On the importance (and absence) of annotation in Next Generation Sequencing Data
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There are data from nearly 30,000 experiments deposited in the Sequence Read Archive, a repository of genomic and transcriptomic data corresponding to approximately 2 x 10^15 nucleotides (equivalent to approximately 600,000 human genomes). This is a huge resource that could be mined for a variety of different purposes. It is also a vast collection of different samples, having been gathered under a variety of different technologies and experimental protocols. Jamie Alnasir and I have demonstrated that the annotation of this data is in general very poor and hence undermines the usefulness of such a resource. We draw some conclusions from this and where such databases need to go in the future.
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Introduzione al software Open Source ed al software libero. Notizie a proposito degli enti (Open Source Software) più importanti e delle licenze più utilizzate.
Formato plano 7th week4_simpl_pasrvspastcont
The document provides lesson plans for a 7th grade English class focusing on teaching the simple past and past continuous tenses. It includes examples of how to form and use these tenses, practice exercises for students, and a reading assignment. The goal is for students to be able to use the simple past and past continuous to talk about past actions.
VPI Ontario
Vincent Porcaro Inc. (VPI) is a third party logistics company founded in 1996 that provides fulfillment services like assembly, fulfillment, distribution and warehousing to over 40 national and international companies out of its headquarters in Providence, RI. VPI has a distribution center located in Ontario, CA near major shipping hubs that has a 50,000 square foot warehouse facility equipped to meet various customer needs. VPI aims to provide extraordinary fulfillment through inventory management, quality control, picking/packing/assembly and shipping services.
Folio
Souk06 is about adapting passion into a lifestyle. Developing both the technical and creative elements to allow richer interaction for both the creator and the user. This lifestyle compliments itself simply by the inspirational individuals and creative environments that are within.
“Your greatest resource is your imagination."
Presentazione Progetto CRio
Presentazione del progetto per il calcolo della posizione di un utente tramite utilizzo del controllore cRIO.
Viernes santo la merced 2012
This short document does not contain any meaningful information to summarize. It consists only of blank lines and punctuation marks. A proper summary requires substantive content to extract and convey the key ideas, but this document lacks any details, facts, or concepts to summarize in 3 sentences or less.
Formato plano 6th week6_future_simple
The document is a lesson plan for a 6th grade English class about future simple tenses and future plans. It includes an indicator of achievement stating that students will be able to talk about future plans. It provides an overview of the future simple tense, explaining that it is used to talk about predictions for the future using will or be going to. It notes that be going to is used when a plan is already in place, while will can show willingness or talk about immediate future plans without prior arrangement. Comparisons are made between will and be going to. The lesson plan continues for 5 pages with sections on exploration, conceptualization, production, modeling, workshop, and evaluation.
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Top Ten Digital Engagement Tools - WASHTO 2013 Annual Meeting
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Similar to On the importance (and absence) of annotation in Next Generation Sequencing Data
Finding and Accessing Human Genomics Datasets
This document summarizes a workshop about finding and accessing human genomic datasets. The workshop covered various data sources such as public repositories, case studies on accessing data from the University of Cambridge, and a demonstration of the Repositive platform which aims to simplify accessing genomic data through a single search. Hands-on sessions allowed participants to search for genomic data themes in small groups using Repositive and report their results. Overall the workshop aimed to educate researchers on challenges of accessing genomic data and introduce Repositive as a tool to help address fragmentation and simplify the workflow for discovering and accessing genomic datasets.
Dia sds2015 web version
The Emerging Discipline of Data Science: Principles and Techniques for Data-Intensive Analysis, Keynote, 2nd Swiss Workshop on Data Science – SDS|2015, Winterthur, Switzerland, 12 June 2015
Abstract and other presentations at: http://michaelbrodie.com/?page_id=17
2016 09 cxo forum
Slides from a Chief-Whatever-Officer (Data, Information, Technology) focused on health care organizations preparing for genomic medicine.
Life sciences big data use cases
Big data use cases for sequencing and life sciences given at the Big Data Management workshop at Imperial College 27 June 2013
Genome sharing projects around the world nijmegen oct 29 - 2015
Genome sharing projects across the world
Did you ever wonder what happened to the exponential increase in genome sequencing data? It is out there around the world and a lot of it is consented for research use. This means that if you just know where to find the data, you can potentially analyse gigabytes of data to power your research.
In this talk Fiona will present community genome initiatives, the genome sharing projects across the world, how you can benefit from this wealth of data in your work, and how you can boost your academic career by sharing and collaboration.
by Fiona Nielsen, Founder and CEO of DNAdigest and Repositive
With a background in software development Fiona pursued her career in bioinformatics research at Radboud University Nijmegen. Now a scientist-turned-entrepreneur Fiona founded DNAdigest and its social enterprise spin-out Repositive Ltd. Both the charity and company focus on efficient and ethical sharing of genetics data for research to accelerate diagnostics and cures for genetic diseases.
From Replication Crisis to Credibility Revolution
The document discusses issues related to the replication crisis in psychology and potential solutions. It notes that questionable research practices like p-hacking and HARKing are common but unintentional. Solutions proposed include transparency through open science, pre-registration of studies including pre-reviews, direct replication of studies, and higher evidentiary standards. Institutional changes are also needed to incentivize practices like pre-registration and increasing acceptance of replication studies. While rigorous methods may initially lower productivity, they can increase it long-term by allowing easier reuse of materials and data and identifying reliable findings sooner.
Activities at the Royal Society of Chemistry to gather, extract and analyze b...
Activities at the Royal Society of Chemistry to gather, extract and analyze b...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The phrase “Big Data” is generally used to describe a large volume of structured and/or unstructured data that cannot be processed using traditional database and software techniques. In the domain of chemistry the Royal Society of Chemistry certainly hosts large structured databases of chemistry data, for example ChemSpider, as well as unstructured content, in the form of our collection of scientific articles. Our research literature provides value to their readership and, at present, as an example of one of our databases, ChemSpider is accessed by many tens of thousands of scientists every day. But do these collections constitute “Big Data” or is it the potential which lies within the collections that can contribute to the Big Data movement. This presentation will discuss our activities to contribute both data, and service-based access to our data sets, to support grant-based projects such as the Innovative Medicines Initiative Open PHACTS project (to support drug discovery) and the PharmaSea initiative (to identify novel natural products from the ocean). We will also provide an overview of our activities to perform data mining of public patent collections and examine what can be done with the data. We are presently extracting physicochemical properties and textual forms of NMR spectra and, with the resulting data, are building predictive models (for melting points at present) and assembling a large NMR spectral database containing many hundreds of thousands of spectral-structure pairs. Our experiences to date have demonstrated that we are working at the edge of current algorithmic and computing capabilities for predictive model building, with over a quarter of a million melting points producing a matrix of over 200 billion descriptors. Our work to produce the NMR spectral database will necessitate batch processing of the data to examine consistency between the spectral-structure pairs and other forms of data validation. The intention is to take our experiences in this work applied to a public patents corpus and apply it to the RSC back file of publications to mine data and enable new paths to the discoverability of both data and the associated publications. Workshop finding and accessing data - fiona - lunteren april 18 2016
Workshop presentation on finding and accessing human genomics data for research.
Including statistics of publicly available data sources and tips on how to save time in your workflow of data access.
Presented at BioSB2016, pre-conference PhD retreat for young researchers in bioinformatics and systems biology at Congrescentrum De Werelt in Lunteren. #BioSB2016 #BioSB16
Link to event:
http://www.youngcb.nl/events/biosb-phd-retreat-2016/
Read more about my work:
http://DNAdigest.org
http://repositive.io
https://uk.linkedin.com/in/fionanielsen
Workshop - finding and accessing data - Cambridge August 22 2016
Finding and accessing human genomic data for research
University of Cambridge, United Kingdom | Seminar Room G
Monday, 22 August 2016 from 10:00 to 12:00 (BST)
Charlotte, Nadia and Fiona presented an overview of data sources around the world where you can find genomics data for your research and gave examples of the data access application for dbGaP and EGA with specific details relevant for University of Cambridge researchers.
CINECA webinar slides: Modular and reproducible workflows for federated molec...
Genetic analysis of molecular traits such as gene expression, splicing and chromatin accessibility requires a number of complex analysis steps that can easily take weeks or months for a analyst to implement from scratch. In the CINECA project, we have developed a number of modular Nextflow workflows that standardise and automate these steps. In this webinar, we will give an overview of the CINECA workflows for genotype imputation, gene expression and splicing quantification, data normalisation and association testing, and demonstrate how these workflows can be used in a federated setting without transferring identifiable personal data between partners.
The CINECA webinar series aims to discuss ways to address common challenges and share best practices in the field of cohort data analysis, as well as distribute CINECA project results. All CINECA webinars include an audience Q&A session during which attendees can ask questions and make suggestions. Please note that all webinars are recorded and available for posterior viewing.
This webinar took place on 10th November 2020 and is part of the CINECA webinar series.
For previous and upcoming CINECA webinars see:
https://www.cineca-project.eu/webinars
The fourth paradigm: data intensive scientific discovery - Jisc Digifest 2016
There is broad recognition within the scientific community that the emerging data deluge will fundamentally alter disciplines in areas throughout academic research. A wide variety of researchers - from scientists and engineers to social scientists and humanities researchers - will require tools, technologies, and platforms that seamlessly integrate into standard scientific methodologies and processes.
'The fourth paradigm' refers to the data management techniques and the computational systems needed to manipulate, visualize, and manage large amounts of research data. This talk will illustrate the challenges researchers will face, the opportunities these changes will afford, and the resulting implications for data-intensive researchers.
In addition, the talk will review the global movement towards open access, research repositories and open science and the importance of curation of digital data. The talk concludes with some comments on the research requirements for campus e-infrastructure and the end-to-end performance of the network.
sience 2.0 : an illustration of good research practices in a real study
a presentation explaining the what, how and why of some of the features of science 2.0 (replication, registration, high power, bayesian statistics, estimation, co-pilot multi-software approach, distinction between confirmatory and exploratory analyses, and open science) using steegen et al. (2014) as a running example.
High Performance Computing and the Opportunity with Cognitive Technology
With the ability to reduce “time to insight” and accelerate research breakthroughs by providing immense computational power, high performance computing is becoming increasingly important in the marketplace. Meanwhile, cognitive technology has risen to prominence, similarly accelerating new insight, but through a very different approach - by analyzing previously ignored unstructured data, which accounts for 80% of new data created today.
By combining the powerful computing power of the HPC market, along with the machine learning, natural language processing, and even computer vision techniques found within cognitive technology, there is a huge opportunity to accelerate breakthroughs and enable better decision making than ever before.
Watch the replay of the webinar: https://www.youtube.com/watch?v=Hxgieboj3W0
In Silico Approaches for Predicting Hazards from Chemical Structure and Exist...
In Silico Approaches for Predicting Hazards from Chemical Structure and Exist...U.S. Army Engineer Research and Development Center
A high level overview of using artificial intelligence and chemical structure information to predict toxicity in various species. Discusses molecular docking, deep learning, quantitative structure activity relationships, Bayesian networks and cats (lots of cat pictures). Part of my artificial intelligence for national security, artificial intelligence for warfighter readiness, and alternative methods for toxicity prediction research portfolios. Escaping Flatland: Interactive High-Dimensional Data Analysis in Drug Discove...
This document describes a project at Novartis to use Apache Spark for high-dimensional data analysis from drug screening. Large datasets from various screening technologies were analyzed using Spark pipelines for quality control, normalization, and classification. Visualizations were built using WebGL. The goals were to speed up multi-day batch jobs, create a unified analysis workflow, and build an application for scientists. Future work includes elastic infrastructure, supervised learning of cell phenotypes, and contributing methods to open source.
RNP support to data-driven research
The document summarizes the results of a survey conducted in Brazil on researchers' practices and perceptions around open access to research data. Some key findings include:
- Most respondents were professors/researchers at public universities conducting research in fields like health sciences, biology and engineering.
- Researchers generate a variety of data types and formats, with estimated volumes mostly under 50GB per year.
- While a majority of researchers are knowledgeable about research data management, top reasons for not sharing data include needing to publish first and lacking infrastructure for sharing.
- Next steps include publishing survey results, deploying a prototype research data repository, and recruiting beta testers.
Workshop finding and accessing data - fiona nadia charlotte - cambridge apr...
Workshop presentation on finding and accessing human genomics data for research.
Including statistics of publicly available data sources and tips on how to save time in your workflow of data access.
Organised in collaboration between DNAdigest and Open Data Cambridge.
Read more about our work:
http://DNAdigest.org
http://repositive.io
https://uk.linkedin.com/in/fionanielsen
http://www.data.cam.ac.uk
Amia tb-review-08
This document provides a review and summary of major scientific events, trends, and publications in translational bioinformatics in 2008 by Russ B. Altman from Stanford University. Some of the key topics covered include the sequencing and analysis of an individual's diploid genome, next-generation sequencing technologies, genome-wide association studies, pharmacogenomics, analysis of high-throughput molecular data, neuroscience datasets, and using molecular information to improve disease detection and treatment. The review highlights over 25 seminal papers from 2008 and provides insights on emerging trends in the field.
Using Machine Learning to Automate Clinical Pathways
The document discusses using machine learning to automate clinical pathways in emergency departments. It describes developing a next-generation electronic health record system that predicts clinical state variables in real-time from patient data to provide alerts, decision support, and trigger clinical pathways. Specifically, it discusses using an "anchor and learn" framework to improve on an existing rule for triggering a cellulitis pathway, by combining simple expert rules with analysis of large clinical databases that does not require manual labeling of data.
Dr. Eliot Siegel: Watson and Deep QA Software in Pursuit of Personalized Medi...
Dr. Eliot Siegel: Watson and Deep QA Software in Pursuit of Personalized Medi...National Cancer Institute National Cancer Informatics Program
The Jeopardy match between the two best human players of all time and the IBM Deep Q/A software, “Watson,” captured the spotlight and stimulated the imagination of the entire world. The subsequent announcement of IBM’s involvement in the creation of “Dr. Watson” has created a high level of interest in the healthcare community about the potential of this breakthrough technology as well as the potential pitfalls of the use of “artificial intelligence” in medicine. Dr. Siegel is currently working together with IBM engineers to explore how Dr. Watson can work together with physicians and medical specialists. His presentation, which was delivered on March 28th, provided a high level overview of the uniqueness of Deep Q/A Software and how it differs from other previous artificial intelligence applications.Similar to On the importance (and absence) of annotation in Next Generation Sequencing Data (20)
Genome sharing projects around the world nijmegen oct 29 - 2015
Genome sharing projects around the world nijmegen oct 29 - 2015
Activities at the Royal Society of Chemistry to gather, extract and analyze b...
Activities at the Royal Society of Chemistry to gather, extract and analyze b...
Workshop finding and accessing data - fiona - lunteren april 18 2016
Workshop finding and accessing data - fiona - lunteren april 18 2016
Workshop - finding and accessing data - Cambridge August 22 2016
Workshop - finding and accessing data - Cambridge August 22 2016
CINECA webinar slides: Modular and reproducible workflows for federated molec...
CINECA webinar slides: Modular and reproducible workflows for federated molec...
The fourth paradigm: data intensive scientific discovery - Jisc Digifest 2016
The fourth paradigm: data intensive scientific discovery - Jisc Digifest 2016
sience 2.0 : an illustration of good research practices in a real study
sience 2.0 : an illustration of good research practices in a real study
High Performance Computing and the Opportunity with Cognitive Technology
High Performance Computing and the Opportunity with Cognitive Technology
In Silico Approaches for Predicting Hazards from Chemical Structure and Exist...
In Silico Approaches for Predicting Hazards from Chemical Structure and Exist...
Escaping Flatland: Interactive High-Dimensional Data Analysis in Drug Discove...
Escaping Flatland: Interactive High-Dimensional Data Analysis in Drug Discove...
Workshop finding and accessing data - fiona nadia charlotte - cambridge apr...
Workshop finding and accessing data - fiona nadia charlotte - cambridge apr...
Using Machine Learning to Automate Clinical Pathways
Using Machine Learning to Automate Clinical Pathways
Dr. Eliot Siegel: Watson and Deep QA Software in Pursuit of Personalized Medi...
Dr. Eliot Siegel: Watson and Deep QA Software in Pursuit of Personalized Medi...
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EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
Aims. In this paper we present the Extended Westerlund 1 and 2 Open Clusters Survey (EWOCS) project, which aims to investigate
the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
Methods. The project is based primarily on recent observations conducted with the Chandra and JWST observatories. Specifically,
the Chandra survey of Westerlund 1 consists of 36 new ACIS-I observations, nearly co-pointed, for a total exposure time of 1 Msec.
Additionally, we included 8 archival Chandra/ACIS-S observations. This paper presents the resulting catalog of X-ray sources within
and around Westerlund 1. Sources were detected by combining various existing methods, and photon extraction and source validation
were carried out using the ACIS-Extract software.
Results. The EWOCS X-ray catalog comprises 5963 validated sources out of the 9420 initially provided to ACIS-Extract, reaching a
photon flux threshold of approximately 2 × 10−8 photons cm−2
s
−1
. The X-ray sources exhibit a highly concentrated spatial distribution,
with 1075 sources located within the central 1 arcmin. We have successfully detected X-ray emissions from 126 out of the 166 known
massive stars of the cluster, and we have collected over 71 000 photons from the magnetar CXO J164710.20-455217.
在线办理(salfor毕业证书)索尔福德大学毕业证毕业完成信一模一样
学校原件一模一样【微信：741003700 】《(salfor毕业证书)索尔福德大学毕业证》【微信：741003700 】学位证，留信认证（真实可查，永久存档）原件一模一样纸张工艺/offer、雅思、外壳等材料/诚信可靠,可直接看成品样本，帮您解决无法毕业带来的各种难题！外壳，原版制作，诚信可靠，可直接看成品样本。行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备。十五年致力于帮助留学生解决难题，包您满意。
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6:个人职称评审加20分
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8:在国家人才网主办的国家网络招聘大会中纳入资料，供国家高端企业选择人才
Compexometric titration/Chelatorphy titration/chelating titration
Classification
Metal ion ion indicators
Masking and demasking reagents
Estimation of Magnisium sulphate
Calcium gluconate
Complexometric Titration/ chelatometry titration/chelating titration, introduction, Types-
1.Direct Titration
2.Back Titration
3.Replacement Titration
4.Indirect Titration
Masking agent, Demasking agents
formation of complex
comparition between masking and demasking agents,
Indicators/Metal ion indicators/ Metallochromic indicators/pM indicators,
Visual Technique,PM indicators (metallochromic), Indicators of pH, Redox Indicators
Instrumental Techniques-Photometry
Potentiometry
Miscellaneous methods.
Complex titration with EDTA.
Cytokines and their role in immune regulation.pptx
This presentation covers the content and information on "Cytokines " and their role in immune regulation .
Bob Reedy - Nitrate in Texas Groundwater.pdf
Presented at June 6-7 Texas Alliance of Groundwater Districts Business Meeting
SAR of Medicinal Chemistry 1st by dk.pdf
In this presentation include the prototype drug SAR on thus or with their examples .
Syllabus of Second Year B. Pharmacy
2019 PATTERN.
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
The debris of the ‘last major merger’ is dynamically young
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
‘last major merger.’ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1–2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the ‘last major merger’
did not collide with the MW proto-disc at early times, as is thought for the GSE, but instead collided with the MW disc within
the last few Gyr, consistent with the body of work surrounding the VRM.
Applied Science: Thermodynamics, Laws & Methodology.pdf
When I was asked to give a companion lecture in support of ‘The Philosophy of Science’ (https://shorturl.at/4pUXz) I decided not to walk through the detail of the many methodologies in order of use. Instead, I chose to employ a long standing, and ongoing, scientific development as an exemplar. And so, I chose the ever evolving story of Thermodynamics as a scientific investigation at its best.
Conducted over a period of >200 years, Thermodynamics R&D, and application, benefitted from the highest levels of professionalism, collaboration, and technical thoroughness. New layers of application, methodology, and practice were made possible by the progressive advance of technology. In turn, this has seen measurement and modelling accuracy continually improved at a micro and macro level.
Perhaps most importantly, Thermodynamics rapidly became a primary tool in the advance of applied science/engineering/technology, spanning micro-tech, to aerospace and cosmology. I can think of no better a story to illustrate the breadth of scientific methodologies and applications at their best.
The binding of cosmological structures by massless topological defects
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
mitigated, at least in part.
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
Slides from talk:
Aleš Zamuda: Remote Sensing and Computational, Evolutionary, Supercomputing, and Intelligent Systems.
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
https://www.etran.rs/2024/en/home-english/Thornton ESPP slides UK WW Network 4_6_24.pdf
ESPP presentation to EU Waste Water Network, 4th June 2024 “EU policies driving nutrient removal and recycling
and the revised UWWTD (Urban Waste Water Treatment Directive)”
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...
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.
3D Hybrid PIC simulation of the plasma expansion (ISSS-14)
3D Particle-In-Cell (PIC) algorithm,
Plasma expansion in the dipole magnetic field.
Deep Software Variability and Frictionless Reproducibility
Deep Software Variability and Frictionless ReproducibilityUniversity 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
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...
Current descriptions of immersive learning cases are often difficult or impossible to compare. This is due to a myriad of different options on what details to include, which aspects are relevant, and on the descriptive approaches employed. Also, these aspects often combine very specific details with more general guidelines or indicate intents and rationales without clarifying their implementation. In this paper we provide a method to describe immersive learning cases that is structured to enable comparisons, yet flexible enough to allow researchers and practitioners to decide which aspects to include. This method leverages a taxonomy that classifies educational aspects at three levels (uses, practices, and strategies) and then utilizes two frameworks, the Immersive Learning Brain and the Immersion Cube, to enable a structured description and interpretation of immersive learning cases. The method is then demonstrated on a published immersive learning case on training for wind turbine maintenance using virtual reality. Applying the method results in a structured artifact, the Immersive Learning Case Sheet, that tags the case with its proximal uses, practices, and strategies, and refines the free text case description to ensure that matching details are included. This contribution is thus a case description method in support of future comparative research of immersive learning cases. We then discuss how the resulting description and interpretation can be leveraged to change immersion learning cases, by enriching them (considering low-effort changes or additions) or innovating (exploring more challenging avenues of transformation). The method holds significant promise to support better-grounded research in immersive learning.
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On the importance (and absence) of annotation in Next Generation Sequencing Data
- 1. The importance (and absence) of annotation in the Next Generation Sequence Data Hugh Shanahan & Jamie Alnasir Hugh.Shanahan@rhul.ac.uk @hughshanahan Results to be published in GigaScience
- 2. It was the best of times • Many exciting experiments based on gathering huge amounts of data. • 100,000 Genomes in the UK, many others • Elixir - Exabytes of biomedical data in the next decade • Large experiments - SKA, LHC • Opening up of Government data • Up ahead - Sensor networks and Monitoring Cities • Machine Learning is now a widely accepted tool in analysing data and in making decisions. • Evidence-based policy becoming the norm.
- 3. It was the worst of times • Leaks appearing in the Scientific process. • In domains with many possible relationships, most published results are wrong (Ioannidis, PLoS Medicine, 2005). • 1/4 of 67 published experiments on drug targets reproduced (Prinz et al., Nat. Rev. Drug Disc., 2011) • 39% of key Psychology experiments could be reproduced (Nature News, 2015).
- 4. Poor statistics? • Naive use of p-value calculations across fields. • Banning use of Null Hypothesis Significance Test Procedure in Basic and Applies Social Psychology (Trafimow and Marks, BASP, 2015) • Not the end of the story…more like the tip of the iceberg (Leek and Peng, Nature 2015)
- 5. Lessons learnt • Results from individual experiments are probably wrong. • Bias in your data means your conclusions are even more likely to be wrong. • Meta-analyses help. • Understand how you got the data you have.
- 6. Sequence Read Archive • Central repository of sequence data. • Nearly 30,000 genomic and transcriptomics experiments stored and freely available. • 2 x 1015 nucleotides stored
- 8. • Based on Next Generation Sequencing • Step reduction in cost of sequencing • ~$thousands for a human genome • Potentially an enormous resource • But how do you get that data?
- 9. Good news • SRA data is open • Stored in a sensible way (uses SQL) • API and documentation to access it
- 10. Mucky business • Data stored in SRA are short reads. • ~100 nucleotide-long fragments which are then assembled. • Very long pipeline to get from a sample to this step. • Pipeline (Protocol in their lingo) is VARIABLE
- 12. Obvious question • Is there any evidence of bias in the data due to varying the protocol?
- 13. Even More Obvious Question • Where is the metadata on the pipeline (protocol)?
- 14. 4% of experiments describe all of the steps
- 15. What’s more… • Metadata are stored as text fields. • Hugely difficult task to parse. • Submitters are not obliged to fill this data in. • Confusion about what level to enter data in.
- 16. Bottom line • For much of the SRA data, there is a “known unknown” about biases due to preparation. • It’s very unlikely we’ll ever be able to figure that out.
- 17. Why should you be paying attention? • As a member of the public - it’s your money down the drain ($108-$109) • As a researcher - all of this undermines confidence in Science as a whole. • If you work with big (and more particularly) complex data - the same issues will crop up for you.
- 18. Answers? • Understand how you got your data - even if it’s a step for modelling. • Metadata is crucial. • Organising your data is crucial. • Use Ontologies • Use discrete keywords • Get people to use it
- 19. In summary :- We want to do all the clever stuff….
- 20. Most of the time we need to deal with a ton of pitchblende to find the milligram of Radium ..