The document discusses the evolution of genomic resources at the National Center for Biotechnology Information (NCBI) over the past 22 years. It shows graphs of the growth in data volumes for resources like GenBank, users accessing services, and the number of human variations cataloged in dbSNP. Key resources highlighted include PubMed, BLAST, Entrez, GenBank, dbSNP, Reference Sequence (RefSeq), Genome Remapping Service, Sequence Read Archive, and more. The document outlines NCBI's role in organizing and providing access to genomic and biomedical literature data.
The document summarizes the evolution of genome data over time at the National Center for Biotechnology Information (NCBI). It describes how the amount of genome data and number of users has grown exponentially since 1989. It also discusses advances in genome assembly, including representing structural variation and alternate loci. The development of the Genome Reference Consortium to maintain updated genome assemblies deposited in public archives is also covered.
The document characterized DNA methylation in the Pacific oyster (Crassostrea gigas). Results showed DNA methylation is present and predictive analysis aligned with experimental measurements. High-throughput bisulfite sequencing of gill tissue revealed methylation in exons, introns, and intergenic regions. Methylation levels correlated negatively with gene expression. Comparisons between tissues identified differentially methylated regions, with half in gene bodies. Methylation may distinguish housekeeping from inducible genes and have a role in tissue-specific functions.
This document summarizes research characterizing DNA methylation in the Pacific oyster Crassostrea gigas. High-throughput bisulfite sequencing was used to analyze DNA methylation patterns at high resolution. Several genes were found to have different levels and patterns of methylation across tissues and developmental stages. The results provide evidence that DNA methylation plays an important regulatory role and may be involved in environmental responses in C. gigas. Future work will investigate how epigenetic mechanisms are affected by environmental stressors.
Consortium to produce_bio_fuels_from_jatropha[1]ehiosa
This document summarizes a consortium project between institutions in Japan, Indonesia, and Botswana to develop Jatropha plants that can produce clean biofuel through molecular breeding. The goals are to increase Jatropha productivity and develop plants that absorb more carbon dioxide. Participating organizations will work on molecular breeding techniques, field testing in different environments, and evaluating fuel production from higher yielding Jatropha varieties. The end goal is to assist energy needs in Asia and Africa through a sustainable Jatropha biofuel production system.
This document discusses the process of analyzing sequencing data from the NA12878 reference sample. It describes the 3 phases required to turn raw sequencing reads into usable variant calls: 1) NGS data processing, 2) variant discovery and genotyping, and 3) integrative analysis. Phase 1 involves tasks like mapping, local realignment, and duplicate marking to produce analysis-ready reads. Phase 2 identifies SNPs, indels and structural variants. Phase 3 performs quality control and combines results with other data. The document emphasizes the extensive processing needed to produce reliable variant calls from raw sequencing data.
This document discusses the evolution of metagenomics from culturing microorganisms to direct high-throughput sequencing using next-generation sequencing (NGS) technologies. It describes how early metagenomics relied on cloning environmental DNA into libraries for Sanger sequencing, but NGS allows direct sequencing without cloning. NGS produces large volumes of sequence data at low cost, enabling assembly of large DNA fragments and reliable annotation of genes and pathways. The future of metagenomics involves comprehensively cataloging human and environmental microbiomes using NGS and exploiting microbial diversity for biotechnology applications like enzymes, antibiotics, and probiotics.
This document describes a comparative analysis of the human gut microbiota of Koreans using barcoded pyrosequencing. It finds that the Korean gut microbiome has high diversity at the species and strain levels, with over 800 species-level phylotypes identified on average per individual. The analysis identifies 14 core genera that are consistently present across Korean guts, including Bacteroides, Prevotella, Clostridium, and Ruminococcus. The phylum-level diversity of the Korean gut microbiome is similar to other human populations.
The document summarizes the evolution of genome data over time at the National Center for Biotechnology Information (NCBI). It describes how the amount of genome data and number of users has grown exponentially since 1989. It also discusses advances in genome assembly, including representing structural variation and alternate loci. The development of the Genome Reference Consortium to maintain updated genome assemblies deposited in public archives is also covered.
The document characterized DNA methylation in the Pacific oyster (Crassostrea gigas). Results showed DNA methylation is present and predictive analysis aligned with experimental measurements. High-throughput bisulfite sequencing of gill tissue revealed methylation in exons, introns, and intergenic regions. Methylation levels correlated negatively with gene expression. Comparisons between tissues identified differentially methylated regions, with half in gene bodies. Methylation may distinguish housekeeping from inducible genes and have a role in tissue-specific functions.
This document summarizes research characterizing DNA methylation in the Pacific oyster Crassostrea gigas. High-throughput bisulfite sequencing was used to analyze DNA methylation patterns at high resolution. Several genes were found to have different levels and patterns of methylation across tissues and developmental stages. The results provide evidence that DNA methylation plays an important regulatory role and may be involved in environmental responses in C. gigas. Future work will investigate how epigenetic mechanisms are affected by environmental stressors.
Consortium to produce_bio_fuels_from_jatropha[1]ehiosa
This document summarizes a consortium project between institutions in Japan, Indonesia, and Botswana to develop Jatropha plants that can produce clean biofuel through molecular breeding. The goals are to increase Jatropha productivity and develop plants that absorb more carbon dioxide. Participating organizations will work on molecular breeding techniques, field testing in different environments, and evaluating fuel production from higher yielding Jatropha varieties. The end goal is to assist energy needs in Asia and Africa through a sustainable Jatropha biofuel production system.
This document discusses the process of analyzing sequencing data from the NA12878 reference sample. It describes the 3 phases required to turn raw sequencing reads into usable variant calls: 1) NGS data processing, 2) variant discovery and genotyping, and 3) integrative analysis. Phase 1 involves tasks like mapping, local realignment, and duplicate marking to produce analysis-ready reads. Phase 2 identifies SNPs, indels and structural variants. Phase 3 performs quality control and combines results with other data. The document emphasizes the extensive processing needed to produce reliable variant calls from raw sequencing data.
This document discusses the evolution of metagenomics from culturing microorganisms to direct high-throughput sequencing using next-generation sequencing (NGS) technologies. It describes how early metagenomics relied on cloning environmental DNA into libraries for Sanger sequencing, but NGS allows direct sequencing without cloning. NGS produces large volumes of sequence data at low cost, enabling assembly of large DNA fragments and reliable annotation of genes and pathways. The future of metagenomics involves comprehensively cataloging human and environmental microbiomes using NGS and exploiting microbial diversity for biotechnology applications like enzymes, antibiotics, and probiotics.
This document describes a comparative analysis of the human gut microbiota of Koreans using barcoded pyrosequencing. It finds that the Korean gut microbiome has high diversity at the species and strain levels, with over 800 species-level phylotypes identified on average per individual. The analysis identifies 14 core genera that are consistently present across Korean guts, including Bacteroides, Prevotella, Clostridium, and Ruminococcus. The phylum-level diversity of the Korean gut microbiome is similar to other human populations.
Personalis is transitioning to using the GRCh38 human reference genome. This new version includes 3.6 Mb of novel sequence and 153 genes not present in the previous assembly. Analysis of variants is more challenging with the new assembly due to additional paralogous and allelic duplications as well as alternate loci. New computational tools are needed to properly align sequences and call variants in these complex genomic regions.
This document provides an introduction to bioinformatics. It defines bioinformatics as the interdisciplinary field that develops methods for storing, organizing, and analyzing vast amounts of biological data generated by new technologies. It discusses the explosive growth of genomic and protein data. It also describes the roles and skills of bioinformaticians, including knowledge of biology, computer science, and quantitative disciplines. Finally, it outlines where bioinformatics is typically conducted, such as specialized centers and universities, and how it is usually done through online and open source solutions.
The document provides instructions for using MyNCBI and linking publications to grants and awards in order to comply with NIH public access policy requirements. It describes how to create a MyNCBI account and link it to an eRA Commons account. It explains how to add publications to My Bibliography and link them to relevant grants or awards. It also discusses designating a delegate and changing a publication's compliance status. The document provides resources for further information on public access policy and using MyNCBI and My Bibliography.
This document contains slides from a lecture on the evolution of DNA sequencing technologies taught by Jonathan Eisen at UC Davis in winter 2014. The lecture covers the timeline of sequencing technology development from early manual Sanger and Maxam-Gilbert sequencing methods through modern next-generation sequencing platforms. It discusses the key innovations that enabled automation and high-throughput sequencing, such as labeled dideoxynucleotides, capillary electrophoresis, emulsion PCR, and sequencing by synthesis using reversible terminators. The slides illustrate sequencing workflows and compare different sequencing platforms such as 454, Illumina, SOLiD, and Helicos.
FAIR Data, Operations and Model management for Systems Biology and Systems Me...Carole Goble
This document discusses the FAIRDOM consortium's efforts to promote FAIR (Findable, Accessible, Interoperable, Reusable) principles for managing data, operations, and models from systems biology and systems medicine projects. It outlines challenges in asset management for multi-partner, multi-disciplinary projects using multiple formats and repositories. FAIRDOM provides pillars of support including community actions, platforms/tools, and a public project commons to help address these challenges and better enable sharing, reuse, and reproducibility of research assets according to FAIR principles.
The document discusses using NCBI databases to design quantitative PCR (qPCR) assays. It describes several NCBI tools that can be used:
1) The NCBI Nucleotide and Gene databases to obtain sequence information for the gene of interest.
2) NCBI BLAST to perform sequence searches and check primer specificity against relevant databases.
3) NCBI dbSNP to search for single nucleotide polymorphisms (SNPs) in the primer binding sites that could affect assay performance.
The document provides guidance on how to use these NCBI tools at various steps of the qPCR assay design process.
This document provides an introduction to next generation sequencing (NGS) technologies. It begins with an outline of topics to be covered, including the evolution of NGS technologies, their descriptions and comparisons, bioinformatics challenges of NGS data analysis, and some aspects of NGS data analysis workflows and tools. The document then delves into explanations of specific NGS platforms, their performance characteristics, and the sequencing processes. It discusses the large computational infrastructure and data management needs of NGS, as well as quality control, preprocessing of NGS data, and popular analysis tools and workflows.
The document describes the sequencing of the wheat genome, specifically chromosome 3B. Key points:
1. An international effort led by the IWGSC sequenced individual wheat chromosomes including 3B using a physical map-based approach.
2. Sequencing of the 1Gb chromosome 3B generated over 1000 scaffolds covering 995Mb with an N50 of 463kb. Genes and markers were annotated.
3. The sequenced and ordered chromosome 3B provides a foundation for accelerating wheat improvement through map-based cloning, marker development, and integrating genetic and genomic resources.
Stephen Friend Nature Genetics Colloquium 2012-03-24Sage Base
This document proposes using data intensive science to build models of disease within a shared computing environment or "commons". It notes that current disease models often oversimplify complex conditions. Five pilot projects are described that could leverage shared clinical and genomic data as well as model building to better represent diseases: 1) sharing comparator arm data from clinical trials, 2) a federated aging analysis project, 3) portable legal consent, 4) a Sage Congress modeling competition, and 5) the BRIDGE initiative for democratizing medical research. The document argues this approach could accelerate disease understanding and new therapy development.
Stephen Friend Fanconi Anemia Research Fund 2012-01-21Sage Base
This document summarizes Stephen Friend's presentation on using data intensive science and bionetworks to build better maps of human diseases. It discusses how collecting and integrating massive amounts of molecular and clinical data using open information systems and computing could enable the development of more comprehensive and probabilistic causal models of diseases. These evolving disease maps may help identify causal genes and pathways involved in various conditions. The presentation outlines Sage Bionetworks' mission to create a commons for scientists to collaborate on building and refining such integrative bionetworks to accelerate the elimination of human disease.
Presentation of Eugeni Belda (LABGeM-Genoscope) at the Biocuration 2012 conference (Georgetown University, Washington DC): From bacterial genome annotation to metabolic pathway curation
The document summarizes a presentation about developing open access tools to maximize the value of genomic data through the Genome Commons. The Genome Commons Database will be a repository of variants and associated traits. The Genome Commons Navigator will integrate this data and external tools to facilitate basic research, clinical applications, and more. Participation in the Critical Assessment of Genome Interpretation initiative aims to improve predictions of variant impacts on molecular, cellular and organismal phenotypes. Analysis of variants in folate pathway genes found classes of effects on yeast growth and folate remediation.
The document discusses the BioHDF project which aims to develop scalable data infrastructure for bioinformatics using HDF5. It notes that next generation DNA sequencing is producing vast amounts of complex data that is challenging to analyze and compare across samples due to lack of consistent data models and structured storage. The BioHDF project seeks to address this by developing HDF5 domain extensions and tools to organize, index, annotate and access sequencing data in a way that enables more efficient analysis, visualization and exploration of results within and between samples.
The document discusses RNA-seq analysis. It begins with an introduction to Mikael Huss, a bioinformatics scientist, and provides an overview of how genomics, RNA profiles, protein profiles, and interactomics relate within systems biology. The document then discusses how gene expression analysis can provide insights into basic research questions regarding tissue and cell identity, as well as insights into diseases by identifying genes that are over- or under-expressed in patients. Finally, it provides a brief overview of the typical workflow for RNA-seq analysis, which involves mapping RNA sequencing reads to a reference genome or transcriptome.
This document discusses lessons learned from building cancer models and realities around sharing, rewards, and affordability. It notes that oncogenes only make good targets in particular molecular contexts, as seen with the EGFR story. Predicting treatment response to known oncogenes is complex and requires detailed understanding of how different genetic backgrounds function. It also discusses preliminary probabilistic models being used to identify genes causal for disease. Extensive publications now substantiate the scientific approach of using probabilistic causal bionetwork models for diseases like metabolism, cardiovascular disease, and bone diseases. Sage Bionetworks is working to build an information commons for biological functions through collaborative disease maps and data repositories to better relate genetic features of cancer to drug efficacy and
This document provides information about a QIIME workshop. It includes instructions on how to get started with QIIME, an overview of the typical QIIME analysis pipeline from raw sequencing data to results, and details on specific QIIME tools and files like the mapping file, OTU table, and parameters file. The document also discusses moving image analysis of the human microbiome using QIIME.
Scratchpads in the Biodiversity Informatics LandscapeVince Smith
Roberts, D., Harman, K., Rycroft, S.D. & Smith, V.S. Stockholm Biodiversity Informatics Symposium 2008, Swedish Museum of Natural History, Stockholm, Sweden 1-4 December 2008.
The GeneArt® Gene Synthesis service consists of chemical synthesis, cloning, and sequence verification of virtually any desired genetic sequence. You will receive a bacterial stab and/or purified plasmid containing your synthesized gene—ready for downstream applications.
Whether you have limited cloning experience or simply want to save time, the GeneArt® Gene Synthesis service helps you move your ideas from the planning stage to the laboratory more quickly. Benefit from our experience in successfully producing over 180,000 constructs for customers as diverse as large pharmaceutical companies, biotechnology start-ups, and basic research institutions. The comparison shown in the figure below highlights the time and effort saved compared to traditional cloning. For more information visit:
https://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Cloning/gene-synthesis.html?CID=genesynthesis-SS-12312
The National Center for Biotechnology Information (NCBI) was created in 1988 as part of the National Library of Medicine at NIH. It establishes public databases for biological research, develops software tools for sequence analysis, and disseminates biomedical information from its location in Bethesda, MD. NCBI houses several integrated databases including PubMed, GenBank, RefSeq, and UniGene that contain literature, sequences, gene information, and more.
Personalis is transitioning to using the GRCh38 human reference genome. This new version includes 3.6 Mb of novel sequence and 153 genes not present in the previous assembly. Analysis of variants is more challenging with the new assembly due to additional paralogous and allelic duplications as well as alternate loci. New computational tools are needed to properly align sequences and call variants in these complex genomic regions.
This document provides an introduction to bioinformatics. It defines bioinformatics as the interdisciplinary field that develops methods for storing, organizing, and analyzing vast amounts of biological data generated by new technologies. It discusses the explosive growth of genomic and protein data. It also describes the roles and skills of bioinformaticians, including knowledge of biology, computer science, and quantitative disciplines. Finally, it outlines where bioinformatics is typically conducted, such as specialized centers and universities, and how it is usually done through online and open source solutions.
The document provides instructions for using MyNCBI and linking publications to grants and awards in order to comply with NIH public access policy requirements. It describes how to create a MyNCBI account and link it to an eRA Commons account. It explains how to add publications to My Bibliography and link them to relevant grants or awards. It also discusses designating a delegate and changing a publication's compliance status. The document provides resources for further information on public access policy and using MyNCBI and My Bibliography.
This document contains slides from a lecture on the evolution of DNA sequencing technologies taught by Jonathan Eisen at UC Davis in winter 2014. The lecture covers the timeline of sequencing technology development from early manual Sanger and Maxam-Gilbert sequencing methods through modern next-generation sequencing platforms. It discusses the key innovations that enabled automation and high-throughput sequencing, such as labeled dideoxynucleotides, capillary electrophoresis, emulsion PCR, and sequencing by synthesis using reversible terminators. The slides illustrate sequencing workflows and compare different sequencing platforms such as 454, Illumina, SOLiD, and Helicos.
FAIR Data, Operations and Model management for Systems Biology and Systems Me...Carole Goble
This document discusses the FAIRDOM consortium's efforts to promote FAIR (Findable, Accessible, Interoperable, Reusable) principles for managing data, operations, and models from systems biology and systems medicine projects. It outlines challenges in asset management for multi-partner, multi-disciplinary projects using multiple formats and repositories. FAIRDOM provides pillars of support including community actions, platforms/tools, and a public project commons to help address these challenges and better enable sharing, reuse, and reproducibility of research assets according to FAIR principles.
The document discusses using NCBI databases to design quantitative PCR (qPCR) assays. It describes several NCBI tools that can be used:
1) The NCBI Nucleotide and Gene databases to obtain sequence information for the gene of interest.
2) NCBI BLAST to perform sequence searches and check primer specificity against relevant databases.
3) NCBI dbSNP to search for single nucleotide polymorphisms (SNPs) in the primer binding sites that could affect assay performance.
The document provides guidance on how to use these NCBI tools at various steps of the qPCR assay design process.
This document provides an introduction to next generation sequencing (NGS) technologies. It begins with an outline of topics to be covered, including the evolution of NGS technologies, their descriptions and comparisons, bioinformatics challenges of NGS data analysis, and some aspects of NGS data analysis workflows and tools. The document then delves into explanations of specific NGS platforms, their performance characteristics, and the sequencing processes. It discusses the large computational infrastructure and data management needs of NGS, as well as quality control, preprocessing of NGS data, and popular analysis tools and workflows.
The document describes the sequencing of the wheat genome, specifically chromosome 3B. Key points:
1. An international effort led by the IWGSC sequenced individual wheat chromosomes including 3B using a physical map-based approach.
2. Sequencing of the 1Gb chromosome 3B generated over 1000 scaffolds covering 995Mb with an N50 of 463kb. Genes and markers were annotated.
3. The sequenced and ordered chromosome 3B provides a foundation for accelerating wheat improvement through map-based cloning, marker development, and integrating genetic and genomic resources.
Stephen Friend Nature Genetics Colloquium 2012-03-24Sage Base
This document proposes using data intensive science to build models of disease within a shared computing environment or "commons". It notes that current disease models often oversimplify complex conditions. Five pilot projects are described that could leverage shared clinical and genomic data as well as model building to better represent diseases: 1) sharing comparator arm data from clinical trials, 2) a federated aging analysis project, 3) portable legal consent, 4) a Sage Congress modeling competition, and 5) the BRIDGE initiative for democratizing medical research. The document argues this approach could accelerate disease understanding and new therapy development.
Stephen Friend Fanconi Anemia Research Fund 2012-01-21Sage Base
This document summarizes Stephen Friend's presentation on using data intensive science and bionetworks to build better maps of human diseases. It discusses how collecting and integrating massive amounts of molecular and clinical data using open information systems and computing could enable the development of more comprehensive and probabilistic causal models of diseases. These evolving disease maps may help identify causal genes and pathways involved in various conditions. The presentation outlines Sage Bionetworks' mission to create a commons for scientists to collaborate on building and refining such integrative bionetworks to accelerate the elimination of human disease.
Presentation of Eugeni Belda (LABGeM-Genoscope) at the Biocuration 2012 conference (Georgetown University, Washington DC): From bacterial genome annotation to metabolic pathway curation
The document summarizes a presentation about developing open access tools to maximize the value of genomic data through the Genome Commons. The Genome Commons Database will be a repository of variants and associated traits. The Genome Commons Navigator will integrate this data and external tools to facilitate basic research, clinical applications, and more. Participation in the Critical Assessment of Genome Interpretation initiative aims to improve predictions of variant impacts on molecular, cellular and organismal phenotypes. Analysis of variants in folate pathway genes found classes of effects on yeast growth and folate remediation.
The document discusses the BioHDF project which aims to develop scalable data infrastructure for bioinformatics using HDF5. It notes that next generation DNA sequencing is producing vast amounts of complex data that is challenging to analyze and compare across samples due to lack of consistent data models and structured storage. The BioHDF project seeks to address this by developing HDF5 domain extensions and tools to organize, index, annotate and access sequencing data in a way that enables more efficient analysis, visualization and exploration of results within and between samples.
The document discusses RNA-seq analysis. It begins with an introduction to Mikael Huss, a bioinformatics scientist, and provides an overview of how genomics, RNA profiles, protein profiles, and interactomics relate within systems biology. The document then discusses how gene expression analysis can provide insights into basic research questions regarding tissue and cell identity, as well as insights into diseases by identifying genes that are over- or under-expressed in patients. Finally, it provides a brief overview of the typical workflow for RNA-seq analysis, which involves mapping RNA sequencing reads to a reference genome or transcriptome.
This document discusses lessons learned from building cancer models and realities around sharing, rewards, and affordability. It notes that oncogenes only make good targets in particular molecular contexts, as seen with the EGFR story. Predicting treatment response to known oncogenes is complex and requires detailed understanding of how different genetic backgrounds function. It also discusses preliminary probabilistic models being used to identify genes causal for disease. Extensive publications now substantiate the scientific approach of using probabilistic causal bionetwork models for diseases like metabolism, cardiovascular disease, and bone diseases. Sage Bionetworks is working to build an information commons for biological functions through collaborative disease maps and data repositories to better relate genetic features of cancer to drug efficacy and
This document provides information about a QIIME workshop. It includes instructions on how to get started with QIIME, an overview of the typical QIIME analysis pipeline from raw sequencing data to results, and details on specific QIIME tools and files like the mapping file, OTU table, and parameters file. The document also discusses moving image analysis of the human microbiome using QIIME.
Scratchpads in the Biodiversity Informatics LandscapeVince Smith
Roberts, D., Harman, K., Rycroft, S.D. & Smith, V.S. Stockholm Biodiversity Informatics Symposium 2008, Swedish Museum of Natural History, Stockholm, Sweden 1-4 December 2008.
The GeneArt® Gene Synthesis service consists of chemical synthesis, cloning, and sequence verification of virtually any desired genetic sequence. You will receive a bacterial stab and/or purified plasmid containing your synthesized gene—ready for downstream applications.
Whether you have limited cloning experience or simply want to save time, the GeneArt® Gene Synthesis service helps you move your ideas from the planning stage to the laboratory more quickly. Benefit from our experience in successfully producing over 180,000 constructs for customers as diverse as large pharmaceutical companies, biotechnology start-ups, and basic research institutions. The comparison shown in the figure below highlights the time and effort saved compared to traditional cloning. For more information visit:
https://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Cloning/gene-synthesis.html?CID=genesynthesis-SS-12312
The National Center for Biotechnology Information (NCBI) was created in 1988 as part of the National Library of Medicine at NIH. It establishes public databases for biological research, develops software tools for sequence analysis, and disseminates biomedical information from its location in Bethesda, MD. NCBI houses several integrated databases including PubMed, GenBank, RefSeq, and UniGene that contain literature, sequences, gene information, and more.
This document discusses the marriage of translational medicine and big data. It notes that predicting treatment response to known oncogenes like EGFR is complex and requires detailed understanding of genetic backgrounds. Networks can identify genes causal for disease. The approach uses probabilistic causal network models, with over 80 publications validating the scientific approach. Sage Bionetworks is building disease maps and data repositories through collaborations with industry, foundations, government and academia. Fundamentally, biological science hasn't changed due to omics but iterative networked approaches are needed to generate, analyze and support new disease models.
NCBI has developed a powerful suite of online biomedical and bioinformatics resources, including old friends like PubMed and OMIM and newer resources such as Genome. This collection of databases and tools are widely used by scientists and medical professionals across the world. With such a wealth of information, it is easy to get overwhelmed. Join us for an overview to NCBI resources for the information professional with an emphasis on biodata connectivity. No science degree required!
Unison: Enabling easy, rapid, and comprehensive proteomic miningReece Hart
Unison is an online database and data integration platform that aggregates proteomic and genomic data from multiple sources and provides over 200 million precomputed predictions on protein sequences, domains, structures, and more. It aims to enable easy, rapid, and comprehensive proteomic mining through semantic integration of distinct data types and automated querying of predictions. Custom data mining projects using Unison have led to discoveries about proteins like Bcl-2 that regulate apoptosis.
Microarrays allow researchers to examine gene expression patterns across thousands of genes simultaneously. A microarray contains probes for known genes that are used to detect complementary mRNA in a biological sample. Microarrays can be used to study gene expression differences between normal and diseased tissues, classify tumor subtypes, and diagnose cancers. They also show promise for personalized cancer treatment by predicting patient prognosis and response to therapy.
The document discusses ways to improve the diagnostic yield of exome sequencing by addressing limitations in analytical and clinical validity. It notes that standard exomes do not fully cover the exome or reference genomes, and clinical interpretation is limited by incomplete knowledge in the literature and databases. Improving coverage, integrating more information sources, and enhancing data processing could help uncover more diagnostic variants.
This document provides information about variation resources available from the National Center for Biotechnology Information (NCBI). It lists the staff members who work on variation resources and key collaborators. It describes some of the major databases hosted by NCBI that contain genetic variation data, including dbSNP, dbVar, ClinVar and GTR. It also summarizes some of the tools and viewers available for exploring genetic variation data from NCBI.
The document discusses the human reference genome assembly. It provides information on what a reference assembly is, how it is constructed, and how it has evolved over time. Key points include:
- The reference assembly is a model of the human genome built from many sequencing reads and is continually improved.
- Early assemblies had gaps and errors that have been improved on in newer releases. The current primary assembly is GRCh38.
- Alternate loci are now included to represent structural and haplotype variations not in the primary assembly.
- The reference assembly is important for mapping variants and interpreting genomic data.
This document discusses analyzing individual genomes and the human reference genome assembly. It provides an overview of how the reference assembly is constructed from sequencing data and improved over time. Key points discussed include how gaps are filled, alternate loci are represented, and new sequences are added to improve representation of structural and sequence variation.
This document discusses the reference genome assembly and how it is changing. It provides an overview of why the reference assembly matters, how the assembly is constructed and updated, and tools for finding assembly and variation data. Key points include: the assembly is a model that may have gaps; the human reference assembly has been updated several times; alternate loci are used to represent structural variants and haplotypes; and ongoing work involves adding novel sequence and fixing rare incorrect bases or assembly problems.
This document discusses the GeT-RM Project and Browser, which provides a resource for clinical testing laboratories to submit and analyze genomic variant call data. It lists the project team members and participating laboratories. The GeT-RM Browser allows laboratories to analyze variant call concordance and validation data across different sequencing platforms. Looking forward, the project aims to improve analysis tools and the browser interface with features like consensus genotype sets, investigation of discordant regions, and improved gene navigation.
This document discusses improvements to the human reference genome assembly (GRCh38) which will be released in September 2013. It highlights several key areas of focus for the new assembly including adding novel sequence from alternate loci, improving problematic regions through patching, increasing contiguity, and masking regions of high identity to aid read alignment and variant calling. The overall goal is to provide a more complete and accurate representation of the human genome sequence.
This document summarizes the challenges of integrating historical human genetic variation data from analog formats into digital genomic databases. It discusses issues with standardizing phenotypic data, variant call formats from clinical labs, reference assemblies, and defining mutations consistently. Harmonizing these diverse data sources will improve access and interpretation of human genetic variation.
This document discusses the Human Genome Project and summarizes two studies related to human genomes. The first study analyzed genetic variation in human meiotic recombination. The second studied population stratification of a common gene deletion polymorphism. Figures from both published studies are included to illustrate their findings.
The document discusses the human reference genome assembly, noting that it is a composite model that is not static, as new versions are periodically released with changes to sequence and coordinates. It emphasizes that accession versions are important for data management when the reference updates, and that tools are available to help with identifying changes between assemblies. The human reference assembly aims to represent the composite human genome but continues to be improved over time.
This document discusses improving the accuracy of variant identification by evolving the reference assembly. It describes how the reference assembly is updated through patches that add novel sequence, coordinate remapping between versions, and collaboration between groups to centralize assembly data. The goal is to facilitate reporting and fixing problems while building tools and managing data.
This document summarizes work on representing genomes and identifying genetic variants. It discusses challenges in genome assembly due to structural variation between haplotypes and the need for new assembly models that represent multiple haplotypes. It also describes the Genome Reference Consortium's efforts to improve the human reference genome sequence through patching and releasing alternate loci and haplotypes. This includes releasing over 70 patches to fix errors and add novel sequences, with patches being released quarterly.
This document discusses the evolution of genome references at the National Center for Biotechnology Information (NCBI). It describes how genomic data is stored and tracked in GenBank, and how reference assemblies are developed and annotated through collaborations between NCBI, other genome centers, and the research community. The goal is to provide consistent, high-quality reference genomes and annotations across multiple assemblies.
The document summarizes an IMGS 2011 bioinformatics workshop. It discusses next-generation sequencing technologies including Roche 454, Illumina/Solexa, and AB SOLiD. It also covers topics like sequence alignments, file formats, tools for analysis including BWA and TopHat, and visualization. The document provides links to video tutorials and resources on sequencing technologies, alignments, and analyzing RNA-seq data.
This is the talk I gave at the 4th annual Sequencing, Finishing, Analysis in the Future meeting. I tried to record my talk onto the slides based on the recording from the meeting, but it didn't work well. You can view the talk here: http://www.scivee.tv/node/11410 to hook the words up to the slides.
Why You Should Replace Windows 11 with Nitrux Linux 3.5.0 for enhanced perfor...SOFTTECHHUB
The choice of an operating system plays a pivotal role in shaping our computing experience. For decades, Microsoft's Windows has dominated the market, offering a familiar and widely adopted platform for personal and professional use. However, as technological advancements continue to push the boundaries of innovation, alternative operating systems have emerged, challenging the status quo and offering users a fresh perspective on computing.
One such alternative that has garnered significant attention and acclaim is Nitrux Linux 3.5.0, a sleek, powerful, and user-friendly Linux distribution that promises to redefine the way we interact with our devices. With its focus on performance, security, and customization, Nitrux Linux presents a compelling case for those seeking to break free from the constraints of proprietary software and embrace the freedom and flexibility of open-source computing.
Generative AI Deep Dive: Advancing from Proof of Concept to ProductionAggregage
Join Maher Hanafi, VP of Engineering at Betterworks, in this new session where he'll share a practical framework to transform Gen AI prototypes into impactful products! He'll delve into the complexities of data collection and management, model selection and optimization, and ensuring security, scalability, and responsible use.
Building RAG with self-deployed Milvus vector database and Snowpark Container...Zilliz
This talk will give hands-on advice on building RAG applications with an open-source Milvus database deployed as a docker container. We will also introduce the integration of Milvus with Snowpark Container Services.
Observability Concepts EVERY Developer Should Know -- DeveloperWeek Europe.pdfPaige Cruz
Monitoring and observability aren’t traditionally found in software curriculums and many of us cobble this knowledge together from whatever vendor or ecosystem we were first introduced to and whatever is a part of your current company’s observability stack.
While the dev and ops silo continues to crumble….many organizations still relegate monitoring & observability as the purview of ops, infra and SRE teams. This is a mistake - achieving a highly observable system requires collaboration up and down the stack.
I, a former op, would like to extend an invitation to all application developers to join the observability party will share these foundational concepts to build on:
20 Comprehensive Checklist of Designing and Developing a WebsitePixlogix Infotech
Dive into the world of Website Designing and Developing with Pixlogix! Looking to create a stunning online presence? Look no further! Our comprehensive checklist covers everything you need to know to craft a website that stands out. From user-friendly design to seamless functionality, we've got you covered. Don't miss out on this invaluable resource! Check out our checklist now at Pixlogix and start your journey towards a captivating online presence today.
GraphSummit Singapore | The Future of Agility: Supercharging Digital Transfor...Neo4j
Leonard Jayamohan, Partner & Generative AI Lead, Deloitte
This keynote will reveal how Deloitte leverages Neo4j’s graph power for groundbreaking digital twin solutions, achieving a staggering 100x performance boost. Discover the essential role knowledge graphs play in successful generative AI implementations. Plus, get an exclusive look at an innovative Neo4j + Generative AI solution Deloitte is developing in-house.
Sudheer Mechineni, Head of Application Frameworks, Standard Chartered Bank
Discover how Standard Chartered Bank harnessed the power of Neo4j to transform complex data access challenges into a dynamic, scalable graph database solution. This keynote will cover their journey from initial adoption to deploying a fully automated, enterprise-grade causal cluster, highlighting key strategies for modelling organisational changes and ensuring robust disaster recovery. Learn how these innovations have not only enhanced Standard Chartered Bank’s data infrastructure but also positioned them as pioneers in the banking sector’s adoption of graph technology.
Communications Mining Series - Zero to Hero - Session 1DianaGray10
This session provides introduction to UiPath Communication Mining, importance and platform overview. You will acquire a good understand of the phases in Communication Mining as we go over the platform with you. Topics covered:
• Communication Mining Overview
• Why is it important?
• How can it help today’s business and the benefits
• Phases in Communication Mining
• Demo on Platform overview
• Q/A
Cosa hanno in comune un mattoncino Lego e la backdoor XZ?Speck&Tech
ABSTRACT: A prima vista, un mattoncino Lego e la backdoor XZ potrebbero avere in comune il fatto di essere entrambi blocchi di costruzione, o dipendenze di progetti creativi e software. La realtà è che un mattoncino Lego e il caso della backdoor XZ hanno molto di più di tutto ciò in comune.
Partecipate alla presentazione per immergervi in una storia di interoperabilità, standard e formati aperti, per poi discutere del ruolo importante che i contributori hanno in una comunità open source sostenibile.
BIO: Sostenitrice del software libero e dei formati standard e aperti. È stata un membro attivo dei progetti Fedora e openSUSE e ha co-fondato l'Associazione LibreItalia dove è stata coinvolta in diversi eventi, migrazioni e formazione relativi a LibreOffice. In precedenza ha lavorato a migrazioni e corsi di formazione su LibreOffice per diverse amministrazioni pubbliche e privati. Da gennaio 2020 lavora in SUSE come Software Release Engineer per Uyuni e SUSE Manager e quando non segue la sua passione per i computer e per Geeko coltiva la sua curiosità per l'astronomia (da cui deriva il suo nickname deneb_alpha).
A tale of scale & speed: How the US Navy is enabling software delivery from l...sonjaschweigert1
Rapid and secure feature delivery is a goal across every application team and every branch of the DoD. The Navy’s DevSecOps platform, Party Barge, has achieved:
- Reduction in onboarding time from 5 weeks to 1 day
- Improved developer experience and productivity through actionable findings and reduction of false positives
- Maintenance of superior security standards and inherent policy enforcement with Authorization to Operate (ATO)
Development teams can ship efficiently and ensure applications are cyber ready for Navy Authorizing Officials (AOs). In this webinar, Sigma Defense and Anchore will give attendees a look behind the scenes and demo secure pipeline automation and security artifacts that speed up application ATO and time to production.
We will cover:
- How to remove silos in DevSecOps
- How to build efficient development pipeline roles and component templates
- How to deliver security artifacts that matter for ATO’s (SBOMs, vulnerability reports, and policy evidence)
- How to streamline operations with automated policy checks on container images
UiPath Test Automation using UiPath Test Suite series, part 6DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 6. In this session, we will cover Test Automation with generative AI and Open AI.
UiPath Test Automation with generative AI and Open AI webinar offers an in-depth exploration of leveraging cutting-edge technologies for test automation within the UiPath platform. Attendees will delve into the integration of generative AI, a test automation solution, with Open AI advanced natural language processing capabilities.
Throughout the session, participants will discover how this synergy empowers testers to automate repetitive tasks, enhance testing accuracy, and expedite the software testing life cycle. Topics covered include the seamless integration process, practical use cases, and the benefits of harnessing AI-driven automation for UiPath testing initiatives. By attending this webinar, testers, and automation professionals can gain valuable insights into harnessing the power of AI to optimize their test automation workflows within the UiPath ecosystem, ultimately driving efficiency and quality in software development processes.
What will you get from this session?
1. Insights into integrating generative AI.
2. Understanding how this integration enhances test automation within the UiPath platform
3. Practical demonstrations
4. Exploration of real-world use cases illustrating the benefits of AI-driven test automation for UiPath
Topics covered:
What is generative AI
Test Automation with generative AI and Open AI.
UiPath integration with generative AI
Speaker:
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
“An Outlook of the Ongoing and Future Relationship between Blockchain Technologies and Process-aware Information Systems.” Invited talk at the joint workshop on Blockchain for Information Systems (BC4IS) and Blockchain for Trusted Data Sharing (B4TDS), co-located with with the 36th International Conference on Advanced Information Systems Engineering (CAiSE), 3 June 2024, Limassol, Cyprus.
Full-RAG: A modern architecture for hyper-personalizationZilliz
Mike Del Balso, CEO & Co-Founder at Tecton, presents "Full RAG," a novel approach to AI recommendation systems, aiming to push beyond the limitations of traditional models through a deep integration of contextual insights and real-time data, leveraging the Retrieval-Augmented Generation architecture. This talk will outline Full RAG's potential to significantly enhance personalization, address engineering challenges such as data management and model training, and introduce data enrichment with reranking as a key solution. Attendees will gain crucial insights into the importance of hyperpersonalization in AI, the capabilities of Full RAG for advanced personalization, and strategies for managing complex data integrations for deploying cutting-edge AI solutions.
Let's Integrate MuleSoft RPA, COMPOSER, APM with AWS IDP along with Slackshyamraj55
Discover the seamless integration of RPA (Robotic Process Automation), COMPOSER, and APM with AWS IDP enhanced with Slack notifications. Explore how these technologies converge to streamline workflows, optimize performance, and ensure secure access, all while leveraging the power of AWS IDP and real-time communication via Slack notifications.
3. ClinVar
140,000 2,500,000
GTR
Twenty Two Years of Growth: Genome Remapping Service
PubMed Health
CloneDB
120,000
NCBI Data and User Services Public Access
Genome Decoration Page
Influenza Seqs.
GenBank Base Pairs GenSAT 2,000,000
Users (Average) GeneTests
PubChem Peptidome
100,000 Trace Archive BioSystems
CCDS Flu H1N1
Cancer Chromosomes
Environmental Samples
Discovery Initiative 1,500,000
Base Pairs (Millions)
80,000 PubMed Central Entrez Genes Entrez Sensors
Users/Weekday
BLINK Mouse Composite Primer BLAST
MapViewer Genome
GEO Gnomon Seq Read Archive
GeneRIFs UniSTS
WGS
RefSeqGene
60,000 HLA Haplotypes
Human Genome Human Genome-TPA Genome Reference
LinkOut Consortium 1,000,000
dbMHC dbVar
PubMed LocusLink Epigenomics
BookShelf
PSI-BLAST RefSeq MyNCBI
BankIt Human Genome-
VAST dbSNP 1000 Genomes
40,000 Genomes Transcripts Alignments
ePCR Project
Taxonomy Microbial Genomes Genome-Wide
PHI-BLAST Association Studies
3D Structure OMIM CGAP dbGap 500,000
Network Entrez GeneMap Entrez Portal
20,000 Cn3D
WWW
GenBank UniGene
dbSTS
Entrez at NCBI
BLAST dbEST
0 0
1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011
4. NCBI
Tools Literature Data
Blast PubMed GenBank
GBench PubMed Central Protein DB
Splign Bookshelf SRA
Cn3D MeSH GEO
e-PCR Gene Reviews dbSNP
e-Utilities … Gene
… RefSeq
…
5. Entrez: Pathway to Discovery
Term frequency
statistics
MEDLINE
abstracts
Literature Literature citations
citations in in sequence
sequence databases
databases
Nucleotide Protein
sequences sequences
Nucleotide Amino acid sequence
sequence similarity Coding region similarity
features
14. GRC Beginnings
Distributed data
Old Assembly Model
Genome not in INSDC Database
15.
16.
17.
18. Build sequence contigs based on contigs
defined in TPF.
Check for orientation consistencies
Select switch points
Instantiate sequence for further analysis
Switch point
Consensus sequence
23. Distributed data
Centralized Data
Old Assembly Model
Genome not in INSDC Database
24. Large-Scale Variation Complicates Genome Assembly
Sequences from haplotype 1
Sequences from haplotype 2
Old Assembly model: compress into a consensus
New Assembly model: represent both haplotypes
27. UGT2B17 MHC MAPT GRCh37 (hg19)
7 alternate haplotypes
at the MHC
Alternate loci released as:
FASTA
AGP
Alignment to chromosome
http://genomereference.org
28.
29. Assembly (e.g. GRCh37)
PAR Non-nuclear
Primary assembly unit
Assembly (e.g. MT)
ALT ALT ALT
Genomic 1 2 3
Region
(MHC)
Genomic
ALT ALT ALT
Region 4 5 6
(UGT2B17)
Genomic
Region
ALT
ALT
(MAPT) 7
8
ALT
9
31. Oh No! Not a new
version of the human
genome!
http://genomereference.org
32.
33. Assembly (e.g. GRCh37.p5)
PAR Non-nuclear
Primary assembly unit
Assembly (e.g. MT)
ALT ALT ALT
Genomic 1 2 3
Region
(MHC)
Genomic
ALT ALT ALT
Region 4 5 6
(UGT2B17)
Genomic
Region
ALT
ALT
(MAPT) 7
Genomic 8
Region
(ABO)
Genomic ALT
Region 9
(SMA)
Genomic
Region
(PECAM1)
Patches
…
34. TBC1D3C TBC1D3 TBC1D3H
TBC1D3C
Myo19 region (17q21)
35. 60 Fix PATCHES: Chromosome will update in GRCh38
(adds >1 Mb of novel sequence to the assembly)
70 Novel PATCHES: Additional sequence added
(adds >800K of novel sequence to the assembly)
Releasing patches quarterly
36. Distributed data
Centralized Data
Old Assembly Model
Updated Assembly Model
Genome not in INSDC Database
Genome in INSDC Database
Editor's Notes
TPFs are loaded to a centralized system for tracking. This system also manages QA on the files as an ongoing process. The first level of QA is to look at the overlap between adjacent sequences on the TPF.
When certifying an overlap, external evidence supporting the alignment must be available. Evidence typically consists of sequence data from another source, spanning clone ends or experimental verification (such as a PCR assay detecting the join).These certificates are reviewed by other GRC members and may be approved or rejected. Certification information is publicly available.
Alignments refer to pairs of sequence. Once you know how a pair of sequences go together, you can look at stringing the pairs along into a contig. The contig is essentially the consensus sequence that is produced from the components.To create a contig, we use the steps shown on this slide.What are switch points? As you create the consensus sequence of the contig, the switch points tell you where to stop using the sequence from one component and begin using the sequence from the next.