Course: Bioinformatics for Biomedical Research (2014).
Session: 4.2- Introduction to Functional Analysis with IPA.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Course: Bioinformatics for Biomedical Research (2014).
Session: 3.2- Basic Aspects of Microarray Technology and Data Analysis.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Tumblr Terms of Service Policy Primer: an Internet Communications student per...alanthall
The length of online policy documents means that many people who use Tumblr are unlikely to have read the terms of service that they agreed to upon registration.
This policy primer provides a cursory overview of Tumblr's policies, focusing on privacy, freedom of expression, and copyright.
Big Data and Superorganism Genomics: Microbial Metagenomics Meets Human GenomicsLarry Smarr
This presentation on February 27, 2014 to NGS and the Future of Medicine at Illumina Headquarters in La Jolla, CA, was made by Calit2 Director Larry Smarr.
Kenya MOICT presentation at the Youth Engagement Summit MauritiusAdrian Hall
Presentation by ICT Officer from the Ministry of ICT Kenya at the Youth Engagement Summit Mauritius, forming part of the Kenya Country Showcase panel session
Moving into the Post-MetagenomicEra of Gut Microbiome ResearchJonathan Clarke
Julian Marchesi's presentation slides from our previous Microbiome R&D and Business Collaboration Forum. For information about this years event please visit http://www.globalengage.co.uk/microbiota.html
This document discusses the relationship between gut microbiota and obesity. It finds that obese individuals have different gut bacteria compositions than lean individuals, with obese individuals tending to have more Firmicutes bacteria, which are more efficient at harvesting energy from food and promoting fat storage. Maintaining a diverse gut microbiota through a high fiber diet can help prevent obesity by encouraging the growth of beneficial bacteria like Bacteroidetes over Firmicutes. Probiotics and prebiotics may also help influence the gut microbiota in ways that impact weight and metabolism.
GSK posted a higher net profit of $24.3 million for 2008, up 17.1% from the previous year. Net sales increased 26.3% to $13.4 billion. GSK also acquired Bristol-Myers Squibb Pakistan for $36.5 million, adding popular branded drugs to its portfolio. Additionally, GSK Biological announced plans to invest more money in Pakistan.
Systems biology - Understanding biology at the systems levelLars Juhl Jensen
The document discusses systems biology and its goal of understanding biology at the systems level. It explains that systems biology studies complete biological systems by integrating multiple types of high-throughput omics data and mathematical modeling. It provides examples of modeling the cell cycle and integrating gene expression, protein interaction, and genetic interaction networks to understand complex multi-layer regulation within biological systems. Interactive online databases are described that allow users to explore omics data, expand networks, and investigate relationships between biological entities and diseases.
Course: Bioinformatics for Biomedical Research (2014).
Session: 3.2- Basic Aspects of Microarray Technology and Data Analysis.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Tumblr Terms of Service Policy Primer: an Internet Communications student per...alanthall
The length of online policy documents means that many people who use Tumblr are unlikely to have read the terms of service that they agreed to upon registration.
This policy primer provides a cursory overview of Tumblr's policies, focusing on privacy, freedom of expression, and copyright.
Big Data and Superorganism Genomics: Microbial Metagenomics Meets Human GenomicsLarry Smarr
This presentation on February 27, 2014 to NGS and the Future of Medicine at Illumina Headquarters in La Jolla, CA, was made by Calit2 Director Larry Smarr.
Kenya MOICT presentation at the Youth Engagement Summit MauritiusAdrian Hall
Presentation by ICT Officer from the Ministry of ICT Kenya at the Youth Engagement Summit Mauritius, forming part of the Kenya Country Showcase panel session
Moving into the Post-MetagenomicEra of Gut Microbiome ResearchJonathan Clarke
Julian Marchesi's presentation slides from our previous Microbiome R&D and Business Collaboration Forum. For information about this years event please visit http://www.globalengage.co.uk/microbiota.html
This document discusses the relationship between gut microbiota and obesity. It finds that obese individuals have different gut bacteria compositions than lean individuals, with obese individuals tending to have more Firmicutes bacteria, which are more efficient at harvesting energy from food and promoting fat storage. Maintaining a diverse gut microbiota through a high fiber diet can help prevent obesity by encouraging the growth of beneficial bacteria like Bacteroidetes over Firmicutes. Probiotics and prebiotics may also help influence the gut microbiota in ways that impact weight and metabolism.
GSK posted a higher net profit of $24.3 million for 2008, up 17.1% from the previous year. Net sales increased 26.3% to $13.4 billion. GSK also acquired Bristol-Myers Squibb Pakistan for $36.5 million, adding popular branded drugs to its portfolio. Additionally, GSK Biological announced plans to invest more money in Pakistan.
Systems biology - Understanding biology at the systems levelLars Juhl Jensen
The document discusses systems biology and its goal of understanding biology at the systems level. It explains that systems biology studies complete biological systems by integrating multiple types of high-throughput omics data and mathematical modeling. It provides examples of modeling the cell cycle and integrating gene expression, protein interaction, and genetic interaction networks to understand complex multi-layer regulation within biological systems. Interactive online databases are described that allow users to explore omics data, expand networks, and investigate relationships between biological entities and diseases.
A little bit of Lamba Calculus.
What is that and how it is applied in functional programming languages.
Currying, High Order Functions, Anonymous Functions
This document analyzes the relationship between food and the intestinal microbiota in humans. It discusses what intestinal microbiomes are, their roles, and their relationship with the host. The document explores how diet can modulate gut microbiome composition and influence enterotypes. It summarizes research studies that link long-term diet to enterotypes and show the gut microbiome of malnourished children remains immature. The conclusion is that food affects the gut flora, which in turn impacts health and development.
The document discusses Parallella, an open source parallel computing platform that aims to democratize access to supercomputing. Parallella uses a low-cost $99 board containing a dual-core ARM processor, programmable FPGA, and 16-64 core Epiphany parallel processor. It provides high performance at a fraction of the cost and power of conventional supercomputers. The document outlines Parallella's architecture, programming model, applications in fields like computing, medical, and communications, and areas for potential improvement.
This document discusses systems biology and provides examples of regulatory networks and dynamics modeling in systems biology. It summarizes that systems biology aims to understand biological processes using a systems-level approach by integrating 'omics data, quantitative analysis, and computational modeling to study biological systems at various scales, from pathways to whole organisms. It also notes the rapid expansion of the field since 2000 and discusses current and future directions, including data integration, modeling dynamics, placing networks in spatial and temporal contexts, and applications to medicine.
1. Ravindra Salukhe owns a small fruit and vegetable shop in Mumbai and uses a Tata ACE mobile grocery unit to earn a higher monthly income than his loan emi payments.
2. Tata Motors developed the Tata ACE to fill a gap in the light commercial vehicle market for an affordable last-mile transport solution.
3. Market research found demand for a vehicle with the price and fuel efficiency of a three-wheeler but the safety, payload, and comfort of a small truck.
Metagenomics is the study of microbial communities directly in their natural environments without isolating individual species in the lab. It involves sequencing DNA from environmental samples and analyzing the metagenomes. Some key points are that metagenomics can identify uncultivable microbes, bypassing the need for culture, and it has led to advances in understanding microbial ecology, evolution, and diversity. The rumen, home to a complex microbial community important for ruminant digestion, is a important target of metagenomics study. Next generation sequencing techniques now allow more accessible exploration of microbial systems through metagenomics.
1. The document discusses metagenomics research on the human gut microbiome using a gene-centric approach.
2. It involves sequencing microbial DNA from gut samples to identify genes and characterize functional profiles of the microbiome.
3. Analysis of Japanese gut microbiome samples identified over 600,000 genes, including many novel to the gut microbiome, providing insight into microbiome composition and functions.
Metagenomics is a set of techniques used to study microbial communities through direct collection and analysis of environmental DNA samples. It allows researchers to study millions of microbial organisms and genetic fragments simultaneously without needing to culture individual microbes in the lab. The main procedures involve sampling an environment, filtering out particles by size, extracting and sequencing DNA fragments. Two common sequencing methods are shotgun sequencing and high-throughput sequencing using platforms like Illumina or SOLiD. Projects like MetaHIT use metagenomics to study the human gut microbiome and its role in health and disease. Potential applications include contributions to earth sciences, life sciences, biomedicine, bioenergy, biotechnology, and microbial forensics.
The document summarizes a functional job analysis that was conducted for the role of Quality and Standards Manager. The analysis involved interviewing an incumbent, reviewing documentation like the job description and organizational charts, and rating tasks on scales related to data, people, things, etc. The analysis identified key tasks, as well as the knowledge, skills, abilities, and competencies required for the role. Some limitations of the analysis are noted, such as only interviewing one incumbent and questions around generalizability. The information collected could be used for purposes like recruitment, training, and performance management. The functional job analysis method provides a standardized way to collect job information, though jobs are evolving and the analysis represents a snapshot in time.
Tata launched the Tata Ace mini-truck in India in 2005 at a price of Rs. 225,000. It targeted the small commercial vehicle segment of 0.75 to 1 ton payload that was dominated by three-wheelers. The Ace was an instant success, achieving its annual sales target of 30,000 units in under a year. Its compact size, low cost of operation, and maneuverability in crowded Indian cities enabled it to capture over half the market share in the segment. The Ace's success encouraged Tata to double its production capacity and launch variants like the Ace Super to expand its market reach.
How to Write Amazing Functional Analysis Documents for your SharePoint Projects GSoft
The document provides an overview of a presentation on how to write functional analysis documents for SharePoint projects. It discusses defining requirements, prioritizing requirements, and a 9-step methodology for functional analysis when using SharePoint. The methodology includes steps like visualizing requirements, describing information types, defining relationships between data, determining data storage and flows, and defining data access points and behaviors. The presentation provides examples and tips for effectively analyzing requirements and functionality for SharePoint solutions.
This document provides an overview of genomics and metagenomics. It begins with an introduction to genomics, describing genome assembly, validation, and metabolic reconstruction. It then covers metagenomics, discussing its history, pitfalls, and potentials. Key points include that genomics analyzes the parts list of a single genome, while metagenomics analyzes the collective genomes of an entire microbial community. Metagenomics has been used to explore novel sequences from various environments, perform comparative analyses between ecosystems, and extract genomes from low-abundance species.
This is Info-Edu slide for learning about 3D. It's introduction to 3D which anyone whose new to 3D can understand. I'll be adding more information on various subjects...
Tata Motors presented the Tata Nano car at the 2008 Auto Expo in New Delhi, aiming to create the world's cheapest car for families in India with two-wheeled transport. The Nano plant was established in Singur, West Bengal with an investment of 1500 crore rupees. The Nano has a 623cc rear-engine and rear-wheel drive with a fuel efficiency of 21.97km/ltr in city and 25.5km/ltr on highways. Tata Motors established relationships with 20 major global automotive suppliers to source components for proprietary designs and those designed in-house in order to produce the Nano at a low cost.
This document discusses the potentials and pitfalls of metagenomics. It begins with an introduction to metagenomics and its history. It describes some of the early applications of metagenomics including exploration of microbial communities and identification of specific functions. Potential pitfalls of metagenomics are then outlined, including issues related to DNA extraction, sequencing depth, and biases. The major pitfall discussed is the incompleteness of databases for assigning taxonomy and functions. The document concludes by describing some of the potentials of metagenomics, including hunting for novel antibiotic resistance genes using functional metagenomics and extracting genomes from metagenomes through reducing microdiversity and binning sequences from multiple related samples.
The document provides information about the Tata Nano car, introduced in 2008 as India's "People's Car." It discusses the car's affordable price of 100,000 rupees, its small size and fuel efficiency. It also summarizes Tata's market research which showed potential for the Nano in India given the country's large family sizes and growing middle class. The document outlines Tata's strategies for manufacturing, marketing and distributing the Nano to make it widely available and increase car ownership across India.
This document provides an introduction to metagenomics. It defines metagenomics as the study of microbial communities directly in their natural environments using modern genomics techniques. The document outlines the historical context and basic purpose of metagenomics. It describes some of the applications of metagenomics, such as understanding the human microbiome, bioremediation, bioenergy production, and smart farming. Finally, it introduces some basic concepts in metagenomics analysis including binning, OTUs, alpha and beta diversity measurements, and challenges around estimating diversity from samples.
Course: Bioinformatics for Biomedical Research (2014).
Session: 4.1- Introduction to RNA-seq and RNA-seq Data Analysis.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Course: Bioinformatics for Biomedical Research (2014).
Session: 3.1- Brief Overview to Amplicon Variant Analysis.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.3- Introduction to NGS Variant Calling Analysis.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.2- Introduction to Galaxy. A web-based genome analysis platform.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.1.3- Next Generation Sequencing. Technologies and Applications. Part III: NGS Applications II.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
A little bit of Lamba Calculus.
What is that and how it is applied in functional programming languages.
Currying, High Order Functions, Anonymous Functions
This document analyzes the relationship between food and the intestinal microbiota in humans. It discusses what intestinal microbiomes are, their roles, and their relationship with the host. The document explores how diet can modulate gut microbiome composition and influence enterotypes. It summarizes research studies that link long-term diet to enterotypes and show the gut microbiome of malnourished children remains immature. The conclusion is that food affects the gut flora, which in turn impacts health and development.
The document discusses Parallella, an open source parallel computing platform that aims to democratize access to supercomputing. Parallella uses a low-cost $99 board containing a dual-core ARM processor, programmable FPGA, and 16-64 core Epiphany parallel processor. It provides high performance at a fraction of the cost and power of conventional supercomputers. The document outlines Parallella's architecture, programming model, applications in fields like computing, medical, and communications, and areas for potential improvement.
This document discusses systems biology and provides examples of regulatory networks and dynamics modeling in systems biology. It summarizes that systems biology aims to understand biological processes using a systems-level approach by integrating 'omics data, quantitative analysis, and computational modeling to study biological systems at various scales, from pathways to whole organisms. It also notes the rapid expansion of the field since 2000 and discusses current and future directions, including data integration, modeling dynamics, placing networks in spatial and temporal contexts, and applications to medicine.
1. Ravindra Salukhe owns a small fruit and vegetable shop in Mumbai and uses a Tata ACE mobile grocery unit to earn a higher monthly income than his loan emi payments.
2. Tata Motors developed the Tata ACE to fill a gap in the light commercial vehicle market for an affordable last-mile transport solution.
3. Market research found demand for a vehicle with the price and fuel efficiency of a three-wheeler but the safety, payload, and comfort of a small truck.
Metagenomics is the study of microbial communities directly in their natural environments without isolating individual species in the lab. It involves sequencing DNA from environmental samples and analyzing the metagenomes. Some key points are that metagenomics can identify uncultivable microbes, bypassing the need for culture, and it has led to advances in understanding microbial ecology, evolution, and diversity. The rumen, home to a complex microbial community important for ruminant digestion, is a important target of metagenomics study. Next generation sequencing techniques now allow more accessible exploration of microbial systems through metagenomics.
1. The document discusses metagenomics research on the human gut microbiome using a gene-centric approach.
2. It involves sequencing microbial DNA from gut samples to identify genes and characterize functional profiles of the microbiome.
3. Analysis of Japanese gut microbiome samples identified over 600,000 genes, including many novel to the gut microbiome, providing insight into microbiome composition and functions.
Metagenomics is a set of techniques used to study microbial communities through direct collection and analysis of environmental DNA samples. It allows researchers to study millions of microbial organisms and genetic fragments simultaneously without needing to culture individual microbes in the lab. The main procedures involve sampling an environment, filtering out particles by size, extracting and sequencing DNA fragments. Two common sequencing methods are shotgun sequencing and high-throughput sequencing using platforms like Illumina or SOLiD. Projects like MetaHIT use metagenomics to study the human gut microbiome and its role in health and disease. Potential applications include contributions to earth sciences, life sciences, biomedicine, bioenergy, biotechnology, and microbial forensics.
The document summarizes a functional job analysis that was conducted for the role of Quality and Standards Manager. The analysis involved interviewing an incumbent, reviewing documentation like the job description and organizational charts, and rating tasks on scales related to data, people, things, etc. The analysis identified key tasks, as well as the knowledge, skills, abilities, and competencies required for the role. Some limitations of the analysis are noted, such as only interviewing one incumbent and questions around generalizability. The information collected could be used for purposes like recruitment, training, and performance management. The functional job analysis method provides a standardized way to collect job information, though jobs are evolving and the analysis represents a snapshot in time.
Tata launched the Tata Ace mini-truck in India in 2005 at a price of Rs. 225,000. It targeted the small commercial vehicle segment of 0.75 to 1 ton payload that was dominated by three-wheelers. The Ace was an instant success, achieving its annual sales target of 30,000 units in under a year. Its compact size, low cost of operation, and maneuverability in crowded Indian cities enabled it to capture over half the market share in the segment. The Ace's success encouraged Tata to double its production capacity and launch variants like the Ace Super to expand its market reach.
How to Write Amazing Functional Analysis Documents for your SharePoint Projects GSoft
The document provides an overview of a presentation on how to write functional analysis documents for SharePoint projects. It discusses defining requirements, prioritizing requirements, and a 9-step methodology for functional analysis when using SharePoint. The methodology includes steps like visualizing requirements, describing information types, defining relationships between data, determining data storage and flows, and defining data access points and behaviors. The presentation provides examples and tips for effectively analyzing requirements and functionality for SharePoint solutions.
This document provides an overview of genomics and metagenomics. It begins with an introduction to genomics, describing genome assembly, validation, and metabolic reconstruction. It then covers metagenomics, discussing its history, pitfalls, and potentials. Key points include that genomics analyzes the parts list of a single genome, while metagenomics analyzes the collective genomes of an entire microbial community. Metagenomics has been used to explore novel sequences from various environments, perform comparative analyses between ecosystems, and extract genomes from low-abundance species.
This is Info-Edu slide for learning about 3D. It's introduction to 3D which anyone whose new to 3D can understand. I'll be adding more information on various subjects...
Tata Motors presented the Tata Nano car at the 2008 Auto Expo in New Delhi, aiming to create the world's cheapest car for families in India with two-wheeled transport. The Nano plant was established in Singur, West Bengal with an investment of 1500 crore rupees. The Nano has a 623cc rear-engine and rear-wheel drive with a fuel efficiency of 21.97km/ltr in city and 25.5km/ltr on highways. Tata Motors established relationships with 20 major global automotive suppliers to source components for proprietary designs and those designed in-house in order to produce the Nano at a low cost.
This document discusses the potentials and pitfalls of metagenomics. It begins with an introduction to metagenomics and its history. It describes some of the early applications of metagenomics including exploration of microbial communities and identification of specific functions. Potential pitfalls of metagenomics are then outlined, including issues related to DNA extraction, sequencing depth, and biases. The major pitfall discussed is the incompleteness of databases for assigning taxonomy and functions. The document concludes by describing some of the potentials of metagenomics, including hunting for novel antibiotic resistance genes using functional metagenomics and extracting genomes from metagenomes through reducing microdiversity and binning sequences from multiple related samples.
The document provides information about the Tata Nano car, introduced in 2008 as India's "People's Car." It discusses the car's affordable price of 100,000 rupees, its small size and fuel efficiency. It also summarizes Tata's market research which showed potential for the Nano in India given the country's large family sizes and growing middle class. The document outlines Tata's strategies for manufacturing, marketing and distributing the Nano to make it widely available and increase car ownership across India.
This document provides an introduction to metagenomics. It defines metagenomics as the study of microbial communities directly in their natural environments using modern genomics techniques. The document outlines the historical context and basic purpose of metagenomics. It describes some of the applications of metagenomics, such as understanding the human microbiome, bioremediation, bioenergy production, and smart farming. Finally, it introduces some basic concepts in metagenomics analysis including binning, OTUs, alpha and beta diversity measurements, and challenges around estimating diversity from samples.
Course: Bioinformatics for Biomedical Research (2014).
Session: 4.1- Introduction to RNA-seq and RNA-seq Data Analysis.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Course: Bioinformatics for Biomedical Research (2014).
Session: 3.1- Brief Overview to Amplicon Variant Analysis.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.3- Introduction to NGS Variant Calling Analysis.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.2- Introduction to Galaxy. A web-based genome analysis platform.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.1.3- Next Generation Sequencing. Technologies and Applications. Part III: NGS Applications II.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.1.2- Next Generation Sequencing. Technologies and Applications. Part II: NGS Applications I.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.1.1- Next Generation Sequencing. Technologies and Applications. Part I: NGS Introduction and Technology Overview.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Course: Bioinformatics for Biomedical Research (2014).
Session: 1.2- Storing and Accessing Information. Databases and Queries.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
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.
Course: Bioinformatics for Biomedical Research (2014).
Session: 1.3- Genome Browsing, Genomic Data Mining and Genome Data Visualization with Ensembl, Biomart and IGV.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
1) The document discusses using the Tiki Wiki CMS system to manage information flows at the Statistics and Bioinformatics Unit at Vall d'Hebron Institut de Recerca.
2) Key features of Tiki that are highlighted include wiki pages, structures and permissions to manage documentation, trackers for databases, and calendars for planning. It also allows connecting R to the web through plugins.
3) Examples provided include using Tiki to create task trackers, study databases, and an interactive heatmap tool powered by R. The system allows automating workflows and sharing results in a customizable centralized system.
This document discusses real-time quantitative PCR (RT-qPCR) data analysis. It outlines topics including normalization, absolute and relative quantification methods, and data analysis pipelines. For normalization, it describes correcting for systematic variation between samples through methods like using housekeeping genes or internal calibrators. It also explains that absolute quantification uses a standard curve of known copy numbers, while relative quantification compares target and reference gene expression ratios, such as through the delta-delta Ct method. The document provides examples of calculating fold changes between samples or tissues.
Este documento presenta un resumen del seminario sobre la técnica de RTqPCR realizado en 2012. Describe las diferentes etapas de un experimento de RTqPCR, incluyendo la definición de la técnica, la terminología asociada, el flujo de trabajo con etapas como el diseño experimental, la preparación y extracción de muestras, la transcripción reversa, la reacción en cadena de la polimerasa cuantitativa y la validación y análisis de los resultados. El documento proporciona información fundamental sobre esta importante técnica de biolog
El resumen analiza los principios básicos del diseño experimental y el proceso de análisis de datos de microarrays. Explica que un buen diseño experimental sigue principios como la aleatorización, la replicación y el bloqueo para minimizar errores sistemáticos y maximizar la precisión. También describe los diferentes tipos de estudios de microarrays, como la comparación de clases y el descubrimiento de clases, así como las herramientas disponibles para el análisis.
Este documento describe un curso sobre tecnologías de alto rendimiento en genómica que se llevará a cabo del 28 de noviembre al 5 de diciembre. El curso cubrirá técnicas como microarrays, RT-qPCR, secuenciación masiva y análisis de resultados de estas técnicas. Los temas incluyen tipos de microarrays, cómo se fabrican, calidad y cantidad de RNA de partida, y procedimientos de microarrays.
Este documento describe la tecnología de arrays de proteínas y su aplicación en el estudio de interacciones proteína-proteína. Se explica el flujo de trabajo de un ensayo con arrays de proteínas reversas utilizando la tecnología Zeptosens. También se detalla la optimización del servicio de arrays de proteínas en la Unidad de Análisis Traslacional mediante el uso de lisados celulares y anticuerpos validados.
This document provides an introduction and overview of next-generation sequencing (NGS) data analysis. It discusses the bioinformatics challenges posed by large NGS datasets, including the need for powerful computing infrastructure and data storage. The document outlines common NGS data analysis workflows and applications, such as quality control, metagenomics, de novo assembly, amplicon analysis and variant detection. It also compares different NGS platforms and provides examples of software tools used in NGS data analysis.
Este documento describe un curso sobre tecnologías de secuenciación de nueva generación. El curso cubre las tecnologías 454 de Roche, comparaciones con otros sistemas de secuenciación masiva paralela, y aplicaciones como el estudio de quasiespecies virales, secuenciación de genomas de novo, metagenómica, RNA-seq, y análisis de exomas y mutaciones en leucemia mediante arrays de captura de secuencia. El curso también cubre el análisis de datos de secuenciación masiva paralela.
More from VHIR Vall d’Hebron Institut de Recerca (20)
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...AbdullaAlAsif1
The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
The debris of the ‘last major merger’ is dynamically youngSérgio Sacani
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
‘last major merger.’ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1–2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the ‘last major merger’
did not collide with the MW proto-disc at early times, as is thought for the GSE, but instead collided with the MW disc within
the last few Gyr, consistent with the body of work surrounding the VRM.
ESPP presentation to EU Waste Water Network, 4th June 2024 “EU policies driving nutrient removal and recycling
and the revised UWWTD (Urban Waste Water Treatment Directive)”
The binding of cosmological structures by massless topological defectsSérgio Sacani
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
mitigated, at least in part.
BREEDING METHODS FOR DISEASE RESISTANCE.pptxRASHMI M G
Plant breeding for disease resistance is a strategy to reduce crop losses caused by disease. Plants have an innate immune system that allows them to recognize pathogens and provide resistance. However, breeding for long-lasting resistance often involves combining multiple resistance genes
ANAMOLOUS SECONDARY GROWTH IN DICOT ROOTS.pptxRASHMI M G
Abnormal or anomalous secondary growth in plants. It defines secondary growth as an increase in plant girth due to vascular cambium or cork cambium. Anomalous secondary growth does not follow the normal pattern of a single vascular cambium producing xylem internally and phloem externally.
Phenomics assisted breeding in crop improvementIshaGoswami9
As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate
change, and increasing global population, crop yield and quality need to be improved in a sustainable way over the coming decades. Genetic improvement by breeding is the best way to increase crop productivity. With the rapid progression of functional
genomics, an increasing number of crop genomes have been sequenced and dozens of genes influencing key agronomic traits have been identified. However, current genome sequence information has not been adequately exploited for understanding
the complex characteristics of multiple gene, owing to a lack of crop phenotypic data. Efficient, automatic, and accurate technologies and platforms that can capture phenotypic data that can
be linked to genomics information for crop improvement at all growth stages have become as important as genotyping. Thus,
high-throughput phenotyping has become the major bottleneck restricting crop breeding. Plant phenomics has been defined as the high-throughput, accurate acquisition and analysis of multi-dimensional phenotypes
during crop growing stages at the organism level, including the cell, tissue, organ, individual plant, plot, and field levels. With the rapid development of novel sensors, imaging technology,
and analysis methods, numerous infrastructure platforms have been developed for phenotyping.
Or: Beyond linear.
Abstract: Equivariant neural networks are neural networks that incorporate symmetries. The nonlinear activation functions in these networks result in interesting nonlinear equivariant maps between simple representations, and motivate the key player of this talk: piecewise linear representation theory.
Disclaimer: No one is perfect, so please mind that there might be mistakes and typos.
dtubbenhauer@gmail.com
Corrected slides: dtubbenhauer.com/talks.html
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
Slides from talk:
Aleš Zamuda: Remote Sensing and Computational, Evolutionary, Supercomputing, and Intelligent Systems.
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
https://www.etran.rs/2024/en/home-english/
Introduction to Functional Analysis with IPA (UEB-UAT Bioinformatics Course - Session 4.2 - VHIR, Barcelona)
1. Hospital Universitari Vall d’Hebron
Institut de Recerca - VHIR
Institut d’Investigació Sanitària de l’Instituto de Salud Carlos III (ISCIII)
Bioinformàtica per la
Recerca Biomèdica
http://ueb.vhir.org/2014BRB
Ferran Briansó
ferran.brianso@vhir.org
22/05/2014
INTRODUCTION TO
FUNCTIONAL ANALYSIS
2. 1. WORKFLOW ANALYSIS EXAMPLE
2. GENE (OR WHATEVER) LIST(S)
3. FROM LISTS TO BIOLOGY
4. BENEFITS (AND DRAWBACKS)
5. BASIC EXAMPLE
6. FUNCTIONAL ANALYSIS TOOLS
7. INGENUITY PATHWAY ANALYSIS
●
The Ingenuity Vision
●
IPA Knowledge Base
●
IPA Definitions
●
Tips & Hints for Expression Analyses
1
2
3
5
6
PRESENTATION OUTLINE
4
7
5. 5
FROM LISTS TO BIOLOGY3
●
Classical approach for gene list analysis: one
by one
– Literature, databases, ...
●
Problem:
– Slow and tedious task, and what is worst...
– Ignores possible interactions
●
Alternative approach: functional analysis (aka
biological significance)
6. 6
BENEFITS (AND DRAWBACKS)4
✔
Authomatic methods for
✔
Identification of biological processes associated with experimental
results.
✔
Determination/Comparison of common functions in selected groups
of genes.
✔
Analisys of connections between genes, molecules and/or diseases
through literature mining, in order to find relevant associations
according with experimental data.
✔
Make auxiliary information more accessible
✔
Contribute to the understanding of the underlying biological
phenomena
✗
Require more sofisticated software & hardware
✗
Depend on the degree of curation of the data sources
10. FUNCTIONAL ANALYSIS TOOLS
10
6
●
Several tools deployed in the last 15 years
http://estbioinfo.stat.ub.es/resources/index.html
●
Direct study of gene lists
– Based on GO or other BD (KEGG...)
●
fatiGO, DAVID, GSEA, Babelomics ... [SerbGO]
●
Ingenuity Pathways Analysis
●
Mining relationships from literature
– PubMed, Scopus, HighWire, GOPubMed, …
– Ingenuity Pathways Analysis
●
Analysis of pathways inferred from the lists
– Pathway Explorer, MappFinder, GenMapp ...
– Ingenuity Pathway Analysis