Libraries & Research Data Management for CO Alliance of Resrch LibrariesCarly Strasser
Keynote presentation for the Colorado Alliance of Research Libraries 2014 Research Data Management Conference, 11 July 2014. Focuses on why data management and sharing is important, and the role of libraries.
Presentation from the “Corporate Data” session of the “Our World, Our Data” conference held at at MIT Media Lab on April 30, 2017. Organized by Safecast with sponsorship from the Shuttleworth Fund. Many thanks to Joi Ito, Director of the MIT Media Lab, and Ethan Zuckerman and Lorrie LeJeune of The Center for Civic Media.
https://www.media.mit.edu/events/our-world-our-data/
Presentation by R. David Lankes at the 2006 Charleston Conference. Describes how librarianship must evolve to adapt to massive scale computing and data.
Linking Scientific Metadata (presented at DC2010)Jian Qin
Linked entity data in metadata records builds a foundation for semantic web. Even though metadata records contain rich entity data, there is no linking between associated entities such as persons, datasets, projects, publications, or organizations. We conducted a small experiment using the dataset collection from the Hubbard Brook Ecosystem Study (HBES), in which we converted the entities and their relationships into RDF triples and linked the URIs contained in RDF triples to the corresponding entities in the Ecological Metadata Language (EML) records. Through the transformation program written in XML Stylesheet Language (XSL), we turned a plain EML record display into an interlinked semantic web of ecological datasets. The experiment suggests a methodological feasibility in incorporating linked entity data into metadata records. The paper also argues for the need of changing the scientific as well as general metadata paradigm.
This webinar will discuss the special needs of digital humanities researchers and help you learn how to talk them about their information management needs.
Topics that will be covered:
What is humanities data?
What special considerations are involved in creating DMPs for humanities data?
Where can you store humanities data?
What will humanities funding agencies be looking for? What regulations apply to humanities data (e.g., data sharing, data management, data availability)?
What librarians should know before meeting with a humanist; how humanists differ from other researchers in the way they think about their version of data.
Libraries & Research Data Management for CO Alliance of Resrch LibrariesCarly Strasser
Keynote presentation for the Colorado Alliance of Research Libraries 2014 Research Data Management Conference, 11 July 2014. Focuses on why data management and sharing is important, and the role of libraries.
Presentation from the “Corporate Data” session of the “Our World, Our Data” conference held at at MIT Media Lab on April 30, 2017. Organized by Safecast with sponsorship from the Shuttleworth Fund. Many thanks to Joi Ito, Director of the MIT Media Lab, and Ethan Zuckerman and Lorrie LeJeune of The Center for Civic Media.
https://www.media.mit.edu/events/our-world-our-data/
Presentation by R. David Lankes at the 2006 Charleston Conference. Describes how librarianship must evolve to adapt to massive scale computing and data.
Linking Scientific Metadata (presented at DC2010)Jian Qin
Linked entity data in metadata records builds a foundation for semantic web. Even though metadata records contain rich entity data, there is no linking between associated entities such as persons, datasets, projects, publications, or organizations. We conducted a small experiment using the dataset collection from the Hubbard Brook Ecosystem Study (HBES), in which we converted the entities and their relationships into RDF triples and linked the URIs contained in RDF triples to the corresponding entities in the Ecological Metadata Language (EML) records. Through the transformation program written in XML Stylesheet Language (XSL), we turned a plain EML record display into an interlinked semantic web of ecological datasets. The experiment suggests a methodological feasibility in incorporating linked entity data into metadata records. The paper also argues for the need of changing the scientific as well as general metadata paradigm.
This webinar will discuss the special needs of digital humanities researchers and help you learn how to talk them about their information management needs.
Topics that will be covered:
What is humanities data?
What special considerations are involved in creating DMPs for humanities data?
Where can you store humanities data?
What will humanities funding agencies be looking for? What regulations apply to humanities data (e.g., data sharing, data management, data availability)?
What librarians should know before meeting with a humanist; how humanists differ from other researchers in the way they think about their version of data.
Hawke's Bay Open Data Conference - 2 May 2019enotsluap
Hawke's Bay Open Data Conference - 2 May 2019. Presentation on open data Policy, data available and innovative ways it is being reused. Also why the private sector could/should release data.
Jason Parker gave a presentation on "Open Data Sources for Grants" to the Tennessee Chapter of the Grant Professionals Association on September 10, 2014. This presentation includes a wide variety of open data resources that grant writers can use to strengthen proposals.
What is research data?
Value and potential of research data and who benefits
What is data sharing? Open/shared/closed models
Benefits of open data
Class discussion: does all data need to be open to get value from it?
Opening the Gates: Will Open Data Initiatives Make Local Governments in the P...Open Data Research Network
A research poster presented as part of the Exploring the Emerging Impacts of Open Data in Developing Countries project at the Research Sharing Event in Berlin, 15th July 2014. For more see http://www.opendataresearch.org/emergingimpacts/
Hawke's Bay Open Data Conference - 2 May 2019enotsluap
Hawke's Bay Open Data Conference - 2 May 2019. Presentation on open data Policy, data available and innovative ways it is being reused. Also why the private sector could/should release data.
Jason Parker gave a presentation on "Open Data Sources for Grants" to the Tennessee Chapter of the Grant Professionals Association on September 10, 2014. This presentation includes a wide variety of open data resources that grant writers can use to strengthen proposals.
What is research data?
Value and potential of research data and who benefits
What is data sharing? Open/shared/closed models
Benefits of open data
Class discussion: does all data need to be open to get value from it?
Opening the Gates: Will Open Data Initiatives Make Local Governments in the P...Open Data Research Network
A research poster presented as part of the Exploring the Emerging Impacts of Open Data in Developing Countries project at the Research Sharing Event in Berlin, 15th July 2014. For more see http://www.opendataresearch.org/emergingimpacts/
Jaimi Dowdell presents "Data Journalism for Business Reporting" during the free, daylong workshop, "Be a Better Business Watchdog -- CAR for Business Journalists."
For more information about free training for business journalists, please visit businessjournalism.org.
This handout accompanies a presentation, "Data-Driven Enterprise off Any Beat," by Manuel Torres, enterprise editor at The Times-Picayune | Nola.com. It details what data journalism can do for a journalist, how to get started with data journalism, how to find data and how to learn more about data journalism. It also lists links to many data sets by beat. NewsTrain is a training initiative of Associated Press Media Editors: http://bit.ly/NewsTrain
Similar to Data Extension for a public-trust resource (20)
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
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 .
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
(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.
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.
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.
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.
10. If these are all public-trust
resources, why do we treat
them differently?
11. Data as a public-trust
resource is scary
Might BecomeYour Data Our Data
orY(our) Data (Y)Our Data
12. Some brief history:
The 1862 Morrill Act authorized the selling of federal
property to fund the creation of state universities
focused on agricultural and technical education;
Need recognized for experts to go beyond teaching on
campus and so the Smith-Lever Act of 1914 authorized
the creation of Land-Grant Cooperative Extension
Services;
Sea Grants, Sun Grants, and Space Grants created
subsequently.
13. The Promises and Challenges
of Open Data
Potential Benefits (Janssen et al. (2012):
Transparency
New services for citizens
Direct democracy
Economic growth
Co-creation & reuse of data
Potential Challenges (Janssen et al. (2012) :
Transparency vs privacy
Access to both original and processed data
Incorporation of user input
Balancing organizational and individual interests
14. Functions for a Data Grant
Serve as an available intermediary to assist in:
Discovering and accessing relevant public data
Identifying available tools to work with data
Crafting workflows
Others?
15. Does a Data Grant already exist?
Signs of movement in this direction:
General Service Administration’s 18F
Commerce Data Service
National Data Service
Libraries (more later)
Others?
16. Are libraries already filling this
role?
Sort of, especially if:
1. You lock the library
2. Sell the books
3. Keep the librarians
4. I’m not suggesting we do any of these things (except #3)
5. A new program or staff in this paradigm would have a
fundamentally different service model
6. A Sea Grant assessment found in 2014 that $2 of federal funds
leveraged an additional $1 of state funds, and provided a 750%
ROI for these combined funds; retained or created 3,400
businesses, and retained or created 15,000 jobs (Sea Grant
Association)
17. Characteristics of Grant-type
programs:
May feature a large one time federal allocation, that
may include resources (e.g. land)
Some state ownership/support
Local presence across region
Extension approach
Support for all sectors
Goes to the customer
18. Data as a public-trust
resource is scary
Might BecomeYour Data Our Data
orYour) Data (Y)Our Data
Extension
Y(our) Data
19. A notional construct:
Dispersed effort and coalition;
Local extension through higher education institutions
from community colleges to flagship universities;
Governor’s Office of Internet Technology as state
partner;
Department of Commerce as federal partner; RFP
2016-NIST-NICE-01
Colorado Data Extension Network (CODEN).
20. References:
Marijn Janssen , Yannis Charalabidis & Anneke Zuiderwijk (2012)
Benefits, Adoption Barriers and Myths of Open Data and Open
Government, Information Systems Management, 29:4, 258-268,
DOI: 10.1080/10580530.2012.716740
A smart investment in our coastal communities, Sea Grant
Association,
http://seagrant.noaa.gov/Portals/0/Documents/network_resources/
communications/WE_SeaGrant_Investment_Final-rev2.pdf