The document describes an ensemble approach for detecting somatic mutations in impure cancer samples. It details the benchmark data set used from TCGA, which includes BAM files for a tumor sample that is 50% tumor cells and 50% normal cells mixed. It then outlines several commonly used somatic mutation callers - SomaticSniper, VarScan2, MuTect - and applies them to the data set. The results from the different callers are then combined using various filtering and consensus approaches to generate a high confidence list of somatic mutations for validation.
This document provides an overview of analyzing RNA-Seq data using the Tuxedo protocol in Galaxy. It describes experimental design considerations, quality control of sequencing data using FastQC, mapping reads to a reference genome using Tophat, determining differential expression with Cuffdiff, and visualizing results using IGV and CummeRbund. The tutorial walks through an example analysis on Drosophila melanogaster RNA-Seq data, covering topics such as setting file formats, running alignment and expression tools, extracting workflows, and useful Galaxy resources.
Big data solution for ngs data analysisYun Lung Li
This document outlines a presentation on big data solutions for NGS data analysis using software containerization and distributed analytics. It discusses Docker containerization and its use at Atgenomix to simplify cluster environments. It also covers NGS genome analysis techniques like read mapping, variant calling, and using Spark and Hadoop for data parallelization. Elasticsearch is introduced for distributed, RESTful search and analytics of variant data.
SeqsLab: a high performance genomics data analysis platform based on Apache S...Yun Lung Li
On the way to precision medicine, personal genomics is an essential topic since the genome holds the most fundamental information of individual. NGS is a comprehensive way to explore human genome, but with the intimidating amount of data and computation effort. Atgenomix SeqsLab is a high performance genomics data analysis platform aiming to close the Bio-IT gap.
NGS Targeted Enrichment Technology in Cancer Research: NGS Tech Overview Webi...QIAGEN
This slidedeck discusses the most biologically efficient, cost-effective method for successful NGS. The GeneRead DNA QuantiMIZE Kits enable determination of the optimum conditions for targeted enrichment of DNA isolated from biological samples, while the GeneRead DNAseq Panels V2 allow you to quickly and reliably deep sequence your genes of interest. Applications in translational and clinical research are highlighted.
Use of CRISPR-Cas9 has revolutionized targeted genome editing. However, rapid design of high-quality guide RNA (gRNA) sequences with high on-target and low off-target editing remains challenging. We implemented a machine learning algorithm to design high-quality gRNA sequences in 5 commonly used species (human, mouse, rat, zebrafish, and nematode). Our tool also designs gRNA sequences against custom targets, and can check existing gRNA designs for quality. In this webinar, we review our data illustrating this tool's performance and demonstrate its use in predicting and designing improved gRNAs for genome editing.
This document describes PrimeTime® qPCR products for gene expression analysis, including probe- and primer-based assays for human, mouse, and rat sequences as well as custom assays. It provides details on master mixes, probes, controls, and an assay design and ordering process to ensure specific and efficient assays. The assays are guaranteed to have high efficiency and sensitivity for accurate quantification of gene expression.
This document provides an introduction and overview of common methods for processing and analyzing next generation sequencing (NGS) data, including mapping NGS reads and de novo assembly of NGS reads. It discusses various NGS applications such as RNA-Seq, epigenetics, structural variation detection, and metagenomics. Key steps in read alignment such as choosing an alignment program and viewing alignments are outlined. Considerations for choosing an alignment program based on library type, read type, and platform are also reviewed. Popular alignment programs including Bowtie, BWA, TopHat, and Novoalign are mentioned.
This document provides an overview of analyzing RNA-Seq data using the Tuxedo protocol in Galaxy. It describes experimental design considerations, quality control of sequencing data using FastQC, mapping reads to a reference genome using Tophat, determining differential expression with Cuffdiff, and visualizing results using IGV and CummeRbund. The tutorial walks through an example analysis on Drosophila melanogaster RNA-Seq data, covering topics such as setting file formats, running alignment and expression tools, extracting workflows, and useful Galaxy resources.
Big data solution for ngs data analysisYun Lung Li
This document outlines a presentation on big data solutions for NGS data analysis using software containerization and distributed analytics. It discusses Docker containerization and its use at Atgenomix to simplify cluster environments. It also covers NGS genome analysis techniques like read mapping, variant calling, and using Spark and Hadoop for data parallelization. Elasticsearch is introduced for distributed, RESTful search and analytics of variant data.
SeqsLab: a high performance genomics data analysis platform based on Apache S...Yun Lung Li
On the way to precision medicine, personal genomics is an essential topic since the genome holds the most fundamental information of individual. NGS is a comprehensive way to explore human genome, but with the intimidating amount of data and computation effort. Atgenomix SeqsLab is a high performance genomics data analysis platform aiming to close the Bio-IT gap.
NGS Targeted Enrichment Technology in Cancer Research: NGS Tech Overview Webi...QIAGEN
This slidedeck discusses the most biologically efficient, cost-effective method for successful NGS. The GeneRead DNA QuantiMIZE Kits enable determination of the optimum conditions for targeted enrichment of DNA isolated from biological samples, while the GeneRead DNAseq Panels V2 allow you to quickly and reliably deep sequence your genes of interest. Applications in translational and clinical research are highlighted.
Use of CRISPR-Cas9 has revolutionized targeted genome editing. However, rapid design of high-quality guide RNA (gRNA) sequences with high on-target and low off-target editing remains challenging. We implemented a machine learning algorithm to design high-quality gRNA sequences in 5 commonly used species (human, mouse, rat, zebrafish, and nematode). Our tool also designs gRNA sequences against custom targets, and can check existing gRNA designs for quality. In this webinar, we review our data illustrating this tool's performance and demonstrate its use in predicting and designing improved gRNAs for genome editing.
This document describes PrimeTime® qPCR products for gene expression analysis, including probe- and primer-based assays for human, mouse, and rat sequences as well as custom assays. It provides details on master mixes, probes, controls, and an assay design and ordering process to ensure specific and efficient assays. The assays are guaranteed to have high efficiency and sensitivity for accurate quantification of gene expression.
This document provides an introduction and overview of common methods for processing and analyzing next generation sequencing (NGS) data, including mapping NGS reads and de novo assembly of NGS reads. It discusses various NGS applications such as RNA-Seq, epigenetics, structural variation detection, and metagenomics. Key steps in read alignment such as choosing an alignment program and viewing alignments are outlined. Considerations for choosing an alignment program based on library type, read type, and platform are also reviewed. Popular alignment programs including Bowtie, BWA, TopHat, and Novoalign are mentioned.
This document discusses relating new genome assemblies to the human reference genome GRCh38. It provides an overview of changes in reference sources, evaluating new sequences, and the future of assembly curation. GRCh38 contains 178 regions with alternative loci comprising 2% of the sequence from multiple whole genome sequencing projects. The Assemblathon project evaluated assemblies of the CHM13 hydatidiform mole genome to assess data quality, aligners, and identify improvements for the reference. Future work will integrate additional platinum genomes and develop local reassembly and graph-based references.
1. The PacBio assembly of the CHM1 genome had an N50 contig length of 4.5 MB and potentially fills gaps in the GRCh38 reference genome.
2. Multiple assemblies of the CHM1 genome were generated using different techniques and are being evaluated based on contiguity, annotation, and concordance with other data to select the best assembly.
3. The goal is to generate a high-quality "Platinum Genome" for CHM1 by improving the best assembly with additional data sources like BAC clones and using it as a new reference genome. A second individual, CHM13, is also being assembled to increase genome diversity.
This document discusses the bioinformatics analysis of ChIP-seq data. It begins with an overview of ChIP-seq experiments and the major steps in processing and analyzing the sequencing data, including quality control, alignment, peak calling, and downstream analyses. Pipelines for automated analysis are described, such as Cluster Flow and Nextflow. The talk emphasizes that there is no single correct approach and the analysis depends on the biological question and experimental design.
Presentation by Tina Graves-Lindsay at GRC/GIAB ASHG 2017 workshop "Getting the most from the reference assembly and reference materials" on production of reference grade assemblies for various human populations.
Real-Time quantitative PCR (qPCR) is a mainstream method that is used in research and diagnostic applications for quantification of gene expression. IDT has developed a robust and affordable qPCR master mix for use with probe-based qPCR in single and multiplex assays. In this presentation, we explore a variety of applications of PrimeTime® Gene Expression Master Mix. We cover the use of PrimeTime master mix with probe based assays from IDT. We also look at the use of PrimeTime master mix in multiplex applications without the loss of sensitivity that is commonly observed. Finally, we demonstrate the unmatched stability of PrimeTime master mix under ambient temperatures, saving your research money and minimizing on shipping delays.
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.
How to cluster and sequence an ngs library (james hadfield160416)James Hadfield
A presentation for people intersted in understanding how Illumina adapter ligation, clustering ands SBS sequencing work. Follow core-genomics http://core-genomics.blogspot.co.uk/
The document discusses gEVAL Browser, a tool for evaluating genome assemblies developed by the Sanger Institute. It allows users to navigate and view annotations of different assemblies, including the GRCh38, GRCh37, and HuRef assemblies. The document also describes the GRC TrackHub, which displays genomic issues and regions of interest identified by the Genome Reference Consortium on the Ensembl and UCSC browsers.
The document discusses new challenges in reference assembly management due to changing sequencing technologies and new resources. It summarizes an evaluation of de novo assemblies of the CHM1 and CHM13 haploid hydatidiform mole samples from different assemblers. Key metrics like contiguity, alignment to reference transcripts and protein coding regions, and error rates are compared between the assemblies and reference. The evaluation aims to assess suitability of the assemblies for use in reference curation.
This document summarizes work being done to improve human reference genomes using alternative samples. It notes that the initial human reference is incomplete and additional sequences are needed to represent diversity. It then describes efforts to generate "platinum" quality assemblies of additional samples, including CHM1 and CHM13, using long read sequencing and scaffolding with optical mapping. Initial assembly stats are provided for CHM13 and NA19240, and future plans include integrating targeted sequences, adding more diversity, and developing tools to utilize alternate haplotypes in the reference.
The human reference genome is incomplete and does not fully represent structural variation. Additional sequences are needed to represent diversity. A hydatidiform mole genome (CHM1) provides an alternate haploid reference with differences from the diploid human reference. The current CHM1 assembly incorporates BAC sequences and Illumina reads. Future work includes improving the assembly using long read technologies and integrating it into the human reference to better represent human variation.
ADAM is an open source, high performance, distributed platform for genomic analysis that defines a data schema and layout on disk using Parquet and Avro, integrates with Spark's Scala and Java APIs, and provides a command line interface. ADAM achieves linear scalability out to 128 nodes for most tasks and provides a 2-4x performance improvement over other tools like GATK and samtools. The platform includes various tools like avocado for efficient local variant calling via de Bruijn graph reassembly of sequencing reads.
Native Code & Off-Heap Data Structures for Solr: Presented by Yonik Seeley, H...Lucidworks
The document discusses native code and off-heap data structures for Solr. It begins by introducing the speaker and their background working on Solr and Lucene projects. It then describes the Heliosearch project, which is a fork of Solr that uses off-heap filters, fieldcache, and native code to improve performance. The document discusses issues with garbage collection in Java and how off-heap structures and native code can help reduce its impact. It provides examples showing performance improvements from using off-heap filters, fieldcache, and native code for faceting.
The human reference genome is becoming more complex, moving from a single consensus sequence to representing multiple haplotypes and genomic diversity. The current assembly model, GRCh38, includes 178 regions with alternative loci sequences totaling 3.6 Mb of novel sequence not present in previous assemblies. Future assemblies will aim to better define sequence contexts and provide coordinate information for multiple genomes and patches. Challenges include developing compatible analysis tools and determining how to best represent updated regions in new assembly releases.
The human reference genome is a work in progress that does not fully represent global genetic diversity. This project aims to improve reference genomes by sequencing additional genomes from diverse populations at high coverage, including genomes from Yoruba, Puerto Rican, Han Chinese, and Colombian individuals. New long read sequencing technologies allow generation of more complete diploid genome assemblies. These "Gold Standard" genomes will help improve and expand the human reference to better represent human genetic variation worldwide.
The document discusses updates to the human reference genome assembly GRCh38. It provides background on reference assemblies and describes how the Genome Reference Consortium manages and models genome assemblies. Key points include that GRCh38 contains refined centromere regions based on new data, novel sequence detections, and 261 alternate loci representing structural variants. The assembly is now incorporated into public sequence databases to improve access and use of the reference genome data.
Discussion about the evolution of metrics in Cassandra from 1.0 to 3.0, how the metric changes impact operational tooling, pros and cons for different metric representations, and how and why DataStax OpsCenter collects and stores metrics. Includes a deep dive on how DataStax OpsCenter represents and stores the different kinds of metrics to provide visibility beyond simple cluster averages both behind the scenes and in the rendering.
About the Speaker
Chris Lohfink Software Engineer, DataStax
I am a Java, Python, and Clojure developer who has been using Cassandra in an application development and operational context for the last five years. The last nearly two years I have been working with the OpsCenter Monitoring team at DataStax to improve the accuracy and breadth of the visualization tooling available.
Struggling with low editing efficiency or delivery problems? IDT has developed a simple and affordable CRISPR-Cas9 solution that outperforms other methods. In this presentation we present the advantages of using a Cas9:tracrRNA:crRNA ribonucleoprotein (RNP) complex in genome editing experiments, and explain why it is the most efficient driver for genome editing compared to alternative methods, such as expression plasmids or the use of sgRNAs. We also review RNP delivery using cationic lipids and electroporation, and provide tips for optimized transfection in your system.
Storm is a fast, scalable, fault-tolerant, and easy to operate distributed realtime computation system. It guarantees that messages will be processed and allows processing big data streams reliably in real time. Storm was originally developed by Nathan Marz at BackType (acquired by Twitter) and is written in Java and Clojure. It uses a simple programming model and can scale to large clusters, making it suitable for processing millions of events per second.
This document discusses approaches for identifying somatic mutations from cancer sequencing data using multiple mutation callers. It compares several popular mutation callers, explores a simple consensus approach, and proposes an integrated ensemble approach. The ensemble approach applies multiple callers, filters using GATK, and assigns a ranking score to variants based on validation rates to generate a high-confidence list of somatic mutations. This strategy aims to leverage the strengths of different callers to improve accuracy over any single caller.
This document provides an overview of using the STRUCTURE software to analyze population structure from genetic data. STRUCTURE is a model-based clustering method that detects underlying genetic populations among individuals genotyped at multiple markers. It takes genotype data as input and computes the proportion of each individual's genome originating from inferred populations. The document discusses input format, parameter configuration, running single and batch runs, and analyzing results to infer the true number of populations.
This document discusses relating new genome assemblies to the human reference genome GRCh38. It provides an overview of changes in reference sources, evaluating new sequences, and the future of assembly curation. GRCh38 contains 178 regions with alternative loci comprising 2% of the sequence from multiple whole genome sequencing projects. The Assemblathon project evaluated assemblies of the CHM13 hydatidiform mole genome to assess data quality, aligners, and identify improvements for the reference. Future work will integrate additional platinum genomes and develop local reassembly and graph-based references.
1. The PacBio assembly of the CHM1 genome had an N50 contig length of 4.5 MB and potentially fills gaps in the GRCh38 reference genome.
2. Multiple assemblies of the CHM1 genome were generated using different techniques and are being evaluated based on contiguity, annotation, and concordance with other data to select the best assembly.
3. The goal is to generate a high-quality "Platinum Genome" for CHM1 by improving the best assembly with additional data sources like BAC clones and using it as a new reference genome. A second individual, CHM13, is also being assembled to increase genome diversity.
This document discusses the bioinformatics analysis of ChIP-seq data. It begins with an overview of ChIP-seq experiments and the major steps in processing and analyzing the sequencing data, including quality control, alignment, peak calling, and downstream analyses. Pipelines for automated analysis are described, such as Cluster Flow and Nextflow. The talk emphasizes that there is no single correct approach and the analysis depends on the biological question and experimental design.
Presentation by Tina Graves-Lindsay at GRC/GIAB ASHG 2017 workshop "Getting the most from the reference assembly and reference materials" on production of reference grade assemblies for various human populations.
Real-Time quantitative PCR (qPCR) is a mainstream method that is used in research and diagnostic applications for quantification of gene expression. IDT has developed a robust and affordable qPCR master mix for use with probe-based qPCR in single and multiplex assays. In this presentation, we explore a variety of applications of PrimeTime® Gene Expression Master Mix. We cover the use of PrimeTime master mix with probe based assays from IDT. We also look at the use of PrimeTime master mix in multiplex applications without the loss of sensitivity that is commonly observed. Finally, we demonstrate the unmatched stability of PrimeTime master mix under ambient temperatures, saving your research money and minimizing on shipping delays.
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.
How to cluster and sequence an ngs library (james hadfield160416)James Hadfield
A presentation for people intersted in understanding how Illumina adapter ligation, clustering ands SBS sequencing work. Follow core-genomics http://core-genomics.blogspot.co.uk/
The document discusses gEVAL Browser, a tool for evaluating genome assemblies developed by the Sanger Institute. It allows users to navigate and view annotations of different assemblies, including the GRCh38, GRCh37, and HuRef assemblies. The document also describes the GRC TrackHub, which displays genomic issues and regions of interest identified by the Genome Reference Consortium on the Ensembl and UCSC browsers.
The document discusses new challenges in reference assembly management due to changing sequencing technologies and new resources. It summarizes an evaluation of de novo assemblies of the CHM1 and CHM13 haploid hydatidiform mole samples from different assemblers. Key metrics like contiguity, alignment to reference transcripts and protein coding regions, and error rates are compared between the assemblies and reference. The evaluation aims to assess suitability of the assemblies for use in reference curation.
This document summarizes work being done to improve human reference genomes using alternative samples. It notes that the initial human reference is incomplete and additional sequences are needed to represent diversity. It then describes efforts to generate "platinum" quality assemblies of additional samples, including CHM1 and CHM13, using long read sequencing and scaffolding with optical mapping. Initial assembly stats are provided for CHM13 and NA19240, and future plans include integrating targeted sequences, adding more diversity, and developing tools to utilize alternate haplotypes in the reference.
The human reference genome is incomplete and does not fully represent structural variation. Additional sequences are needed to represent diversity. A hydatidiform mole genome (CHM1) provides an alternate haploid reference with differences from the diploid human reference. The current CHM1 assembly incorporates BAC sequences and Illumina reads. Future work includes improving the assembly using long read technologies and integrating it into the human reference to better represent human variation.
ADAM is an open source, high performance, distributed platform for genomic analysis that defines a data schema and layout on disk using Parquet and Avro, integrates with Spark's Scala and Java APIs, and provides a command line interface. ADAM achieves linear scalability out to 128 nodes for most tasks and provides a 2-4x performance improvement over other tools like GATK and samtools. The platform includes various tools like avocado for efficient local variant calling via de Bruijn graph reassembly of sequencing reads.
Native Code & Off-Heap Data Structures for Solr: Presented by Yonik Seeley, H...Lucidworks
The document discusses native code and off-heap data structures for Solr. It begins by introducing the speaker and their background working on Solr and Lucene projects. It then describes the Heliosearch project, which is a fork of Solr that uses off-heap filters, fieldcache, and native code to improve performance. The document discusses issues with garbage collection in Java and how off-heap structures and native code can help reduce its impact. It provides examples showing performance improvements from using off-heap filters, fieldcache, and native code for faceting.
The human reference genome is becoming more complex, moving from a single consensus sequence to representing multiple haplotypes and genomic diversity. The current assembly model, GRCh38, includes 178 regions with alternative loci sequences totaling 3.6 Mb of novel sequence not present in previous assemblies. Future assemblies will aim to better define sequence contexts and provide coordinate information for multiple genomes and patches. Challenges include developing compatible analysis tools and determining how to best represent updated regions in new assembly releases.
The human reference genome is a work in progress that does not fully represent global genetic diversity. This project aims to improve reference genomes by sequencing additional genomes from diverse populations at high coverage, including genomes from Yoruba, Puerto Rican, Han Chinese, and Colombian individuals. New long read sequencing technologies allow generation of more complete diploid genome assemblies. These "Gold Standard" genomes will help improve and expand the human reference to better represent human genetic variation worldwide.
The document discusses updates to the human reference genome assembly GRCh38. It provides background on reference assemblies and describes how the Genome Reference Consortium manages and models genome assemblies. Key points include that GRCh38 contains refined centromere regions based on new data, novel sequence detections, and 261 alternate loci representing structural variants. The assembly is now incorporated into public sequence databases to improve access and use of the reference genome data.
Discussion about the evolution of metrics in Cassandra from 1.0 to 3.0, how the metric changes impact operational tooling, pros and cons for different metric representations, and how and why DataStax OpsCenter collects and stores metrics. Includes a deep dive on how DataStax OpsCenter represents and stores the different kinds of metrics to provide visibility beyond simple cluster averages both behind the scenes and in the rendering.
About the Speaker
Chris Lohfink Software Engineer, DataStax
I am a Java, Python, and Clojure developer who has been using Cassandra in an application development and operational context for the last five years. The last nearly two years I have been working with the OpsCenter Monitoring team at DataStax to improve the accuracy and breadth of the visualization tooling available.
Struggling with low editing efficiency or delivery problems? IDT has developed a simple and affordable CRISPR-Cas9 solution that outperforms other methods. In this presentation we present the advantages of using a Cas9:tracrRNA:crRNA ribonucleoprotein (RNP) complex in genome editing experiments, and explain why it is the most efficient driver for genome editing compared to alternative methods, such as expression plasmids or the use of sgRNAs. We also review RNP delivery using cationic lipids and electroporation, and provide tips for optimized transfection in your system.
Storm is a fast, scalable, fault-tolerant, and easy to operate distributed realtime computation system. It guarantees that messages will be processed and allows processing big data streams reliably in real time. Storm was originally developed by Nathan Marz at BackType (acquired by Twitter) and is written in Java and Clojure. It uses a simple programming model and can scale to large clusters, making it suitable for processing millions of events per second.
This document discusses approaches for identifying somatic mutations from cancer sequencing data using multiple mutation callers. It compares several popular mutation callers, explores a simple consensus approach, and proposes an integrated ensemble approach. The ensemble approach applies multiple callers, filters using GATK, and assigns a ranking score to variants based on validation rates to generate a high-confidence list of somatic mutations. This strategy aims to leverage the strengths of different callers to improve accuracy over any single caller.
This document provides an overview of using the STRUCTURE software to analyze population structure from genetic data. STRUCTURE is a model-based clustering method that detects underlying genetic populations among individuals genotyped at multiple markers. It takes genotype data as input and computes the proportion of each individual's genome originating from inferred populations. The document discusses input format, parameter configuration, running single and batch runs, and analyzing results to infer the true number of populations.
Project plan for generating a somatic data truth set for NGS cancer assay validation using the COLO-829 and COLO-829BL cell lines as well as synthetic fusion spike-in materials. Whole genome sequencing is being performed on the cell lines by multiple labs to generate consensus somatic variant calls. Synthetic fusion transcripts were created and preliminary tests show they can be detected down to certain concentration thresholds, highlighting their potential as validation standards. The data set will be made publicly available to facilitate cancer assay development and validation. Feedback is welcomed on the suitability of these reference materials.
This document provides an agenda for a workshop on NGS analysis using Galaxy. The agenda includes introductions to Galaxy, examples of using Galaxy for various NGS analyses, Galaxy installation instructions, demonstrations of customizing Galaxy tools, and how to use Galaxy on grid and cloud systems. The workshop aims to educate participants on using the open-source Galaxy platform for integrated computational analysis of next generation sequencing data.
This document contains slides from a PowerPoint presentation on genetics concepts related to cancer. It discusses somatic mutations that can cause cancer within an individual's lifetime. The slides show diagrams of the genetic basis for both sporadic cancers caused by mutations in somatic cells and inherited cancer syndromes caused by a heritable mutation. Mosaicism is also described, where a post-zygotic mutation results in some cells having a normal genotype and others an abnormal one. The slides can be used non-commercially for educational purposes.
Lopez-Bigas talk at the EBI/EMBL Cancer Genomics WorkshopNuria Lopez-Bigas
The document describes an oncogenomics workshop discussing methods for identifying cancer driver genes from tumor sequencing data. It introduces two computational methods developed by the speaker's group called OncodriveFM and OncodriveCLUST that identify drivers by looking at the functional impact of mutations and regional mutation clustering, respectively. These methods can be applied across multiple cancer sequencing projects in a scalable way without needing raw sequencing data. The International Cancer Genome Consortium's IntOGen database currently analyzes over 3,000 tumor samples across 27 cancer projects using these and other methods.
Presentation used for my oral Master's Thesis defense for the Universtat Autònoma de Barcelona. It shows the development of a Perl script for the automated generation of a report of the somatic mutations found in a Normal/Tumor cancer experiment.
Incidental findings throughout multigene panel testing in cancer geneticsPasteur_Tunis
Présentation d'Aurélie Fabre réalisée durant le cours du réseau international des instituts Pasteur de "Médecine Génomique: du diagnostic à la thérapie " (17-21 octobre 2016)
Part 5 of RNA-seq for DE analysis: Detecting differential expressionJoachim Jacob
Fifth part of the training session 'RNA-seq for Differential expression analysis'. We explain the most important concepts of detecting DE expression based on a count table, explaining DESeq2 algorithm. Interested in following this session? Please contact http://www.jakonix.be/contact.html
DESeq models read counts with a negative binomial distribution to account for biological variability between samples, which a Poisson distribution underestimates. It estimates variance for each gene based on a local regression of variance against mean expression of other genes. This allows it to better control false positives compared to EdgeR or a Poisson model. DESeq also estimates sequencing depth differently than EdgeR to improve differential expression testing across the dynamic range of expression levels.
This document compares different methods for differential expression analysis of RNA-seq data, including DESeq, voom, and vst. It provides background on RNA-seq analysis, describes the statistical models and code used in each method, and summarizes results from simulations comparing their performance in accuracy, numbers of differentially expressed genes identified, and running time. Overall, voom and vst performed best in accuracy and speed, though sample size greatly impacts performance for all methods.
Computational genomics approaches to precision medicineAltuna Akalin
The document announces a computational genomics conference from September 12-23, 2016 in Berlin, Germany that will focus on approaches to precision medicine. The conference will include lectures from experts in computational genomics and nine course modules covering topics like RNA-seq analysis, ChIP-seq analysis, variant calling, data integration, and cancer classification using high-throughput sequencing data. The application deadline for the conference is July 1, 2016.
2015 Computational genomics course poster. There will be theoretical lectures followed by practical session where students apply what they learned. The programming will be mainly done in R. The course will be beneficial for first year computational biology PhD students or experimental biologists who want to start data analysis or seeking a better understanding of computational genomics.
영어 논문쓰기 능력 배양을 '쓰기와 읽기의 통합'이라는 관점에서 정리해 보았습니다. 대략 반학기 강의 내용을 압축해 놓은 문서라고 생각됩니다. 구석구석 세세한 내용까지 이해하기는 힘드시겠지만 영어로 학술논문을 쓰시고자 하는 분들께 작은 도움이 되리라 생각합니다.
참고로 이 문서는 "영어로 논문쓰기 레퍼토리를 늘리는 4가지 전략"의 업그레이드 버전입니다. (아래 링크 참조)
http://www.slideshare.net/SungwooKim/4-53134196
вестник южно уральского-государственного_университета._серия_математика._меха...Иван Иванов
- The article deals with surfaces of negative Gaussian curvature that can be bijectively projected onto a circle.
- The author provides sufficient conditions for the existence of an estimate of the circle radius onto which the surface can be projected.
- Specifically, if the Gaussian curvature is bounded above by a negative constant, an estimate of the minimum possible radius of the projecting circle can be determined.
Apache HBase Improvements and Practices at XiaomiHBaseCon
Duo Zhang and Liangliang He (Xiaomi)
In this session, we’ll discuss the various practices around HBase in use at Xiaomi, including those relating to HA, tiered compaction, multi-tenancy, and failover across data centers.
The document provides an overview of the features and specifications of the Lenovo ThinkPad T400 and R400 laptop models. It describes the ThinkPad notebooks' hardware components, preinstalled software applications like ThinkVantage and Rescue and Recovery, security features and user support options through Access Help. The document is intended to help users understand and make full use of the capabilities and services available on their ThinkPad computer.
This document describes the rapid deployment feature of Pathloss 4.0 software for designing high frequency networks. It allows for automated transmission design, interference analysis under clear and rain conditions, and generation of pathloss data files. The process involves setting a high/low frequency plan, polarizations, running transmission design and interference calculations, and outputting individual pathloss files. It supports both standard and adaptive ATPC radios and can test for network stability under rain interference scenarios.
This document provides an overview of the Python programming language across multiple sections. It covers fundamental Python concepts like data types, lists, strings, tuples, dictionaries, control flow, functions, modules and packages. It also discusses object-oriented programming concepts in Python including classes, inheritance and exceptions. Further sections explore using Python in integrated development environments like Emacs and debugging tools. Regular expressions and system commands in Python are also summarized. The document serves as a comprehensive reference to the Python language.
This TaqMan® Gene Expression Assays Protocol provides instructions for performing
real-time reverse transcription-PCR (real-time RT-PCR) using TaqMan Gene
Expression Assays and TaqMan Non-coding RNA Assays.
For more information visit:
http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/PCR/real-time-pcr/real-time-pcr-assays/taqman-gene-expression/single-tube-taqman-gene-expression-analysis.html?ICID=search-product?CID=TaqManGeneProducts-SS-12312
This document provides an overview of the key tools and features in Expedition PCB, a printed circuit board design software. It describes the main interface components like the library manager and padstack editor. It also explains how to work with design elements such as cells, parts, and layout templates. Finally, it outlines the design capture and routing processes and provides guidance on settings and preferences.
Clinical significance of transcript alignment discrepancies gne - 20141016Reece Hart
The document discusses the clinical significance of transcript alignment discrepancies and tools to help deal with them. It provides several motivations for why accurate transcript alignments are important, such as different exon coordinates being reported between databases, indels confounding mappings, and data management challenges. It then introduces the Universal Transcript Archive (UTA) as a solution to consolidate transcript alignment data from multiple sources and versions into a single database. The UTA allows comparisons of exon structures and fingerprints to determine RefSeq-Ensembl transcript equivalences. Statistics on reference agreement and alignment simplicity are also characterized for transcripts with significant alignment discrepancies between NCBI and UCSC. Finally, the document discusses using HGVS nomenclature and an HGVS Python package
Unveiling the Secrets of Gaokao Essays to Stand Out in IB Chinese Exams 揭秘高考作...LEGOO MANDARIN
“Unveiling the Secrets of Gaokao Essays to Stand Out in IB Chinese Exams 揭秘高考作文的秘密,在IB中文考试中脱颖而出 -Compilation of Chinese Gaokao Essay Topics, Sample Essays, and Writing Techniques Year 2023, June 07- 中国高考作文题目、范文及写作技巧汇编 2023 ” , FREE Sample Book, BEST price at Our SHOPIFY Shop @ https://1salesforce.com/products/gaokao-essays-2023 OR at our own website: https://edeo.biz/product/gaokao-essays-2023/ Thanks for your support in us creating better content for you! Get 30% EXTRA discount, use code "Edeo30", applies to all products! For Hardcopy or Paperback books at best price with reduced postage @ https://www.amazon.com/dp/B0C7T7ZNMQ More PDF books and Video courses in our own website at best price @ https://1salesforce.com/ // OR visit Our Amazon Kindle Author Central page: http://bit.ly/david-amazon-kdp
Burst TCP: an approach for benefiting mice flowsGlauco Gonçalves
This document summarizes Glauco Estácio Gonçalves' 2007 master's dissertation on a proposed modification to TCP congestion control called Burst TCP (B-TCP). The dissertation examines problems faced by short "mice" flows under standard TCP, which was designed for long "elephant" flows, and reviews proposals to address these problems. It then presents B-TCP, which employs a responsive congestion window growth scheme based on the current window size to improve performance for small flows. Simulation experiments show B-TCP can significantly reduce transfer times and packet losses for mice flows without harming elephants. The dissertation contributes an intuitive TCP modification and evaluates its effectiveness through network simulation.
This document discusses a study on generating tooth profiles of curvic couplings. It begins with an introduction to curvic couplings and their applications. Then, it describes the conventional manufacturing method using a Gleason No.120 grinding machine. The study aims to develop an alternative manufacturing method.
The study investigates the geometric characteristics of a novel gear tooth profile. It derives the cutting tool profile equation for curvic couplings using a spatial transformation matrix theorem. It then constructs a mathematical model of the generating tool envelope surface (i.e. gear surface) based on the tool motion trajectory and tool-workpiece meshing equations. Finally, it establishes a solid model based on the mathematical model and compares it to a conventional curvic coupling.
2_DOF_Inverted_Pendulum_Laboratory_SessionPeixi Gong
This document provides an introduction and overview of a lab session on controlling a 2-DOF inverted pendulum system. It describes the equipment, typical steps in the control project including modeling and controller design. It also presents the nonlinear and linearized mathematical models of the system and exercises for students to analyze stability, observability and derive the state space models.
YCT 1 Chinese Intensive Reading for Kids Y10900 Official Mock 少儿汉语考试模拟考题 sampleLEGOO MANDARIN
YCT 1 Chinese Intensive Reading for Kids Y10900 Official Mock 少儿汉语考试模拟考题 -Exam-oriented Skills to Improve in Unique Smart Way! Version 2021 新中小学生汉语考试 New Book Launching, More details and Best Price @ https://bit.ly/3D4sTC1
By referring YCT and HSK (version 2009 and the latest version 2021) AP Syllabus, we edited a series of Chinese Vocabulary for those who are studying Chinese or preparing international examinations, such as IB, SAT, AP, IGCSE, GCSE Chinese.
This book gives students a quick revision for their coming exam! Combining our 26 years’ expertise in Teaching and editing our own materials, here is the “LIFE SAVING” book called by many students for their exams. Grab it! Thanks for your support for us creating better contents for you!
This paper aims to provide a benchmark study of three established bearing diagnostic techniques applied to vibration data from the Case Western Reserve University Bearing Data Center. The techniques include envelope analysis of the raw signal, cepstrum prewhitening, and a benchmark method. The results and diagnostic outcomes of each technique are discussed in detail for different bearing fault types and conditions in the data sets. Recommendations are provided on how to best use the data for testing new diagnostic algorithms and how to generate benchmark data in the future.
This thesis investigates methods for integrative analysis of multiple data types. It extends the Joint and Individual Variation Explained (JIVE) method by incorporating a fused lasso penalty. A novel rank selection algorithm is also proposed. The methods are evaluated on simulated data and applied to analyze The Cancer Genome Atlas glioblastoma data to identify shared mutational processes between chromosomes.
This PhD thesis presents a mathematical model of the signalling pathways regulating endothelial cell responses to fluid shear stress. The model consists of 8 interconnected modules describing processes such as calcium dynamics, calpain activity, integrin activation, and the phosphorylation of proteins like FAK and Src. Differential equations are used to simulate the dynamic behaviour of molecular species over time under varying shear stress conditions. The model aims to improve understanding of how fluid flow stimulation is converted into biochemical signals in endothelial cells and how this relates to the development of atherosclerosis.
This chapter discusses brickwork materials and construction techniques. Bricks are one of the oldest man-made building materials, dating back over 4000 years. Bricks are typically made from clay but can also contain sand, lime, or cement. Common types of bricks include clay bricks, fly ash bricks and kiln-burnt bricks. Mortar is used to join bricks and consists of cement, sand and water. There are various bonding patterns used in brickwork such as stretcher bond, header bond and Flemish bond. Equipment used includes trowels, jointers, spirit levels and bricklayers' tools. Proper construction techniques such as joint spacing, bonding and laying patterns are important for quality and durable brickwork.
Coriolis rct1000 manual badger meter rct1000ENVIMART
This document provides an overview of Coriolis flow meter batch control capabilities. It describes the Badger Meter software used for configuration and monitoring. Key features of the batch control include single-stage or two-stage batch shutdown options and batch measurement by mass, volume, or other parameters. The document reviews setup and operation of batch control from the transmitter interface or remotely via inputs and outputs.
Similar to Detecting Somatic Mutations in Impure Cancer Sample - Ensemble Approach (20)
Genome Wide SNP Analysis for Inferring the Population Structure and Genetic H...Hong ChangBum
Study of genome-wide SNPs, mitochondrial DNA and Y-chromosomal DNA variation can provide a valuable information about the population structure and peopling of human populations. To explain a genetic homogeneity of Koreans and population structure of Koreans and the East Asian populations, we analyzed 153 individuals from the Korea and 77 individuals from the East Asia at 46,559 common single-nucleotide polymorphic loci. The 137 CHB and 113 JPT individuals at 25,769 common SNPs from the International HapMap project were further analyzed to reveal the population structure of the East Asians. Principal Component analyses (PCA) and population differentiation ( ) are examined. In the PCA test, the Jeju individuals were slightly different from other Koreans but their values were not significant. This reflect the genetic homogeneity of Korea population. In general, all the individual samples studied here were clustered into subset of ethnic origin according to their geographical location except Mongolians. Whole genome sequencing of Koreans and other population genome by next generation sequencing technology will provide great opportunity to understand the population expansion and peopling of Korea better.
1. BioSMACK is a Linux Live CD customized for analysis of genome-wide association studies (GWAS).
2. It provides pre-compiled, installed and configured software for GWAS analysis like PLINK, EIGENSTRAT, STRUCTURE, and others from a bootable CD/USB without installing on the hard disk.
3. Future works include supporting cloud and cluster computing for parallel GWAS analysis on large datasets.
Next-generation genomics: an integrative approachHong ChangBum
This document summarizes a presentation on next-generation genomics and integrative analysis. It discusses the types of genomic data available from techniques like genome sequencing, RNA sequencing, ChIP-seq, and epigenomics. It explains that integrative analysis can help annotate functional features, infer variant function, and understand gene regulation. Approaches to integration include data reduction, unsupervised clustering, and supervised Bayesian networks. Large-scale datasets can be accessed through browsers, add-ons, and standalone tools to generate novel hypotheses. Future work includes more integrated community resources with search capabilities.
This document summarizes a study that analyzed population differentiation at disease-associated SNPs in over 1,000 individuals from 53 global populations. The study genotyped 25 SNPs related to 6 complex human diseases in populations from 7 geographic regions. It found genetic differentiation between populations, with some SNPs showing strong differentiation within East Asia or between Korea and Jeju Island. Allele frequencies of disease SNPs varied between populations and were not always predictive between races. The study also examined selection resources to identify signals of selection, like thicker hair, and found differences in selected regions between East Asia, Middle East and Europe. It concluded that analyzing a large number of populations can help replicate findings and better characterize allele frequency differences globally.
Perspectives of identifying Korean genetic variationsHong ChangBum
This document summarizes research on identifying genetic variations in the Korean population using single-nucleotide polymorphisms (SNPs). It describes analyzing the population structure based on SNP genotypes, using SNPs to determine kinship, and identifying monozygotic twins using copy number variations (CNVs). It also discusses using SNPs to study physical traits in Koreans and developing ancestry informative markers and a database of genomic variants for Korea.
Genome Browser based on Google Maps APIHong ChangBum
The document discusses using the Google Maps API to embed maps on web pages. It allows users to manipulate maps and add content. Key details include how to position maps using longitude and latitude coordinates, how genomic sequence data is tiled into images at different zoom levels, and how those images are named algorithmically based on their position. Components like panels and a search box for interacting with the embedded map are also mentioned.
The document describes the Korean Database of Genomic Variants (KDGV), which is available online at http://ksnp.cdc.go.kr. It was established in 2009 to catalog genomic variants in the Korean population. The KDGV integrates data from other Korean genomic databases including KSNP, KARE, and GWASaid to provide information on SNPs, genes, and genomic regions of interest. It allows users to search and browse genomic data through the customizable genome browser interface.
This document provides an overview of various direct-to-consumer genetic testing companies and the types of genetic tests they offer. It shows that 23andMe, DeCODE, Navigenics, and Knome offer the widest range of tests related to health, traits, and ancestry. Most companies focus on specific health conditions like cancer, cardiovascular disease, or pharmacogenomics. The tests range from single gene tests to more comprehensive scans of parts of the genome.
Direct-to-Consumer Genetic Testing Companies is a document that lists various genetic tests that can be obtained directly from companies without a doctor. It includes tests related to health conditions like cardiovascular disease, diabetes, osteoporosis, cancer, and neurological disorders. The document also lists tests for traits like athletic performance and tests targeted at certain ethnic populations like those of Ashkenazi Jewish descent.
This document discusses genomic variation research and personalized medicine. It mentions tools used for sequence alignment, database management, text analysis, and machine learning algorithms. Genome browsers and clusters are referenced as computational resources. Challenges around analyzing large genomic datasets within reasonable timeframes are also noted.
This document discusses GenomeBrowser. It mentions that the UCSC Human Genome Browser receives 50,000 hits per day and 3,000 users per day, while another receives 1,257 hits per day and 10 users per day. It also discusses various features of GenomeBrowser like being lightweight, configurable, and promoting data sharing.
The document discusses Genome Browser, a lightweight and portable genome browsing software. It can be configured and customized easily. It promotes data sharing through tracks and supports the Distributed Annotation System (DAS) for adding third-party data. The software uses common bioinformatics libraries and has easy installation methods for various operating systems.
The document discusses project management tools for developers including a developer blog, version control systems like SVN and issue tracking systems like trac. It also mentions tools for documentation projects like moniWiki and describes using FTP for file transfers.
This document provides information about various Linux clusters and distributed resource managers available at the Center for Genome Science and NIH. It lists several Linux cluster machines including KHAN, KGENE, LOGIN, LOGINDB, and DEV. Details are provided about the KHAN cluster, which has a total of 94 nodes, including specifications of the nodes and storage and software information. It also briefly mentions distributed resource managers.
This document provides information about various Linux clusters and distributed resource managers available at the Center for Genome Science and NIH. It lists several Linux cluster machines including KHAN with 94 nodes, KGENE with 28 nodes, and LOGIN and LOGINDB servers. Details are provided about the KHAN cluster including its node configuration, storage space, and available software. It also briefly mentions distributed resource managers.
How Can Hiring A Mobile App Development Company Help Your Business Grow?ToXSL Technologies
ToXSL Technologies is an award-winning Mobile App Development Company in Dubai that helps businesses reshape their digital possibilities with custom app services. As a top app development company in Dubai, we offer highly engaging iOS & Android app solutions. https://rb.gy/necdnt
WMF 2024 - Unlocking the Future of Data Powering Next-Gen AI with Vector Data...Luigi Fugaro
Vector databases are transforming how we handle data, allowing us to search through text, images, and audio by converting them into vectors. Today, we'll dive into the basics of this exciting technology and discuss its potential to revolutionize our next-generation AI applications. We'll examine typical uses for these databases and the essential tools
developers need. Plus, we'll zoom in on the advanced capabilities of vector search and semantic caching in Java, showcasing these through a live demo with Redis libraries. Get ready to see how these powerful tools can change the game!
A neural network is a machine learning program, or model, that makes decisions in a manner similar to the human brain, by using processes that mimic the way biological neurons work together to identify phenomena, weigh options and arrive at conclusions.
UI5con 2024 - Keynote: Latest News about UI5 and it’s EcosystemPeter Muessig
Learn about the latest innovations in and around OpenUI5/SAPUI5: UI5 Tooling, UI5 linter, UI5 Web Components, Web Components Integration, UI5 2.x, UI5 GenAI.
Recording:
https://www.youtube.com/live/MSdGLG2zLy8?si=INxBHTqkwHhxV5Ta&t=0
Boost Your Savings with These Money Management AppsJhone kinadey
A money management app can transform your financial life by tracking expenses, creating budgets, and setting financial goals. These apps offer features like real-time expense tracking, bill reminders, and personalized insights to help you save and manage money effectively. With a user-friendly interface, they simplify financial planning, making it easier to stay on top of your finances and achieve long-term financial stability.
Why Apache Kafka Clusters Are Like Galaxies (And Other Cosmic Kafka Quandarie...Paul Brebner
Closing talk for the Performance Engineering track at Community Over Code EU (Bratislava, Slovakia, June 5 2024) https://eu.communityovercode.org/sessions/2024/why-apache-kafka-clusters-are-like-galaxies-and-other-cosmic-kafka-quandaries-explored/ Instaclustr (now part of NetApp) manages 100s of Apache Kafka clusters of many different sizes, for a variety of use cases and customers. For the last 7 years I’ve been focused outwardly on exploring Kafka application development challenges, but recently I decided to look inward and see what I could discover about the performance, scalability and resource characteristics of the Kafka clusters themselves. Using a suite of Performance Engineering techniques, I will reveal some surprising discoveries about cosmic Kafka mysteries in our data centres, related to: cluster sizes and distribution (using Zipf’s Law), horizontal vs. vertical scalability, and predicting Kafka performance using metrics, modelling and regression techniques. These insights are relevant to Kafka developers and operators.
Superpower Your Apache Kafka Applications Development with Complementary Open...Paul Brebner
Kafka Summit talk (Bangalore, India, May 2, 2024, https://events.bizzabo.com/573863/agenda/session/1300469 )
Many Apache Kafka use cases take advantage of Kafka’s ability to integrate multiple heterogeneous systems for stream processing and real-time machine learning scenarios. But Kafka also exists in a rich ecosystem of related but complementary stream processing technologies and tools, particularly from the open-source community. In this talk, we’ll take you on a tour of a selection of complementary tools that can make Kafka even more powerful. We’ll focus on tools for stream processing and querying, streaming machine learning, stream visibility and observation, stream meta-data, stream visualisation, stream development including testing and the use of Generative AI and LLMs, and stream performance and scalability. By the end you will have a good idea of the types of Kafka “superhero” tools that exist, which are my favourites (and what superpowers they have), and how they combine to save your Kafka applications development universe from swamploads of data stagnation monsters!
Preparing Non - Technical Founders for Engaging a Tech AgencyISH Technologies
Preparing non-technical founders before engaging a tech agency is crucial for the success of their projects. It starts with clearly defining their vision and goals, conducting thorough market research, and gaining a basic understanding of relevant technologies. Setting realistic expectations and preparing a detailed project brief are essential steps. Founders should select a tech agency with a proven track record and establish clear communication channels. Additionally, addressing legal and contractual considerations and planning for post-launch support are vital to ensure a smooth and successful collaboration. This preparation empowers non-technical founders to effectively communicate their needs and work seamlessly with their chosen tech agency.Visit our site to get more details about this. Contact us today www.ishtechnologies.com.au
14 th Edition of International conference on computer visionShulagnaSarkar2
About the event
14th Edition of International conference on computer vision
Computer conferences organized by ScienceFather group. ScienceFather takes the privilege to invite speakers participants students delegates and exhibitors from across the globe to its International Conference on computer conferences to be held in the Various Beautiful cites of the world. computer conferences are a discussion of common Inventions-related issues and additionally trade information share proof thoughts and insight into advanced developments in the science inventions service system. New technology may create many materials and devices with a vast range of applications such as in Science medicine electronics biomaterials energy production and consumer products.
Nomination are Open!! Don't Miss it
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DevOps Consulting Company | Hire DevOps Servicesseospiralmantra
Spiral Mantra excels in providing comprehensive DevOps services, including Azure and AWS DevOps solutions. As a top DevOps consulting company, we offer controlled services, cloud DevOps, and expert consulting nationwide, including Houston and New York. Our skilled DevOps engineers ensure seamless integration and optimized operations for your business. Choose Spiral Mantra for superior DevOps services.
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Benefits of Artificial Intelligence in Healthcare!Prestware
Benefits of AI in Healthcare
Faster Diagnoses
AI speeds up the diagnostic process, helping doctors identify conditions quickly and accurately.
Personalized Treatments
AI creates customized treatment plans based on individual patient data, improving outcomes.
Predictive Healthcare
AI anticipates health issues before they arise, allowing for preventative measures.
Improved Accuracy
AI reduces human error in diagnostics and treatment, leading to better patient care.
Enhanced Imaging
AI improves the clarity and precision of medical imaging, aiding in early detection of diseases.
Efficient Drug Development
AI accelerates the drug discovery process, bringing new treatments to market faster.
Streamlined Operations
AI automates administrative tasks, reducing the burden on healthcare professionals and improving efficiency.
24/7 Patient Support
AI-powered virtual assistants and chatbots provide round-the-clock support and information to patients.
Cost Reduction
AI optimizes resource use and reduces operational costs, making healthcare more affordable.
Continuous Monitoring
AI continuously monitors patient health, enabling timely interventions and better management of chronic conditions.
Experience the Future of Healthcare with AI!
#AIinHealthcare #MedicalInnovation #HealthTech #BetterCare
Most important New features of Oracle 23c for DBAs and Developers. You can get more idea from my youtube channel video from https://youtu.be/XvL5WtaC20A
Flutter is a popular open source, cross-platform framework developed by Google. In this webinar we'll explore Flutter and its architecture, delve into the Flutter Embedder and Flutter’s Dart language, discover how to leverage Flutter for embedded device development, learn about Automotive Grade Linux (AGL) and its consortium and understand the rationale behind AGL's choice of Flutter for next-gen IVI systems. Don’t miss this opportunity to discover whether Flutter is right for your project.
Liberarsi dai framework con i Web Component.pptxMassimo Artizzu
In Italian
Presentazione sulle feature e l'utilizzo dei Web Component nell sviluppo di pagine e applicazioni web. Racconto delle ragioni storiche dell'avvento dei Web Component. Evidenziazione dei vantaggi e delle sfide poste, indicazione delle best practices, con particolare accento sulla possibilità di usare web component per facilitare la migrazione delle proprie applicazioni verso nuovi stack tecnologici.
The Rising Future of CPaaS in the Middle East 2024Yara Milbes
Explore "The Rising Future of CPaaS in the Middle East in 2024" with this comprehensive PPT presentation. Discover how Communication Platforms as a Service (CPaaS) is transforming communication across various sectors in the Middle East.
Microservice Teams - How the cloud changes the way we workSven Peters
A lot of technical challenges and complexity come with building a cloud-native and distributed architecture. The way we develop backend software has fundamentally changed in the last ten years. Managing a microservices architecture demands a lot of us to ensure observability and operational resiliency. But did you also change the way you run your development teams?
Sven will talk about Atlassian’s journey from a monolith to a multi-tenanted architecture and how it affected the way the engineering teams work. You will learn how we shifted to service ownership, moved to more autonomous teams (and its challenges), and established platform and enablement teams.
26. Detecting Somatic Mutations in Impure Cancer Sample - Ensemble Approach 26
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$ cd
$ cp /BIO/app/bwa -0.7.4. tar.bz2 ./
$ tar xvf bwa -0.7.4. tar.bz2
$ cd bwa -0.7.4
$ make
$ ./bwa
Program: bwa (alignment via Burrows -Wheeler transformation )
Version: 0.7.4 - r385
Contact: Heng Li <lh3@sanger.ac.uk >
Usage: bwa <command > [options]
Command: index index sequences in the FASTA format
mem BWA -MEM algorithm
fastmap identify super -maximal exact matches
pemerge merge overlapping paired ends (EXPERIMENTAL)
aln gapped/ungapped alignment
samse generate alignment (single ended)
sampe generate alignment (paired ended)
bwasw BWA -SW for long queries
fa2pac convert FASTA to PAC format
pac2bwt generate BWT from PAC
pac2bwtgen alternative algorithm for generating BWT
bwtupdate update .bwt to the new format
bwt2sa generate SA from BWT and Occ
$ bwa
Program: bwa (alignment via Burrows -Wheeler transformation )
Version: 0.6.2 - r126
Contact: Heng Li <lh3@sanger.ac.uk >
Usage: bwa <command > [options]