Presentation for the Open Science Week in Dublin, 2022. The presentation outlines motivations and solutions from the "Replacing Academic Journals" proposal:
https://doi.org/10.5281/zenodo.5526634
Good Riddance: Academic Publishers are Abandoning PublishingBjörn Brembs
Talk at RIOT science club on the myriad ways in which science would do so much better if scholarly institutions took their money and spent it on modern information technology instead of antiquated and counter-productive journals.
Scott Edmunds slides from class 7 from the HKU Data Curation (module MLIM7350 from the Faculty of Education) course covering open data policy and practice, and the Hong Kong context.
Good Riddance: Academic Publishers are Abandoning PublishingBjörn Brembs
Talk at RIOT science club on the myriad ways in which science would do so much better if scholarly institutions took their money and spent it on modern information technology instead of antiquated and counter-productive journals.
Scott Edmunds slides from class 7 from the HKU Data Curation (module MLIM7350 from the Faculty of Education) course covering open data policy and practice, and the Hong Kong context.
What's wrong with our scholarly infrastructure?Björn Brembs
First of a two-part series on the issues scientists face with their expensive, antiquated infrastructure and how to overcome these problems. First part on problems, second part (upcoming) on solutions.
EarthCube Monthly Community Webinar- Nov. 22, 2013EarthCube
This webinar features project overviews of all EarthCube Awards (Building Blocks, Research Coordination Networks, Conceptual Designs, and Test Governance), followed by a call for involvement, and a Q&A session.
Agenda:
EarthCube Awards – Project Overviews
1.. EarthCube Web Services (Building Block)
2. EC3: Earth-Centered Community for Cyberinfrastructure (RCN)
3. GeoSoft (Building Block)
4. Specifying and Implementing ODSIP (Building Block)
5. A Broker Framework for Next Generation Geoscience (BCube) (Building Block)
6. Integrating Discrete and Continuous Data (Building Block)
7. EAGER: Collaborative Research (Building Block)
8. A Cognitive Computer Infrastructure for Geoscience (Building Block)
9. Earth System Bridge (Building Block)
10. CINERGI – Community Inventory of EC Resources for Geoscience Interoperability (BB)
11. Building a Sediment Experimentalist Network (RCN)
12. C4P: Collaboration and Cyberinfrastructure for Paleogeosciences (RCN)
13. Developing a Data-Oriented Human-centric Enterprise for Architecture (CD)
14. Enterprise Architecture for Transformative Research and Collaboration (CD)
15. EC Test Enterprise Governance: An Agile Approach (Test Governance)
A Call for Involvement!
Incentives for infrastructure modernizationBjörn Brembs
Slides for EUA meeting explaining a strategy for open science infrastructure reform. The strategy is laid out in detail here:
http://bjoern.brembs.net/2018/11/maybe-try-another-kind-of-mandate/
Field of Study and Research Methods for an Effect of Cognitive and Informatio...Yury Solonitsyn
Authors show one of the possible approaches to the experimental research of the cognitive and information load on PC’s users – the mental load or amount of efforts, spent because of the necessity to recognise screen form’s elements and to process the data presented.
Andrei Balkanskii, Artem Smolin, Yury Solonitsyn
ITMO University, Saint Petersburg, Russia
RepliCHI - 8 Challenges in Replicating a StudyMax L. Wilson
A presentation of the 8 challenges we experienced when 6 novice MSC students tried to replicate a study of collaborative information seeking as part of their methods class, and how the original authors supported the process.
Keynote speech - Carole Goble - Jisc Digital Festival 2015Jisc
Carole Goble is a professor in the school of computer science at the University of Manchester.
In this keynote, Carole offered her insights into research data management and data centres.
RARE and FAIR Science: Reproducibility and Research ObjectsCarole Goble
Keynote at JISC Digifest 2015 on Reproducibility and Research Objects in Scholarly Communication
Includes hidden slides
All material except maybe the IT Crowd screengrab reusable
Apollo and i5K: Collaborative Curation and Interactive Analysis of GenomesMonica Munoz-Torres
Precise elucidation of the many different biological features encoded in a genome requires a careful curation process that involves reviewing all available evidence to allow researchers to resolve discrepancies and validate automated gene models, protein alignments, and other biological elements. Genome annotation is an inherently collaborative task; researchers only rarely work in isolation, turning to colleagues for second opinions and insights from those with expertise in particular domains and gene families.
The i5k initiative seeks to sequence the genomes of 5,000 insect and related arthropod species. The selected species are known to be important to worldwide agriculture, food safety, medicine, and energy production as well as many used as models in biology, those most abundant in world ecosystems, and representatives in every branch of the insect phylogeny in an effort to better understand arthropod evolution and phylogeny. Because computational genome analysis remains an imperfect art, each of these new genomes sequenced will require visualization and curation.
Apollo is an instantaneous, collaborative, genome annotation editor, and the new JavaScript based version allows researchers real-time interactivity, breaking down large amounts of data into manageable portions to mobilize groups of researchers with shared interests. The i5K is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process and Apollo is serving as the platform to empower this community. Here we offer details about this collaboration.
Experiences as a producer, consumer and observer of open dataProgCity
Peter Mooney, is an Environmental Protection Agency (EPA) funded Research Fellow at the Department of Computer Science, NUI Maynooth. He has been working with the EPA on making environmental data publicly accessibly for the last ten years.
Presentation was part of The 1st Seminar of the ERC Funded Programmable City Project based at NIRSA, NUI Maynooth, Republic of Ireland.
Big Data in Biomedicine – An NIH PerspectivePhilip Bourne
Keynote at the IEEE International Conference on Bioinformatics and Biomedicine, Washington DC, November 10, 2015.
https://cci.drexel.edu/ieeebibm/bibm2015/
New ways to communicate in science: perspectives from biodiversity researchVince Smith
A presentation given at the co-ordination workshop on Open Access to Scientific Information on Wednesday 4th May 2011 at the EU DG Information Society & Media, Avenue de Beaulieu 25, Brussels.
What's wrong with our scholarly infrastructure?Björn Brembs
First of a two-part series on the issues scientists face with their expensive, antiquated infrastructure and how to overcome these problems. First part on problems, second part (upcoming) on solutions.
EarthCube Monthly Community Webinar- Nov. 22, 2013EarthCube
This webinar features project overviews of all EarthCube Awards (Building Blocks, Research Coordination Networks, Conceptual Designs, and Test Governance), followed by a call for involvement, and a Q&A session.
Agenda:
EarthCube Awards – Project Overviews
1.. EarthCube Web Services (Building Block)
2. EC3: Earth-Centered Community for Cyberinfrastructure (RCN)
3. GeoSoft (Building Block)
4. Specifying and Implementing ODSIP (Building Block)
5. A Broker Framework for Next Generation Geoscience (BCube) (Building Block)
6. Integrating Discrete and Continuous Data (Building Block)
7. EAGER: Collaborative Research (Building Block)
8. A Cognitive Computer Infrastructure for Geoscience (Building Block)
9. Earth System Bridge (Building Block)
10. CINERGI – Community Inventory of EC Resources for Geoscience Interoperability (BB)
11. Building a Sediment Experimentalist Network (RCN)
12. C4P: Collaboration and Cyberinfrastructure for Paleogeosciences (RCN)
13. Developing a Data-Oriented Human-centric Enterprise for Architecture (CD)
14. Enterprise Architecture for Transformative Research and Collaboration (CD)
15. EC Test Enterprise Governance: An Agile Approach (Test Governance)
A Call for Involvement!
Incentives for infrastructure modernizationBjörn Brembs
Slides for EUA meeting explaining a strategy for open science infrastructure reform. The strategy is laid out in detail here:
http://bjoern.brembs.net/2018/11/maybe-try-another-kind-of-mandate/
Field of Study and Research Methods for an Effect of Cognitive and Informatio...Yury Solonitsyn
Authors show one of the possible approaches to the experimental research of the cognitive and information load on PC’s users – the mental load or amount of efforts, spent because of the necessity to recognise screen form’s elements and to process the data presented.
Andrei Balkanskii, Artem Smolin, Yury Solonitsyn
ITMO University, Saint Petersburg, Russia
RepliCHI - 8 Challenges in Replicating a StudyMax L. Wilson
A presentation of the 8 challenges we experienced when 6 novice MSC students tried to replicate a study of collaborative information seeking as part of their methods class, and how the original authors supported the process.
Keynote speech - Carole Goble - Jisc Digital Festival 2015Jisc
Carole Goble is a professor in the school of computer science at the University of Manchester.
In this keynote, Carole offered her insights into research data management and data centres.
RARE and FAIR Science: Reproducibility and Research ObjectsCarole Goble
Keynote at JISC Digifest 2015 on Reproducibility and Research Objects in Scholarly Communication
Includes hidden slides
All material except maybe the IT Crowd screengrab reusable
Apollo and i5K: Collaborative Curation and Interactive Analysis of GenomesMonica Munoz-Torres
Precise elucidation of the many different biological features encoded in a genome requires a careful curation process that involves reviewing all available evidence to allow researchers to resolve discrepancies and validate automated gene models, protein alignments, and other biological elements. Genome annotation is an inherently collaborative task; researchers only rarely work in isolation, turning to colleagues for second opinions and insights from those with expertise in particular domains and gene families.
The i5k initiative seeks to sequence the genomes of 5,000 insect and related arthropod species. The selected species are known to be important to worldwide agriculture, food safety, medicine, and energy production as well as many used as models in biology, those most abundant in world ecosystems, and representatives in every branch of the insect phylogeny in an effort to better understand arthropod evolution and phylogeny. Because computational genome analysis remains an imperfect art, each of these new genomes sequenced will require visualization and curation.
Apollo is an instantaneous, collaborative, genome annotation editor, and the new JavaScript based version allows researchers real-time interactivity, breaking down large amounts of data into manageable portions to mobilize groups of researchers with shared interests. The i5K is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process and Apollo is serving as the platform to empower this community. Here we offer details about this collaboration.
Experiences as a producer, consumer and observer of open dataProgCity
Peter Mooney, is an Environmental Protection Agency (EPA) funded Research Fellow at the Department of Computer Science, NUI Maynooth. He has been working with the EPA on making environmental data publicly accessibly for the last ten years.
Presentation was part of The 1st Seminar of the ERC Funded Programmable City Project based at NIRSA, NUI Maynooth, Republic of Ireland.
Big Data in Biomedicine – An NIH PerspectivePhilip Bourne
Keynote at the IEEE International Conference on Bioinformatics and Biomedicine, Washington DC, November 10, 2015.
https://cci.drexel.edu/ieeebibm/bibm2015/
New ways to communicate in science: perspectives from biodiversity researchVince Smith
A presentation given at the co-ordination workshop on Open Access to Scientific Information on Wednesday 4th May 2011 at the EU DG Information Society & Media, Avenue de Beaulieu 25, Brussels.
Publish or perish: how our literature serves the anti-science agendaBjörn Brembs
Online presentation at the Leibniz-Institute of Freshwater Ecology and Inland Fisheries on how our journals are one of the core reasons for the reliability, affordability and functionality issues science is experiencing today and how to fix them.
Modernisierung der Infrastruktur - so viel mehr als nur Zugang.Björn Brembs
Vortrag über die Ursachen warum die digitale informationsinfrastruktur in der Wissenschaft so hoffnungslos veraltet ist und welche verheerenden Konsequenzen das für die Wissenschaft hat.
The neurobiological nature of free willBjörn Brembs
Our own experience of our free will has been classified as either supernatural or an illusion because it is difficult to reconcile with macroscopic determinism as well as with microscopic quantum randomness. The former constituting a prison in which no freedom can exist, the latter signifying destructive chaos rather than creative action. Lost in this dichotomy is the demonstrated constructive combination of chance and necessity in complex systems, such as evolution. Recent converging evidence from neuroscience, ecology and genetics suggests that nervous systems, including human brains, have evolved neural circuits that harness (potentially quantum) chance events by embedding them in the controlling architecture of neuronal rules, in order to carefully inject them as creative components into ongoing goal-directed behavior. This presentation contains evidence that this form of behavioral variability may constitute a necessary neural mechanism for free will to evolve in humans.
The evolutionary conserved neurobiology of operant learningBjörn Brembs
Presentation at the 2016 annual meeting of the Mind and Brain College of the University of Lisbon on the multiple learning systems interacting during operant learning.
A replication crisis in the making: how we reward unreliable scienceBjörn Brembs
Presentation at the 2016 annual meeting of the Mind and Brain College of the university of Lisbon on the infrastructural causes for the apparent replication crisis in the experimental/biomedical sciences.
General brain function: Action – Outcome EvaluationBjörn Brembs
My presentation for the brain and behavior symposium entitled "Brain, Cognition, Behavior, Evolution: Polyglot to Monoglot?" organized by Jerry Hogan at the Institute of advanced studies of the University of Sao Paulo, Brazil.
Journal Club: Behavioral variability in C. elegansBjörn Brembs
My journal club presentation for Tuesday, March 17, 2015 on the paper: Feedback from Network States Generates Variability in a Probabilistic Olfactory Circuit http://dx.doi.org/10.1016/j.cell.2015.02.018
My presentation for the General ONline Research Conference in Cologn, Germany on March 6, 2014. On these slides I detail our proof-of-concept of making all our digital data openly accessible online by default, automatically, whenever the researcher who collected them evaluates them using our custom R-Scripts.
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.
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.
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 .
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.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
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.
13. Brembs, B., Button, K., & Munafò, M. (2013). Deep impact: unintended consequences of journal rank. Frontiers in Human Neuroscience, 7. doi:10.3389/fnhum.2013.00291
20. • Obsolete modes of access
• Journal prestige correlates with unreliability
• No scientific impact analysis
• Suboptimal peer-review
• Massive transparency issues
• No effective sort, filter and discover solution
• No functional hyperlinks
• Static data visualizations
• No content mining
• No social component
• No global search
• Hardly any user statistics
• etc.
…it’s like the internet in 1995!
25. • Obsolete modes of access
• Journal prestige correlates with unreliability
• No scientific impact analysis
• Suboptimal peer-review
• Massive transparency issues
• No effective sort, filter and discover solution
• No functional hyperlinks
• Static data visualizations
• No content mining
• No social component
• No global search
• Hardly any user statistics
• etc.
…it’s like the internet in 1995!
27. Report on Integration of Data and Publications, ODE Report 2011
http://www.alliancepermanentaccess.org/wp-content/plugins/download-monitor/download.php?id=ODE+Report+on+Integration+of+Data+and+Publications
36. • Current journal payments allowed only via “single source
exemption”
37.
38.
39.
40. • Current journal payments for content allowed only via “single
source exemption”
• Publishing services cannot be covered by this exemption and
must be awarded by tender/bidding:
– Open Research Europe
– Hardware, Software, Services
41.
42.
43.
44. 216.35
5000
SERVICE CONTENT
per
article
cost
[US$]
Potential
for
reform:
US$
9.56
billion
p.a.
tomorrow today
• Substitutable Services (-> competition!)
• No author facing costs
• Journal functionalities can be copied
• Cost-neutral solutions for data/code
• No individual mandates necessary
• No journals, no need to judge journal quality
• …
• …
• …
• …
• …
• …
• Side effect: permanent, legal, public access
A sustainable scholarly infrastructure:
45. • Dynamic, version controlled
• Can be searched and text-
mined
• Near-immediate publication
• Different models for post-
publication review exist
• Contributorship in diverse
roles
• Open to everyone
Data
Code
Preregistration
DMP
Interpretations
Materials
Review/Quality
control
46. • Dynamic, version controlled
• Can be searched and text-
mined
• Near-immediate publication
• Different models for post-
publication review exist
• Contributorship in diverse
roles
• Open to everyone
48. 1. Enforce procurement rules once substitutability is established:
-> publication payments awarded only via tenders
2. Funders incentivize institutions to make investments in
modern infrastructure via eligibility rules:
-> antiquated infrastructure, no funding