Talk for the workshop on the Future of the Commons, November 18, 2015: http://cendievents.infointl.com/CENDI_NFAIS_RDA_2015/
Slides distributed under under CC-by license: https://creativecommons.org/licenses/by/2.0/
Open Source Tools Facilitating Sharing/Protecting Privacy: Dataverse and Data...Merce Crosas
Presentation for the NFAIS Webinar series: Open Data Fostering Open Science: Meeting Researchers' Needs
http://www.nfais.org/index.php?option=com_mc&view=mc&mcid=72&eventId=508850&orgId=nfais
DataTags, The Tags Toolset, and Dataverse IntegrationMichael Bar-Sinai
This presentation describes the concept of DataTags, which simplifies handling of sensitive datasets. It then shows the Tags toolset, and how it is integrated with Dataverse, Harvard's popular dataset repository.
The DataTags System: Sharing Sensitive Data with ConfidenceMerce Crosas
This talk was part of a session at the Research Data Alliance (RDA) 8th Plenary on Privacy Implications of Research Data Sets, during International Data Week 2016:
https://rd-alliance.org/rda-8th-plenary-joint-meeting-ig-domain-repositories-wg-rdaniso-privacy-implications-research-data
Slides in Merce Crosas site:
http://scholar.harvard.edu/mercecrosas/presentations/datatags-system-sharing-sensitive-data-confidence
Data Publishing at Harvard's Research Data Access SymposiumMerce Crosas
Data Publishing: The research community needs reliable, standard ways to make the data produced by scientific research available to the community, while giving credit to data authors. As a result, a new form of scholarly publication is emerging: data publishing. Data publishing - or making data reusable, citable, and accessible for long periods - is more than simply providing a link to a data file or posting the data to the researcher’s web site. We will discuss best practices, including the use of persistent identifiers and full data citations, the importance of metadata, the choice between public data and restricted data with terms of use, the workflows for collaboration and review before data release, and the role of trusted archival repositories. The Harvard Dataverse repository (and the Dataverse open-source software) provides a solution for data publishing, making it easy for researchers to follow these best practices, while satisfying data management requirements and incentivizing the sharing of research data.
Talk for the workshop on the Future of the Commons, November 18, 2015: http://cendievents.infointl.com/CENDI_NFAIS_RDA_2015/
Slides distributed under under CC-by license: https://creativecommons.org/licenses/by/2.0/
Open Source Tools Facilitating Sharing/Protecting Privacy: Dataverse and Data...Merce Crosas
Presentation for the NFAIS Webinar series: Open Data Fostering Open Science: Meeting Researchers' Needs
http://www.nfais.org/index.php?option=com_mc&view=mc&mcid=72&eventId=508850&orgId=nfais
DataTags, The Tags Toolset, and Dataverse IntegrationMichael Bar-Sinai
This presentation describes the concept of DataTags, which simplifies handling of sensitive datasets. It then shows the Tags toolset, and how it is integrated with Dataverse, Harvard's popular dataset repository.
The DataTags System: Sharing Sensitive Data with ConfidenceMerce Crosas
This talk was part of a session at the Research Data Alliance (RDA) 8th Plenary on Privacy Implications of Research Data Sets, during International Data Week 2016:
https://rd-alliance.org/rda-8th-plenary-joint-meeting-ig-domain-repositories-wg-rdaniso-privacy-implications-research-data
Slides in Merce Crosas site:
http://scholar.harvard.edu/mercecrosas/presentations/datatags-system-sharing-sensitive-data-confidence
Data Publishing at Harvard's Research Data Access SymposiumMerce Crosas
Data Publishing: The research community needs reliable, standard ways to make the data produced by scientific research available to the community, while giving credit to data authors. As a result, a new form of scholarly publication is emerging: data publishing. Data publishing - or making data reusable, citable, and accessible for long periods - is more than simply providing a link to a data file or posting the data to the researcher’s web site. We will discuss best practices, including the use of persistent identifiers and full data citations, the importance of metadata, the choice between public data and restricted data with terms of use, the workflows for collaboration and review before data release, and the role of trusted archival repositories. The Harvard Dataverse repository (and the Dataverse open-source software) provides a solution for data publishing, making it easy for researchers to follow these best practices, while satisfying data management requirements and incentivizing the sharing of research data.
Managing and sharing confidential data in Australian social scienceARDC
The “problem” of “sensitive data” - the 5 Safes model
The “problem” of open and transparent research – the FAIR principles
From problems to solutions – Access to sensitive data in Australia – ADA as a model for journal data access system
Data Citation Implementation at DataverseMerce Crosas
Presentation at the Data Citation Implementation Pilot Workshop in Boston, February 3rd, 2016.
https://www.force11.org/group/data-citation-implementation-pilot-dcip/pilot-project-kick-workshop
Data Repositories: Recommendation, Certification and Models for Cost RecoveryAnita de Waard
Talk at NITRD Workshop "Measuring the Impact of Digital Repositories" February 28 – March 1, 2017 https://www.nitrd.gov/nitrdgroups/index.php?title=DigitalRepositories
Mitigating the Risk: identifying Strategic University Partnerships for Compli...Andrea Payant
Payant, A., Rozum, B., Woolcott, L. (2016). Mitigating the Risk: Identifying Strategic University Partnerships for Compliance Tracking of Research Data and Publications. International Federation of Library Associations (IFLA) Satellite Conference: Data in Libraries: The Big Picture
February 18 2015 NISO Virtual Conference Scientific Data Management: Caring for Your Institution and its Intellectual Wealth
Keynote Address: Data Management Plan Requirements at the US Department of Energy
Laura J. Biven, Ph.D., Senior Science and Technology Advisor, Office of the Deputy Director for Science Programs, Office of Science, US Department of Energy
This presentation was provided by Melissa Levine of the University of Michigan during a NISO Virtual Conference on the topic of data curation, held on Wednesday, August 31, 2016
An introduction to the FAIR principles and a discussion of key issues that must be addressed to ensure data is findable, accessible, interoperable and re-usable. The session explored the role of the CDISC and DDI standards for addressing these issues.
Presented by Gareth Knight at the ADMIT Network conference, organised by the Association for Data Management in the Tropics, in Antwerp, Belgium on December 1st 2015.
ESA Ignite talk on UC3 Dash platform for data sharingCarly Strasser
Ignite talk (20 slides / 15 seconds per slide) for ESA 2014 meeting in Sacramento, CA 12 August 2014. On the Dash platform for helping researchers manage and share their data via institutional repositories
Open science can contribute to AI trustworthiness. This talk is a categorization of scientific data platforms, and a framing of AI trustworthiness with pointers to open science contributions.
5-14-13 An Introduction to VIVO Presentation SlidesDuraSpace
“Hot Topics: The DuraSpace Community Webinar Series, "Series Five: VIVO: Research Discovery and Networking.” Webinar #1: An Introduction to VIVO, May 14, 2013
Presented by: Dean Krafft, Chief Technology Strategist at Cornell University Library and Chair of the VIVO-DuraSpace Management Committee, Brian Lowe, Semantic Applications Programmer, Cornell and Jon Corson-Rikert, VIVO Development Lead, Cornell
Managing and sharing confidential data in Australian social scienceARDC
The “problem” of “sensitive data” - the 5 Safes model
The “problem” of open and transparent research – the FAIR principles
From problems to solutions – Access to sensitive data in Australia – ADA as a model for journal data access system
Data Citation Implementation at DataverseMerce Crosas
Presentation at the Data Citation Implementation Pilot Workshop in Boston, February 3rd, 2016.
https://www.force11.org/group/data-citation-implementation-pilot-dcip/pilot-project-kick-workshop
Data Repositories: Recommendation, Certification and Models for Cost RecoveryAnita de Waard
Talk at NITRD Workshop "Measuring the Impact of Digital Repositories" February 28 – March 1, 2017 https://www.nitrd.gov/nitrdgroups/index.php?title=DigitalRepositories
Mitigating the Risk: identifying Strategic University Partnerships for Compli...Andrea Payant
Payant, A., Rozum, B., Woolcott, L. (2016). Mitigating the Risk: Identifying Strategic University Partnerships for Compliance Tracking of Research Data and Publications. International Federation of Library Associations (IFLA) Satellite Conference: Data in Libraries: The Big Picture
February 18 2015 NISO Virtual Conference Scientific Data Management: Caring for Your Institution and its Intellectual Wealth
Keynote Address: Data Management Plan Requirements at the US Department of Energy
Laura J. Biven, Ph.D., Senior Science and Technology Advisor, Office of the Deputy Director for Science Programs, Office of Science, US Department of Energy
This presentation was provided by Melissa Levine of the University of Michigan during a NISO Virtual Conference on the topic of data curation, held on Wednesday, August 31, 2016
An introduction to the FAIR principles and a discussion of key issues that must be addressed to ensure data is findable, accessible, interoperable and re-usable. The session explored the role of the CDISC and DDI standards for addressing these issues.
Presented by Gareth Knight at the ADMIT Network conference, organised by the Association for Data Management in the Tropics, in Antwerp, Belgium on December 1st 2015.
ESA Ignite talk on UC3 Dash platform for data sharingCarly Strasser
Ignite talk (20 slides / 15 seconds per slide) for ESA 2014 meeting in Sacramento, CA 12 August 2014. On the Dash platform for helping researchers manage and share their data via institutional repositories
Open science can contribute to AI trustworthiness. This talk is a categorization of scientific data platforms, and a framing of AI trustworthiness with pointers to open science contributions.
5-14-13 An Introduction to VIVO Presentation SlidesDuraSpace
“Hot Topics: The DuraSpace Community Webinar Series, "Series Five: VIVO: Research Discovery and Networking.” Webinar #1: An Introduction to VIVO, May 14, 2013
Presented by: Dean Krafft, Chief Technology Strategist at Cornell University Library and Chair of the VIVO-DuraSpace Management Committee, Brian Lowe, Semantic Applications Programmer, Cornell and Jon Corson-Rikert, VIVO Development Lead, Cornell
Shaping Ethics in the Digital Age - Connected and Open Research Ethics (CORE)Gayle Simon
@CamilleNebeker, Ed.D., M.S., gave the keynote address at an OHRP sponsored RCF in Hartford, Connecticut, speaking about the ethical use of personal health data and data from mobile technologies in research. Dr. Nebeker is an Assistant Professor of Behavioral Medicine, Family Medicine, and Public Health in the UC San Diego School of Medicine.
Bridging Gaps and Broadening Participation inToday's and Future Research Com...Sandra Gesing
Research computing is in an exciting era and has never as fast evolved as in the last 20 years. We can nowadays answer research questions that we could not even ask two decades ago. This has led to discoveries such as the analyses of DNA from Next-Generation Sequencing technologies. The increased complexity of software, data, hardware and lab instruments demands for more openness and sharing of data and methods. Researchers and educators are not necessarily IT specialists though. Thus, a further trend in research computing is the shift from system-centric design to user-centric design and interdisciplinary teams – complex solutions are offered in self-explanatory user interfaces, so-called science gateways or virtual research environments. I will present solutions and projects supporting users to be able to focus on their research questions without the need to become acquainted with the nitty-gritty details of the complex research computing infrastructure. Key aspects of the presented projects are usability and interoperability of computational methods, reproducibility of research results as well as sustainability of research software. Sustainability of research software has many facets. I advocate for improving the diversity in workforce development, career paths for research software engineers and for incentivizing their work via means beyond the traditional academic rewarding system.
Research Integrity Advisor and Data ManagementARDC
Dr Paul Wong from the Australian Research Data Commons presented at the University of Technology Sydney's RIA Data Management Workshop on 21 June 2018. In partnership with the Australian Research Council, the National Health and Medical Research Council, the Australian Research Data Commons, and RMIT University, this is part of a national workshop series in data management for research integrity advisors.
Presentation at the MOC Workshop, at Boston University.
Cloud Dataverse will be a new service for accessing and processing public data sets in a the Massachusetts Open Cloud (MOC). It is based on Dataverse, a popular software framework for sharing, archiving, and analyzing research data. Cloud Dataverse extends Dataverse to replicate datasets from institution repositories to a cloud-based repository and store their data files in Swift, making data processing faster for in-situ application running in the cloud.
Cloud Dataverse is a collaborative effort between two open source projects: Massachusetts Open Cloud (MOC) and Dataverse. The Dataversesoftware is being developed at Harvard's Institute for Quantitative Social Science (IQSS) with contributors worldwide providing 21 Dataverse installations. The Harvard Dataverse installation alone hosts more than 60,000 datasets from 300 institutions by 15,000 data authors. The MOC is a collaboration between higher education (BU, NEU, Harvard, MIT and UMass), government, and industry. Its mission is to create a self-sustaining at-scale public cloud based on the Open Cloud eXchange model.
VIVO: enabling the discovery of research and scholarshipPaul Albert
An introduction to VIVO, an open source, semantic web application that enables discovery of research and scholarship across institutions and one library's role in its implementation and development.
Introduction to research data management. Presented by Natasha Simons at the C3DIS post conference workshop: Managed data – trusted research: an introduction to Research Data Management, Melbourne 31st may 2018
RDA Fourth Plenary Keynote - Prof. Christine L. Borgman, Professor Presidential Chair in Information Studies at UCLA: "Data, Data, Everywhere, Nor Any Drop to Drink." Tuesday 23rd Sept 2014, Amsterdam, the Netherlands
https://rd-alliance.org/plenary-meetings/fourth-plenary/plenary4-programme.html
Keynote address 'Opening Science' at NORFest 2023 on November 2, 2023 at the Royal Irish Academy in Dublin Ireland. Keynote speaker: Chelle Gentemann, science lead for NASA’s Transform to Open Science Mission and co-chair of the U.S. White House Office for Science and Technology and Policy (OSTP) Sub-working group on the Year of Open Science
December 9, 2015 NISO Webinar: Two-Part Webinar: Emerging Resource Types - Pa...DeVonne Parks, CEM
Addressing the New Challenges in Data Sharing: Large-Scale Data and Sensitive Data
Mercè Crosas, Chief Data Science and Technology Officer, IQSS, Harvard University
Opening science to interdisciplinarity: balancing trade-offs while creating, ...Kate Hertweck
Presentation by Kate Hertweck at the Association for Environmental Studies and Sciences (AESS) meeting in Portland, Oregon in July 2023, https://aessconference.org/
Talk given at the Data Visualisation and the Future of Academic Publishing event. https://www.eventbrite.com/e/data-visualisation-and-the-future-of-academic-publishing-tickets-25372801733?password=dataviz
Similar to Sharing Sensitive Data With Confidence: The DataTags system (20)
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
(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.
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 .
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
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.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
32. Datatags Levels
Tag Type Description Security Features Access Requirements
Blue Public Clear storage
Clear transmission Open
Green Controlled
public
Clear storage
Clear transmission
Email, OAuth verified
registration
Yellow Accountable Clear storage
Encrypted transmit
Password, Registered ,
Approval, Click DUA
Orange More
accountable
Encrypted storage
Encrypted transmit
Password, Registered,
Approval, Signed DUA
Red Fully
accountable
Encrypted storage
Encrypted transmit
Two-factor authentication,
Approval, Signed DUA
Crimson Maximally
restricted
MultiEncrypt store
Encrypted transmit
Two-factor authentication,
Approval, Signed DUA
47. Betty: Global Research Repository
Ingestion and
Decision-making
Knowledge
IRB determination or an interview system.
Codification and
Infrastructure
Blue, Green, Yellow, Orange, Red, Crimson.
Credentials and
Retrieval
Different files may additionally require specific terms of use based on
legal or regulatory requirements or adopted best practices.
(Same use case as Dataverse)