Genomic Futures v2
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Heres a talk on: Human Genomic Variants – Chronic Disease and Cancer Viruses – Zika Bacteria – Food Borne Pathogens Data Transfer and Storage That I am giving in SF later today I think this set is particularly good. Please feel free to repurpose them for any non-malicious purpose.
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Genomic futures v_pitt_kent_osu
This document summarizes Ben Busby's presentation on leveraging commercial and open source bioinformatics tools for clinical and research discoveries from large datasets. The presentation covers analyzing human genomic variants related to chronic disease and cancer, viruses like Zika, and bacteria responsible for foodborne pathogens. It also discusses data transfer, storage, popular metagenomics tools, genome analysis using graphs, and matching expressed variants in memory. The document lists Busby's contact information and links to slides and provides information on NCBI training workshops on bioinformatics.
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This document summarizes genomic variation and individual genome sequencing. It discusses the rising number of subjects with genome sequences available, from 14,201 in 2007 to over 1 million in 2015. It also provides information about genomic analysis tools from NCBI including the SAM format, genome browsers, E-Utilities, Entrez Direct, and upcoming APIs. Finally, it advertises upcoming hackathons in January and March for developing tools and apps to work with NCBI genomic data and APIs.
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The document discusses data integration and sharing principles for genomics data. It describes metadata search, using non-SQL databases, integrating data sources, using non-ambiguous identifiers, transferring small amounts of validated data, and making data accessible to domain experts. Metrics for data uploads and downloads are proposed. User review post-publication and linking data to outside resources are also discussed. Future directions include more integration into discovery frameworks, command line APIs, moving from FTP to on-demand APIs, and hackathons to generate apps that work with genomic data structures and metadata.
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The document discusses the National Center for Biotechnology Information (NCBI) and the services and databases it provides. NCBI develops and maintains molecular databases and software tools for searching and analyzing data. It provides a web portal for accessing these data and tools. The databases include those related to biomedical literature, sequences, gene expression, genome maps, structures, pathways and genetic variation. NCBI databases include primary data directly submitted as well as curated data maintained by NCBI. Key databases discussed are GenBank, PubMed, dbSNP, Protein Data Bank and Gene. NCBI provides integrated access to these resources through Entrez and tools for analysis like BLAST, Cn3D and Genome Workbench.
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The document discusses the history and evolution of the tire industry from its origins to modern technological advancements. It covers the development of major tire brands like MRF, Bridgestone, Michelin and Goodyear over time. The document also examines emerging transportation technologies like electric vehicles, flying cars and autonomous vehicles and how they will impact the future of tires. The Indian tire industry is discussed in the context of its growth since economic liberalization in the 1990s.
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The document discusses the tyre manufacturing industry in India using Porter's Five Forces model. It notes that the industry faces high competition, cost pressures, and increasing raw material costs despite growing demand. The top 5 companies control over 80% of production. Bargaining power of suppliers is high due to few suppliers and lack of substitutes, while buyers have moderate-to-high power. Potential entrants face very high barriers to entry due to the capital intensive nature and risks. Threat of substitutes is currently low but increasing.
Recommended
Genomic futures v_pitt_kent_osu
This document summarizes Ben Busby's presentation on leveraging commercial and open source bioinformatics tools for clinical and research discoveries from large datasets. The presentation covers analyzing human genomic variants related to chronic disease and cancer, viruses like Zika, and bacteria responsible for foodborne pathogens. It also discusses data transfer, storage, popular metagenomics tools, genome analysis using graphs, and matching expressed variants in memory. The document lists Busby's contact information and links to slides and provides information on NCBI training workshops on bioinformatics.
Umcp cs talk_11_3_16_v1
This document summarizes genomic variation and individual genome sequencing. It discusses the rising number of subjects with genome sequences available, from 14,201 in 2007 to over 1 million in 2015. It also provides information about genomic analysis tools from NCBI including the SAM format, genome browsers, E-Utilities, Entrez Direct, and upcoming APIs. Finally, it advertises upcoming hackathons in January and March for developing tools and apps to work with NCBI genomic data and APIs.
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The document discusses data integration and sharing principles for genomics data. It describes metadata search, using non-SQL databases, integrating data sources, using non-ambiguous identifiers, transferring small amounts of validated data, and making data accessible to domain experts. Metrics for data uploads and downloads are proposed. User review post-publication and linking data to outside resources are also discussed. Future directions include more integration into discovery frameworks, command line APIs, moving from FTP to on-demand APIs, and hackathons to generate apps that work with genomic data structures and metadata.
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The document discusses the National Center for Biotechnology Information (NCBI) and the services and databases it provides. NCBI develops and maintains molecular databases and software tools for searching and analyzing data. It provides a web portal for accessing these data and tools. The databases include those related to biomedical literature, sequences, gene expression, genome maps, structures, pathways and genetic variation. NCBI databases include primary data directly submitted as well as curated data maintained by NCBI. Key databases discussed are GenBank, PubMed, dbSNP, Protein Data Bank and Gene. NCBI provides integrated access to these resources through Entrez and tools for analysis like BLAST, Cn3D and Genome Workbench.
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The document discusses the history and evolution of the tire industry from its origins to modern technological advancements. It covers the development of major tire brands like MRF, Bridgestone, Michelin and Goodyear over time. The document also examines emerging transportation technologies like electric vehicles, flying cars and autonomous vehicles and how they will impact the future of tires. The Indian tire industry is discussed in the context of its growth since economic liberalization in the 1990s.
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The document discusses the tyre manufacturing industry in India using Porter's Five Forces model. It notes that the industry faces high competition, cost pressures, and increasing raw material costs despite growing demand. The top 5 companies control over 80% of production. Bargaining power of suppliers is high due to few suppliers and lack of substitutes, while buyers have moderate-to-high power. Potential entrants face very high barriers to entry due to the capital intensive nature and risks. Threat of substitutes is currently low but increasing.
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- Raw materials like natural rubber, butyl rubber, and nylon account for 63% of industry costs. India imports some raw materials due to insufficient domestic production.
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- Leading tyre manufacturers include MRF,
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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.
CCDI Kibbe Big Data Training May 2022
Purdue Big Data Training for Cancer Research. Overview of the NCI Childhood Cancer Data Initiative (CCDI) and resources available from the CCDI.
Biobanking: The Australian Experience
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.
Similar to Genomic Futures v2 (20)
Functional Analysis & Screening Technologies Congress
Functional Analysis & Screening Technologies Congress
Precision Medicine in the Age of NCI MATCH and the Beau Biden Cancer Moonshot
Precision Medicine in the Age of NCI MATCH and the Beau Biden Cancer Moonshot
The australian experience issues and solutions-Dr.Daniel Catchpoole
The australian experience issues and solutions-Dr.Daniel Catchpoole
More from Ben Busby
Addressing privacy concerns_in_the_age_of_federated_data_access
A talk presented at NIH-STRIDES on the Future of Biomedical Knowledge Extraction, Data Security, and Data Structures
Containerized attribute indexing and graph genomes for federated data access
This document discusses federating genomic sequencing data across cloud platforms for discovery. It presents four topic areas as examples: 1) virus characterization and discovery through building an index of viral signatures, 2) generating systems to analyze genome graphs to compare individuals to communities, 3) annotating haplotypes and graphs to query complex disease, and 4) indexing data flexibly for federated discovery anywhere through APIs. It emphasizes that metadata is needed to contextualize data and maximize its utility for answering biological questions.
Artificial_Intelligence_for_Data_Reuse_2019
Talk given at this conference covering prototypes involving ML, as well as data indexing hackathons capturing community consensus and where we are going with this.
Dream.recomb.ncbi.hackathons v003
Ben Busby is the founder of the Department of Bioinformatics and Data Science at the National Institutes of Health. He discusses hosting numerous data hackathons in 2019 focused on topics like RNA sequencing, human pan-genomics, variant datasets, computational medicine, prokaryotic virulence factors, single cell genomics, and structural variants. The hackathons bring researchers together to collaborate on bioinformatics tools and resources. Busby emphasizes the importance of open communication and creating a community to advance genomic and biomedical research.
Human_Pangenomics_Bio-IT_2019
Description of a large, international human pangenomics hackathon at UCSC in March 2019. Graphs, Mapping,
RNAML_Bio-IT_2019
Ben Busby is the founder of the Department of Bioinformatics and Data Science at NIH. He discusses several hackathon projects focused on analyzing RNAseq data and developing machine learning applications for genomics. These include tools for polygenic SNP search, genomic robots, and phenogenomics. Upcoming hackathons are planned on topics like RNAseq, human pan-genomics, variant datasets, and virus discovery. The goal is to create an open community around bioinformatics and data science.
Hackathon_Bio-IT_2019
Ben Busby is the founder of the Department of Bioinformatics and Data Science at NIH. He discusses several bioinformatics tools and resources developed during NIH hackathons, including tools for polygenic SNP search, RNAseq analysis, and virus discovery. Upcoming hackathon events focus on RNAseq, human pan-genomics, variant datasets, and more. The goal is to create an open bioinformatics community.
Data science futures_v_vu2
Talking about computational medicine, genomics and other fun biomedical datasciency stuff at Vanderbilt!
Sage 2 19_v5_busby
This document contains information about various bioinformatics tools and resources developed by Ben Busby at NCBI, including links to BLAST cloud software, Docker images, and GitHub repositories. It also lists upcoming hackathons focused on data analysis and encourages participation in the bioinformatics community through communication on LinkedIn and contributing to existing events.
Bb health ai_jan26_v2
This document discusses NCBI health resources and hackathons. It provides information about new BLAST features like CloudBLAST and Docker images. It also discusses using BLAST Docker images and magicBLAST. The document describes how to find data when metadata is insufficient by using the taxonomically indexed SRA. It lists several hackathon projects related to virus discovery, gene expression aging, and variant calling. It promotes creating a bioinformatics community and announces upcoming data analysis hackathons.
BB_NCBI_PAG_2019_Workshop
This document summarizes new features in NCBI BLAST that allow for more targeted searches based on taxonomy. It provides examples of using BLAST to search for Argonaute proteins in S. pombe, Ascomycota fungi, and excluding Viridiplantae. Execution times for each search are included. The document also demonstrates using BLAST docker images to search for Shiga toxin proteins in E. coli without needing the entire nr database locally. It concludes by advertising upcoming NCBI hackathons.
Hackathons lightning v_nbs
Groups of prototype software that we have built in Biological Data Science Hackathons which were essentially free to run!
Cmu oss 18
Slides for CMU open science symposium. Outlining tools that can be used to index and extract open data easily and quickly!
Genome web v_repro1
This document appears to be a slide deck presentation given by Ben Busby on making the transition from sharing data to sharing knowledge. Some of the key points covered in the presentation include EUtilities command line and EDirect tools for accessing NCBI resources, PubMed and PMC open FTP, tools like Pubrunner.org as an alternative to PubMed FTP, examples of bioinformatics resources and tools developed through NCBI hackathons posted on GitHub, and an opportunity to work at NCBI for 4-6 weeks through their bioinformatics training program.
Data science futures_v_une
A vast compendium of bioinformatics techniques and prototypes presented to Bioinformaticians at the University of New England
Variant and disease_grs_kickoff
This document discusses making the transition from simply sharing genomic data to sharing knowledge and insights gained from the data. It provides information on various tools from NCBI for searching, accessing, and analyzing genomic data including EUtils, EDirect, magicblast, and genomic analysis tools on GitHub. It also encourages creating an open community around sharing knowledge gained from genomic data analysis.
Ncbi resources i5_k_v4
The document appears to be from a presentation given by Ben Busby on making the transition from sharing data to sharing knowledge. It discusses various tools and resources for accessing genomic data from the National Center for Biotechnology Information including EUtils, EDirect, PubMed FTP, and more. The presentation also highlights several genomic analysis tools and hackathon projects developed by the NCBI community.
Ncbi resources abrf_v3
This document summarizes Ben Busby's presentation on making the transition from sharing data to sharing knowledge at NCBI. The presentation discusses NCBI tools and resources like EUtils, EDirect, PubMed FTP, and SRA. It also highlights several genomic analysis tools developed through NCBI hackathons and available on GitHub. The document lists Busby's contact information and encourages attendees to check his SlideShare profile and NCBI's bioinformatics training program for more details.
Data science futures_v_lbirn
The next generation of large dataset analysis, with examples from NCBI, plus tools made in hackathons, and community resources for bioinformatics!
Pag three ways_to_ngs_at_ncbi
This document discusses three simple ways to analyze next generation sequencing (NGS) data at the National Center for Biotechnology Information (NCBI). It introduces magicBLAST, which can be used to align NGS reads to a reference genome or transcriptome. It also discusses using the SRA Toolkit to extract reads from the Sequence Read Archive (SRA) and view analysis results. The document encourages attendees to check the slideshare presentation for more details on these NGS analysis methods.
More from Ben Busby (20)
Addressing privacy concerns_in_the_age_of_federated_data_access
Addressing privacy concerns_in_the_age_of_federated_data_access
Containerized attribute indexing and graph genomes for federated data access
Containerized attribute indexing and graph genomes for federated data access
Recently uploaded
Randomised Optimisation Algorithms in DAPHNE
Slides from talk:
Aleš Zamuda: Randomised Optimisation Algorithms in DAPHNE .
Austrian-Slovenian HPC Meeting 2024 – ASHPC24, Seeblickhotel Grundlsee in Austria, 10–13 June 2024
https://ashpc.eu/
The debris of the ‘last major merger’ is dynamically young
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
‘last major merger.’ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1–2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the ‘last major merger’
did not collide with the MW proto-disc at early times, as is thought for the GSE, but instead collided with the MW disc within
the last few Gyr, consistent with the body of work surrounding the VRM.
Thornton ESPP slides UK WW Network 4_6_24.pdf
ESPP presentation to EU Waste Water Network, 4th June 2024 “EU policies driving nutrient removal and recycling
and the revised UWWTD (Urban Waste Water Treatment Directive)”
Immersive Learning That Works: Research Grounding and Paths Forward
We will metaverse into the essence of immersive learning, into its three dimensions and conceptual models. This approach encompasses elements from teaching methodologies to social involvement, through organizational concerns and technologies. Challenging the perception of learning as knowledge transfer, we introduce a 'Uses, Practices & Strategies' model operationalized by the 'Immersive Learning Brain' and ‘Immersion Cube’ frameworks. This approach offers a comprehensive guide through the intricacies of immersive educational experiences and spotlighting research frontiers, along the immersion dimensions of system, narrative, and agency. Our discourse extends to stakeholders beyond the academic sphere, addressing the interests of technologists, instructional designers, and policymakers. We span various contexts, from formal education to organizational transformation to the new horizon of an AI-pervasive society. This keynote aims to unite the iLRN community in a collaborative journey towards a future where immersive learning research and practice coalesce, paving the way for innovative educational research and practice landscapes.
Shallowest Oil Discovery of Turkiye.pptx
The Petroleum System of the Çukurova Field - the Shallowest Oil Discovery of Türkiye, Adana
ESA/ACT Science Coffee: Diego Blas - Gravitational wave detection with orbita...
ESA/ACT Science Coffee: Diego Blas - Gravitational wave detection with orbita...Advanced-Concepts-Team
Presentation in the Science Coffee of the Advanced Concepts Team of the European Space Agency on the 07.06.2024.
Speaker: Diego Blas (IFAE/ICREA)
Title: Gravitational wave detection with orbital motion of Moon and artificial
Abstract:
In this talk I will describe some recent ideas to find gravitational waves from supermassive black holes or of primordial origin by studying their secular effect on the orbital motion of the Moon or satellites that are laser ranged.SAR of Medicinal Chemistry 1st by dk.pdf
In this presentation include the prototype drug SAR on thus or with their examples .
Syllabus of Second Year B. Pharmacy
2019 PATTERN.
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
The cost of acquiring information by natural selection
This is a short talk that I gave at the Banff International Research Station workshop on Modeling and Theory in Population Biology. The idea is to try to understand how the burden of natural selection relates to the amount of information that selection puts into the genome.
It's based on the first part of this research paper:
The cost of information acquisition by natural selection
Ryan Seamus McGee, Olivia Kosterlitz, Artem Kaznatcheev, Benjamin Kerr, Carl T. Bergstrom
bioRxiv 2022.07.02.498577; doi: https://doi.org/10.1101/2022.07.02.498577
Micronuclei test.M.sc.zoology.fisheries.
Current Ms word generated power point presentation covers major details about the micronuclei test. It's significance and assays to conduct it. It is used to detect the micronuclei formation inside the cells of nearly every multicellular organism. It's formation takes place during chromosomal sepration at metaphase.
The binding of cosmological structures by massless topological defects
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
mitigated, at least in part.
8.Isolation of pure cultures and preservation of cultures.pdf
Isolation of pure culture, its various method.
Direct Seeded Rice - Climate Smart Agriculture
Direct Seeded Rice - Climate Smart AgricultureInternational Food Policy Research Institute- South Asia Office
PPT on Direct Seeded Rice presented at the three-day 'Training and Validation Workshop on Modules of Climate Smart Agriculture (CSA) Technologies in South Asia' workshop on April 22, 2024.
20240520 Planning a Circuit Simulator in JavaScript.pptx
Evaporation step counter work. I have done a physical experiment.
(Work in progress.)
Authoring a personal GPT for your research and practice: How we created the Q...
Thematic analysis in qualitative research is a time-consuming and systematic task, typically done using teams. Team members must ground their activities on common understandings of the major concepts underlying the thematic analysis, and define criteria for its development. However, conceptual misunderstandings, equivocations, and lack of adherence to criteria are challenges to the quality and speed of this process. Given the distributed and uncertain nature of this process, we wondered if the tasks in thematic analysis could be supported by readily available artificial intelligence chatbots. Our early efforts point to potential benefits: not just saving time in the coding process but better adherence to criteria and grounding, by increasing triangulation between humans and artificial intelligence. This tutorial will provide a description and demonstration of the process we followed, as two academic researchers, to develop a custom ChatGPT to assist with qualitative coding in the thematic data analysis process of immersive learning accounts in a survey of the academic literature: QUAL-E Immersive Learning Thematic Analysis Helper. In the hands-on time, participants will try out QUAL-E and develop their ideas for their own qualitative coding ChatGPT. Participants that have the paid ChatGPT Plus subscription can create a draft of their assistants. The organizers will provide course materials and slide deck that participants will be able to utilize to continue development of their custom GPT. The paid subscription to ChatGPT Plus is not required to participate in this workshop, just for trying out personal GPTs during it.
ESR spectroscopy in liquid food and beverages.pptx
With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...
Current descriptions of immersive learning cases are often difficult or impossible to compare. This is due to a myriad of different options on what details to include, which aspects are relevant, and on the descriptive approaches employed. Also, these aspects often combine very specific details with more general guidelines or indicate intents and rationales without clarifying their implementation. In this paper we provide a method to describe immersive learning cases that is structured to enable comparisons, yet flexible enough to allow researchers and practitioners to decide which aspects to include. This method leverages a taxonomy that classifies educational aspects at three levels (uses, practices, and strategies) and then utilizes two frameworks, the Immersive Learning Brain and the Immersion Cube, to enable a structured description and interpretation of immersive learning cases. The method is then demonstrated on a published immersive learning case on training for wind turbine maintenance using virtual reality. Applying the method results in a structured artifact, the Immersive Learning Case Sheet, that tags the case with its proximal uses, practices, and strategies, and refines the free text case description to ensure that matching details are included. This contribution is thus a case description method in support of future comparative research of immersive learning cases. We then discuss how the resulting description and interpretation can be leveraged to change immersion learning cases, by enriching them (considering low-effort changes or additions) or innovating (exploring more challenging avenues of transformation). The method holds significant promise to support better-grounded research in immersive learning.
Recently uploaded (20)
The debris of the ‘last major merger’ is dynamically young
The debris of the ‘last major merger’ is dynamically young
Immersive Learning That Works: Research Grounding and Paths Forward
Immersive Learning That Works: Research Grounding and Paths Forward
ESA/ACT Science Coffee: Diego Blas - Gravitational wave detection with orbita...
ESA/ACT Science Coffee: Diego Blas - Gravitational wave detection with orbita...
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
The cost of acquiring information by natural selection
The cost of acquiring information by natural selection
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
The binding of cosmological structures by massless topological defects
The binding of cosmological structures by massless topological defects
8.Isolation of pure cultures and preservation of cultures.pdf
8.Isolation of pure cultures and preservation of cultures.pdf
20240520 Planning a Circuit Simulator in JavaScript.pptx
20240520 Planning a Circuit Simulator in JavaScript.pptx
Authoring a personal GPT for your research and practice: How we created the Q...
Authoring a personal GPT for your research and practice: How we created the Q...
ESR spectroscopy in liquid food and beverages.pptx
ESR spectroscopy in liquid food and beverages.pptx
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...
Genomic Futures v2
- 1. Ben Busby, Ph.D. Lead, Bioinformatics Training, NCBI Chair, Department of Bioinformatics and Data Science, FAES ben.busby@nih.gov Efficiently Leveraging Commercial and Open Source Bioinformatics Tools for Clinical Interventions and Research Discoveries from Very Large Datasets
- 2. Please note that all views are my own and not necessarily those of any Federal agency. No mention of any commercial or non- profit entity should be considered an endorsement. • Human Genomic Variants – Chronic Disease and Cancer • Viruses – Zika • Bacteria – Food Borne Pathogens • Data Transfer and Storage
- 5. © Martine Zilversmit 2013
- 6. http://1.usa.gov/1J1xmYs NCBI NGS Online Workshop – Available on the NCBI YouTube Channel!
- 9. 14,201 53,216 139,311 374,464 485,727 566,181 660,665 876,849 1,002,935 2007 2008 2009 2010 2011 2012 2013 2014 2015 Subjects
- 22. Combined score is the average of SVs, mappability, GC.. NCBI region list Encode blacklist
- 23. Genome in a Bottle
- 24. Combined score is the average of SVs, mappability, GC.. NCBI region list Encode blacklist
- 26. Matching Expressed Variants in-memory; Analyzing with Graphs https://f1000research.com/articles/5-674/v1
- 28. Variants are Often Pleiotropic
- 31. Carpentries, MOOCs, Semi-Traditional Coursework and Mentoring
- 32. NCBI Webinars
- 41. • Escherichia and Shigella • Campylobacter • Acinetobacter • Salmonella • Klebsiella • Listeria
- 44. 44 • Qiime • Mothur • Nepthele • MetAMOS • MetaViz • mash Popular Metagenomics Tools!
- 45. Another example – Cas9
- 48. • March 20-22, NIH Campus • May 22-24, UC BioFrontiers Institute Boulder CO • June 19-21, NYGC • August 17-19, NIH Campus • September 25-27, Pittsburgh, PA • October 11-13, Microbial and Metagenomics, NCBI (with ASM and CDC)
- 49. Come work at NCBI for 4-6 weeks! Email bioinformatics-training@ncbi.nlm.nih.gov for more information!
- 50. My View of Data Transfer Principles • Metadata Search • Rapid NoSQL (for now) • Integration • Non-ambiguous identifiers • Transferring Small amounts of Data • Data still gets transferred in the cloud • Underlying structure • Finding specific data from validated formats • Democratization of Data • Rapid comparison by domain experts • Reporting • Metrics to report data upload and [unique IP] download of datasets • Post-publication User Review
- 52. 52 EDirect (Search API) Cookbook
- 53. 53 New APIs!
Editor's Notes
- Now… with AMR data!
- Now… with AMR data!
- Now… with AMR data!
- Now… with AMR data!
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- Now… with AMR data!
- Now… with AMR data!
- Now… with AMR data!
- Now… with AMR data!
- Now… with AMR data!
- Now… with AMR data!
- Now… with AMR data!
- Now… with AMR data!
- Now… with AMR data!
- Show suggestive search..
- Now… with AMR data!
- Now… with AMR data!