The panel will focus on a pilot project to ensure that all stakeholders understand the services and infrastructures to be included in the DMPs by the granting councils and CFI.
Islandora Webinar: Highlighting CUHK Chinese Digital CollectionsErin Tripp
The webinar will feature a presentation and Q&A session with Jeff Liu, Digital Services Librarian and Louisa Lam, Head, Research Support and Digital Initiatives at the CUHK Library.
The CUHK Library has curated a collection of over five million digital objects in the past 20 years. It features Chinese literature, culture, arts, politics, society and religion. Until recently, the collection was stored in a broad range of different systems, complicating the discovery of these precious digital assets.
In 2015, librarians at CUHK embarked on a project to find a permanent, single platform for digital content. Objectives of the project included enhanced discoverability, multi-language support (Chinese, Japanese & Korean) and custom development capability to modify display and viewing features that would showcase Chinese literature in its true form.
Islandora met all the functional requirements and more, including support for digital humanities projects and access to a user-driven open source software community.
The CUHK library was also attracted to the vendor services and support available through discoverygarden. We provided advice, support and custom development assistance; contributing to the launch of the digital repository every step of the way.
The repository (http://repository.lib.cuhk.edu.hk) officially launched in February 2016, making the CUHK Library digital initiatives pioneers in Hong Kong.
A presentation on the ways in which digital preservation capability is being embedded within Hydra, given at the 2016 Spring meeting of the international Preservation and Archiving Special Interest Group
Networking Repositories, Optimizing Impact: Georgia Knowledge Repository MeetingKaren S Calhoun
Prepared as the keynote for the Georgia Knowledge Repository's annual meeting, this presentation discusses why repositories are important, the challenges they face, and solutions or opportunities for networking repositories and optimizing their impact for local, regional and global communities.
"Filling the Digital Preservation Gap" with ArchivematicaJenny Mitcham
A webinar given by Jenny Mitcham and Simon Wilson to Digital Preservation Coalition members on 25th November 2015. It describes work underway in the "Filling the Digital Preservation Gap" project using Archivematica to preserve research data
Islandora Webinar: Highlighting CUHK Chinese Digital CollectionsErin Tripp
The webinar will feature a presentation and Q&A session with Jeff Liu, Digital Services Librarian and Louisa Lam, Head, Research Support and Digital Initiatives at the CUHK Library.
The CUHK Library has curated a collection of over five million digital objects in the past 20 years. It features Chinese literature, culture, arts, politics, society and religion. Until recently, the collection was stored in a broad range of different systems, complicating the discovery of these precious digital assets.
In 2015, librarians at CUHK embarked on a project to find a permanent, single platform for digital content. Objectives of the project included enhanced discoverability, multi-language support (Chinese, Japanese & Korean) and custom development capability to modify display and viewing features that would showcase Chinese literature in its true form.
Islandora met all the functional requirements and more, including support for digital humanities projects and access to a user-driven open source software community.
The CUHK library was also attracted to the vendor services and support available through discoverygarden. We provided advice, support and custom development assistance; contributing to the launch of the digital repository every step of the way.
The repository (http://repository.lib.cuhk.edu.hk) officially launched in February 2016, making the CUHK Library digital initiatives pioneers in Hong Kong.
A presentation on the ways in which digital preservation capability is being embedded within Hydra, given at the 2016 Spring meeting of the international Preservation and Archiving Special Interest Group
Networking Repositories, Optimizing Impact: Georgia Knowledge Repository MeetingKaren S Calhoun
Prepared as the keynote for the Georgia Knowledge Repository's annual meeting, this presentation discusses why repositories are important, the challenges they face, and solutions or opportunities for networking repositories and optimizing their impact for local, regional and global communities.
"Filling the Digital Preservation Gap" with ArchivematicaJenny Mitcham
A webinar given by Jenny Mitcham and Simon Wilson to Digital Preservation Coalition members on 25th November 2015. It describes work underway in the "Filling the Digital Preservation Gap" project using Archivematica to preserve research data
Libraries and Research Data Management – What Works? Summary of a Pre-Survey.LIBER Europe
This presentation by Rob Grim was given at the Scholarly Communication and Research Infrastructures Steering Committee Workshop. The workshop title was Libraries and Research Data Management – What Works?
ESI Supplemental 1 E-research Support SlidesDuraSpace
E-Research Support at
Johns Hopkins University & Purdue University
Supplemental Webinar
Wednesday, October 17, 2012
Presented by Sayeed Choudhurry & James Mullins
DuraSpace is OPEN presented by:
Debra Hanken Kurtz, CEO Jonathan Markow, CSO at the
11th Annual International Conference on Open Repositories 2016, Dublin
This slideshow was used in an Introduction to Research Data Management course taught for the Mathematical, Physical and Life Sciences Division, University of Oxford, on 2017-02-15. It provides an overview of some key issues, looking at both day-to-day data management, and longer term issues, including sharing, and curation.
This slideshow was used in a research data management planning course taught at IT Services, University of Oxford, on 2017-02-01. It provides an overview of the elements of a data management plan, plus an introduction to some tools that can be used to build one. (The presentation has been very slightly edited: references to resources provided to course participants have been replaced with web links.)
This slideshow was used in a Preparing Your Research Material for the Future course for the Humanities Division, University of Oxford, on 2017-02-22. It provides an overview of some key issues, focusing on the long-term management of data and other research material, including sharing and curation.
Presented by Peter Burnhill at the ost ALA Annual Holdings Update Forum, Universal and repurposed holdings information -- Emerging initiatives and projects, Morial Convention Center, New Orleans, Louisiana, USA, 25 June 2011
A brief overview of the development and current workflows for Research Data Management at Imperial College London, presented to colleagues at the University of Copenhagen and Roskilde University in Denmark.
Federation and Interoperability in the Nectar Research CloudOpenStack
Audience Level
Beginner
Synopsis
The Nectar Research Cloud provides an OpenStack cloud for Australia’s academic researchers. Since its inception in 2012 it has grown steadily to over 30,000 CPUs, with over 10,000 registered users from more than 50 research institutions. It is different to many clouds in being a federation across eight organisations, each of which runs cloud infrastructure in one or more data centres and contributes to a distributed help desk and user support. A Nectar core services team runs centralised cloud services. This presentation will give an overview of the experiences, challenges and benefits of running a federated OpenStack cloud and a short demonstration on using the Nectar cloud. We will also describe some current approaches that are looking to extend this federation to encompass other institutions including some in New Zealand, to extend the infrastructure using commercial cloud providers, and to move towards interoperability with the growing number of international science and research clouds through the new Open Research Cloud initiative.
Speaker Bio
Dr Paul Coddington is a Deputy Director of Nectar, responsible for the Nectar national Research Cloud, and also Deputy Director of eResearch SA. He has over 30 years experience in eResearch including computational science, high performance and distributed computing, cloud computing, software development, and research data management.
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Libraries and Research Data Management – What Works? Summary of a Pre-Survey.LIBER Europe
This presentation by Rob Grim was given at the Scholarly Communication and Research Infrastructures Steering Committee Workshop. The workshop title was Libraries and Research Data Management – What Works?
ESI Supplemental 1 E-research Support SlidesDuraSpace
E-Research Support at
Johns Hopkins University & Purdue University
Supplemental Webinar
Wednesday, October 17, 2012
Presented by Sayeed Choudhurry & James Mullins
DuraSpace is OPEN presented by:
Debra Hanken Kurtz, CEO Jonathan Markow, CSO at the
11th Annual International Conference on Open Repositories 2016, Dublin
This slideshow was used in an Introduction to Research Data Management course taught for the Mathematical, Physical and Life Sciences Division, University of Oxford, on 2017-02-15. It provides an overview of some key issues, looking at both day-to-day data management, and longer term issues, including sharing, and curation.
This slideshow was used in a research data management planning course taught at IT Services, University of Oxford, on 2017-02-01. It provides an overview of the elements of a data management plan, plus an introduction to some tools that can be used to build one. (The presentation has been very slightly edited: references to resources provided to course participants have been replaced with web links.)
This slideshow was used in a Preparing Your Research Material for the Future course for the Humanities Division, University of Oxford, on 2017-02-22. It provides an overview of some key issues, focusing on the long-term management of data and other research material, including sharing and curation.
Presented by Peter Burnhill at the ost ALA Annual Holdings Update Forum, Universal and repurposed holdings information -- Emerging initiatives and projects, Morial Convention Center, New Orleans, Louisiana, USA, 25 June 2011
A brief overview of the development and current workflows for Research Data Management at Imperial College London, presented to colleagues at the University of Copenhagen and Roskilde University in Denmark.
Federation and Interoperability in the Nectar Research CloudOpenStack
Audience Level
Beginner
Synopsis
The Nectar Research Cloud provides an OpenStack cloud for Australia’s academic researchers. Since its inception in 2012 it has grown steadily to over 30,000 CPUs, with over 10,000 registered users from more than 50 research institutions. It is different to many clouds in being a federation across eight organisations, each of which runs cloud infrastructure in one or more data centres and contributes to a distributed help desk and user support. A Nectar core services team runs centralised cloud services. This presentation will give an overview of the experiences, challenges and benefits of running a federated OpenStack cloud and a short demonstration on using the Nectar cloud. We will also describe some current approaches that are looking to extend this federation to encompass other institutions including some in New Zealand, to extend the infrastructure using commercial cloud providers, and to move towards interoperability with the growing number of international science and research clouds through the new Open Research Cloud initiative.
Speaker Bio
Dr Paul Coddington is a Deputy Director of Nectar, responsible for the Nectar national Research Cloud, and also Deputy Director of eResearch SA. He has over 30 years experience in eResearch including computational science, high performance and distributed computing, cloud computing, software development, and research data management.
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The Canadian Linked Data Initiative: Charting a Path to a Linked Data FutureNASIG
As libraries prepare to shift away from MARC to a linked data framework, new convergences in the metadata production activities of our libraries' technical services units, special collections, and digital libraries are becoming possible. In September 2015, the Canadian Linked Data Initiative (CLDI) was formed to leverage the existing collaboration between the Technical Services departments of Canada’s top 5 research libraries and the Library and Archives of Canada. Working cooperatively, our objective is to provide a path to linked data readiness for our institutions and leadership for the adoption of linked data by libraries across Canada. To achieve this goal, partner libraries are working across departments and institutions to create new workflows and tools and adapt to a new conceptual understanding of descriptive metadata. This presentation is a preliminary report on the progress made in five key areas of interest: digital collections, education and training, MARC record enhancement, evaluation of linked data tools and vendor supplied metadata. Building on existing initiatives, the CLDI is investigating the potential of integrating linked data elements into digitized collections, as well as MARC-based bibliographic and authority records, with the aim of fostering new and interesting pathways for resource discovery. To strengthen and expand the professional knowledge of staff, partner institutions are collaborating in the production of educational and training materials related to linked data principles and practices. The evaluation and potential development of linked data tools is another area of concentration. Finally, with the goal of changing workflows upstream, the CLDI is working to engage publishers and vendors in the linked data conversation. In addition to reporting on the work undertaken in the first year of the project, this presentation will also cover lessons learned and outline some of the new opportunities gained from working on a collaborative project that spans across multiple boundaries.
Marlene van Ballegooie, Metadata Librarian,
University of Toronto
Juliya Borie, University of Toronto Libraries
Andrew Senior, Coordinator,
E-Resources and Serials, McGill University
A collaborative approach to "filling the digital preservation gap" for Resear...Jenny Mitcham
A presentation given by Chris Awre, Jenny Mitcham and Sarah Romkey at RDMF14 (the DCC's Research Data Management Forum) on 9th November 2015 in York. It describes work underway in the "Filling the Digital Preservation Gap" project using Archivematica to preserve research data
Preservation of Research Data: Dataverse / Archivematica Integration by Allan...datascienceiqss
Scholars Portal, a program of the Ontario Council of University Libraries (OCUL), provides the technical infrastructure to store, preserve, and provide access to shared digital library collections in Ontario - including hosting a local instance of Dataverse since 2011. As part of a national project known as Portage (a project of the Canadian Association of Research Libraries), Scholars Portal is partnering with Artefactual Systems, Dataverse, the University of British Columbia, the University of Alberta, and others, to integrate Dataverse with preservation software Archivematica. When completed, this project will facilitate the long-term preservation of research data according to the Open Archival Information System (OAIS) Reference Model.
Presentació a càrrec de Mireia Alcalá, tècnica de Recursos d'Informació al CSUC, duta a terme al workshop en línia "Research Data Management & Open Science" organitzat per l'IDIBELL el 2 de novembre de 2020.
Jenny Mitcham from the University of York and Chris Awre from the University of Hull share lessons learned from their project to explore the potential of the digital preservation solution Archivematica to help manage research data that academics within the University produce. The project 'Filling the Digital Preservation Gap' has been carried out with funding from Jisc as part of their Research Data Spring program and was a collaboration of the University of York and the University of Hull. The project did not only explore Archivematica as a possible solution but also how it could integrate with the repositories and other systems for the management of research data.
The Series is jointly sponsored by ANDS and CAUL.
Overview of the UKRDDS pilot project at Univwersity of Edinburgh employing PhD interns to validate metadata about research data created by University of Edinburgh researchers and held in local RDM services solutions. This was presented at IASSIST in June 2016, Bergen, Norway.
Presented by Robin Rice at the "IRs dealing with data" workshop at the Open Repositories 2013 Conference in Charlottetown, Prince Edward Island, Canada, on 8 July 2013.
In order to be reused, research data must be discoverable.
The EPSRC Research Data Expectations* requires research organisations to maintain a data catalogue to record metadata about research data generated by EPSRC-funded research projects.
Universities are increasingly making research data assets available through repositories or other data portals.
The requirement for a UK research data discovery service has grown as universities become more involved in RDM and capacity develops.
Relationship Building and Advocacy Across the CampusUCD Library
Presentation given by Julia Barrett, Research Services Manager at University College Dublin Library, to the ANLTC Seminar: Supporting the Activities of Your Research Community - Issues and Initiatives, held on December 3, 2014 at the Royal Irish Academy, Dublin, Ireland.
RDAP14: An analysis and characterization of DMPs in NSF proposals from the Un...ASIS&T
Research Data Access and Preservation Summit, 2014
San Diego, CA
March 26-28, 2014
Lightning Talks
William Mischo, University of Illinois at Urbana-Champaign
Similar to L&P Humphrey Stewart-Shearer-Joint Session Project ARC & Federated DMP Pilot (20)
Optimising benefits from Canadian Research - Jim WoodgettCASRAI
Janet Halliwell, Chair CASRAI; Co-Chair Admin Burden Canada collective; Chair CSPC
Dominique Bérubé, Vice-President Research Programs, SSHRC
Jim Woodgett, Director of Research, Lunenfeld-Tanenbaum Research Institute
Optimising benefits from Canadian Research - Janet HalliwellCASRAI
Janet Halliwell, Chair CASRAI; Co-Chair Admin Burden Canada collective; Chair CSPC
Dominique Bérubé, Vice-President Research Programs, SSHRC
Jim Woodgett, Director of Research, Lunenfeld-Tanenbaum Research Institute
Admin Burden in Canada (ABC) Introductory Panel Discussion (CA, UK and US ove...CASRAI
Admin Burden in Canada (ABC) Introductory Panel Discussion (CA, UK and US overview)
David Robinson
Executive Vice Provost & Professor
Oregon Health & Science University (US)
ABC Project 1 - Piloting Auto-upload of Standardized Funding Award Results - ...CASRAI
ABC Project 1 - Piloting Auto-upload of Standardized Funding Award Results
Judith L. Chadwick
Assistant Vice-President, Research Services
University of Toronto
Bob Dirstein
Dirstein Consulting Inc.
w/University of Toronto
ABC Project 2 - Launching an ORCID Consortia in Canada - Clare Appavoo & Geof...CASRAI
Launching an ORCID Consortia in Canada
Clare Appavoo
Executive Director
Canadian Research Knowledge Network (CRKN)
Geoffrey Harder
Associate University Librarian
University of Alberta
Mark Leggott
Executive Director
Research Data Canada (RDC)
Introduction to the Federal Demonstration Partnership (FDP) of the US - David...CASRAI
Introduction to the Federal Demonstration Partnership (FDP) of the US
David Robinson
Executive Vice Provost & Professor
Oregon Health & Science University (US)
Tutorial: the new Portage Research Data Management Planning Tool - Chuck Hump...CASRAI
Tutorial: the new Portage Research Data Management Planning Tool
Chuck Humphrey
Director, Portage Network
University of Alberta
Dylanne Dearborn
Physics Library
University of Toronto Libraries
How Do I Know Thee? Let Me Count the Ways: Panel 2: Jeffrey Alexander & Patri...CASRAI
All R&D organizations classify their research activities, either implicitly (e.g., by laboratory or department) or explicitly (e.g., by creating taxonomies to define and map research disciplines and domains). However the lack of clear standards for doing so impedes the sharing and aggregation of data on R&D activities. In this panel the speakers will provide an overview of the organizational needs driving the development of a classification of R&D activities, use cases for such a classification, and the potential advantages of international coordination across such classifications.
Classifying R&D: Why and How Organizations Develop Taxonomies for Research Fi...CASRAI
All R&D organizations classify their research activities, either implicitly (e.g., by laboratory or department) or explicitly (e.g., by creating taxonomies to define and map research disciplines and domains). However the lack of clear standards for doing so impedes the sharing and aggregation of data on R&D activities. In this workshop, Jeff Alexander and Patrick Lambe will provide an overview of the organizational needs driving the development of a classification of R&D activities, use cases for such a classification, and the potential advantages of international coordination across such classifications. The workshop, based heavily on a study they conducted for the National Center for Science & Engineering Statistics at the U.S. National Science Foundation, will review alternate approaches to both developing R&D classifications, and streamlining the process of classifying research programs and projects. Topics to be covered include examples of international R&D classifications and their development (such as the Australia-New Zealand Standard Research Classification), design principles for R&D classifications, and new automated and semi-automated classification techniques using semantic analysis and machine learning.
How Do I Know Thee? Let Me Count the Ways: Sarah Moreault, Monica Valsangkar-...CASRAI
Classification of research plays an integral role in the functioning of research funding organizations. As such it is important to have a classification system for efficient research data collection, use, analysis and reporting. Hear about lessons learned as well as key limitations and challenges for the implementation of a standard approach to classification through the analyses of different international standards currently in use with respect to their governance, development, implementation and maintenance
Over the past 10 years, research systems have evolved from systems that focused on how to structure and record information on research, to systems capable of allowing significant insights to be derived based upon years of high quality information. In 2015, the maturity of the information now collected within many Current Research Information Systems, and the insights that this can provide is of equal or greater value than the insights that could be gleaned from established externally provided research metrics platforms alone. The ability to intersect these external and internal worlds provides new levels of strategic insight not previously available. With the addition of platforms that track altmetrics, and their ability to connect university publications data with a constant flow of real time attention level metrics, an image of a dynamic network of systems emerges, connected together by ever turning ‘cogs’ pushing and translating information. Add to this, the success of ORCID as pervasive researcher identifier infrastructure, and CASRAI as the emerging social contract for information exchange, and it becomes possible to extend this network back from the systems that track and record research information, through to the platforms through which research knowledge is created. The ‘Mechanics’ of this network of systems is more than just getting the ‘plumbing’ right. As research information moves through the network, its audience and purpose changes, the requirements for contextual metadata can also change. This presentation will explore the lived experience of Research Data Mechanics at Digital Science though illustrating how connections between Figshare, Altmetric, Symplectic Elements, and Dimensions can both enhance research system capability and reduce the burden on researchers, and research administration.
Provincial Perspectives on Research Impacts: Eddy Nason, Renata Osika, Krista...CASRAI
When we say “Research Impact” many things come to mind and the reasons for why we are concerned with it vary. The underlying concepts are complex and often require expert knowledge, and there is also no one single interpretation or answer. Stakeholders are diverse and so are the means of communication. Therefore across Canada, we continue to seek more consistent and harmonized ways of telling the “Impact Story.” The panel will reflect on harmonization efforts across provinces.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
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.
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.
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 .
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
3. THE TREND TOWARDS SHARED SERVICES
• Other countries are developing shared services and
infrastructure to support research data
management services.
• Why? To address cost redundancies, pools
knowledge, breaks down silos across disciplines.
• Common shared services are: discovery, data
registries, support and expertise, training, shared
repositories and preservation.
• General trend towards domain-based services to
generic RDM infrastructure. There are common
infrastructure and service requirements across
domains!
4. PROJECT ARC
• Initiated and supported by CARL
• December 2013 initial stakeholders meeting
• March 2014 working group launched, for 1 year
• Working group members represent
– CARL
– all four regional academic library associations:
CAUL, COPPUL, OCUL and Quebec
– CRKN
• Includes some of Canada’s top research data
management experts
5. PROJECT ARC
Builds on previous efforts by CARL to improve capacity
at Canadian universities in the area of research data
management:
• 2009 Research Data Management Toolkit: Unseen
Opportunities
• 2010 Library Roles in Management Research Data
• 2011-2012 Proposal: “Canadian National
Collaborative Data Infrastructure Project”
• 2013 RDM Course: Introduction to Research Data
Management Services
6. PROJECT ARC AIM AND VISION
• A future in which Canada capitalizes on the
trend towards data intensive research and is
a world leader in research and innovation
• This future is achievable, with comprehensive
support for research data management at a
national scale.
• Project ARC aim is to improve our national
capacity for the management, preservation,
and re-use of research data.
7. PROJECT ARC – SCOPE
• Bring together existing library-based initiatives to
better coordinate activities and build capacity across
the country
• Lay the foundation for a library-based research data
management network
• Work closely with other stakeholders (e.g. CANARIE,
Compute Canada, Research Data Canada) to ensure
integration with and support for other infrastructures
and initiatives in Canada
8. PROJECT ARC - PRINCIPLES
• Data are a public good
• Intelligent access: openness, with respect for privacy
• Collaborative approaches: cost savings and sharing expertise
• Inclusiveness: aim to serve all researchers and create a more level
playing field
• Commitment to standards and interoperability
• International relationships: liaise internationally and ensure our work is
in keeping with international practices
• Respect for differences: flexibility to meet the needs of different regions,
institutions, and disciplines
• Open source: Tools will be contributed back to the community
• Stewardship: a sense of responsibility for managing research data over
the long term
9. OBJECTIVES OF PROJECT ARC
Liaising closely with all relevant stakeholder in this
arena,
1. Provide support for institutions to deliver data
management plans (DMPs)
2. Develop a plan for the implementation of a centre
of expertise for the curation of research data in
Canada
3. Undertake a pilot that will act as an exemplar for
a national preservation service for research data
4. Develop an organizational framework and
operational plan for a library-based research data
management network in Canada
10. PORTAGE
At Project ARC mid-point (September 2014), a
network name was proposed and concepts were
refined…
The Portage network will have two major
components:
• A distributed centre of expertise for research data
management, and
• A national preservation system for research data
that will evolve and expand over time
11. NETWORK CENTRE OF EXPERTISE
1) Comprehensive set of resources to support data management planning
– How-to guides, case studies, training materials
– Cooperation with UK Digital Curation Centre (DCC)
– Currently being collected on Project ARC website
2) National DMP automated tool to assist Canadian researchers in
developing management plans
– DMP online (originally developed by DCC) selected
3) Consulting services
– Draw on expertise of librarians and others from across the country
– Support data curation, training, DMPs, discovery, preservation,
privacy-security-ethics
– Build human capacity across the country
12. NATIONAL PRESERVATION SYSTEM
(more from Chuck and Walter)
Advice and support for researchers depends on viable technical
solutions!
• Continue a pilot in close collaboration with Compute Canada
and RDC, including some of the domain data centres
• Domain data centres currently involved are Canadian
Astronomy Data Centre and C-Brain, whose creation was
supported by the CANARIE research software program
• Goal is to enable all interested academic libraries to
participate, whether or not they have their own local
infrastructure
• Complements high performance computing infrastructure and
domain repositories and contributes integration layer
15. A COLLABORATIVE EFFORT AMONG RDC, CARL
Project Arc, Compute Canada, CANARIE,
Scholar’s Portal, SFU Libraries, CANFAR, C-
Brain, CPDN
Born at the DI Summit2014
16. THE CONTEXT:
• Data are both a product and a resource for 21st
century discovery.
• The TC3+ are preparing to require Data
Management Plans as part of the funding
application process.
• The federal government has extended its
commitment to open government and open data
to cover federally funded research:
17. THE CONTEXT:
The Government of Canada will maximize access to
federally funded scientific research to encourage greater
collaboration and engagement with the scientific
community, the private sector, and the public.
Among the commitments for 2014 to 2016:
Launch of open access to publications and data resulting
from federally funded scientific activities
Canada's Action Plan on Open Government 2014-16
http://open.canada.ca/
18. THE PROBLEM:
• Data that cannot be discovered cannot be open!
• Data that are only on someone’s hard drive or
memory stick cannot be open!
• Data that are not curated cannot be open for
long!
19. THE PROBLEM:
• Currently in Canada, most researchers lack
access to the services and the infrastructure
that would permit them to be good stewards of
their research data and to make it accessible.
• Outside of some data intensive disciplines, little
is in place to provide for the long-term curation
and preservation of data
20. THE OPPORTUNITY:
• Many of the elements for a national system of
data stewardship are in place – the networks
that are required with CANARIE and the ORANS;
storage systems at Compute Canada; data
expertise in research libraries and the ARC
Project of CARL; significant experience in
developing repositories with CANFAR, C-Brain,
and CPDN among others.
21. THE CHALLENGE:
• Can we integrate those elements at a pilot level?
• Can we work with a small set of researchers to
ingest their data into a storage and curation
environment easily and seamlessly in a manner
that provides for easy retrieval?
• Can we create this opportunity first at a local
level and then demonstrate integration among a
few local sites into a proto-typical national
network that provides appropriate replication
and the basis for long-term preservation?
22. THE ANTICIPATED RESULT:
• Anticipating meeting the challenge successfully,
we hope to be able to arrive at a set of
conclusions that will allow us to make
recommendations on what would be required to
grow such a prototypical system into a truly
national network that would serve those parts of
the research community currently unserved and
would provide further support and backup for
existing repositories, some of which have
concerns about their long-term viability.
23. PROGRESS TO DATE:
• We have a model identified about which Chuck
Humphrey will speak in a moment.
• Building on a local scale project at SFU, we have
researcher data being moved into Compute
Canada storage resources by library staff
• We have a plan for a similar activity at the
University of Toronto to get underway in 2015
24. NEXT STEPS:
• We will shortly start having researchers do their own
ingest directly into the repository and archive
environment at SFU
• We will be looking at establishing a duplicative
installation at another university
• We will be looking to test replication services
• We will look to have researchers use the system at a
distance
• We will minutely detail the processes
• We will begin to discuss what it would take to scale
26. The Pilot
Working with existing digital technology and
expertise, the Pilot is to assemble a research
data management infrastructure
demonstrating interoperability among data
repositories and the archiving of research
data.
27. LEVELS OF DATA STEWARDSHIP
• Research data management infrastructure supports data
stewardship that occurs at different levels across the
research lifecycle.
o The researcher at the project level
o The data repository level
o The interoperability level at the regional and national
level
28. EXCHANGES AMONG LEVELS
• The exchange of research data and metadata
among these three levels can encounter barriers
or gaps.
• A Data Management Plan is helpful in identifying
a pathway for data and metadata across levels,
bridging gaps and overcoming barriers.
29. KEY OBJECTIVES
Because no national RDM infrastructure
exists today, the pilot is building
pathways across levels and assembling an
operational system to demonstrate a
community response to providing RDM
infrastructure.