This document discusses issues with the current scholarly publishing system, including the impact factor metric and paywalls limiting access to research. It advocates for reforming the system by publishing in venues that are open access and evaluate works based on usage and sharing of data/code rather than journal prestige. Open and reproducible research could better serve scientists and maximize the impact of their findings.
Recomendations for infrastructure and incentives for open science, presented to the Research Data Alliance 6th Plenary. Presenter: William Gunn, Director of Scholarly Communications for Mendeley.
Recomendations for infrastructure and incentives for open science, presented to the Research Data Alliance 6th Plenary. Presenter: William Gunn, Director of Scholarly Communications for Mendeley.
Data Journalism lecture - Week 9: Social Data Visualisation
Lecture date: 4 Nov 2015
MA in Journalism
National University of Ireland, Galway
Title slide image from The Data Journalism Handbook
“Open Research Data: Implications for Science and Society”, Warsaw, Poland, May 28–29, 2015, conference organized by the Open Science Platform — an initiative of the Interdisciplinary Centre for Mathematical and Computational Modelling at the University of Warsaw. pon.edu.pl @OpenSciPlatform #ORD2015
Using R to enhance numeracy in geography: some pros and cons Rich Harris
A short presentation for the 2011 Geography, Earth and Environmental Sciences conference (Teaching and Learning for GEES Students, Birmingham) exploring how R might help improve the statistical numeracy of undergraduate students.
Laurie Goodman on "Overcoming Hurdles to Data Publication" for the Alan Turing Institute Symposium on Reproducibility for Data-Intensive Research, Oxford, 7th April 2016.
ACS National Meeting - Libraries as Hubs for Emerging Technologies - 14_0813jeffreylancaster
Presentation at the National Meeting of the American Chemical Society in San Francisco, CA, entitled, "Libraries as Hubs for Emerging Technologies" presented on August 13, 2014
A dystopian view of our evolving knowledge infrastructure. Talk in session "Reproducibility in new digital scholarship – bigger, faster, better?" at the Alan Turing Institute Symposium on Reproducibility for Data Centric Research, St Hugh's, Oxford, 7th April 2016
1000 days in the life of a science advisorSciAdvice14
Keynote by Anne Glover, chief science advisor to the European Commission at the Science Advice to Governments conference. For more information see www.globalscienceadvice.org
Data Journalism lecture - Week 9: Social Data Visualisation
Lecture date: 4 Nov 2015
MA in Journalism
National University of Ireland, Galway
Title slide image from The Data Journalism Handbook
“Open Research Data: Implications for Science and Society”, Warsaw, Poland, May 28–29, 2015, conference organized by the Open Science Platform — an initiative of the Interdisciplinary Centre for Mathematical and Computational Modelling at the University of Warsaw. pon.edu.pl @OpenSciPlatform #ORD2015
Using R to enhance numeracy in geography: some pros and cons Rich Harris
A short presentation for the 2011 Geography, Earth and Environmental Sciences conference (Teaching and Learning for GEES Students, Birmingham) exploring how R might help improve the statistical numeracy of undergraduate students.
Laurie Goodman on "Overcoming Hurdles to Data Publication" for the Alan Turing Institute Symposium on Reproducibility for Data-Intensive Research, Oxford, 7th April 2016.
ACS National Meeting - Libraries as Hubs for Emerging Technologies - 14_0813jeffreylancaster
Presentation at the National Meeting of the American Chemical Society in San Francisco, CA, entitled, "Libraries as Hubs for Emerging Technologies" presented on August 13, 2014
A dystopian view of our evolving knowledge infrastructure. Talk in session "Reproducibility in new digital scholarship – bigger, faster, better?" at the Alan Turing Institute Symposium on Reproducibility for Data Centric Research, St Hugh's, Oxford, 7th April 2016
1000 days in the life of a science advisorSciAdvice14
Keynote by Anne Glover, chief science advisor to the European Commission at the Science Advice to Governments conference. For more information see www.globalscienceadvice.org
Presentation by Aaron Griffiths, Research Officer at the Research Information Network at the Embedding Institutional Data Curation Services in Research (EIDSCR) workshop on 14 October 2009.
http://eidcsr.blogspot.com/2009/09/eidcsr-workshop-on-14-october.html
Find out how to do brand-based social media to engage customers, clients and employees.
Your organization has the opportunity to harness social media in a way that creates sustainable relationships beyond the product sale to create a community around your brand, a community that can drive innovation, business strategy & more.
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.
Scott Edmunds: Channeling the Deluge: Reproducibility & Data Dissemination in...GigaScience, BGI Hong Kong
Scott Edmunds talk at the 7th Internation Conference on Genomics: "Channeling the Deluge: Reproducibility & Data Dissemination in the “Big-Data” Era. ICG7, Hong Kong 1st December 2012
"
ISMB/ECCB 2013 Keynote Goble Results may vary: what is reproducible? why do o...Carole Goble
Keynote given by Carole Goble on 23rd July 2013 at ISMB/ECCB 2013
http://www.iscb.org/ismbeccb2013
How could we evaluate research and researchers? Reproducibility underpins the scientific method: at least in principle if not practice. The willing exchange of results and the transparent conduct of research can only be expected up to a point in a competitive environment. Contributions to science are acknowledged, but not if the credit is for data curation or software. From a bioinformatics view point, how far could our results be reproducible before the pain is just too high? Is open science a dangerous, utopian vision or a legitimate, feasible expectation? How do we move bioinformatics from one where results are post-hoc "made reproducible", to pre-hoc "born reproducible"? And why, in our computational information age, do we communicate results through fragmented, fixed documents rather than cohesive, versioned releases? I will explore these questions drawing on 20 years of experience in both the development of technical infrastructure for Life Science and the social infrastructure in which Life Science operates.
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
Presentazione all'interno del seminario "Servizi e strumenti per la ricerca a Ca’ Foscari". 29 maggio 2019 ore 9.15 – 14.30. Aula Morelli, Palazzo Malcanton Marcorà, Venezia.
Cite as:
Sarretta, Alessandro. (2019, May). Pubblicare: la parola ai ricercatori (Publishing Open). Zenodo. http://doi.org/10.5281/zenodo.3234169
Scott Edmunds talk at G3 (Great GigaScience & Galaxy) workshop: Open Data: th...GigaScience, BGI Hong Kong
Scott Edmunds talk at G3 (Great GigaScience & Galaxy) workshop: Open Data: the reproducibility crisis, and the need for transparency. Melbourne University 19th September 2014
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.
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.
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.
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/
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.
Richard's aventures in two entangled wonderlandsRichard 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.
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.
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.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
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.
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 .
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
(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.
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/
3. Van Noorden, R. (2013). Open access: The true cost of science publishing. Nature 495, 426–9
House of Commons Select Committee on Science and Technology (2004). APPENDIX 138. Supplementary evidence from Nature Publishing Group
4. Introduced in 1950’s by Eugene Garfield: ISI
A1 A2
C12
citations
published
time
articles
published
year 1 year 2 year 3
퐼퐹(푦푒푎푟 3) = +
5. Introduced in 1950’s by Eugene Garfield: ISI
40 60
100
citations
published
time
articles
published
year 1 year 2 year 3
퐼퐹(푦푒푎푟 3) = +
=1
6. Journal X IF 2013=
All citations from TR indexed journals in 2013 to papers in journal X
Number of citable articles published in journal X in 20011/12
€30,000-130,000/year subscription rates
Covers ~11,500 journals (Scopus covers ~16,500)
8. • PLoS Medicine, IF 2-11 (8.4)
(The PLoS Medicine Editors (2006) The Impact Factor Game. PLoS Med 3(6): e291.
http://www.plosmedicine.org/article/info:doi/10.1371%2Fjournal.pmed.0030291)
• Current Biology IF from 7 to 11 in
2003
– Bought by Cell Press (Elsevier) in 2001…
9.
10.
11.
12.
13.
14. • Rockefeller University Press bought their data from Thomson Reuters
• Up to 19% deviation from published records
• Second dataset still not correct
Rossner M, van Epps H, Hill E (2007): Show me the data. The Journal of Cell
Biology, Vol. 179, No. 6, 1091-1092 http://jcb.rupress.org/cgi/content/full/179/6/1091
15. • Left-skewed distributions
• Weak correlation of individual
article citation rate with journal IF
Seglen PO (1997): Why the impact factor of journals should not be used for evaluating research. BMJ 1997;314(7079):497http://www.bmj.com/cgi/content/full/314/7079/497
16. The weakening relationship between the Impact Factor and papers' citations in the digital age (2012): George A. Lozano, Vincent Lariviere, Yves Gingras arXiv:1205.4328
17. 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
18. Munafò, M., Stothart, G., & Flint, J. (2009). Bias in genetic association studies and impact factor Molecular Psychiatry, 14 (2), 119-120 DOI: 10.1038/mp.2008.77
19. Brown, E. N., & Ramaswamy, S. (2007).
Quality of protein crystal structures. Acta
Crystallographica Section D Biological
Crystallography, 63(9), 941–950.
doi:10.1107/S0907444907033847
20. Fang et al. (2012): Misconduct accounts for the majority of retracted scientific publications. PNAS 109 no. 42 17028-17033
21. Data from: Fang, F., & Casadevall, A. (2011). RETRACTED SCIENCE AND THE RETRACTION INDEX Infection and Immunity DOI: 10.1128/IAI.05661-11
26. • Limited access
• No scientific impact
analysis
• No global search
• No functional hyperlinks
• No flexible data
visualization
• No submission
standards
• (Almost) no statistics
• No text/data-mining
• No effective way to sort,
filter and discover
• No networking feature
• etc.
…it’s like the
web in 1995!
27. Costs [thousand US$/article]
Legacy SciELO
(Sources: Van Noorden, R. (2013). Open access: The true cost of science publishing. Nature 495, 426–9; Packer, A. L. (2010). The SciELO Open
Access: A Gold Way from the South. Can. J. High. Educ. 39, 111–126)
30. Report on Integration of Data and Publications, ODE Report 2011
http://www.alliancepermanentaccess.org/wp-content/plugins/download-monitor/download.php?id=ODE+Report+on+Integration+of+Data+and+Publications
38. Potential for innovation: 9.8b p.a.
Costs [thousand US$/article]
Legacy SciELO
(Sources: Van Noorden, R. (2013). Open access: The true cost of science publishing. Nature 495, 426–9; Packer, A. L. (2010). The SciELO Open
Access: A Gold Way from the South. Can. J. High. Educ. 39, 111–126)
39.
40.
41.
42. 1) Publish in the “Journal of Unreliable Research”
of your field – or take your chances
43. 2) Publish everything else where publication is
quick and where it can be widely read
44. 3) Ask your PI what will happen to all the work
you put into your code & data and how you can
get as many people as possible to use it
45. 1. Publish in the “Journal of Unreliable
Research” of your field – or take your chances
2. Publish everything else where publication is
quick and where it can be widely read
3. Ask your PI what will happen to all the work
you put into your code & data and how you
can get as many people as possible to use it
46. What we are doing: One person is
not an institutional infrastructure
61. Same type of experiments → same
script
Default: → same categories
→ same tags
→ same authors
→ same links
→ same description
→ One complete article, in one click.
Update the figure:
Higher sample size directly published
while analysed, your boss may see the
results before you do! (or you may see
the results of your student before they
do)
Possibility to make it public and citable
in one click or directly in the R code.