seminar by Neil Chue Hong, reflecting on the rise of Grid and Web 2.0, and how this might enable increased participation and use of computing infrastructure for e-Science and research.
El nuevo superordenador Mare Nostrum y el futuro procesador europeoAMETIC
Presentación a cargo de Mateo Valero, del BSC-CNC, en el 33er Encuentro de la Economía Digital y las Telecomunicaciones organizado por AMETIC y Santander Empresas en colaboración con la UIMP
An update on BeSTGRID activity and plans, in particular in preparation for the planned future developments of a unified approach to high performance and distributed computing in NZ.
Keep taking the tablets? The graduation of the iPad generationMartin Hamilton
Over the last ten years, smartphones and tablets and pervasive Internet connectivity have taken over our lives, and more importantly the lives of our children. In this talk for Loughborough University's 2018 Learning and Teaching conference I reflect on how higher education could respond to this trend. I invite the audience to consider what children who have always had access to the sum total of human knowledge will will expect and need from universities in the future, and how we might best support learners from disadvantaged backgrounds to thrive
The Intelligent Campus - Where the Internet of Things meets AI - HESCA June 2018Martin Hamilton
In this talk for the Higher Education Smart Card Assocation (HESCA) I introduce Jisc's Intelligent Campus initiative, which is looking at how we can connect data from Internet of Things sensors to Learning Analytics services to improve learning outcomes and attainment whilst also delivering institutional efficiency savings and exploring new delivery models for higher education
The Digital Book Thief has a Napster Moment - Edinburgh Near Future Library S...Martin Hamilton
We’ve grown accustomed to being able to call up any information, anywhere, any time - but what happens when our digital landlord forecloses? When that service we entrusted our data to goes to the Startup Graveyard? In this talk for the University of Edinburgh's Near Future Library Symposium I highlight some of the risks to our culture and the scientific record, and what the near future library can do to help
Martin Hamilton - The wind from nowhere - Horizon scanning in an uncertain ag...Martin Hamilton
Does it feel like the world has recently become much less certain and predictable? We tend to expect that each day will be like the last, more or less, but incremental change is increasingly feeling like a thing of the past. In this talk for the 2018 Scientia EMEA User Conference I look at how we can read the signals around us to better predict the future, and consider the impact of technologies and trends like blockchain, artificial intelligence and Brexit on further and higher education
From Blockchain to Brexit - edtech trends for 2018 - BETT 2018Martin Hamilton
In this talk for BETT 2018 I take a look at a few of the socio-technical trends that are set to have a big impact on universities and colleges in 2018 from blockchain to Brexit, and data vandalism to UK spaceports. I look at some approaches that institutions can take to help plan for an uncertain future, and consider how the community can mobilise to protect the progressive values that now often seem to be under threat.
Martin Hamilton - Digital skills: You won't believe what happened next!Martin Hamilton
We're often told how it's vitally important for everyone to develop their digital skills, but what digital skills will we need for near future careers, and how can we go about developing them? In this talk for the Manchester Digital Skills Festival 2018 I take a look at a few examples, including some that are literally out of this world
Martin Hamilton - Librarians in Outer Space - CILIP invited talkMartin Hamilton
We are becoming used to living in an interconnected world, with vast amounts of data at our fingertips, but what happens when our preconceptions are challenged? What happens when the things that we take for granted simply don’t work any more? How can librarians rise to the challenge? In this invited talk for CILIP, I reflect on the impact for libraries and librarians of some of the defining narratives of the late Anthropocene era: from climate change and failed states to cheap space travel and artificial intelligence
Martin Hamilton - The impact of technology on the higher education sector - L...Martin Hamilton
How digital is your university? In this talk for the Leadership Foundation for Higher Education (LFHE) I invite viewers to think about the impact of technology on the sector, with some examples of disruptive technologies and trends, like Udacity's self-driving car engineering nanodegree
Martin Hamilton - Robots and AI, the calm before the Singularity? - BCS invit...Martin Hamilton
In this invited talk for the BCS I look at the state of the art in robots and artificial intelligence, and what this tells us about the near-term future that our children and grandchildren will live in. Will the imminent arrival of AI powered self-driving vehicles mean redundancies for truck and taxi drivers? What will these people do next? I also show how robots and AI are already becoming commonplace, working in places like shops, restaurants and distribution centres
Martin Hamilton - What did your AI make today? - BCS invited talkMartin Hamilton
Artificial intelligence and machine learning are used extensively by Internet services to help us find and classify information. This is how products like Google Photos can "magically" find all your photos of cats or trees - or cats up trees! But there's a new wave of AI called generative adversarial neural networks that's all about using AI to make things. In this invited talk for the British Computer Society (BCS) I reflect on what we could use this technology for and the implications for people and society.
Blockchain in research and education - UKSG Webinar - September 2017Martin Hamilton
There’s a lot of hype right now about blockchain, the technology that underpins the Bitcoin virtual currency, with speculation that it could transform just about every aspect of our lives. In this talk for UKSG I consider possible blockchain applications in research and education, and do a little myth-busting about when and where it makes sense to use blockchain.
HPC in the cloud comes of age - Red Oak HPC SeminarMartin Hamilton
What does HPC in the cloud look like in 2017, and how did we get there? In this talk for Red Oak's HPC Seminar, I look at the origins of cloud HPC, and how it has become mainstream through technologies like Amazon Web Services and OpenStack. I also offer a sneak preview of the 2017 UK national e-Infrastructure survey results, and some thoughts about what's next in cloud HPC, from hyperscale providers to the momentum behind container technologies from Docker and the Open Container Initiative.
Imagining Mars University - Universities UK 2017 conferenceMartin Hamilton
In this talk from the Universities UK 2017 annual conference I update delegates on the latest developments in brain computer interfaces, artificial intelligence, robotics and affordable space travel, and encourage them to consider what Mars University might look like.
In this talk for the University of Glasgow's Future Proof IT event I explore a few near future careers and technologies that will impact learners and institutions, such as self-driving vehicles, and how we might respond to them.
Tech in exams - SQA Assessment Expert Group - June 2017Martin Hamilton
Is it time to start looking at how we can embrace technology in exams, instead of banning it? My elevator pitch to the Scottish Qualifications Authority assessment expert group meeting in June 2017.
Through the Overton Window - Health Education England horizon scanning worksh...Martin Hamilton
Video of my talk for Health Education England's horizon scanning workshop in June 2017, looking at how we can break out of our comfort zone and move our own personal Overton Window to think about teaching and learning in healthcare in the near future.
A new life awaits you in the off world colonies - UCISA Spotlight on Digital ...Martin Hamilton
The chance to begin again in a golden land of opportunity and adventure? In this talk for the 2017 UCISA Spotlight on Digital Capabilities event I invite the audience to consider what and how the DNA editors and asteroid miners of tomorrow will be learning, and what digital capability and digital skills will mean for them.
Help! My robot is a teacher! - Future Edtech 2017Martin Hamilton
Robots and AI powered digital assistants are increasingly becoming part of our lives.But one person's utopia could be another's dypstopia. This talk for Future Edtech 2017 looks at how could we use these new technologies to help teachers and learners, and what to do if it all goes horribly wrong.
Towards a UK Edtech Strategy - Edtech Vision 2020Martin Hamilton
Do we need an Edtech Strategy for the UK, and what would that look like? Some thoughts on blockers and potential enablers from myself and Jisc CIO Phil Richards, presented at our joint June Edtech Vision 2020 event with EdtechUK
Bridging the digital divide - Digital Skills Summit 2017Martin Hamilton
My talk on Jisc support for digital skills, digitally enabled apprenticeships and building digital capability in organisations, from the 2017 Sunderland Software City Digital Skills Summit #DSS17
The increased availability of biomedical data, particularly in the public domain, offers the opportunity to better understand human health and to develop effective therapeutics for a wide range of unmet medical needs. However, data scientists remain stymied by the fact that data remain hard to find and to productively reuse because data and their metadata i) are wholly inaccessible, ii) are in non-standard or incompatible representations, iii) do not conform to community standards, and iv) have unclear or highly restricted terms and conditions that preclude legitimate reuse. These limitations require a rethink on data can be made machine and AI-ready - the key motivation behind the FAIR Guiding Principles. Concurrently, while recent efforts have explored the use of deep learning to fuse disparate data into predictive models for a wide range of biomedical applications, these models often fail even when the correct answer is already known, and fail to explain individual predictions in terms that data scientists can appreciate. These limitations suggest that new methods to produce practical artificial intelligence are still needed.
In this talk, I will discuss our work in (1) building an integrative knowledge infrastructure to prepare FAIR and "AI-ready" data and services along with (2) neurosymbolic AI methods to improve the quality of predictions and to generate plausible explanations. Attention is given to standards, platforms, and methods to wrangle knowledge into simple, but effective semantic and latent representations, and to make these available into standards-compliant and discoverable interfaces that can be used in model building, validation, and explanation. Our work, and those of others in the field, creates a baseline for building trustworthy and easy to deploy AI models in biomedicine.
Bio
Dr. Michel Dumontier is the Distinguished Professor of Data Science at Maastricht University, founder and executive director of the Institute of Data Science, and co-founder of the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. His research explores socio-technological approaches for responsible discovery science, which includes collaborative multi-modal knowledge graphs, privacy-preserving distributed data mining, and AI methods for drug discovery and personalized medicine. His work is supported through the Dutch National Research Agenda, the Netherlands Organisation for Scientific Research, Horizon Europe, the European Open Science Cloud, the US National Institutes of Health, and a Marie-Curie Innovative Training Network. He is the editor-in-chief for the journal Data Science and is internationally recognized for his contributions in bioinformatics, biomedical informatics, and semantic technologies including ontologies and linked data.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
Comparative structure of adrenal gland in vertebrates
UK e-Infrastructure for Research - UK/USA HPC Workshop, Oxford, July 2015
1. UK e-Infrastructure for Research
Michael Ball, BBSRC
Frances Collingborn, NERC
Martin Hamilton, Jisc
David de Roure, ESRC / University of Oxford
Photo credit: STFC 1UKUSAHPC - July 201509/07/2015
2. UK e-Infrastructure for research
1. UK e-Infrastructure for research
– Public funding for major science facilities and institutes
– Support for translation from R&D into business
2. e-Infrastructure survey
– Build inventory of the e-Infrastructure
– Operating systems and software environment
– Funding and budgeting models
– Training and support arrangements
– Academic and industrial impact
3. RCUK e-Infrastructure roadmap
– Vision and aspirations
– Investment plan
Photo credit EPCC / EPSRC
4. UK e-Infrastructure for research
HPC Project RC Amount/£M
National Service EPSRC, NERC 43
Hartree Centre STFC 30
DIRAC STFC 15
GRIDPP STFC 3
The Genome Analysis Centre
(TGAC)
BBSRC 8
Monsoon NERC/Met Office 1
JASMIN2 & CEMS NERC, & UKSA 7.75
Regional Centres: N8, SES5,
MID+, HPC Midlands, ARCHIE-
WeSt
EPSRC 6.5
JANET Network and
Authentication Moonshot
Jisc 31
HPC Data Storage EPSRC, STFC 15
Total 160
Investments by BIS, the Research Councils and HEIs
have resulted in core elements of the national e-
Infrastructure being put in place.
» 2011-2012 - £160m
Investments were made in core HPC and
Networking infrastructure. In addition investments
were made in the Authentication Infrastructure
Moonshot (now known as Jisc Assent).
» 2012-2013 - £189m
» 2014-2015 - £257m
6. UK e-Infrastructure for research
Big Data Project RC Amount/£M
Digital transformations in arts and
humanities
AHRC 8
E-infrastructure for biosciences BBSRC 13
Research data facility and software
Development
EPSRC 8
Administrative data centres ESRC 36
Understanding populations ESRC 12
Business datasafe ESRC 14
Biomedical informatics MRC 55
Environmental virtual observatory NERC 13
Square Kilometre Array STFC 11
Energy Efficiency Computing
Hartree Centre
STFC 19
Total 189
Investments by BIS, the Research Councils and HEIs
have resulted in core elements of the national e-
Infrastructure being put in place.
» 2011-2012 - £160m
» 2012-2013 - £189m
Big Data projects using funds announced by the
Government in December 2012 were funded at this
time. Major Awards have been made to 18 centres
in the UK, 16 of whom are HEIs.The pre-eminent
role of HEIs in managing and providing national
and Large Specialist data and compute services to
UK academia is emphasised by these awards.
» 2014-2015 - £257m
7. UK e-Infrastructure for research
Energy Efficient
Computing
Infrastructure
(STFC)
De-identified admin
(including health) data
Busines
s data
Open data
(public
sector)
Social media
data
Researc
h data
Longitudin
al survey
data
Open data
Securely held data
Environme
nt data
Business Datasafe
(ESRC)
Admin Data Research
Centres (ESRC)
High Performance
Data Environment
(NERC)
Clinical
data
Medical Bioinformatics (MRC)
Understanding Populations
(ESRC)
Clinical Practice Datalink
(MHRA, NIHR)
100,000 Genome Project NHS)
Research Data Facility (EPSRC)
European Bioinformatics
Institute (EMBL)
Bioscience E-Infrastructure
(BBSRC)
Square Kilometre Array (STFC)
Digital Transformations
(AHRC)
Archive
data
Open Data
Institute
Commercial
Research
Understanding
Populations (ESRC)
RCUK Big Data
21st century raw material
9. UK e-Infrastructure for research
Investments by BIS, the Research Councils and HEIs
have resulted in core elements of the national e-
Infrastructure being put in place.
» 2011-2012 - £160m
» 2012-2013 - £189m
» 2014-2015 - £257m
Three major investments dominated this period:
» Centre for Cognitive Computing at the Hartree Centre.
This was funded at the £115M level with a further £230M from IBM
» A 10 Pflop Supercomputer for the Met Office (£100M)
» AlanTuring Centre for Data Science (£42M)
In addition it was announced that a further £100M would be made available to the SKA Project as
part of Big Data Investments.
Photo credit: EPSRC
10. April 2015 BBSRC bioscience big data infrastructure funding:
» £1.79M to build a next generation image repository, to make available original scientific image
data that underpins life sciences research.
» £2M for big data infrastructure for crop genomics, stimulating new opportunities in crop
development to help improve some of the world's most important crops.
» £1.9M to establish infrastructure for functional annotation of farmed animal genomes, to
help feed us in the future by providing an important framework for the discovery of genetic
variation in domesticated animals and how that influences their characteristics.
» £1.78M to create cyber infrastructure for the plant sciences.The UK iPlant node that will help
to spread expertise and best practice between the UK and US. UK/US collaboration with
University of Arizona and theTexas Advanced Computing Center.
UK e-Infrastructure for research
11. UK e-Infrastructure for research
bit.ly/dowlingreport bit.ly/bis8great
Context:
› Reviews, e.g. Pearce,
Diamond, Dowling,
Shadbolt
– Demonstrable efficiency,
effectiveness and
productivity
› UK Government
Industrial Strategy
– 8 GreatTechnologies
– CatapultCentres
› Cultural shifts
– Open Science
– OpenAccess
– Open Research Data
12. UK e-Infrastructure for research
bit.ly/hauserreportbit.ly/jischpc
Drivers:
› Shared facilities and
industry access
– Finding them
– Using them (kit & people)
› Big push for translation
and consolidation
– New Catapult Centres
– Farr Institute,
FrancisCrick Institute,
AlanTuring Institute
› Impact of Austerity 2.0
– Comprehensive Spending
Review, Autumn 2015
14. e-Infrastructure Survey
What we did:
› Build an inventory of UK research e-Infrastructure
– Including interconnects, storage, accelerators etc
– Gathering data on use of cloud technologies
› Itemize operating environment
– e.g. OS distributions, schedulers, filesystems, authentication
& authorization
› Funding and budgeting models
– Power costs, PUE, split between CAPEX/OPEX,
location of scientific computing in the institution
› Training and support arrangements
– Where is support effort spent, role of women in HPC
› Academic and industrial impact
– Grants, papers, businesses using the facilities
Photo credit: CC-BY HPC Midlands
20. e-Infrastructure Survey
› Top 9
Large &
Specialist
(by number
of users)
1. Large and Specialist Services
Organisation name System name
What are the top three research
areas the system is used for?
Total number
of processor
cores in the
system
Total usable
storage for
HPC users
(TB)
Number of
registered
users
Theoretical
Peak
Performance
(Tflop/s)
NERC (operated by STFC) JASMIN
Climate Science, Earth
Observation, environmental
genomics 4,500 25 Over 10,000
STFC Hartree Centre Blue Wonder
Modelling & Simulation (CFD,
Materials, and Computer Aided
Formulation) 24,000 9000 750 - 1,000 200
Norwich Bioscience Institutes
(TGAC, JIC, IFR, TSL)
Bioinformatics, mathematical
modelling. 9,000 4,000 750 - 1,000
DiRAC @ University of
Cambridge (HPCS) Darwin
Life Sciences. Atomic structure.
Computational Fluid Dynamics. 9,600 2,847 750 - 1,000 200
STFC Scientific Computing
Division
UK e-Science Certification
Authority
Supports all UK research. Major
users Particle Physics 750 - 1,000
STFC Scientific Computing
Division SCARF
Computational Chemistry Plasma
Physics, Processing Satellite
images Support of ISIS, CLF,
RAPSP, DLS user communities 7,000 320 500 - 750 165
STFC Hartree Centre Blue Joule
Modelling & Simulation (CFD,
Materials, and Computer Aided
Formulation) 98,000 6000 200 - 500 1,200
EMBL-EBI - European
Bioinformatics Institute Embassy Cloud Life science research 31,000 3,200 200 - 500
DiRAC @ EPCC DIRAC BG/Q QCD, Soft Matter Physics 98,304 1,000 200 - 500 1,258
21. e-Infrastructure Survey
› Top 9
Large &
Specialist
(by number
of users)
1. Large and Specialist Services
Organisation name System name
What are the top three research
areas the system is used for?
Total number
of processor
cores in the
system
Total usable
storage for
HPC users
(TB)
Number of
registered
users
Theoretical
Peak
Performance
(Tflop/s)
NERC (operated by STFC) JASMIN
Climate Science, Earth
Observation, environmental
genomics 4,500 25 Over 10,000
STFC Hartree Centre Blue Wonder
Modelling & Simulation (CFD,
Materials, and Computer Aided
Formulation) 24,000 9000 750 - 1,000 200
Norwich Bioscience Institutes
(TGAC, JIC, IFR, TSL)
Bioinformatics, mathematical
modelling. 9,000 4,000 750 - 1,000
DiRAC @ University of
Cambridge (HPCS) Darwin
Life Sciences. Atomic structure.
Computational Fluid Dynamics. 9,600 2,847 750 - 1,000 200
STFC Scientific Computing
Division
UK e-Science Certification
Authority
Supports all UK research. Major
users Particle Physics 750 - 1,000
STFC Scientific Computing
Division SCARF
Computational Chemistry Plasma
Physics, Processing Satellite
images Support of ISIS, CLF,
RAPSP, DLS user communities 7,000 320 500 - 750 165
STFC Hartree Centre Blue Joule
Modelling & Simulation (CFD,
Materials, and Computer Aided
Formulation) 98,000 6000 200 - 500 1,200
EMBL-EBI - European
Bioinformatics Institute Embassy Cloud Life science research 31,000 3,200 200 - 500
DiRAC @ EPCC DIRAC BG/Q QCD, Soft Matter Physics 98,304 1,000 200 - 500 1,258
22. e-Infrastructure Survey
› Regional centres (by total cores)
2. Regional Systems
Organisation name System name
What are the top three research areas
the system is used for?
Total number of
processor cores
in the system
Total usable
storage for HPC
users (TB)
Number of
registered users
Theoretical
Peak
Performance
(Tflop/s)
HPC Wales Various (distributed system)
Advanced Materials & Manufacturing,
Life Sciences and Energy &
Environment 16,816 702 2,000 - 5,000 319
N8HPC Polaris 5,312 175 200 - 500 138
ARCHIE-WeSt ARCHIE
Molecular dynamics, CFD, Plasma
Physics 3,920 148 200 - 500 38
HPC Midlands Hera
Advanced Materials Energy Efficient
Transport 3,008 120 100 - 200 48
23. e-Infrastructure Survey
› Regional centres (by total cores)
2. Regional Systems
Organisation name System name
What are the top three research areas
the system is used for?
Total number of
processor cores
in the system
Total usable
storage for HPC
users (TB)
Number of
registered users
Theoretical
Peak
Performance
(Tflop/s)
HPC Wales Various (distributed system)
Advanced Materials & Manufacturing,
Life Sciences and Energy &
Environment 16,816 702 2,000 - 5,000 319
N8HPC Polaris 5,312 175 200 - 500 138
ARCHIE-WeSt ARCHIE
Molecular dynamics, CFD, Plasma
Physics 3,920 148 200 - 500 38
HPC Midlands Hera
Advanced Materials Energy Efficient
Transport 3,008 120 100 - 200 48
24. e-Infrastructure Survey
› Top 8 HEIs
(by total
cores)
3. HEI Systems
Organisation name System name
What are the top three
research areas the system is
used for?
Total
number of
processor
cores in
the
system
Total
usable
storage
for HPC
users (TB)
Number of
registered
users
Theoretica
l Peak
Performan
ce
(Tflop/s)
Imperial College London cx1 21,558 2,000 750 - 1,000
University of Bristol BlueCrystal
Chemistry, Aerospace Eng,
Geographical Sciences 9,000 740 750 - 1,000 240
University College
London Legion
Chemistry, Physics, Biological
Sciences (according to REF
Categories) 7,816 356 500 - 750 115
Imperial College London cx2 7,000 500 0 - 100 60
University of
Manchester
Computational Shared
Facility
Computational Chemistry /
MD CFD FEA 6,288 750 750 - 1,000 111
Durham University Hamilton
Condensed Matter Molecular
Dynamics Fluid Dynamics 5,600 350 200 - 500 75
University of Oxford Arcus-B 5,440 432
2,000 -
5,000 538
Lancaster University HEC (High End Cluster)
High Energy Physics
Condensed Matter Theory
CFD 4,784 1,530 200 - 500
31. RCUK e-Infrastructure roadmap
From the roadmap document:
“Our aspiration is for the UK to have an integrated e-
infrastructure: one that is run and managed as a whole without
silos or boundaries, where there are simple processes by which
users can get access to the e-infrastructure they need across the
eco-system, as appropriate for the type or stage of research
they are doing.We need to consider how best to integrate:
» Vertically up and down the eco-system pyramid, so users
have easy access to the most appropriate type of e-
infrastructure they need;
» Horizontally across the different elements, as shown in the
diagram;
» Across the different research communities and the
different stakeholders;
» Internationally, across other national e-infrastructures to
deliver end-to-end services in the global environment of
collaborative research.”
bit.ly/eroadmap
33. That’s all, folks…
33
Except where otherwise noted, this
work is licensed under CC-BY
Martin Hamilton
Futurist, Jisc, London
@martin_hamilton
martin.hamilton@jisc.ac.uk
UKUSAHPC - July 201509/07/2015