HiGlass & Friends

•

0 likes•270 views

This document highlights new features of HiGlass, including a split matrix view, built-in view config editor, and cross-track annotations. It also lists several new HiGlass-based tools from various institutions for genomic data visualization, such as PEAX from Harvard and Novartis, and Epilogos from Altius Institute. Finally, it provides links to learn more about HiGlass' Python integration, a SciPy 2019 talk, and encourages following the HiGlass Twitter account for updates.

Science

HiGlass & Friends
Nils Gehlenborg
Harvard Medical School
@ngehlenborg

Peter Kerpedjiev
Zymergen
@pkerpedjiev
Nezar Abdennur
MIT
@nv1ctus
Fritz Lekschas
Harvard
@flekschas

http://higlass.io
Built-In
View
Config
Editor

http://higlass.io
Cross Track
Annotations

https://ﬂekschas.github.io/higlass-fancy/
Cross Track
Annotations

http://peax.lekschas.de
PEAX
Harvard +
Novartis

https://epilogos.altius.org
Epilogos
Altius
Institute

http://scalable-insets.lekschas.de
Scalable
Insets
Harvard

https://onlinelibrary.wiley.com/doi/epdf/10.1111/cgf.13727
Tasks,
Techniques,
and Tools for
Genomic Data
Visualization

https://github.com/higlass/higlass-python
higlass-
python

https://github.com/higlass/scipy19
SciPy 2019
Talk + Demo

https://www.youtube.com/watch?v=v62k4Ok1S8g&feature=youtu.be&t=1489
Jupyter
Notebook
Integration

https://twitter.com/higlass_io
Follow
@higlass_io

Most scientific developments are recorded in published papers and communicated via presentations. Scientific findings are presented within organizations, at conferences, via Webinars and other fora. Yet after delivery to an audience, important information is often left to wither on hard drives, document management systems and even the Web. Accessing the underlying data for scientific findings has been the Achilles Heel of researchers due to closed and proprietary systems. This presentation shows an alternative to sharing scientific information using a Linked Data approach.

FHIR Developer Days 2015. Study on db implementations for FHIR server

Igor Bossenko

Managing & sharing your data and code for openness

Phoebe Ayers

Methanol toxin

LanHngPhm3

Linked Data for improved organization of research data

Samuel Lampa

Avoid Scientific Misconduct

Nader Ale Ebrahim

One of the most important research ethical issues that should be taken into consideration is “scientific misconduct” such as fabrication, falsification and plagiarism. Plagiarism can occur at any stage of the research activities such as reporting, communicating, authoring, and peer review. The purpose of this workshop is to engage researchers in their responsibility to conduct an ethical research.

Multi-Scale Visualization Tools for Exploration of Chromosome Interaction ...

Nils Gehlenborg

How do you visualize a 3 million x 3 million matrix and allow users to explore features across a wide range of different scales? We built HiGlass and HiPiler, web-based visualization tools for analysis of Hi-C and other genome-wide chromosome interaction data that enables comparison of multiple contact matrices and integration of other data types. In my talk, I will discuss several use cases and describe how we architected HiGlass and HiPiler.

Presentation at BOSC 2013 / ISMB 2013. (PowerPoint 2013 source) PDF: https://www.slideshare.net/soilandreyes/2013-0719bosc-2013myexperimentresearchobjectsslides See also poster at http://www.slideshare.net/soilandreyes/2013-0718bosc-2013myexperimentresearchobjectsposter-24242509 or submitted abstract: https://docs.google.com/document/d/1jaAuPV-EnbsyI14L56HKHBQP7eDVfeXGLlK-LwohnWw/edit?usp=sharing We have evolved Research Objects as a mechanism to preserve digital resources related to research, by providing mechanisms, formats and architecture for describing aggregated resources (hypothesis, workflow, datasets, scripts, services), their relations (is input for, explains, used by), provenance (graph was derived from dataset A, B and C) and attribution (who contributed what, and when?). The website myExperiment is already popular for collaborating on, publishing and sharing scientific workflows, however we have found that for understanding and preserving a workflow over time, its definition is not enough, specially faced with workflow decay, services and tools that change over time. We have therefore adapted the research object model as a foundation for the myExperiment packs, allowing uploading of workflow runs, inputs, outputs and other files relevant to the workflow, relating them with annotations and integrated the Wf4Ever architecture for performing decay analysis and tracking a research object’s evolution as it and its constituent resources change over time.

Being Reproducible: SSBSS Summer School 2017

Carole Goble

Lecture 2: Being Reproducible: Models, Research Objects and R* Brouhaha Reproducibility is a R* minefield, depending on whether you are testing for robustness (rerun), defence (repeat), certification (replicate), comparison (reproduce) or transferring between researchers (reuse). Different forms of "R" make different demands on the completeness, depth and portability of research. Sharing is another minefield raising concerns of credit and protection from sharp practices. In practice the exchange, reuse and reproduction of scientific experiments is dependent on bundling and exchanging the experimental methods, computational codes, data, algorithms, workflows and so on along with the narrative. These "Research Objects" are not fixed, just as research is not “finished”: the codes fork, data is updated, algorithms are revised, workflows break, service updates are released. ResearchObject.org is an effort to systematically support more portable and reproducible research exchange. In this talk I will explore these issues in more depth using the FAIRDOM Platform and its support for reproducible modelling. The talk will cover initiatives and technical issues, and raise social and cultural challenges.

2017-11-03 Provenance and Research Object

Stian Soiland-Reyes

TAMALE Seminar: Evaluating scientific hypotheses using Semantic Web technologies

alison.callahan

Open PHACTS April 2017 Science webinar Workflow tools

open_phacts

Final Johnson Research Libraries and Computational Research

National Information Standards Organization (NISO)

2017-11-03 Provenance and Research Object

Stian Soiland-Reyes

Donders neuroimage toolkit - open science and good practices

Robert Oostenveld

Shift Left Security

gjdevos

HyQue: Evaluating scientific Hypotheses using semantic web technologiesMichel Dumontier

Algorithm of Reading Scientific Research Article

VIT-AP University

Agenda 1. Algorithm of Reading Scientific Research Article 2. Importance of ORCID ID 3. Benefit of ORCiD 4. Process of Connecting Scopus database to ORCiD iD 5. Registration of ORCiD iD Account 6. Scopus Database connected to ORCiD iD 7. BibTeX Entry to add all the publication at the same time in ORCiD iD 8. Process of importing BibTex into ORCiD Database 9. Using Bibtex include all the research article in one time

Verifiable, linked open knowledge that anyone can edit

Dario Taraborelli

Analytic and Visual Elements on Researcher Profiling Systems

Michael Bales

Making Use of NGS Data: From Reads to Trees and Annotations

João André Carriço

Citing & Searching : Tools and Trics

Guus van den Brekel

Mtsr2015 goble-keynote

Carole Goble

Metadata and Semantics Research Conference, Manchester, UK 2015 Research Objects: why, what and how, In practice the exchange, reuse and reproduction of scientific experiments is hard, dependent on bundling and exchanging the experimental methods, computational codes, data, algorithms, workflows and so on along with the narrative. These "Research Objects" are not fixed, just as research is not “finished”: codes fork, data is updated, algorithms are revised, workflows break, service updates are released. Neither should they be viewed just as second-class artifacts tethered to publications, but the focus of research outcomes in their own right: articles clustered around datasets, methods with citation profiles. Many funders and publishers have come to acknowledge this, moving to data sharing policies and provisioning e-infrastructure platforms. Many researchers recognise the importance of working with Research Objects. The term has become widespread. However. What is a Research Object? How do you mint one, exchange one, build a platform to support one, curate one? How do we introduce them in a lightweight way that platform developers can migrate to? What is the practical impact of a Research Object Commons on training, stewardship, scholarship, sharing? How do we address the scholarly and technological debt of making and maintaining Research Objects? Are there any examples I’ll present our practical experiences of the why, what and how of Research Objects.

Research software and Dataverse

philipdurbin

Working with data.open.ac.uk, the Linked Data Platform of the Open University

Mathieu d'Aquin

B Chapman - Toolkit for variation comparison and analysis

Jan Aerts

Power to the People: Data Visualization in Biology and Medicine

Nils Gehlenborg

Cancer Genomics Visualization across Scales: Nucleotides to Cohorts

Nils Gehlenborg

Similar to HiGlass & Friends

Reproducibility 1

Khalid Belhajjame

2013-07-19 myExperiment research objects, beyond workflows and packs (PPTX)

Stian Soiland-Reyes

Being Reproducible: SSBSS Summer School 2017

Carole Goble

2017-11-03 Provenance and Research Object

Stian Soiland-Reyes

TAMALE Seminar: Evaluating scientific hypotheses using Semantic Web technologies

alison.callahan

Open PHACTS April 2017 Science webinar Workflow tools

open_phacts

Final Johnson Research Libraries and Computational Research

National Information Standards Organization (NISO)

2017-11-03 Provenance and Research Object

Stian Soiland-Reyes

Donders neuroimage toolkit - open science and good practices

Robert Oostenveld

Shift Left Security

gjdevos

HyQue: Evaluating scientific Hypotheses using semantic web technologiesMichel Dumontier

Algorithm of Reading Scientific Research Article

VIT-AP University

Verifiable, linked open knowledge that anyone can edit

Dario Taraborelli

Analytic and Visual Elements on Researcher Profiling Systems

Michael Bales

Making Use of NGS Data: From Reads to Trees and Annotations

João André Carriço

Citing & Searching : Tools and Trics

Guus van den Brekel

Mtsr2015 goble-keynote

Carole Goble

Research software and Dataverse

philipdurbin

Working with data.open.ac.uk, the Linked Data Platform of the Open University

Mathieu d'Aquin

B Chapman - Toolkit for variation comparison and analysis

Jan Aerts

Similar to HiGlass & Friends (20)

Reproducibility 1

2013-07-19 myExperiment research objects, beyond workflows and packs (PPTX)

Being Reproducible: SSBSS Summer School 2017

2017-11-03 Provenance and Research Object

TAMALE Seminar: Evaluating scientific hypotheses using Semantic Web technologies

Open PHACTS April 2017 Science webinar Workflow tools

Final Johnson Research Libraries and Computational Research

2017-11-03 Provenance and Research Object

Donders neuroimage toolkit - open science and good practices

Shift Left Security

HyQue: Evaluating scientific Hypotheses using semantic web technologies

Algorithm of Reading Scientific Research Article

Verifiable, linked open knowledge that anyone can edit

Analytic and Visual Elements on Researcher Profiling Systems

Making Use of NGS Data: From Reads to Trees and Annotations

Citing & Searching : Tools and Trics

Mtsr2015 goble-keynote

Research software and Dataverse

Working with data.open.ac.uk, the Linked Data Platform of the Open University

B Chapman - Toolkit for variation comparison and analysis

More from Nils Gehlenborg

Power to the People: Data Visualization in Biology and Medicine

Nils Gehlenborg

Cancer Genomics Visualization across Scales: Nucleotides to Cohorts

Nils Gehlenborg

A Unified Approach to Exploration, Authoring, and Communication with Reproduc...

Nils Gehlenborg

Visualization plays two essential roles in data-driven scientific discovery. First, visualization is a key tool for data exploration and hypothesis generation. Second, visualization facilitates communication of insights and findings. In a typical analysis scenario, however, visualization for exploration and visualization for communication are two separate processes. They often involve different software tools and data representations. Even though sophisticated interactive visualization tools are available to explore data sets, findings are usually shared in form of static images or functionally limited interactive visualizations. While these capture a particular state, they do not include any information about the exploration process that lead to the finding. In this talk I will describe how by capturing the visual exploration process, visualizations can be made reproducible and sharable. My collaborators and I leverage such data about the analysis process to allow analysts to create "vistories", which are interactive and annotated figures, that communicate insights and findings.

EMBL John Kendrew Award Lecture 2018

Nils Gehlenborg

Receiving the John Kendrew Award is a great honour for me, and I am humbled to be joining the ranks of the previous recipients. None of this would have been possible without the many people who influenced my career at EMBL and Harvard Medical School, in particular, my past and present mentors. To me, the John Kendrew Award is not only a recognition of my achievements. I also consider it an acknowledgment of the importance of my field—visualisation of biomedical data—which was in its infancy when I started my PhD at the EMBL-EBI in 2006. https://www.embl.de/aboutus/alumni/news/news_2018/20180302_gehlenborg/index.html

Mining Gems from the Data Visualization Literature

Nils Gehlenborg

Patients, Genomes, Time: Visualizing Disease Cohorts

Nils Gehlenborg

Interpreting data from cohort studies where clinical and molecular data across hundreds to thousands of patient samples need to be integrated, potentially spanning multiple time points, is challenging. In this presentation, I will discuss how data visualization can be used to drive or support this process, using tools that are applying the concept of “divide and conquer” to visual exploration. I will be presenting our early work on StratomeX and illustrate how this approach led to techniques such as Domino and LineUp, and will also introduce OncoThreads and Lineage, tools that we designed for visualization of cohorts with temporal and genealogical information, respectively.

Data Visualization in Biomedical Sciences: More than Meets the Eye

Nils Gehlenborg

In science, data visualization serves two primary purposes. The first is to explore data sets interactively and the second is to communicate discoveries. However, the requirements for visualizations employed in these activities are very different. Therefore, the software tools used for these purposes are typically disconnected, creating significant challenges for reproducibility and effective communication of discoveries in data-driven biomedical science. In this presentation, I will address how a new approach to creating data visualization tools can connect data analysts and other stakeholders inside and outside the scientific community. I will introduce and demonstrate the "Vistories" approach that was motivated by these question. Presented at the 5th Cancer Research UK Big Data Analytics Conference on Data Visualization.

Visualizing Patient Cohorts: Integrating Data Types, Relationships, and Time

Nils Gehlenborg

Visualization of 3D Genome Data

Nils Gehlenborg

Bayer Data Science Meetup

Nils Gehlenborg

HiGlass + HiPiler: Making Sense of Chromosome Interaction Data with Multi-Sca...

Nils Gehlenborg

How can we visualize a 3,000,000 x 3,000,000 cell matrix and allow analysts to explore features across a wide range of different scales? We built HiGlass, a web-based visualization tool for analysis of Hi-C and other genome-wide chromosome interaction data that enables comparison of multiple contact matrices and integration of other data types. To complement this functionality, we also created HiPiler, which enables investigators to view and explore thousands of features such as loops or TADs and correlate their appearance with their genomic locations and experimental conditions. In my talk, I will discuss the design of HiGlass and HiPiler and present a range of use cases for these applications. (Thanks to Fritz Lekschas for providing many of the slides.)

Relaxation Techniques for the Upset Data Scientist

Nils Gehlenborg

SMC-RNA BioVis Data Visualization DREAM Challenge Preview

Nils Gehlenborg

Tracing the Origins of Data and Ideas - Provenance Visualization for Biomedic...

Nils Gehlenborg

Approaches for the Integration of Visual and Computational Analysis of Biomed...

Nils Gehlenborg

The integration of computational and statistical approaches with visualization tools is becoming crucial as biomedical data sets are rapidly growing in size. Finding efficient solutions that address the interplay between data management, algorithmic and visual analysis tools is challenging. I will discuss some of these challenges and demonstrate how we are addressing them in our Refinery Platform project (http://www.refinery-platform.org).

Data Visualization to Enhance our Understanding of the Cancer Genome

Nils Gehlenborg

BioVis Meetup @ IEEE VIS 2015

Nils Gehlenborg

The international Symposium on Biological Data Visualization (BioVis) is an interdisciplinary event covering all aspects of visualization in biology. The Symposium brings together researchers from the visualization, bioinformatics, and biology communities with the purpose of educating, inspiring, and engaging visualization researchers in problems in biological data visualization as well as bioinformatics and biology researchers in state-of-the-art visualization research. In order to further engage with a biological audience, the fourth and fifth editions were organized in collaboration with the International Society for Computational Biology and held jointly with their ISMB annual conference. We are keen to maintain a presence with the VIS community and this meetup will serve as a focus for researchers in BioVis to meet up at VIS to discuss ideas for further development of the Biological Visualisation Community. In particular, this meetup will bring together BioVis researchers and groups of interest within the City of Chicago, who runs a regular Data Visualization Meetup in Chicago. Website: http://www.meetup.com/The-Chicago-Data-Visualization-Group/

Visualization Tools for the Refinery Platform - Supporting reproducible resea...

Nils Gehlenborg

The Refinery Platform (http://www.refinery-platform.org) is a web-based data visualization and analysis system for epigenomic and genomic data designed to support reproducible biomedical research. The analysis backend employs the Galaxy Workbench and connects to a data repository based on the ISA-Tab data description format. In my talk I will discuss the exploratory visualization tools that we have integrated into Refinery.

Visualization Approaches for Biomedical Omics Data: Putting It All Together

Nils Gehlenborg

Keynote Talk presented at the 1st Annual BiVi Community Annual Meeting (17 December 2014) http://bivi.co/page/bivi-annual-meeting-16-17th-december-2014 Visualization Approaches for Biomedical Omics Data: Putting It All Together The rapid proliferation of high quality, low cost genome-wide measurement technologies such as whole-genome and transcriptome sequencing, as well as advances in epigenomics and proteomics, are enabling researchers to perform studies that generate heterogeneous datasets for cohorts of thousands of individuals. A common feature of these studies is that a collection of genome-wide, molecular data types and phenotypic or clinical characterizations are available for each individual. These data can be used to identify the molecular basis of diseases and to characterize and describe the variations that are relevant for improved diagnosis, prognosis and targeted treatment of patients. An example for a study in which this approach has been successfully applied is The Cancer Genome Atlas project (http://cancergenome.nih.gov). In my talk I will discuss how visualization approaches can be applied to enable exploration and support analysis of data generated by such studies. Specifically, I will review techniques and tools for visual exploration of individual omics data types, their ability to scale to large numbers of individuals or samples, and emerging techniques that integrate multiple omics data types for interactive visual analysis. I will also examine technical and legal challenges that developers of such visualization tools are facing. To conclude my talk, I will outline research opportunities for the biological data visualization community that address major challenges in this domain.

Biological Visualization Community Meetup 2014

Nils Gehlenborg

More from Nils Gehlenborg (20)

Power to the People: Data Visualization in Biology and Medicine

Cancer Genomics Visualization across Scales: Nucleotides to Cohorts

A Unified Approach to Exploration, Authoring, and Communication with Reproduc...

EMBL John Kendrew Award Lecture 2018

Mining Gems from the Data Visualization Literature

Patients, Genomes, Time: Visualizing Disease Cohorts

Data Visualization in Biomedical Sciences: More than Meets the Eye

Visualizing Patient Cohorts: Integrating Data Types, Relationships, and Time

Visualization of 3D Genome Data

Bayer Data Science Meetup

HiGlass + HiPiler: Making Sense of Chromosome Interaction Data with Multi-Sca...

Relaxation Techniques for the Upset Data Scientist

SMC-RNA BioVis Data Visualization DREAM Challenge Preview

Tracing the Origins of Data and Ideas - Provenance Visualization for Biomedic...

Approaches for the Integration of Visual and Computational Analysis of Biomed...

Data Visualization to Enhance our Understanding of the Cancer Genome

BioVis Meetup @ IEEE VIS 2015

Visualization Tools for the Refinery Platform - Supporting reproducible resea...

Visualization Approaches for Biomedical Omics Data: Putting It All Together

Biological Visualization Community Meetup 2014

Recently uploaded

SAR of Medicinal Chemistry 1st by dk.pdf

KrushnaDarade1

Nutraceutical market, scope and growth: Herbal drug technology

Lokesh 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.

Leaf Initiation, Growth and Differentiation.pdf

RenuJangid3

Chapter 12 - climate change and the energy crisis

tonzsalvador2222

Mudde & Rovira Kaltwasser. - Populism - a very short introduction [2017].pdf

frank0071

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.

DERIVATION OF MODIFIED BERNOULLI EQUATION WITH VISCOUS EFFECTS AND TERMINAL V...

Wasswaderrick3

In this book, we use conservation of energy techniques on a fluid element to derive the Modified Bernoulli equation of flow with viscous or friction effects. We derive the general equation of flow/ velocity and then from this we derive the Pouiselle flow equation, the transition flow equation and the turbulent flow equation. In the situations where there are no viscous effects , the equation reduces to the Bernoulli equation. From experimental results, we are able to include other terms in the Bernoulli equation. We also look at cases where pressure gradients exist. We use the Modified Bernoulli equation to derive equations of flow rate for pipes of different cross sectional areas connected together. We also extend our techniques of energy conservation to a sphere falling in a viscous medium under the effect of gravity. We demonstrate Stokes equation of terminal velocity and turbulent flow equation. We look at a way of calculating the time taken for a body to fall in a viscous medium. We also look at the general equation of terminal velocity.

THEMATIC APPERCEPTION TEST(TAT) cognitive abilities, creativity, and critic...

Abdul Wali Khan University Mardan,kP,Pakistan

hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skills

Phenomics assisted breeding in crop improvement

IshaGoswami9

As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate change, and increasing global population, crop yield and quality need to be improved in a sustainable way over the coming decades. Genetic improvement by breeding is the best way to increase crop productivity. With the rapid progression of functional genomics, an increasing number of crop genomes have been sequenced and dozens of genes influencing key agronomic traits have been identified. However, current genome sequence information has not been adequately exploited for understanding the complex characteristics of multiple gene, owing to a lack of crop phenotypic data. Efficient, automatic, and accurate technologies and platforms that can capture phenotypic data that can be linked to genomics information for crop improvement at all growth stages have become as important as genotyping. Thus, high-throughput phenotyping has become the major bottleneck restricting crop breeding. Plant phenomics has been defined as the high-throughput, accurate acquisition and analysis of multi-dimensional phenotypes during crop growing stages at the organism level, including the cell, tissue, organ, individual plant, plot, and field levels. With the rapid development of novel sensors, imaging technology, and analysis methods, numerous infrastructure platforms have been developed for phenotyping.

Nucleic Acid-its structural and functional complexity.

Nistarini College, Purulia (W.B) India

Richard's aventures in two entangled wonderlands

Richard 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.

Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...

Travis Hills MN

Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.

Lateral Ventricles.pdf very easy good diagrams comprehensive

silvermistyshot

Deep Software Variability and Frictionless Reproducibility

University of Rennes, INSA Rennes, Inria/IRISA, CNRS

The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions. Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability. Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields. I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating). I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems. Exposé invité Journées Nationales du GDR GPL 2024

Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...

University of Maribor

Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...

Sérgio Sacani

Since volcanic activity was first discovered on Io from Voyager images in 1979, changes on Io’s surface have been monitored from both spacecraft and ground-based telescopes. Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images show that a plume deposit from a powerful eruption at Pillan Patera has covered part of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive optics at visible wavelengths.

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.

DMARDs Pharmacolgy Pharm D 5th Semester.pdf

fafyfskhan251kmf

Unveiling the Energy Potential of Marshmallow Deposits.pdf

Erdal Coalmaker

What is greenhouse gasses and how many gasses are there to affect the Earth.

moosaasad1975