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
Cross-Kingdom Standards in Genomics, Epigenomics and MetagenomicsChristopher Mason
Challenges and biases in preparing, characterizing, and sequencing DNA and RNA can have significant impacts on research in genomics across all kingdoms of life, including experiments in single cells, RNA profiling, and metagenomics. Technical artifacts and contaminations can arise at each point of sample manipulation, extraction, sequencing, and analysis. Thus, the measurement and benchmarking of these potential sources of error are of paramount importance as next-generation sequencing (NGS) projects become more global and ubiquitous.
Fortunately, a variety of methods, standards, and technologies have recently emerged that improve measurements in genomics and sequencing, from the initial input material to the computational pipelines that process and annotate the data.
This webinar will review work to develop standards and their applications in genomics, including the ABRF-NGS Phase II NGS Study on DNA Sequencing; the FDA’s Sequencing Quality Control Consortium (SEQC2); metagenomics standards efforts (ABRF, ATCC, Zymo, Metaquins), and the Epigenomics QC group of the SEQC2. The webinar will also review he computational methods for detection, validation, and implementation of these genomic measures.
Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...Larry Smarr
06.09.15
Invited Talk
2006 Synthetic Biology Symposium
Aliso Creek Inn
Title: Building a Community Cyberinfrastructure to Support Marine Microbial Ecology Metagenomics
Laguna Beach, CA
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
Cross-Kingdom Standards in Genomics, Epigenomics and MetagenomicsChristopher Mason
Challenges and biases in preparing, characterizing, and sequencing DNA and RNA can have significant impacts on research in genomics across all kingdoms of life, including experiments in single cells, RNA profiling, and metagenomics. Technical artifacts and contaminations can arise at each point of sample manipulation, extraction, sequencing, and analysis. Thus, the measurement and benchmarking of these potential sources of error are of paramount importance as next-generation sequencing (NGS) projects become more global and ubiquitous.
Fortunately, a variety of methods, standards, and technologies have recently emerged that improve measurements in genomics and sequencing, from the initial input material to the computational pipelines that process and annotate the data.
This webinar will review work to develop standards and their applications in genomics, including the ABRF-NGS Phase II NGS Study on DNA Sequencing; the FDA’s Sequencing Quality Control Consortium (SEQC2); metagenomics standards efforts (ABRF, ATCC, Zymo, Metaquins), and the Epigenomics QC group of the SEQC2. The webinar will also review he computational methods for detection, validation, and implementation of these genomic measures.
Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...Larry Smarr
06.09.15
Invited Talk
2006 Synthetic Biology Symposium
Aliso Creek Inn
Title: Building a Community Cyberinfrastructure to Support Marine Microbial Ecology Metagenomics
Laguna Beach, CA
Clinical Metagenomics for Rapid Detection of Enteric Pathogens and Characteri...QIAGEN
High-throughput sequencing, combined with high-resolution metagenomic analysis, provides a powerful diagnostic tool for clinical management of enteric disease. Forty-five patient samples of known and unknown disease etiology and 20 samples from health individuals were subjected to next-generation sequencing. Subsequent metagenomic analysis identified all microorganisms (bacteria, viruses, fungi and parasites) in the samples, including the expected pathogens in the samples of known etiology. Multiple pathogens were detected in the individual samples, providing evidence for polymicrobial infection. Patients were clearly differentiated from healthy individuals based on microorganism abundance and diversity. The speed, accuracy and actionable features of CosmosID bioinformatics and curated GenBook® databases, implemented in the QIAGEN Microbial Genomics Pro Suite, and the functional analysis, leveraging the QIAGEN functional metagenomics workflow, provide a powerful tool contributing to the revolution in clinical diagnostics, prophylactics and therapeutics that is now in progress globally.
This presents a number of case studies on the application on high-throughput sequencing (HTS), next generation sequencing (NGS), to biological problems ranging from human genome sequencing, identification of disease mutations, metagenomics, virus discovery, epidemic, transmission chains and viral populations. Presented at the University of Glasgow on Friday 26th June 2015.
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.
Clinical Metagenomics for Rapid Detection of Enteric Pathogens and Characteri...QIAGEN
High-throughput sequencing, combined with high-resolution metagenomic analysis, provides a powerful diagnostic tool for clinical management of enteric disease. Forty-five patient samples of known and unknown disease etiology and 20 samples from health individuals were subjected to next-generation sequencing. Subsequent metagenomic analysis identified all microorganisms (bacteria, viruses, fungi and parasites) in the samples, including the expected pathogens in the samples of known etiology. Multiple pathogens were detected in the individual samples, providing evidence for polymicrobial infection. Patients were clearly differentiated from healthy individuals based on microorganism abundance and diversity. The speed, accuracy and actionable features of CosmosID bioinformatics and curated GenBook® databases, implemented in the QIAGEN Microbial Genomics Pro Suite, and the functional analysis, leveraging the QIAGEN functional metagenomics workflow, provide a powerful tool contributing to the revolution in clinical diagnostics, prophylactics and therapeutics that is now in progress globally.
This presents a number of case studies on the application on high-throughput sequencing (HTS), next generation sequencing (NGS), to biological problems ranging from human genome sequencing, identification of disease mutations, metagenomics, virus discovery, epidemic, transmission chains and viral populations. Presented at the University of Glasgow on Friday 26th June 2015.
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.
Heute sind die Möglichkeiten von Social Media erkannt, die Werkzeuge etabliert, der Umgang tägliche Praxis – nicht überall, aber doch in weiten Unternehmenskreisen. Dort haben wir uns umgehört, Kolleginnen und Kollegen auf Unternehmensseite um ihre Einschätzungen gebeten, ihre An- und Einsichten ausgewertet. Was heute sinnvoll ist, was noch nicht so gut klappt, was zukünftig wichtig sein wird, das erfahren Sie auf den folgenden Seiten und auf http://www.ergo-komm.de/newsroom/news/unternehmen-und-social-media/. Eine Publikation von ergo Kommunikation, erschienen im Pressesprecher 05/2013.
Whipepaper Open Educational Resources in Ausbildung und WeiterbildungBertelsmann Stiftung
Im Jahr 2015 sind digitale Lehr-Lern-Materialien („Educational Resources“) im Bildungsbereich zum Normalfall geworden. Inhalte sind digital einfacher zu kopieren und zu bearbeiten, besser miteinander zu kombinieren und schneller zu verbreiten. Auch die Lernenden schätzen die Vorteile von Materialien, die sie nach Belieben abspeichern und bearbeiten können, ganz zu schweigen von multimedialen und interaktiven Inhalten.
In der Praxis stoßen die erweiterten Möglichkeiten häufig an urheberrechtliche Grenzen. Die Folge sind Unsicherheit und Zurückhaltung bei der Bearbeitung, beim Austausch und Verbreiten digitaler Materialien. Hier setzt die Idee von Open Educational Resources (OER) an. Offene Lizenzen erlauben all das, was traditionell eingeschränkt ist. Entsprechend groß sind die Hoffnungen, die mit OER verbunden werden: Die UNESCO erkennt in OER „ein gewaltiges Potential zur Verbesserung der Qualität und Effektivität von Bildung“. Bei der OECD sieht man OER als „Treiber für Innovation im Bildungsbereich“, und auch die Europäische Kommission erwartet eine „Chance für die Neugestaltung der Bildung in der EU“. Eine gemeinsame Arbeitsgruppe von Kultusministerkonferenz (KMK) und Bundesministerium für Bildung und Forschung (BMBF) stellte im März 2015 fest: „OER können einen Mehrwert bei der Vermittlung und Aneignung von Wissen darstellen und pädagogische Ziele wie zum Beispiel die Individualisierung von Lehr-Lern-Prozessen fördern.“ Nicht zuletzt ist die Bereitstellung von OER aber auch eine zivilgesellschaftliche Frage der erhöhten Partizipation sowie des ökonomischen Nutzens; Zugang zu Wissen ist die entscheidende Voraussetzung, um auf den globalisierten Arbeitsmärkten in Zukunft zu bestehen.
Die Erwartungen sind also hoch. Passt die OER- Idee aber überhaupt in ein System, in dem Dozenten und Trainer in Konkurrenz zueinander stehen und sich auch über ihre Materialien voneinander unterscheiden? Wissen die Entscheider um die Potenziale und Herausforderungen von OER? Auch auf politischer Ebene ist das Thema relevant, wie das 2014 gegründete zivilgesellschaftliche „Bündnis freie Bildung“ deutlich macht. Eine der zentralen Forderungen des Bündnisses lautet: Materialien, deren Erstellung öffentlich finanziert sind, sollen offen lizenziert sein. Das vorliegende Whitepaper will einen Beitrag dazu leisten, das Grundlagenwissen zu OER zu verbreitern und die Diskussion um OER voranzutreiben. Denn bisher sind alle Versprechungen zu OER vor allem eins: Versprechungen. Um das Potenzial der OER zu entfalten, braucht es eine Debatte auf allen Ebenen des Bildungswesen.
Autoren: Ingo Blees, Markus Deimann, Hedwig Seipel, Doris Hirschmann, Jöran Muuß-Merholz
Koller Dekorative Graphik Auktion - Old Master Prints Auction Koller Auctions
Koller Auctions - English descriptions available on the site via the links in the catalogue, then hit EN top of the site.
http://kollerauktionen.auctioneersvault.com/catalogues/A176f/
Helvetica
Ausländische Veduten
Künstler-Graphik des 15. bis 20. Jh.
Dekorative Graphik
Lot 3601 - 3651
Auktion: Dienstag, 22. März 2016, 10.00 Uhr
Vorbesichtigung: 8. bis 16. März 2016
Old Master Prints
Koller Zurich A176
Auction 22.03.2016, 10.00 AM
Koller is the leading Swiss auction house, with offices in London, Munich, Dusseldorf, Milan, Hamburg, Beijing, Moscow and New York. Each year Koller holds over thirty auctions, covering all of the major collecting categories in the fine and decorative arts, jewelry, Asian art and wine. Koller regularly sets record prices and benefits from a large base of international bidders. With its team of highly experienced specialists, as well as its membership in the worldwide group “International Auctioneers,” the family-owned auction house combines the distinct advantages of an internationally active auction house with Swiss reliability and efficiency.
(in German) Praesentation von Martin Engstler vom Fraunhofer IAO auf der IBM-Bankenfachtagung am 8. Maerz 2007 zu den Inhalten und Ergebnissen der aktuellen Studie "Bank und Zukunft" 2007.
Domains of unknown function are essential in yeastLaura Berry
Presented in the Synthetic Biology & Gene Editing strand of the 4Bio Summit. For more information, visit:
www.global-engage.com
~25% of yeast essential domains of unknown function (yeDUFs) are broadly conserved across all kingdoms of life (including Bacteria), while a small number are found in large numbers of proteins in mammals. In this presentation, Norman Goodacre from the FDA discusses 68 yeDUFs and their roles in alternative carbohydrate metabolism, mitochondrial transport, nuclear pore complex, mRNA processing, initiation of translation, protein complex assembly, and membrane-binding.
Using methylation patterns to determine origin of biological material and ageQIAGEN
In this QIAGEN sponsored webinar, our guest speakers from the San Francisco Police Department (SFPD) Crime Lab and Florida International University (FIU) discuss their research on the potential of epigenetic methylation as a procedure for body fluid identification and age estimation from DNA left at crime scenes. Several approaches have been studied, including an analysis of methyl array data and an initial validation of procedures such as pyrosequencing and real-time PCR. The presentation focuses on a number of tissue-specific epigenetic markers for body fluid and age determination with a promise of future integration of these markers into the forensic lab due to the simplicity of analysis and the ease of application.
Learn more about the Pyrosequencing technology and our solutions at
https://www.qiagen.com/resources/technologies/pyrosequencing-resource-center/
Genomics on the Half Shell: Making Science more Opensr320
Abstract
Technology has significantly changed how research is done in biology. Along with this shift, it is increasingly easier and advantageous to operate in an open science framework. In this presentation I will begin by providing an overview of our research efforts with particularly attention to challenges in data analysis. Research in our lab focuses on characterizing physiological responses of shellfish to environmental change, examining impacts and adaptive potential from the nucleotide to organism level. A core component of this includes investigating the functional relationship of genetics, epigenetics, and transcription. In our research we leverage several computing infrastructure solutions that I will describe. In addition, our lab practices Open Notebook Science. I will describe the practical aspects of how we accomplish this including addressing some of the concerns and realized advantages. Beyond online lab notebooks, we are continually experimenting with different ways to use online resources to engage with a larger audience and improve science communication. I have found this is a complex balance of time and effort versus impact and will discuss how our lab group attempts to reach this balance.
Bio
Steven Roberts is an Associate Professor in the School of Aquatic and Fishery Sciences where his research centers around characterizing the response of aquatic organisms to environmental change. Prior to coming to the University of Washington, in 2007 he was at the Marine Biological Laboratory in Woods Hole, Massachusetts and received his PhD from the University of Notre Dame. In graduate school he spent most of his time transferring agarose gels, and now he spends most of his time transferring files.
Are you interested in the pGLO™ experiment? Learn more about this hands-on laboratory activity with a FREE download of BioRad’s pGLO™ experiment power point.
Lecture from whole-cell modeling summer school March 3-9, 2015 at the University of Rostock. See http://sites.google.com/site/vwwholecellsummerschool/ for more information.
Science Communication and Impact: A Researcher's Perspectivesr320
Presentation given at Special Libraries Association - Vancouver, Canada - June 2014. Part of the panel discussion - Staying in the Game: New Roles for Libraries in Research Support
The French Revolution, which began in 1789, was a period of radical social and political upheaval in France. It marked the decline of absolute monarchies, the rise of secular and democratic republics, and the eventual rise of Napoleon Bonaparte. This revolutionary period is crucial in understanding the transition from feudalism to modernity in Europe.
For more information, visit-www.vavaclasses.com
Operation “Blue Star” is the only event in the history of Independent India where the state went into war with its own people. Even after about 40 years it is not clear if it was culmination of states anger over people of the region, a political game of power or start of dictatorial chapter in the democratic setup.
The people of Punjab felt alienated from main stream due to denial of their just demands during a long democratic struggle since independence. As it happen all over the word, it led to militant struggle with great loss of lives of military, police and civilian personnel. Killing of Indira Gandhi and massacre of innocent Sikhs in Delhi and other India cities was also associated with this movement.
How to Make a Field invisible in Odoo 17Celine George
It is possible to hide or invisible some fields in odoo. Commonly using “invisible” attribute in the field definition to invisible the fields. This slide will show how to make a field invisible in odoo 17.
Introduction to AI for Nonprofits with Tapp NetworkTechSoup
Dive into the world of AI! Experts Jon Hill and Tareq Monaur will guide you through AI's role in enhancing nonprofit websites and basic marketing strategies, making it easy to understand and apply.
June 3, 2024 Anti-Semitism Letter Sent to MIT President Kornbluth and MIT Cor...Levi Shapiro
Letter from the Congress of the United States regarding Anti-Semitism sent June 3rd to MIT President Sally Kornbluth, MIT Corp Chair, Mark Gorenberg
Dear Dr. Kornbluth and Mr. Gorenberg,
The US House of Representatives is deeply concerned by ongoing and pervasive acts of antisemitic
harassment and intimidation at the Massachusetts Institute of Technology (MIT). Failing to act decisively to ensure a safe learning environment for all students would be a grave dereliction of your responsibilities as President of MIT and Chair of the MIT Corporation.
This Congress will not stand idly by and allow an environment hostile to Jewish students to persist. The House believes that your institution is in violation of Title VI of the Civil Rights Act, and the inability or
unwillingness to rectify this violation through action requires accountability.
Postsecondary education is a unique opportunity for students to learn and have their ideas and beliefs challenged. However, universities receiving hundreds of millions of federal funds annually have denied
students that opportunity and have been hijacked to become venues for the promotion of terrorism, antisemitic harassment and intimidation, unlawful encampments, and in some cases, assaults and riots.
The House of Representatives will not countenance the use of federal funds to indoctrinate students into hateful, antisemitic, anti-American supporters of terrorism. Investigations into campus antisemitism by the Committee on Education and the Workforce and the Committee on Ways and Means have been expanded into a Congress-wide probe across all relevant jurisdictions to address this national crisis. The undersigned Committees will conduct oversight into the use of federal funds at MIT and its learning environment under authorities granted to each Committee.
• The Committee on Education and the Workforce has been investigating your institution since December 7, 2023. The Committee has broad jurisdiction over postsecondary education, including its compliance with Title VI of the Civil Rights Act, campus safety concerns over disruptions to the learning environment, and the awarding of federal student aid under the Higher Education Act.
• The Committee on Oversight and Accountability is investigating the sources of funding and other support flowing to groups espousing pro-Hamas propaganda and engaged in antisemitic harassment and intimidation of students. The Committee on Oversight and Accountability is the principal oversight committee of the US House of Representatives and has broad authority to investigate “any matter” at “any time” under House Rule X.
• The Committee on Ways and Means has been investigating several universities since November 15, 2023, when the Committee held a hearing entitled From Ivory Towers to Dark Corners: Investigating the Nexus Between Antisemitism, Tax-Exempt Universities, and Terror Financing. The Committee followed the hearing with letters to those institutions on January 10, 202
Unit 8 - Information and Communication Technology (Paper I).pdfThiyagu K
This slides describes the basic concepts of ICT, basics of Email, Emerging Technology and Digital Initiatives in Education. This presentations aligns with the UGC Paper I syllabus.
Instructions for Submissions thorugh G- Classroom.pptxJheel Barad
This presentation provides a briefing on how to upload submissions and documents in Google Classroom. It was prepared as part of an orientation for new Sainik School in-service teacher trainees. As a training officer, my goal is to ensure that you are comfortable and proficient with this essential tool for managing assignments and fostering student engagement.
Palestine last event orientationfvgnh .pptxRaedMohamed3
An EFL lesson about the current events in Palestine. It is intended to be for intermediate students who wish to increase their listening skills through a short lesson in power point.
Epigenetic and Environmental Influences on the Shellfish Immune Response
1. Epigenetic and Environmental
Influences on the Shellfish
Immune Response
Steven B. Roberts
Assistant Professor
School of Aquatic and Fishery Sciences
University of Washington
Seattle - Washington - US
2. Open Science
•You are free to Share!
•Our lab practices open notebook
science
•Slides, links, and related material are
available @
oystergen.es/vigo
17. e
Characterization of genes involved in ceramide metabolism in the Pacific oyster
(Crassostrea gigas).
Timmins-Schiffman and Roberts 2012
Immune Function
18. e
Rapid accumulation of an interleukin 17 homolog transcript in Crassostrea gigas
hemocytes following bacterial exposure.
Roberts et al 2008
Analysis of genes isolated from plated hemocytes of the Pacific Oyster,
Crassostrea gigas.
Roberts et al 2009
Characterization of genes involved in ceramide metabolism in the Pacific oyster
(Crassostrea gigas).
Timmins-Schiffman and Roberts 2012
20. e
Characterizing short read sequencing for gene discovery and
RNA-Seq analysis in Crassostrea gigas.
Gavery and Roberts 2012
Elevated pCO2 causes developmental delay in early larval Pacific oysters, Crassostrea gigas.
Timmins-Schiffman et al 2012
O c e a n A c i d i f i c a t i o n
22. e
O c e a n A c i d i f i c a t i o n
unpublished
Proteomic Response
23. e
O c e a n A c i d i f i c a t i o n
unpublished
Proteomic Response
oxidation reduction
signal transduction
oxidative stress
response
cellular stress &
transport
Elevated (7.2) Control (8)
28. e
unpublished
Puta%ve
cytochrome
P450
Isocitrate
dehydrogenase
[NAD]
subunit
beta
Alpha-‐soluble
NSF
aCachment
protein
C16orf62
homolog
Radial
spoke
head
protein
4
homolog
A
Flo%llin-‐2
Small
nuclear
ribonucleoprotein-‐associated
protein
ES1
protein
homolog
Sterile
alpha
and
TIR
mo%f-‐containing
protein
1
Twinfilin-‐2
Lachesin
Syntaxin-‐5
Serine
dehydratase-‐like
Caspase-‐3
tRNA
methyltransferase
112
homolog
Circularly
permutated
Ras
protein
1
Contac%n
Caspase-‐7
Apopto%c
chroma%n
condensa%on
inducer
Calcium-‐binding
protein
Vacuolar
protein
sor%ng-‐associated
protein
13C
Cullin-‐1
Control
58. Biology
In species that experience a diverse range of
environmental conditions, processes have evolved to
increase the number of potential phenotypes in a
population in order to improve the chances for an
individual’s survival.
59. M M M M M M M M M M
germline methylation
conventional transcription
5’ UTR promotor
ubiquitously expressed,
critical genes
Transcriptional opportunities
60. x x
M M M M
sparse methylation
alternative start sites
sequence mutation
change AA, premature stop codon
conventional transcription
transient methylation
alternate transcript
exon skipping
tissue / temporal specific and
inducible genes
Transcriptional opportunities
Roberts and Gavery 2012
69. Profiling the DNA methylomes of plants exposed
to bacterial pathogen, avirulent bacteria, or salicylic acid
hormone revealed numerous stress-induced
differentially methylated regions, many of which
were intimately associated with differentially
expressed genes.
70. ChIP-seq analysis of four
histone modifications
revealed that the priming
treatment altered the
epigenomic landscape; ....
preferentially targeted
transcription factors.
84. Open Notebook Science
... there is a URL to a laboratory notebook that is
freely available and indexed on common search
engines. It does not necessarily have to look like a
paper notebook but it is essential that all of the
information available to the researchers to make
their conclusions is equally available to the rest of
the world.
—Jean-Claude Bradley
89. Open Notebook Science
Hello,
I was doing a search for what
concentrations of MgSO4 to use as a
bivalve relaxant and came across
Katie’s Notebook. What a cool idea!
Please say thanks to Katie :). My boss
said MgSO4 but most of the literature
was MgCl2.... So g’day from the
University of Queensland in Brisbane,
Australia.
Cheers
KA
email June 22, 2013
90. R e p r o d u c i b i l i t y
usable data formats
Sharing
91. R e p r o d u c i b i l i t y
usable data formats
Sharing
Platforms
FigShare
Dryad
GitHub
runmycode
92. R e p r o d u c i b i l i t y
usable data formats
Sharing
looking for patterns