This is a presentation from the Canadian Bovine Genomics Workshop held in Calgary, Alberta on Sept.14, 2009.
The workshop was the first step in developing a national bovine genomics strategy for Canada.
This document provides an update on the Genome in a Bottle Consortium. Key points include:
- Two papers characterizing small variants in GIAB genomes have been published or are in press. GIAB products are being widely used for benchmarking and training AI methods.
- The consortium is developing new long read sequencing data from PacBio and Oxford Nanopore, as well as strand-seq data. Goals include fully characterizing structural variants and difficult regions.
- NIST is working to establish a repository to host GIAB samples and ensure long-term access. Six admixed cell lines have been identified for potential development as reference samples.
- Upcoming workshops will focus on benchmarking assemblies,
Thinkshop cells as packaging for giab genomesGenomeInABottle
Cells are proposed as packaging for genome samples because they can be regenerated by users, but there are risks like contamination, stability issues, and unethical use that would need to be addressed. If distributing live cell samples, considerations include quality assurance, distribution terms, access policies, and what cell types would be most appropriate.
This document outlines a strategy for developing genomic reference materials (GIAB). It discusses identifying the principles that will guide product development decisions, including the unique value GIAB provides through open access to data, materials and analyses. It addresses how comprehensive a GIAB call set needs to be and what is required to generate a GIAB genome product, such as sequencing and characterization. The document also covers commitments to ongoing maintenance and making improvements, with ambitions for more genomes, somatic references and finished assemblies. The overall goal is to establish a strategic framework for GIAB product development.
How giab fits in the rest of the world mdic somatic reference samplesGenomeInABottle
This document provides an overview of the Cancer Genomic Somatic Reference Samples initiative, a collaborative effort to develop reference samples to improve next-generation sequencing (NGS) cancer tests. The initiative is working in phases to prioritize clinically relevant variants, analyze existing reference material efforts, define desired sample characteristics, and issue requests for information and proposals. The goal is to make reference samples available publicly to help diagnostic companies validate NGS tests and streamline regulatory processes, providing transparency. Upcoming webinars will focus on selecting tumor suppressor genes and genomic signatures for inclusion.
How giab fits in the rest of the world introductionGenomeInABottle
GIAB is one of several projects working to develop genomic reference samples and improve reference assemblies. These include the Human Genome Reference Program maintaining the current reference, funding to develop a human pangenome reference, the Vertebrate Genome Project developing assembly metrics, and the Telomere-to-Telomere Project working on chromosome-length assemblies using long reads. The new Human Genome Reference Program will connect GIAB with the Reference Center and include elements like reference genomes, reference representations R&D, sequencing R&D, and pangenome informatics tools.
The roles communities play in improving bioinformatics: better software, bett...Iddo
Discussing three community strategies to improve bioinformatics: collective open source development (biopython), critical assessment challenge (CAFA), and crowdsourcing (maize phenomics).
The document discusses principles for disseminating samples from the Genome in a Bottle (GIAB) reference collection. It raises several issues to consider, including whether every GIAB sample needs to be openly distributed, how essential open and unrestricted availability is, and whether an independent repository is needed to ensure this. Other topics discussed are the representativeness and diversity of available samples, reliability and stability concerns with disseminating cell lines, and ensuring quality control as technologies advance.
The document provides an update and roadmap for the Genome in a Bottle (GIAB) Consortium. Key points include: progress made in developing benchmarking methods and data for small variants, structural variants, and difficult regions; adoption of GIAB resources in clinical and research settings; plans to develop new germline and tumor samples from diverse populations; and ongoing work to characterize genomes using long reads, linked reads, and other technologies. The document outlines goals for an upcoming workshop, including reviewing progress, discussing dissemination principles, and planning future sample types.
This document provides an update on the Genome in a Bottle Consortium. Key points include:
- Two papers characterizing small variants in GIAB genomes have been published or are in press. GIAB products are being widely used for benchmarking and training AI methods.
- The consortium is developing new long read sequencing data from PacBio and Oxford Nanopore, as well as strand-seq data. Goals include fully characterizing structural variants and difficult regions.
- NIST is working to establish a repository to host GIAB samples and ensure long-term access. Six admixed cell lines have been identified for potential development as reference samples.
- Upcoming workshops will focus on benchmarking assemblies,
Thinkshop cells as packaging for giab genomesGenomeInABottle
Cells are proposed as packaging for genome samples because they can be regenerated by users, but there are risks like contamination, stability issues, and unethical use that would need to be addressed. If distributing live cell samples, considerations include quality assurance, distribution terms, access policies, and what cell types would be most appropriate.
This document outlines a strategy for developing genomic reference materials (GIAB). It discusses identifying the principles that will guide product development decisions, including the unique value GIAB provides through open access to data, materials and analyses. It addresses how comprehensive a GIAB call set needs to be and what is required to generate a GIAB genome product, such as sequencing and characterization. The document also covers commitments to ongoing maintenance and making improvements, with ambitions for more genomes, somatic references and finished assemblies. The overall goal is to establish a strategic framework for GIAB product development.
How giab fits in the rest of the world mdic somatic reference samplesGenomeInABottle
This document provides an overview of the Cancer Genomic Somatic Reference Samples initiative, a collaborative effort to develop reference samples to improve next-generation sequencing (NGS) cancer tests. The initiative is working in phases to prioritize clinically relevant variants, analyze existing reference material efforts, define desired sample characteristics, and issue requests for information and proposals. The goal is to make reference samples available publicly to help diagnostic companies validate NGS tests and streamline regulatory processes, providing transparency. Upcoming webinars will focus on selecting tumor suppressor genes and genomic signatures for inclusion.
How giab fits in the rest of the world introductionGenomeInABottle
GIAB is one of several projects working to develop genomic reference samples and improve reference assemblies. These include the Human Genome Reference Program maintaining the current reference, funding to develop a human pangenome reference, the Vertebrate Genome Project developing assembly metrics, and the Telomere-to-Telomere Project working on chromosome-length assemblies using long reads. The new Human Genome Reference Program will connect GIAB with the Reference Center and include elements like reference genomes, reference representations R&D, sequencing R&D, and pangenome informatics tools.
The roles communities play in improving bioinformatics: better software, bett...Iddo
Discussing three community strategies to improve bioinformatics: collective open source development (biopython), critical assessment challenge (CAFA), and crowdsourcing (maize phenomics).
The document discusses principles for disseminating samples from the Genome in a Bottle (GIAB) reference collection. It raises several issues to consider, including whether every GIAB sample needs to be openly distributed, how essential open and unrestricted availability is, and whether an independent repository is needed to ensure this. Other topics discussed are the representativeness and diversity of available samples, reliability and stability concerns with disseminating cell lines, and ensuring quality control as technologies advance.
The document provides an update and roadmap for the Genome in a Bottle (GIAB) Consortium. Key points include: progress made in developing benchmarking methods and data for small variants, structural variants, and difficult regions; adoption of GIAB resources in clinical and research settings; plans to develop new germline and tumor samples from diverse populations; and ongoing work to characterize genomes using long reads, linked reads, and other technologies. The document outlines goals for an upcoming workshop, including reviewing progress, discussing dissemination principles, and planning future sample types.
sbv IMPROVER: an industry initiative to harness the wisdom of the crowd in sc...Crowdsourcing Week
The document describes sbv IMPROVER, an initiative led by Philip Morris International that uses crowdsourcing to verify scientific data and methods. It provides examples of past challenges that asked participants to verify biological networks and diagnostic signatures. The initiative aims to complement peer review and drive innovation through collaboration. It works by engaging scientists through online challenges, publications, conferences and incentives to collaboratively refine computational models and methods.
The document discusses the Genome in a Bottle Consortium's efforts to develop reference materials and reference methods to help validate whole genome sequencing for clinical applications. This includes developing well-characterized reference genomes and reference data from these genomes to enable evaluation of variant calling accuracy and help standardize performance metrics. The consortium is working to generate integrated variant calls from multiple sequencing platforms and technologies for different reference genomes to serve as benchmarks for evaluation.
2014 agbt giab data integration poster 140206GenomeInABottle
This document summarizes efforts by the Genome in a Bottle Consortium to develop an integrated set of genotype calls for the NA12878 reference sample using data from 14 sequencing datasets. They identify characteristics of bias and errors in the different datasets to arbitrate between discordant variant calls. The resulting high-confidence SNP and indel calls are being used as a benchmark to evaluate the performance of sequencing and analysis methods. The integrated calls appear to have higher sensitivity than previous microarray-based assessments. The consortium is exploring expanding this approach to structural variants and using pedigree relationships.
The document discusses a knowledge management platform developed at Genentech to manage pre-clinical animal studies.
The platform called DIVOS manages over 12,000 in vivo studies dating back to 1998 across multiple therapeutic areas conducted both in-house and by CROs. The technical approach involved developing a structured yet flexible platform to capture study details while enabling data reuse. People were key to change through various teams guiding strategy, tactics and operations. New capabilities like improved study logistics, enhanced collaboration and new insights from data analysis provide evidence of the platform's success.
Application of adverse outcome pathways in chemical risk assessment, Dan Vill...OECD Environment
On 30 April 2019, the OECD organised a webinar on the Adverse Outcome Pathway (AOP) framework. The AOP framework is a collaborative tool that applies an innovative approach for collecting mechanistic knowledge from various sources that can eventually support chemical safety assessment.
The following questions were addressed:
What is the AOP framework and why should you care?
Why are we developing AOPs?
Why collaborations are encouraged and why should scientific societies be brought in?
What are the opportunities for collaboration in AOP development?
Giab jan2016 analysis team breakout SNP indel update zookGenomeInABottle
This document summarizes the process used to integrate SNP and indel calls from multiple datasets. It finds consensus calls supported by two or more technologies, uses consensus calls to train models to identify outlier calls from each dataset, and then uses callable regions and outlier calls to arbitrate between datasets and identify high-confidence calls. It also provides preliminary comparisons of SNP/indel calls between versions 2.19 and 3.0 for chromosome 20 in the NA12878 genome. The document discusses how to add more difficult calls and regions to the high-confidence set and lists potential topics for breakout discussions, including benchmarking and validating structural variants and establishing confident regions without variants.
This is a presentation from the Canadian Bovine Genomics Workshop held in Calgary, Alberta on Sept.14, 2009.
The workshop was the first step in developing a national bovine genomics strategy for Canada.
Validating microbiome claims – including the latest DNA techniquesEagle Genomics
Abel Ureta-Vidal, Founder and CEO of Eagle Genomics, discusses how advanced DNA techniques help us to identify and characterise the microbiome, leading us to ways to prove cosmetic claims at the in-cosmetics formulation summit, 25th October 2017.
This document provides materials for an activity where students match organisms to the percentage of DNA they share with humans. The organisms included are fruit fly, chimpanzee, zebrafish, bacteria, mustard grass, and roundworm. Students are asked to draw lines connecting each organism to its DNA percentage. They are then prompted to think about whether the DNA similarities make sense and if they are surprised by any matches.
The diagnosis of viral pathogens is a crucial component of plant biosecurity surveillance and preventing the introduction of exotic plant viruses and viroids at the border. Existing quarantine procedures can be time-consuming and require detailed knowledge of potential infecting viral pathogens. Currently, imported plants can spend as long as two years in quarantine, with associated costs.
To simplify the post-entry quarantine process researchers have developed a plant diagnostic toolkit for plant viruses and viroids. The toolkit takes advantage of the natural antiviral system of plants, using small RNA next generation sequencing (sRNA-seq) technology to detect nearly all known viruses and viroids in a single test. The new test, and associated toolkit, will reduce the time imported plant material spends in Australia’s quarantine system while improving accuracy of detection in a single sRNA-seq experiment.
Marker assisted selection can be used to accelerate genetic change for economic and production traits in cattle. It allows for more direct selection compared to phenotype-based selection alone. This can increase profitability through improved feed efficiency, carcass value, and other traits. While marker assisted selection may increase uniformity across breeds, variation is still important for adaptation to different environments. Breeders need to consider how to balance selection for market traits while maintaining breed distinctions and ability to adapt. Genomic technology can help improve the accuracy of estimated breeding values by linking DNA information to performance data.
This is a presentation from the Canadian Bovine Genomics Workshop held in Calgary, Alberta on Sept.14, 2009.
The workshop was the first step in developing a national bovine genomics strategy for Canada.
This is a presentation from the Canadian Bovine Genomics Workshop held in Calgary, Alberta on Sept.14, 2009.
The workshop was the first step in developing a national bovine genomics strategy for Canada.
This is a presentation from the Canadian Bovine Genomics Workshop held in Calgary, Alberta on Sept.14, 2009.
The workshop was the first step in developing a national bovine genomics strategy for Canada.
Application of molecular biology to conventional disease strategies ( M.Phil ...Satya Prakash Chaurasia
As resistance to disease in plants is genetically controlled, molecular tools like breeding resistant cultivars has been an intensively used approach for crop protection since near beginning of human civilization, the time when we did not know its molecular aspects. Even today, molecular biology is applied in multiple ways to control plant diseases. Some of which are breeding, tissue culture, marker assisted breeding, QTL- mapping, identification of novel resistance genes etc. With the commencement of advanced technologies in the recent past, we are now able to genetically modify a plant without wasting a lot of time and avoiding problems of sexual incompatibility which we encounter in breeding programs.
Presentation on "Choosing the Right Social Media Tools to Get Your Message Out". Some of the tools may have changes since 2012 but this is all about the basics to help you no matter what comes and goes.
This is a presentation from the Canadian Bovine Genomics Workshop held in Calgary, Alberta on Sept.14, 2009.
The workshop was the first step in developing a national bovine genomics strategy for Canada.
The document summarizes the Canadian Beef Breeds Council (CBBC) and their Beef InfoXchange System (BIXS) initiative. CBBC/BIXS aims to build value in the Canadian beef brand and value chain by creating a single-source information system. This system would link purebred beef producers and allow for information sharing around animal genetics and performance data. The goals are to identify and increase demand for superior genetics, reduce risk, and make the industry more profitable, quality-driven and globally competitive.
12 Tweets for Using Digital Media for Internal CommunicationGenome Alberta
1) The document discusses using digital media and social media for internal communications within organizations.
2) It provides 12 tweets that each highlight a key consideration or best practice for using these tools effectively, such as letting business needs drive the strategy, sticking to basic digital principles, and managing potential unintended consequences.
3) The overall message is that internal digital media can be a useful tool if implemented with the right philosophy, principles, and awareness of its opportunities and challenges.
Workshop finding and accessing data - fiona - lunteren april 18 2016Fiona Nielsen
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
sbv IMPROVER: an industry initiative to harness the wisdom of the crowd in sc...Crowdsourcing Week
The document describes sbv IMPROVER, an initiative led by Philip Morris International that uses crowdsourcing to verify scientific data and methods. It provides examples of past challenges that asked participants to verify biological networks and diagnostic signatures. The initiative aims to complement peer review and drive innovation through collaboration. It works by engaging scientists through online challenges, publications, conferences and incentives to collaboratively refine computational models and methods.
The document discusses the Genome in a Bottle Consortium's efforts to develop reference materials and reference methods to help validate whole genome sequencing for clinical applications. This includes developing well-characterized reference genomes and reference data from these genomes to enable evaluation of variant calling accuracy and help standardize performance metrics. The consortium is working to generate integrated variant calls from multiple sequencing platforms and technologies for different reference genomes to serve as benchmarks for evaluation.
2014 agbt giab data integration poster 140206GenomeInABottle
This document summarizes efforts by the Genome in a Bottle Consortium to develop an integrated set of genotype calls for the NA12878 reference sample using data from 14 sequencing datasets. They identify characteristics of bias and errors in the different datasets to arbitrate between discordant variant calls. The resulting high-confidence SNP and indel calls are being used as a benchmark to evaluate the performance of sequencing and analysis methods. The integrated calls appear to have higher sensitivity than previous microarray-based assessments. The consortium is exploring expanding this approach to structural variants and using pedigree relationships.
The document discusses a knowledge management platform developed at Genentech to manage pre-clinical animal studies.
The platform called DIVOS manages over 12,000 in vivo studies dating back to 1998 across multiple therapeutic areas conducted both in-house and by CROs. The technical approach involved developing a structured yet flexible platform to capture study details while enabling data reuse. People were key to change through various teams guiding strategy, tactics and operations. New capabilities like improved study logistics, enhanced collaboration and new insights from data analysis provide evidence of the platform's success.
Application of adverse outcome pathways in chemical risk assessment, Dan Vill...OECD Environment
On 30 April 2019, the OECD organised a webinar on the Adverse Outcome Pathway (AOP) framework. The AOP framework is a collaborative tool that applies an innovative approach for collecting mechanistic knowledge from various sources that can eventually support chemical safety assessment.
The following questions were addressed:
What is the AOP framework and why should you care?
Why are we developing AOPs?
Why collaborations are encouraged and why should scientific societies be brought in?
What are the opportunities for collaboration in AOP development?
Giab jan2016 analysis team breakout SNP indel update zookGenomeInABottle
This document summarizes the process used to integrate SNP and indel calls from multiple datasets. It finds consensus calls supported by two or more technologies, uses consensus calls to train models to identify outlier calls from each dataset, and then uses callable regions and outlier calls to arbitrate between datasets and identify high-confidence calls. It also provides preliminary comparisons of SNP/indel calls between versions 2.19 and 3.0 for chromosome 20 in the NA12878 genome. The document discusses how to add more difficult calls and regions to the high-confidence set and lists potential topics for breakout discussions, including benchmarking and validating structural variants and establishing confident regions without variants.
This is a presentation from the Canadian Bovine Genomics Workshop held in Calgary, Alberta on Sept.14, 2009.
The workshop was the first step in developing a national bovine genomics strategy for Canada.
Validating microbiome claims – including the latest DNA techniquesEagle Genomics
Abel Ureta-Vidal, Founder and CEO of Eagle Genomics, discusses how advanced DNA techniques help us to identify and characterise the microbiome, leading us to ways to prove cosmetic claims at the in-cosmetics formulation summit, 25th October 2017.
This document provides materials for an activity where students match organisms to the percentage of DNA they share with humans. The organisms included are fruit fly, chimpanzee, zebrafish, bacteria, mustard grass, and roundworm. Students are asked to draw lines connecting each organism to its DNA percentage. They are then prompted to think about whether the DNA similarities make sense and if they are surprised by any matches.
The diagnosis of viral pathogens is a crucial component of plant biosecurity surveillance and preventing the introduction of exotic plant viruses and viroids at the border. Existing quarantine procedures can be time-consuming and require detailed knowledge of potential infecting viral pathogens. Currently, imported plants can spend as long as two years in quarantine, with associated costs.
To simplify the post-entry quarantine process researchers have developed a plant diagnostic toolkit for plant viruses and viroids. The toolkit takes advantage of the natural antiviral system of plants, using small RNA next generation sequencing (sRNA-seq) technology to detect nearly all known viruses and viroids in a single test. The new test, and associated toolkit, will reduce the time imported plant material spends in Australia’s quarantine system while improving accuracy of detection in a single sRNA-seq experiment.
Marker assisted selection can be used to accelerate genetic change for economic and production traits in cattle. It allows for more direct selection compared to phenotype-based selection alone. This can increase profitability through improved feed efficiency, carcass value, and other traits. While marker assisted selection may increase uniformity across breeds, variation is still important for adaptation to different environments. Breeders need to consider how to balance selection for market traits while maintaining breed distinctions and ability to adapt. Genomic technology can help improve the accuracy of estimated breeding values by linking DNA information to performance data.
This is a presentation from the Canadian Bovine Genomics Workshop held in Calgary, Alberta on Sept.14, 2009.
The workshop was the first step in developing a national bovine genomics strategy for Canada.
This is a presentation from the Canadian Bovine Genomics Workshop held in Calgary, Alberta on Sept.14, 2009.
The workshop was the first step in developing a national bovine genomics strategy for Canada.
This is a presentation from the Canadian Bovine Genomics Workshop held in Calgary, Alberta on Sept.14, 2009.
The workshop was the first step in developing a national bovine genomics strategy for Canada.
Application of molecular biology to conventional disease strategies ( M.Phil ...Satya Prakash Chaurasia
As resistance to disease in plants is genetically controlled, molecular tools like breeding resistant cultivars has been an intensively used approach for crop protection since near beginning of human civilization, the time when we did not know its molecular aspects. Even today, molecular biology is applied in multiple ways to control plant diseases. Some of which are breeding, tissue culture, marker assisted breeding, QTL- mapping, identification of novel resistance genes etc. With the commencement of advanced technologies in the recent past, we are now able to genetically modify a plant without wasting a lot of time and avoiding problems of sexual incompatibility which we encounter in breeding programs.
Presentation on "Choosing the Right Social Media Tools to Get Your Message Out". Some of the tools may have changes since 2012 but this is all about the basics to help you no matter what comes and goes.
This is a presentation from the Canadian Bovine Genomics Workshop held in Calgary, Alberta on Sept.14, 2009.
The workshop was the first step in developing a national bovine genomics strategy for Canada.
The document summarizes the Canadian Beef Breeds Council (CBBC) and their Beef InfoXchange System (BIXS) initiative. CBBC/BIXS aims to build value in the Canadian beef brand and value chain by creating a single-source information system. This system would link purebred beef producers and allow for information sharing around animal genetics and performance data. The goals are to identify and increase demand for superior genetics, reduce risk, and make the industry more profitable, quality-driven and globally competitive.
12 Tweets for Using Digital Media for Internal CommunicationGenome Alberta
1) The document discusses using digital media and social media for internal communications within organizations.
2) It provides 12 tweets that each highlight a key consideration or best practice for using these tools effectively, such as letting business needs drive the strategy, sticking to basic digital principles, and managing potential unintended consequences.
3) The overall message is that internal digital media can be a useful tool if implemented with the right philosophy, principles, and awareness of its opportunities and challenges.
Workshop finding and accessing data - fiona - lunteren april 18 2016Fiona Nielsen
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
9 28-2012 surveys phenotypic drug discovery sigJonathan Lee
The survey gathered feedback from over 350 members of the Phenotypic Drug Discovery LinkedIn group on how the group can better serve their needs such as through discussion forums, networking opportunities, and sharing of practical implementation techniques. The responses provided insights into both the achievements and obstacles encountered when using phenotypic approaches for target identification, siRNA screening, and drug discovery including issues around reproducibility, validation of hits, and difficulty identifying molecular targets. Overall, the surveys aimed to understand how the group could improve and provide a useful overview of the field despite the low response rate typical for online surveys.
The Role of Libraries in Data Management and CurationNicole Vasilevsky
The Role of Libraries in Data Management and Curation, presented at the American Library Association conference in Las Vegas, NV, 07/29/14.
Abstract:
As increasing amounts of data are being generated, applying best practices in handling data is important, and librarians are well poised to assist users. During this session, we will discuss the role of libraries in assisting with data management, application of metadata, ontologies, data standards, and the publication of data in repositories and on the Semantic Web. This talk will describe best data practices and engage the attendees in interactive activities to demonstrate these principles.
Genome sharing projects around the world nijmegen oct 29 - 2015Fiona Nielsen
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.
Genomic epidemiology uses whole genome sequencing data from pathogens combined with epidemiological investigations to track the spread of infectious diseases. The document discusses making genomic epidemiology a widespread reality in public health. It outlines key requirements including building a user-friendly analysis platform, developing portable analysis pipelines, providing training to public health personnel, and improving information sharing between organizations.
How Can We Make Genomic Epidemiology a Widespread Reality? - William HsiaoWilliam Hsiao
The document discusses genomic epidemiology and the requirements to bring genomic sequencing into routine public health practice. It outlines two parts: (1) what genomic epidemiology is and why it is important; and (2) the requirements for genomic sequencing to be used routinely in public health. Whole genome sequencing is seen as a way to generate high quality pathogen genomes quickly and allow for more detailed tracking of disease spread compared to traditional methods. However, bringing genomic sequencing into public health practice requires overcoming barriers such as the need for user-friendly analysis platforms, training public health personnel in genomics, and improving information sharing between organizations.
The document discusses issues related to building sustainable biobanks. It outlines key factors for biobanks including having a clear purpose that determines their potential for generating knowledge, obtaining sufficient funding, and having a mandate and governance structure. It also stresses the importance of measuring success not just by the number of samples collected but by whether the biobank has accelerated research and discovery. The document uses the example of the Tumour Bank at the Children's Hospital at Westmead, which has supported over 90 projects, contributed samples to studies worldwide, and resulted in numerous publications despite being a small single-institution biobank.
The australian experience issues and solutions-Dr.Daniel CatchpooleData Science NIH
The document discusses issues related to building sustainable biobanks. It outlines key factors for biobanks including having a clear purpose that determines their potential for generating knowledge, obtaining sufficient funding, and having a mandate and governance structure. It also stresses the importance of measuring success not just by the number of samples collected but by whether the biobank has accelerated research and discovery. The document uses the example of the Tumour Bank at the Children's Hospital in Australia that has supported over 90 projects, contributed samples to studies worldwide, and led to numerous publications advancing the understanding of childhood cancers.
Daniel Catchpoole describes institutional experience with Biobanking in Australia.
This talk was sponsored by the NIH Data Science Special Interest Group and part of a webinar panel on June 23, 2017 on Global Biobanking and Access to Specimens.
This document describes the Continuous Update Project, a novel approach developed by the World Cancer Research Fund to systematically review mechanistic evidence on diet, nutrition, physical activity and cancer. The approach involves conducting systematic reviews and meta-analyses of both epidemiological and mechanistic studies to make judgements on causal relationships. It emphasizes reproducibility, predefined criteria, and reviews evidence separately from making judgements. The goal is to help identify causal links between exposures and cancer outcomes.
This document summarizes a project aiming to develop a comprehensive open-access database of cutaneous neurofibroma (cNF) expression and mutation data to facilitate systems biology analysis. The project has assembled an initial cNF dataset and conducted exploratory analyses to better understand cNF biology. Challenges include the need for more data to power studies given tumor heterogeneity. Next steps involve expanding the dataset by integrating additional public and project-generated cNF data to guide future research and therapeutic development.
Wheat Data Interoperability (1) by Esther DZALE YEUMO KABORE and Richard FULSSCIARD Movement
This document discusses the work of the Wheat Data Interoperability Working Group. The working group aims to provide a common framework for describing, representing, linking and publishing wheat data using open standards. It will initially focus on several key data types. The working group's deliverables include a report on existing resources, a cookbook with guidelines for data managers, a library of linked vocabularies and ontologies, and a prototype for integrating and publishing linked wheat data. A survey of 196 wheat researchers found that over half have no data management guidelines. Key data types identified were phenotypes, SNPs, genomic annotations, germplasm, genetic maps and physical maps. The document outlines next steps including a workshop to provide guidance and discuss standards and use
This file includes the SLAS2013 presentations of Paul A. Johnston of University of Pittsburgh; Douglas Auld of Novartis Institutes for Biomedical Research; and Lisa Minor of In Vitro Strategies, LLC.
CLARITY BPA: a Novel Approach to study EDCsDES Daughter
by the Collaborative on Health and the Environment
On this call Retha Newbold, MS, Researcher Emeritus, National Toxicology Program, National Institute of Environmental Health Sciences, discussed the program called “The Consortium Linking Academic and Regulatory Insights on the Toxicity of Bisphenol A (CLARITY-BPA)” which is an interagency agreement, conducted under the auspices of the National Toxicology Program (NTP), between The National Institute of Environmental Health Sciences (NIEHS) supported grantees, the staff of the Division of the National Toxicology Program (DNTP) at NIH/NIEHS, and the Food and Drug Administration at the National Center for Toxicological Research (FDA/NCTR). The goals of the consortium are to enhance the utility of a perinatal 2-year GLP chronic toxicity study on BPA for regulatory decision-making by incorporating a wide range of doses and some additional disease-related endpoints that are not usually covered.
To this end, 12 NIEHS grantees are studying hypothesis-driven mechanisms by investigating specific endpoints that maybe altered by BPA including behavioral/neuroendocrine, immune function, cardiac, reproductive tract, cancer, thyroid, and other organ systems. This consortium is unique in that it combines the knowledge and skills of the NTP staff with experts from the academic field who are covering more mechanistic studies. Although this program focuses on BPA, it may provide an example of how to better study effects of other endocrine disrupting chemicals especially since numerous organ systems may be involved.
Sources: http://www.healthandenvironment.org/partnership_calls/14639
This document discusses ways to help advance research for rare and orphan diseases through open collaboration and data sharing. It provides examples of how collaborative platforms and tools can help organizations with limited resources pool data and expertise. Specifically, it describes a secure web-based platform that allows private and public data to be simultaneously searched to facilitate partnerships across various sectors.
ROI from social media and online tools can be difficult to determine - especially for government or not for profits who aren't selling widgets. Back to basics to align your efforts with your departmental objectives.
If antibiotics quit working we would see deaths from otherwise treatable infections rise rapidly. This presentation from Genome Alberta President & CEO Dr. David Bailey looks at the rising problem of antibiotic resistant microbes, or AMR. It was part of the Beef Value Chain Roundtable held in Ottawa, Ontario.
Ali washington sept 2013 spear presentationGenome Alberta
Mike Spear's slide deck on social media tools and a bit of theory behind it, presented to the ALI Social Media & Government workshop in Washington DC, September 2013.
Genomics is the study of an organism's entire genetic makeup. New genomic technologies allow cattle producers to select for economically important traits like growth rate, feed efficiency, and disease resistance. The beef industry is interested in using these tools to improve breed performance and validate superior cattle through traits like growth, carcass quality, and animal welfare. Genomic data could be integrated with performance records to enhance selection accuracy and identify new traits of economic value.
Mike Spear outlines a social media strategy for Genome Alberta to raise awareness, provide education, and position the organization as an information source. The strategy focuses on platforms like GenOmics, Twitter, blogs and newsletters to engage different audiences. Social media is seen as a fundamental shift in communication that provides new opportunities despite serving audiences with limited internet access. The goal is to connect various stakeholders through an integrated approach across multiple online channels.
The document summarizes two upcoming Genome Canada competitions: a large-scale applied research competition with $60 million available for projects in forestry, environment, and other sectors, and a $24 million competition for innovation center operations support. It outlines the application process, timelines, eligibility requirements, and criteria for each competition. Key dates include a June 15 registration deadline for the large-scale competition and August 20/December 8 deadlines for letters of intent and full applications, respectively, for the innovation center support competition.
This is a presentation from the Canadian Bovine Genomics Workshop held in Calgary, Alberta on Sept.14, 2009.
The workshop was the first step in developing a national bovine genomics strategy for Canada.
This is a presentation from the Canadian Bovine Genomics Workshop held in Calgary, Alberta on Sept.14, 2009.
The workshop was the first step in developing a national bovine genomics strategy for Canada.
This is a presentation from the Canadian Bovine Genomics Workshop held in Calgary, Alberta on Sept.14, 2009.
The workshop was the first step in developing a national bovine genomics strategy for Canada.
This is a presentation from the Canadian Bovine Genomics Workshop held in Calgary, Alberta on Sept.14, 2009.
The workshop was the first step in developing a national bovine genomics strategy for Canada.
This is a presentation from the Canadian Bovine Genomics Workshop held in Calgary, Alberta on Sept.14, 2009.
The workshop was the first step in developing a national bovine genomics strategy for Canada.
Conversational agents, or chatbots, are increasingly used to access all sorts of services using natural language. While open-domain chatbots - like ChatGPT - can converse on any topic, task-oriented chatbots - the focus of this paper - are designed for specific tasks, like booking a flight, obtaining customer support, or setting an appointment. Like any other software, task-oriented chatbots need to be properly tested, usually by defining and executing test scenarios (i.e., sequences of user-chatbot interactions). However, there is currently a lack of methods to quantify the completeness and strength of such test scenarios, which can lead to low-quality tests, and hence to buggy chatbots.
To fill this gap, we propose adapting mutation testing (MuT) for task-oriented chatbots. To this end, we introduce a set of mutation operators that emulate faults in chatbot designs, an architecture that enables MuT on chatbots built using heterogeneous technologies, and a practical realisation as an Eclipse plugin. Moreover, we evaluate the applicability, effectiveness and efficiency of our approach on open-source chatbots, with promising results.
Your One-Stop Shop for Python Success: Top 10 US Python Development Providersakankshawande
Simplify your search for a reliable Python development partner! This list presents the top 10 trusted US providers offering comprehensive Python development services, ensuring your project's success from conception to completion.
Northern Engraving | Modern Metal Trim, Nameplates and Appliance PanelsNorthern Engraving
What began over 115 years ago as a supplier of precision gauges to the automotive industry has evolved into being an industry leader in the manufacture of product branding, automotive cockpit trim and decorative appliance trim. Value-added services include in-house Design, Engineering, Program Management, Test Lab and Tool Shops.
Discover top-tier mobile app development services, offering innovative solutions for iOS and Android. Enhance your business with custom, user-friendly mobile applications.
5th LF Energy Power Grid Model Meet-up SlidesDanBrown980551
5th Power Grid Model Meet-up
It is with great pleasure that we extend to you an invitation to the 5th Power Grid Model Meet-up, scheduled for 6th June 2024. This event will adopt a hybrid format, allowing participants to join us either through an online Mircosoft Teams session or in person at TU/e located at Den Dolech 2, Eindhoven, Netherlands. The meet-up will be hosted by Eindhoven University of Technology (TU/e), a research university specializing in engineering science & technology.
Power Grid Model
The global energy transition is placing new and unprecedented demands on Distribution System Operators (DSOs). Alongside upgrades to grid capacity, processes such as digitization, capacity optimization, and congestion management are becoming vital for delivering reliable services.
Power Grid Model is an open source project from Linux Foundation Energy and provides a calculation engine that is increasingly essential for DSOs. It offers a standards-based foundation enabling real-time power systems analysis, simulations of electrical power grids, and sophisticated what-if analysis. In addition, it enables in-depth studies and analysis of the electrical power grid’s behavior and performance. This comprehensive model incorporates essential factors such as power generation capacity, electrical losses, voltage levels, power flows, and system stability.
Power Grid Model is currently being applied in a wide variety of use cases, including grid planning, expansion, reliability, and congestion studies. It can also help in analyzing the impact of renewable energy integration, assessing the effects of disturbances or faults, and developing strategies for grid control and optimization.
What to expect
For the upcoming meetup we are organizing, we have an exciting lineup of activities planned:
-Insightful presentations covering two practical applications of the Power Grid Model.
-An update on the latest advancements in Power Grid -Model technology during the first and second quarters of 2024.
-An interactive brainstorming session to discuss and propose new feature requests.
-An opportunity to connect with fellow Power Grid Model enthusiasts and users.
Essentials of Automations: Exploring Attributes & Automation ParametersSafe Software
Building automations in FME Flow can save time, money, and help businesses scale by eliminating data silos and providing data to stakeholders in real-time. One essential component to orchestrating complex automations is the use of attributes & automation parameters (both formerly known as “keys”). In fact, it’s unlikely you’ll ever build an Automation without using these components, but what exactly are they?
Attributes & automation parameters enable the automation author to pass data values from one automation component to the next. During this webinar, our FME Flow Specialists will cover leveraging the three types of these output attributes & parameters in FME Flow: Event, Custom, and Automation. As a bonus, they’ll also be making use of the Split-Merge Block functionality.
You’ll leave this webinar with a better understanding of how to maximize the potential of automations by making use of attributes & automation parameters, with the ultimate goal of setting your enterprise integration workflows up on autopilot.
High performance Serverless Java on AWS- GoTo Amsterdam 2024Vadym Kazulkin
Java is for many years one of the most popular programming languages, but it used to have hard times in the Serverless community. Java is known for its high cold start times and high memory footprint, comparing to other programming languages like Node.js and Python. In this talk I'll look at the general best practices and techniques we can use to decrease memory consumption, cold start times for Java Serverless development on AWS including GraalVM (Native Image) and AWS own offering SnapStart based on Firecracker microVM snapshot and restore and CRaC (Coordinated Restore at Checkpoint) runtime hooks. I'll also provide a lot of benchmarking on Lambda functions trying out various deployment package sizes, Lambda memory settings, Java compilation options and HTTP (a)synchronous clients and measure their impact on cold and warm start times.
This talk will cover ScyllaDB Architecture from the cluster-level view and zoom in on data distribution and internal node architecture. In the process, we will learn the secret sauce used to get ScyllaDB's high availability and superior performance. We will also touch on the upcoming changes to ScyllaDB architecture, moving to strongly consistent metadata and tablets.
Session 1 - Intro to Robotic Process Automation.pdfUiPathCommunity
👉 Check out our full 'Africa Series - Automation Student Developers (EN)' page to register for the full program:
https://bit.ly/Automation_Student_Kickstart
In this session, we shall introduce you to the world of automation, the UiPath Platform, and guide you on how to install and setup UiPath Studio on your Windows PC.
📕 Detailed agenda:
What is RPA? Benefits of RPA?
RPA Applications
The UiPath End-to-End Automation Platform
UiPath Studio CE Installation and Setup
💻 Extra training through UiPath Academy:
Introduction to Automation
UiPath Business Automation Platform
Explore automation development with UiPath Studio
👉 Register here for our upcoming Session 2 on June 20: Introduction to UiPath Studio Fundamentals: https://community.uipath.com/events/details/uipath-lagos-presents-session-2-introduction-to-uipath-studio-fundamentals/
What is an RPA CoE? Session 1 – CoE VisionDianaGray10
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Topics covered:
• The role of a steering committee
• How do the organization’s priorities determine CoE Structure?
Speaker:
Chris Bolin, Senior Intelligent Automation Architect Anika Systems
Taking AI to the Next Level in Manufacturing.pdfssuserfac0301
Read Taking AI to the Next Level in Manufacturing to gain insights on AI adoption in the manufacturing industry, such as:
1. How quickly AI is being implemented in manufacturing.
2. Which barriers stand in the way of AI adoption.
3. How data quality and governance form the backbone of AI.
4. Organizational processes and structures that may inhibit effective AI adoption.
6. Ideas and approaches to help build your organization's AI strategy.
Connector Corner: Seamlessly power UiPath Apps, GenAI with prebuilt connectorsDianaGray10
Join us to learn how UiPath Apps can directly and easily interact with prebuilt connectors via Integration Service--including Salesforce, ServiceNow, Open GenAI, and more.
The best part is you can achieve this without building a custom workflow! Say goodbye to the hassle of using separate automations to call APIs. By seamlessly integrating within App Studio, you can now easily streamline your workflow, while gaining direct access to our Connector Catalog of popular applications.
We’ll discuss and demo the benefits of UiPath Apps and connectors including:
Creating a compelling user experience for any software, without the limitations of APIs.
Accelerating the app creation process, saving time and effort
Enjoying high-performance CRUD (create, read, update, delete) operations, for
seamless data management.
Speakers:
Russell Alfeche, Technology Leader, RPA at qBotic and UiPath MVP
Charlie Greenberg, host
Northern Engraving | Nameplate Manufacturing Process - 2024Northern Engraving
Manufacturing custom quality metal nameplates and badges involves several standard operations. Processes include sheet prep, lithography, screening, coating, punch press and inspection. All decoration is completed in the flat sheet with adhesive and tooling operations following. The possibilities for creating unique durable nameplates are endless. How will you create your brand identity? We can help!
Have you ever been confused by the myriad of choices offered by AWS for hosting a website or an API?
Lambda, Elastic Beanstalk, Lightsail, Amplify, S3 (and more!) can each host websites + APIs. But which one should we choose?
Which one is cheapest? Which one is fastest? Which one will scale to meet our needs?
Join me in this session as we dive into each AWS hosting service to determine which one is best for your scenario and explain why!
AppSec PNW: Android and iOS Application Security with MobSFAjin Abraham
Mobile Security Framework - MobSF is a free and open source automated mobile application security testing environment designed to help security engineers, researchers, developers, and penetration testers to identify security vulnerabilities, malicious behaviours and privacy concerns in mobile applications using static and dynamic analysis. It supports all the popular mobile application binaries and source code formats built for Android and iOS devices. In addition to automated security assessment, it also offers an interactive testing environment to build and execute scenario based test/fuzz cases against the application.
This talk covers:
Using MobSF for static analysis of mobile applications.
Interactive dynamic security assessment of Android and iOS applications.
Solving Mobile app CTF challenges.
Reverse engineering and runtime analysis of Mobile malware.
How to shift left and integrate MobSF/mobsfscan SAST and DAST in your build pipeline.
3. Questions What is the international situation – U.S.? Is there an International Genomics Strategy? How is Canada positioned to influence and/or align with this strategy? What can we learn?
4. U.S. Example Discovery Tools 1 – Methodology 2 – Higher density panels Validation -------------------------------------- Demonstration
5. Discovery This period between BFI Canada and now has seen an amazing number of animals genotyped with the 50K panel. Applied to: Bull repositories – focus on traits with data collection infrastructure Animal phenotypes – focus on novel traits
6. Discovery ARS (beef and dairy) US MARC (phenotype and 2000 bulls) Beltsville (dairy bull repository)
7. Discovery NBCEC (field populations) Healthfulness (Iowa State) Feedlot Health (Colorado State) Reproduction and Stayability (Cornell) Industry partner: Pfizer Animal Genetics
8. Discovery University Programs Examples: University of Missouri - Beef bull repository University of Illinois – Genetic defects Texas A and M, UC Davis, Washington State….
9. Discovery USDA Competitive Grants Examples with an NBCEC flavor (all interrelated): Milt Thomas, NMSU – Reproduction Alison Van Eenennaam, UCD – Integrated Dorian Garrick, ISU – Bioinformatics Van Tassell, Taylor and Pollak – Whole Genome Enabled Animal Selection
10. Discovery Industry Major DNA genetic service providers have R&D programs. Projects in collaboration with university researchers and independent projects
11. U.S. Example Discovery Tools 1 – Methodology 2 – Higher density panels Validation Demonstration
12. Tools Methodology The advent of large SNP panels presents a challenge to analysis of data. Software for the implementation of procedure like Bayes “B” (and derivates) is being developed. GenSel – Iowa State University (freeware)
13. Tools Methodology There are many advantages to universal software to include eliminating duplication of effort and having a system that is understood and tested by all.
14. Tools Methodology Integration of information for selection Optimal use of DNA-derived information and EPDs comes from appropriately indexing all sources of information.
15. Tools Blending of results: Indexing the MBVs and traditional genetic predictions.
16. Tools Using genotypes: Either fitting directly or through the genomic relationship matrix Misztal – University of Georgia
17. Tools Fitting MBVs: Using the molecular predictions as correlated information in genetic evaluation Kachman – University of Nebraska (American Angus Association application)
18. U.S. Example Discovery Tools 1 – Methodology 2 – Higher density panels Validation Demonstration
19. Tools Larger panel: Is 50K enough? In all of the discovery efforts, we are leaving a lot of unexplained genetic variation on the table. The proportion of the genetic variation explained by MBVs is typically quite good in the discovery populations but most often disappointing (< 20%) in validation populations. We also are seeing that the MBVs developed in one breed do not work as effectively in other breeds.
20. Tools Larger panel: Is 50K enough? Some Issues: Variation from rare minor alleles. LD issues leading to lack of “portability” of discovery from one breed to another.
21. Tools How will we apply the new “larger panel”? We have exhausted a lot of financial resources using the 50K. Will it be cost effective to consider redoing all animals genotyped with the 50K? I have not seen a strategic plan in academia for the most efficient, cost effective use of the new panel.
22. U.S. Example Discovery Tools 1 – Methodology 2 – Higher density panels Validation Demonstration
23. Validations Process of replicating discovery results in “ independent ” populations. Past validations are examples of joint efforts of the U.S., Australia and Canada.
24. Validations Running out of populations: We don’t have populations with phenotypes for all traits needing validation. We are using populations we do have phenotyped for discovery. We also have problems with populations being disproportionately related to the discovery group.
25. Validation: Step Two We have not developed an in-depth strategy for “assessment” of DNA tools. We are looking across breeds. Not assessing differences across management schemes or environments.
26. ISSUE: Phenotypes From the process of discovery to broader assessment, the major issue is lack of phenotypic information. We simply do not have enough at this time, and efforts towards collaboration in pooling resources are necessary.
27. Is There a U.S. Genomics Strategy? Positive: A large number of projects with a wide range of target traits and approaches. We also have projects in: Developing methodology for delivery. Developing extension materials. In validation.
28. Is There a U.S. Genomics Strategy? Negative: Disjointed. We have not found efficient ways of combining our resources for discovery or for validation. There is a strategy within ARS, within NBCEC, within USDA competitive grants and in the commercialization companies but not necessarily across organizations.
29. Questions Is there a U.S. Genomics Strategy? At the 30,000 foot level,,,,,, = kind of.
30. U.S. Example Discovery Tools 1 – Methodology 2 – Higher density panels Validation Demonstration
31. Demonstration There is still a lot of inertia impeding adoption and there is the need to develop consumer confidence in the process. The EPD lesson: EPDs were eventually accepted as producers gained confidence that the predictions matched what they saw in their records. The Weight Trait Project
36. 2 Collaborators 4 Collaborators 6 Collaborators 7 Collaborators 1 Collaborator North Dakota Iowa South Dakota Nebraska Kansas 1 Collaborator Colorado 21 Ranches Collecting ~ 18,000 DNA samples
37. Demonstration Concept in this project is to force collaboration among the different organizations through the need to deliver the demonstration project.