Building SADI Services Tutorial - SIB Workshop, Geneva, December 2015Mark Wilkinson
The primary slide deck for the SADI tutorial. We explain the motivation, simple SADI services, more complex SADI services, and then do a detailed walk-through of building a service, including the Perl service code and examples of service invocation at the command line, and using the SHARE client. You will want to look at the sample data/queries in this slide deck: http://www.slideshare.net/markmoby/sample-data-and-other-ur-ls-55737183 and the example service code in this slide deck: http://www.slideshare.net/markmoby/example-code-for-the-sadi-bmi-calculator-web-service?related=1
Este documento ofrece recomendaciones de alimentos y sus beneficios para la salud para diferentes problemas de salud como dolor de cabeza, fiebre, derrame cerebral, insomnio, asma, artritis, estómago revuelto, infección en la vejiga, huesos, falta de memoria, resfriados, tos, cáncer de mama, cáncer de pulmón, úlceras, diarrea, endurecimiento de arterias, alta presión sanguínea, irregularidades en los niveles de azúcar en la sangre y más
Este documento describe cómo varios alimentos se asemejan a diferentes órganos y partes del cuerpo humano, y cómo cada uno de estos alimentos ayuda a mantener la salud de la parte del cuerpo a la que se asemeja. Se proporcionan ejemplos como las zanahorias que se parecen a los ojos y ayudan a la vista, los tomates que se parecen al corazón y son buenos para el corazón, y las nueces que se parecen al cerebro y son buenas para el cerebro. El documento sugiere que Dios diseñó
The document describes how to install and use the SADI plugin in Taverna to build a workflow querying biological data from various SADI services. The workflow is designed to take a KEGG pathway as input and output the genes, proteins and protein sequences involved in that pathway by connecting three SADI services: getKEGGGenesByPathway to retrieve genes from a pathway, getUniprotByKeggGene to get corresponding proteins, and UniProt info to get protein sequences. The workflow is executed using the sample pathway "hsa00232" and the results are viewed in Taverna.
Apache Sirona is an open source monitoring solution for Java applications. It provides simple Gauge and Counter objects to collect metrics. Gauges measure values like memory usage and thread counts, while Counters aggregate metrics like response times and concurrency levels. Metrics can be stored in memory, Cassandra, or Graphite. A central Collector webapp is available to view aggregated reports from multiple instances. Sirona uses a plugin architecture and aims to integrate monitoring natively into applications without external dependencies.
SWAT4LS 2011: SADI Knowledge Explorer Plug-inMark Wilkinson
my presentation of the SADI plug-in to the IO Informatics' Knowledge Explorer. Presented at SWAT4LS (Semantic Web Applications and Tools for Life Sciences), London, UK, December, 2011. It describes how we resolve identifiers to semantic metadata in a variety of ways in order to boot-strap the semantics required to do service discovery and matching. It also describes how we convert OWL classes into approximately matching SPARQL queries, and store these queries in the SADI registry such that, after service discovery, it is simple to extract the data a service requires as its input.
Science in the Web, from hypothesis to result. Publishing in silico experiments IN the Web allows us to immediately and precisely disseminate new knowledge that can affect other Web Science experiments. This is the "singularity" where a new discovery is immediately put into practice
Este documento proporciona orientaciones para que las instituciones de formación para el trabajo ajusten sus programas bajo el enfoque de competencias. Explica las características de una oferta basada en competencias y analiza los momentos clave de la implementación de programas por competencias, como el enfoque del proyecto educativo institucional, la pertinencia de la oferta, la denominación, los perfiles y mapas de competencias, el diseño curricular, los procesos de formación y la evaluación de aprendizajes. Adicionalmente, brinda recom
Building SADI Services Tutorial - SIB Workshop, Geneva, December 2015Mark Wilkinson
The primary slide deck for the SADI tutorial. We explain the motivation, simple SADI services, more complex SADI services, and then do a detailed walk-through of building a service, including the Perl service code and examples of service invocation at the command line, and using the SHARE client. You will want to look at the sample data/queries in this slide deck: http://www.slideshare.net/markmoby/sample-data-and-other-ur-ls-55737183 and the example service code in this slide deck: http://www.slideshare.net/markmoby/example-code-for-the-sadi-bmi-calculator-web-service?related=1
Este documento ofrece recomendaciones de alimentos y sus beneficios para la salud para diferentes problemas de salud como dolor de cabeza, fiebre, derrame cerebral, insomnio, asma, artritis, estómago revuelto, infección en la vejiga, huesos, falta de memoria, resfriados, tos, cáncer de mama, cáncer de pulmón, úlceras, diarrea, endurecimiento de arterias, alta presión sanguínea, irregularidades en los niveles de azúcar en la sangre y más
Este documento describe cómo varios alimentos se asemejan a diferentes órganos y partes del cuerpo humano, y cómo cada uno de estos alimentos ayuda a mantener la salud de la parte del cuerpo a la que se asemeja. Se proporcionan ejemplos como las zanahorias que se parecen a los ojos y ayudan a la vista, los tomates que se parecen al corazón y son buenos para el corazón, y las nueces que se parecen al cerebro y son buenas para el cerebro. El documento sugiere que Dios diseñó
The document describes how to install and use the SADI plugin in Taverna to build a workflow querying biological data from various SADI services. The workflow is designed to take a KEGG pathway as input and output the genes, proteins and protein sequences involved in that pathway by connecting three SADI services: getKEGGGenesByPathway to retrieve genes from a pathway, getUniprotByKeggGene to get corresponding proteins, and UniProt info to get protein sequences. The workflow is executed using the sample pathway "hsa00232" and the results are viewed in Taverna.
Apache Sirona is an open source monitoring solution for Java applications. It provides simple Gauge and Counter objects to collect metrics. Gauges measure values like memory usage and thread counts, while Counters aggregate metrics like response times and concurrency levels. Metrics can be stored in memory, Cassandra, or Graphite. A central Collector webapp is available to view aggregated reports from multiple instances. Sirona uses a plugin architecture and aims to integrate monitoring natively into applications without external dependencies.
SWAT4LS 2011: SADI Knowledge Explorer Plug-inMark Wilkinson
my presentation of the SADI plug-in to the IO Informatics' Knowledge Explorer. Presented at SWAT4LS (Semantic Web Applications and Tools for Life Sciences), London, UK, December, 2011. It describes how we resolve identifiers to semantic metadata in a variety of ways in order to boot-strap the semantics required to do service discovery and matching. It also describes how we convert OWL classes into approximately matching SPARQL queries, and store these queries in the SADI registry such that, after service discovery, it is simple to extract the data a service requires as its input.
Science in the Web, from hypothesis to result. Publishing in silico experiments IN the Web allows us to immediately and precisely disseminate new knowledge that can affect other Web Science experiments. This is the "singularity" where a new discovery is immediately put into practice
Este documento proporciona orientaciones para que las instituciones de formación para el trabajo ajusten sus programas bajo el enfoque de competencias. Explica las características de una oferta basada en competencias y analiza los momentos clave de la implementación de programas por competencias, como el enfoque del proyecto educativo institucional, la pertinencia de la oferta, la denominación, los perfiles y mapas de competencias, el diseño curricular, los procesos de formación y la evaluación de aprendizajes. Adicionalmente, brinda recom
The document discusses rules for using the library. It states that the library is a place for study, investigation, and learning. Children are learning to use the library, while older students must set a good example by following rules such as placing bags in lockers upon entrance, remaining quiet, not using electronics, and being respectful of others. Following the rules properly maintains the library as a productive learning environment.
El documento presenta un "menú cuaresmal" con alimentos y bebidas espirituales recomendadas para la Cuaresma, incluyendo la caridad, la atención a los desamparados, la alegría y el perdón, en contraste con vicios como los chismes y la envidia que se deben evitar. El autor anónimo finalmente recomienda sobre todo "el alimento espiritual" de recibir el cuerpo y la sangre de Cristo para tener vida eterna, de acuerdo con Juan 6:54-56.
Este documento ofrece consejos sobre cómo enfrentar los buenos y malos días, y cómo aprender y crecer de las experiencias. Afirma que los buenos días traen felicidad, los malos días traen experiencia, la felicidad y los intentos nos mantienen positivos, y solo Dios puede guiarnos a través de todo.
This document provides steps to run an enrichment analysis in Gitools to test which KEGG pathways are enriched among genes significantly up-regulated in different cancer types. The steps include: 1) selecting enrichment analysis, 2) loading a continuous data matrix and selecting significantly up-regulated genes, 3) running a binomial test, 4) naming and saving the analysis, and 5) viewing results in a heatmap where columns are cancer types and rows are enriched KEGG pathways.
This document provides steps to export the results of an enrichment analysis as an image heatmap, table, or matrix from the Gitools analysis platform. It describes exporting the heatmap image in various formats, exporting a table with selected analysis parameters and their order, and exporting a matrix file with values for a selected parameter. The exports create new files that contain visualizations or data from the enrichment analysis for further use.
The document outlines the speakers and topics at the 2015 UX Munich conference, including efficient design processes that contribute to products, lean design approaches like crafting and building together, prototyping with different focuses and branding, creating flexible modules instead of pixel-perfect screens, knowing your skills and potentials, having an attitude and philosophy, learning from failures, and making your employees happy at work.
The Semantic Web - This time... its PersonalMark Wilkinson
My presentation on SADI, SHARE, CardioSHARE, and the new iConsent project. Presented to the faculty and students at Stanford Medical Informatics, Palo Alto, USA. May 14th, 2010.
How do we make the semantic web, and medical research, more personal? (both for the researcher and for the patient) I present some ideas we're exploring
This is a brief version of earlier talks, but I think it might explain more emphatically what I think Web Science is, and why I believe it is realistic, and how SADI/SHARE technologies (or technologies like them) are important to achieve the vision
Encouraging Curriculum Change in the NetherlandsLuc Sluijsmans
In the contribution we will discuss the challenges of schools and teachers in taking up local curriculum development activities and the challenges of educational partners at various system levels (such as policy-makers, support agencies, test developers, textbook developers, pre- and in-service education, and inspectorate) to encourage schools and teachers to address curriculum change. Moreover, we will propose a mutual adaptation approach as the best fit. This approach would consist of public curriculum debates, attention to curriculum capacity building of teachers and school leaders, balanced curriculum autonomy and guidance, and balanced curriculum dynamics and stability, all of which will lead to common responsibility for curriculum change.
This document provides steps to explore and customize the results of an enrichment analysis in a heatmap visualization tool. It describes how to sort and filter rows and columns, change the labels to use more descriptive names instead of IDs, and modify the color scale to better represent p-value results. The goal is to interactively investigate and understand the relationships between enriched gene sets and conditions from the analysis.
Cristóvão Buarque, ministro de educación de Brasil, respondió a la sugerencia de internacionalizar la Amazonía diciendo que, aunque los gobiernos no la cuidan debidamente, la Amazonía pertenece a Brasil y los países amazónicos. Sin embargo, desde una perspectiva humanista, otros recursos naturales y culturales deberían internacionalizarse antes, como las reservas de petróleo, el capital financiero de los países ricos, y los principales museos del mundo. Buarque argumentó que si los estadounidenses quieren internacionalizar
Final version of my presentation to BioIT World Congress, Boston MA, April 22, 2010.
Describes how we're using the SADI Semantic Web Service framework to begin personalizing medical research.
The document discusses the motivation for developing Semantic Automated Discovery and Integration (SADI) services as a way to represent important information that cannot be represented directly on the Semantic Web, such as data from analytical algorithms and statistical analyses, and presents SADI as a design pattern for making web services interoperable with the Semantic Web by explicitly labeling the relationships between entities.
The document outlines various customer relationship marketing blueprints using iMarketing automation. It provides visual step-by-step templates for lead generation, nurture campaigns, newsletters, sales qualification, targeted campaigns, and multimode upsells. The blueprints are designed to illustrate typical communication interactions with prospective and current customers from initial lead generation through event marketing and retaining customers.
This tutorial summarizes the steps to analyze gene modules from a dataset using the Gitools analysis platform. The key steps are:
1. Import a continuous data matrix file from IntOGen containing corrected p-values for gene upregulation in different cancer types.
2. Load the continuous data matrix and transform it to a binary matrix using a p-value threshold of 0.05.
3. Load a file containing gene modules to analyze for enrichment.
4. Run a binomial test enrichment analysis and view the results heatmap showing enriched modules for each cancer type.
5. Use the properties window to change column labels from IDs to actual cancer type names for easier interpretation.
Exploring the power and benefits of using WordPress plugins, how to build a WordPress plugin in a few simple steps, plus a good solid list of plugin resources.
The document discusses rules for using the library. It states that the library is a place for study, investigation, and learning. Children are learning to use the library, while older students must set a good example by following rules such as placing bags in lockers upon entrance, remaining quiet, not using electronics, and being respectful of others. Following the rules properly maintains the library as a productive learning environment.
El documento presenta un "menú cuaresmal" con alimentos y bebidas espirituales recomendadas para la Cuaresma, incluyendo la caridad, la atención a los desamparados, la alegría y el perdón, en contraste con vicios como los chismes y la envidia que se deben evitar. El autor anónimo finalmente recomienda sobre todo "el alimento espiritual" de recibir el cuerpo y la sangre de Cristo para tener vida eterna, de acuerdo con Juan 6:54-56.
Este documento ofrece consejos sobre cómo enfrentar los buenos y malos días, y cómo aprender y crecer de las experiencias. Afirma que los buenos días traen felicidad, los malos días traen experiencia, la felicidad y los intentos nos mantienen positivos, y solo Dios puede guiarnos a través de todo.
This document provides steps to run an enrichment analysis in Gitools to test which KEGG pathways are enriched among genes significantly up-regulated in different cancer types. The steps include: 1) selecting enrichment analysis, 2) loading a continuous data matrix and selecting significantly up-regulated genes, 3) running a binomial test, 4) naming and saving the analysis, and 5) viewing results in a heatmap where columns are cancer types and rows are enriched KEGG pathways.
This document provides steps to export the results of an enrichment analysis as an image heatmap, table, or matrix from the Gitools analysis platform. It describes exporting the heatmap image in various formats, exporting a table with selected analysis parameters and their order, and exporting a matrix file with values for a selected parameter. The exports create new files that contain visualizations or data from the enrichment analysis for further use.
The document outlines the speakers and topics at the 2015 UX Munich conference, including efficient design processes that contribute to products, lean design approaches like crafting and building together, prototyping with different focuses and branding, creating flexible modules instead of pixel-perfect screens, knowing your skills and potentials, having an attitude and philosophy, learning from failures, and making your employees happy at work.
The Semantic Web - This time... its PersonalMark Wilkinson
My presentation on SADI, SHARE, CardioSHARE, and the new iConsent project. Presented to the faculty and students at Stanford Medical Informatics, Palo Alto, USA. May 14th, 2010.
How do we make the semantic web, and medical research, more personal? (both for the researcher and for the patient) I present some ideas we're exploring
This is a brief version of earlier talks, but I think it might explain more emphatically what I think Web Science is, and why I believe it is realistic, and how SADI/SHARE technologies (or technologies like them) are important to achieve the vision
Encouraging Curriculum Change in the NetherlandsLuc Sluijsmans
In the contribution we will discuss the challenges of schools and teachers in taking up local curriculum development activities and the challenges of educational partners at various system levels (such as policy-makers, support agencies, test developers, textbook developers, pre- and in-service education, and inspectorate) to encourage schools and teachers to address curriculum change. Moreover, we will propose a mutual adaptation approach as the best fit. This approach would consist of public curriculum debates, attention to curriculum capacity building of teachers and school leaders, balanced curriculum autonomy and guidance, and balanced curriculum dynamics and stability, all of which will lead to common responsibility for curriculum change.
This document provides steps to explore and customize the results of an enrichment analysis in a heatmap visualization tool. It describes how to sort and filter rows and columns, change the labels to use more descriptive names instead of IDs, and modify the color scale to better represent p-value results. The goal is to interactively investigate and understand the relationships between enriched gene sets and conditions from the analysis.
Cristóvão Buarque, ministro de educación de Brasil, respondió a la sugerencia de internacionalizar la Amazonía diciendo que, aunque los gobiernos no la cuidan debidamente, la Amazonía pertenece a Brasil y los países amazónicos. Sin embargo, desde una perspectiva humanista, otros recursos naturales y culturales deberían internacionalizarse antes, como las reservas de petróleo, el capital financiero de los países ricos, y los principales museos del mundo. Buarque argumentó que si los estadounidenses quieren internacionalizar
Final version of my presentation to BioIT World Congress, Boston MA, April 22, 2010.
Describes how we're using the SADI Semantic Web Service framework to begin personalizing medical research.
The document discusses the motivation for developing Semantic Automated Discovery and Integration (SADI) services as a way to represent important information that cannot be represented directly on the Semantic Web, such as data from analytical algorithms and statistical analyses, and presents SADI as a design pattern for making web services interoperable with the Semantic Web by explicitly labeling the relationships between entities.
The document outlines various customer relationship marketing blueprints using iMarketing automation. It provides visual step-by-step templates for lead generation, nurture campaigns, newsletters, sales qualification, targeted campaigns, and multimode upsells. The blueprints are designed to illustrate typical communication interactions with prospective and current customers from initial lead generation through event marketing and retaining customers.
This tutorial summarizes the steps to analyze gene modules from a dataset using the Gitools analysis platform. The key steps are:
1. Import a continuous data matrix file from IntOGen containing corrected p-values for gene upregulation in different cancer types.
2. Load the continuous data matrix and transform it to a binary matrix using a p-value threshold of 0.05.
3. Load a file containing gene modules to analyze for enrichment.
4. Run a binomial test enrichment analysis and view the results heatmap showing enriched modules for each cancer type.
5. Use the properties window to change column labels from IDs to actual cancer type names for easier interpretation.
Exploring the power and benefits of using WordPress plugins, how to build a WordPress plugin in a few simple steps, plus a good solid list of plugin resources.
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