Presentation at STARMUS Science Festival - Life and the Universe. An overview of the evolution of the LifeScanner project in light of insights from the Maker movement.
Presentation from the ECDC expert consultation on Whole Genome Sequencing organised by the European Centre of Disease Prevention and Control - Stockholm, 19 November 2015
CD Genomics provides viral genome sequencing service within Illumina and PacBio Platforms. We can create high-quality de novo assembly of large viral genomes and highest possible data quality at low cost.
Viral metagenomics is the study of viral genetic material sourced directly from the environment rather than from a host or natural reservoir. The goal is to ascertain the viral diversity in the environment that is often missed in studies targeting specific potential reservoirs.
Stay informed! Mills CBST is funded by the National Science Foundation, Chemical, Bioengineering, Environmental, and Transport Systems (CBET) division. This highlight describes in detail the work of Mills CBST, led by Dr. Susan Spiller.
Presentation from the ECDC expert consultation on Whole Genome Sequencing organised by the European Centre of Disease Prevention and Control - Stockholm, 19 November 2015
CD Genomics provides viral genome sequencing service within Illumina and PacBio Platforms. We can create high-quality de novo assembly of large viral genomes and highest possible data quality at low cost.
Viral metagenomics is the study of viral genetic material sourced directly from the environment rather than from a host or natural reservoir. The goal is to ascertain the viral diversity in the environment that is often missed in studies targeting specific potential reservoirs.
Stay informed! Mills CBST is funded by the National Science Foundation, Chemical, Bioengineering, Environmental, and Transport Systems (CBET) division. This highlight describes in detail the work of Mills CBST, led by Dr. Susan Spiller.
Next Generation Sequencing for Identification and Subtyping of Foodborne Pat...nist-spin
"Next Generation Sequencing for Identification and Subtyping of Foodborne Pathogens" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by National Institute for Standards and Technology October 2014 by Rebecca Lindsey, PhD from Enteric Diseases Laboratory Branch of the CDC.
Microbiome Isolation and DNA Enrichment Protocol: Pathogen Detection Webinar ...QIAGEN
This slidedeck presents an easy-to-use workflow that allows selective isolation of microbial DNA from samples that are intrinsically rich in host DNA. This protocol includes steps for efficient depletion of host DNA while providing optimized conditions specific for bacterial lysis. This workflow is also specific for the identification of live bacteria, avoiding false results due to nucleic acids from dead bacteria. Enriched microbial DNA can be directly used in other molecular methods such as whole genome sequencing, qPCR and microarray assays.
Building bioinformatics resources for the global communityExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Building bioinformatics resources for the global community. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management and GMI-9, 23-25 May 2016, Rome, Italy.
Shining a light on virus infection with high-resolution microscopyRoland Remenyi, PhD
Each year the Astbury Centre holds a research retreat to promote interdisciplinary activity, to discuss and present latest findings and to promote and encourage interdisciplinary research at the highest level. I communicated my results from a Chikungunya virus project in a 15-min presentation. Slides from this presentation are shown here.
HGP was conceived in 1984 & officially begun in earnest in October 1990.
HGP is a large multicentric, international collaborative venture, the main aim of which is to determine the nucleotide sequence of the entire human nuclear genome.
In 1997, United States established the National Human Genome Research Institute (NHGRI).
The HGP was an international research groups from six countries- USA, UK, France, Germany, Japan and China, & several laboratories and a large no. of scientists and technicians from various disciplines.
With the loss of chemical control options such as Fenthion and Dimethoate for postharvest treatment of horticulture commodities susceptible to fruit fly infestation, it has become even more important to understand how stress-based control techniques such as heat, cold, irradiation and bacteria parasite
can be used most effectively for disinfestation. This project aims to explore the stress-induced molecular response of two fruit fly species of horticultural significance, Mediterranean fruit fly (Ceratitis capitata) and Queensland fruit fly (Bactrocera tryoni), by characterising the cellular pathways involved in both overall and stressor-specific responses.
Application of Whole Genome Sequencing in the infectious disease’ in vitro di...ExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Applications of WGS in industry. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management -23-25 May 2016, Rome, Italy.
American Society for Microbiology NGS 2020 Aine O'TooleÁine Niamh O'Toole
200,001: A tree-space odyssey. Pandemic phylogenetics and reporting in 2020. Aine O'Toole Plenary
Pipe Dreams: Analytical Methods, Bioinformatic Tools and Pipelines
Based on historical data, Australia and New Zealand (NZ) form a single epidemiological unit for cereal rusts. Until 2001, pathotype analysis of cereal rust pathogens for NZ was conducted at the University of Sydney, Plant Breeding Institute. The first year of pathotype analysis in New Zealand provided evidence for pathotype exchange in both directions across the Tasman. The second year of pathotype analysis has provided more detail on the evolution of rust pathotypes within New
Zealand. From these results a fuller picture of the pathotype diversity of New Zealand cereal rusts is emerging with important consequences for the cereal industry in both New Zealand and Australia.
Quantified Self On Being A Personal Genomic ObservatoryLarry Smarr
Larry Smarr's presentation on the "Quantified Self On Being A Personal Genomic Observatory", Keynote in the "Humans as Genomic Observatories" Meeting Session in the Genomics Standards Consortium, GSC 15, April 24, 2013
Next Generation Sequencing for Identification and Subtyping of Foodborne Pat...nist-spin
"Next Generation Sequencing for Identification and Subtyping of Foodborne Pathogens" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by National Institute for Standards and Technology October 2014 by Rebecca Lindsey, PhD from Enteric Diseases Laboratory Branch of the CDC.
Microbiome Isolation and DNA Enrichment Protocol: Pathogen Detection Webinar ...QIAGEN
This slidedeck presents an easy-to-use workflow that allows selective isolation of microbial DNA from samples that are intrinsically rich in host DNA. This protocol includes steps for efficient depletion of host DNA while providing optimized conditions specific for bacterial lysis. This workflow is also specific for the identification of live bacteria, avoiding false results due to nucleic acids from dead bacteria. Enriched microbial DNA can be directly used in other molecular methods such as whole genome sequencing, qPCR and microarray assays.
Building bioinformatics resources for the global communityExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Building bioinformatics resources for the global community. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management and GMI-9, 23-25 May 2016, Rome, Italy.
Shining a light on virus infection with high-resolution microscopyRoland Remenyi, PhD
Each year the Astbury Centre holds a research retreat to promote interdisciplinary activity, to discuss and present latest findings and to promote and encourage interdisciplinary research at the highest level. I communicated my results from a Chikungunya virus project in a 15-min presentation. Slides from this presentation are shown here.
HGP was conceived in 1984 & officially begun in earnest in October 1990.
HGP is a large multicentric, international collaborative venture, the main aim of which is to determine the nucleotide sequence of the entire human nuclear genome.
In 1997, United States established the National Human Genome Research Institute (NHGRI).
The HGP was an international research groups from six countries- USA, UK, France, Germany, Japan and China, & several laboratories and a large no. of scientists and technicians from various disciplines.
With the loss of chemical control options such as Fenthion and Dimethoate for postharvest treatment of horticulture commodities susceptible to fruit fly infestation, it has become even more important to understand how stress-based control techniques such as heat, cold, irradiation and bacteria parasite
can be used most effectively for disinfestation. This project aims to explore the stress-induced molecular response of two fruit fly species of horticultural significance, Mediterranean fruit fly (Ceratitis capitata) and Queensland fruit fly (Bactrocera tryoni), by characterising the cellular pathways involved in both overall and stressor-specific responses.
Application of Whole Genome Sequencing in the infectious disease’ in vitro di...ExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Applications of WGS in industry. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management -23-25 May 2016, Rome, Italy.
American Society for Microbiology NGS 2020 Aine O'TooleÁine Niamh O'Toole
200,001: A tree-space odyssey. Pandemic phylogenetics and reporting in 2020. Aine O'Toole Plenary
Pipe Dreams: Analytical Methods, Bioinformatic Tools and Pipelines
Based on historical data, Australia and New Zealand (NZ) form a single epidemiological unit for cereal rusts. Until 2001, pathotype analysis of cereal rust pathogens for NZ was conducted at the University of Sydney, Plant Breeding Institute. The first year of pathotype analysis in New Zealand provided evidence for pathotype exchange in both directions across the Tasman. The second year of pathotype analysis has provided more detail on the evolution of rust pathotypes within New
Zealand. From these results a fuller picture of the pathotype diversity of New Zealand cereal rusts is emerging with important consequences for the cereal industry in both New Zealand and Australia.
Quantified Self On Being A Personal Genomic ObservatoryLarry Smarr
Larry Smarr's presentation on the "Quantified Self On Being A Personal Genomic Observatory", Keynote in the "Humans as Genomic Observatories" Meeting Session in the Genomics Standards Consortium, GSC 15, April 24, 2013
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.1.2- Next Generation Sequencing. Technologies and Applications. Part II: NGS Applications I.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Next generation Sequencing or massive parallel sequencing is a high throughput approach to sequence genetic material using the concept of massively parallel processing. It is also called second generation sequencing.This enables researchers a wide variety of applications & study biological systems.
An overview of genomic epidemiology, Canada's IRIDA project for genome-based outbreak investigation, and a breathless romp through the awesome potential of the MinION
Medicine of the Future—The Transformation from Reactive to Proactive (P4) Med...Ryan Squire
Medicine of the Future—The Transformation from Reactive to Proactive (P4) Medicine as presented at the Ohio State University Medical Center Personalized Health Care National Conference.
Leroy Hood, MD, PhD, is the president and founder of the Institute of Systems Biology. Dr. Hood is a member of the National Academy of Sciences, the American Philosophical Society, the American Academy of Arts and Sciences, the Institute of Medicine and the National Academy of Engineering. His professional career began at Caltech where he and his colleagues pioneered four instruments — the DNA gene sequencer and synthesizer and the protein synthesizer and sequencer — which comprise the technological foundation for contemporary molecular biology. In particular, the DNA sequencer played a crucial role in contributing to the successful mapping of the human genome during the 1990s.
http://www.systemsbiology.org/Scientists_and_Research
Using Supercomputers and Supernetworks to Explore the Ocean of LifeLarry Smarr
07.06.07
Director's Colloquium
Los Alamos National Laboratory
Title: Using Supercomputers and Supernetworks to Explore the Ocean of Life
Los Alamos, NM
WGS in public health microbiology - MDU/VIDRL Seminar - wed 17 jun 2015Torsten Seemann
How genomics is changing the practice of public health microbiology. The role of whole genome sequencing as the "one true assay". Another powerful tool for the epidemiologist.
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.
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.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
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/
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
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.
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.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
10. Role of Technology: 23andMe
500K SNPs – Illumina Beadchip Array
77 Peer Reviewed Articles in Top Tier Journals Since 2010
+1 Millions Users To Date
12. 23 and Me: BMI
This gene encodes apolipoprotein (apo-) A-2, which is the second most abundant protein
of the high density lipoprotein particles. The protein is found in plasma as a monomer,
homodimer, or heterodimer with apolipoprotein D. Defects in this gene may result in
apolipoprotein A-II deficiency or hypercholesterolemia.
-RefSeq, June 2013
16. 1000+ Institutions from 94 countries sharing data on BOLD
AcrossNations
Within Nations
100K+
10K – 100K
1K – 10K
BOLD User Network - 2015
17. Collection of Rich Data
Specimen IDs
Trace Data
Geography
DNA Sequence
Audit Trail
Taxonomy
Images
Specimen
Descriptions
Primers
Mass
Chemical
Properties
Isotopes
Ecology
Morphology
???
Project Metadata
Links
18. Barcode Index Number (BIN)
Algorithm
Registry
• Tuned to the marker (COX1)
• Fixed parameters for balanced OTU generation
• Uses prior threshold but refines for each group
• Occurrence of DNA Barcode (place and time)
• Aggregation of all associated metadata
• Reusable - works across studies
36. Contents (Left to Right):
• 1 x Compact quad core GPU
accelerated mini –server
• 1 x iPhone macro lens
• 2 x Pipettes
• 1 x iPhone (bring your own)
• 1 x 8 channel thermocycler
• 20 x LifeScanner v2 kits
• 1 x Oxford Nanopore
MinION sequencer
• 1 x Vortex
• 1 x Microcentrifuge
Add a two sided network – within institute network on top and between institute network on the bottom – metaphor of tip of the iceberg
Lantana camara (wild sage) – invasive plant although ornamental and historical botanical uses
Notioplusia illustrata – native to the Greater Antilles with type locality in st.kitts
304 species/bins
41 new species
We are solving the problems of access and understanding – this creates opportunities in unexpected areas