Este documento presenta una revista mensual sobre seguridad informática y hacking. Proporciona definiciones de términos como "hacker" y discute la intención de la publicación de educar a lectores sobre tecnología sin fomentar actividades ilegales. También incluye una lista de hackers y pioneros de la tecnología famosos.
Este documento presenta una revista mensual sobre seguridad informática y hacking. Proporciona definiciones de términos como "hacker" y discute la intención de la publicación de educar a lectores sobre tecnología sin fomentar actividades ilegales. También incluye una lista de hackers y pioneros de la tecnología famosos.
Este documento presenta un artículo de la revista "Los Cuadernos de HACK X CRACK" que trata sobre los rootkits y su impacto en la seguridad informática. El artículo comienza con una introducción sobre los rootkits y su capacidad de ocultar su presencia en un sistema comprometido, lo que representa una pesadilla para los administradores. Además, incluye secciones sobre aprender a compilar programas, explotar vulnerabilidades de NetBIOS y otras técnicas de hacking.
Global Medical Cures™ | New York Cancer Incidence Rates
DISCLAIMER-
Global Medical Cures™ does not offer any medical advice, diagnosis, treatment or recommendations. Only your healthcare provider/physician can offer you information and recommendations for you to decide about your healthcare choices.
Resumo em evento. Citação:
GONÇALVES, P. A. S.;BOFF, P. PREPARADOS HOMEOPÁTICOS NO MANEJO FITOSSANITÁRIO E RENDIMENTO DE CEBOLA EM SISTEMA ORGÂNICO . In: SIMPÓSIO INTERNACIONAL CIÊNCIA, SAÚDE E TERRITÓRIO, 4, 2017, Lages. Anais... Lages: UNIPLAC, 2017. p. 442-448.
Solving Cross-Domain Issues When Building Mashupsmehmetakin
When building Mashups, you need to consider different techniques to solve the cross-domain issue that is caused by the browser's Same Origin Policy. This session gives you an overview of possible techniques to overcome that problem. Starting with client-side solutions including JSONP, iframes and usage of the browser window object, server-side solutions like Apache’s mod_rewrite module or IBM’s Ajax Proxy as well as proprietary solutions including browser plug-ins, applets, signed scripts and Internet Explorer 8’s XDomainRequest are explored. The session will also cover cross-document messaging that was added in HTML 5 and give an overview of other cross-domain access proposals.
Here are the steps to visualize a potential indel region after realignment:
1. Run GATK IndelRealigner on the target list:
java -jar $EBROOTGATK/GenomeAnalysisTK.jar -T IndelRealigner -R ../human_g1k_v37.fasta -I sample.dedup.bam -targetIntervals sample.intervals -o sample.realigned.bam
2. Index the realigned BAM:
samtools index sample.realigned.bam
3. Load the realigned BAM into IGV and navigate to a region of interest from the target list (sample.intervals).
4. In I
This document discusses phylogenetic analysis and tree building. It introduces the Bioinformatics and Computational Biology Branch (BCBB) group and their work analyzing biological sequences and constructing phylogenetic trees. The document explains why biological sequences are important to analyze and compares sequences to understand relatedness and evolution. It also covers multiple sequence alignment, substitution models, and algorithms for building trees, including neighbor-joining.
The webinar covered new features and updates to the Nephele 2.0 bioinformatics analysis platform. Key updates included a new website interface, improved performance through a new infrastructure framework, the ability to resubmit jobs by ID, and interactive mapping file submission. New pipelines for 16S analysis using DADA2 and quality control preprocessing were introduced, and the existing 16S mothur pipeline was updated. The quality control pipeline provides tools to assess data quality before running microbiome analyses through FastQC, primer/adapter trimming with cutadapt, and additional quality filtering options. The webinar emphasized the importance of data quality checks and highlighted troubleshooting tips such as examining the log file for error messages when jobs fail.
1) METAGENOTE is a new web-based tool for annotating genomic samples and submitting metadata and sequencing files to the Sequence Read Archive (SRA) at the National Center for Biotechnology Information (NCBI).
2) It provides templates and controlled vocabularies to streamline sample metadata annotation using existing ontologies and standards. This allows for easier cross-study comparisons.
3) The demonstration showed how to use METAGENOTE's interface to annotate a mouse ear skin sample with terms from relevant ontologies, import additional annotations in batch, and submit the metadata and files to NCBI SRA through a 5-step wizard.
This document provides an introduction to homology modeling using computational tools like I-TASSER and Phyre2. It discusses how homology modeling can be used to generate 3D structural models of proteins when an experimental structure is not available. The document addresses common questions from users and outlines the I-TASSER modeling pipeline. Hands-on exercises are provided to allow users to run homology modeling tools and examine the resulting models.
This document summarizes different computational methods for protein structure prediction, including homology modeling, fold recognition, threading, and ab initio modeling. Homology modeling relies on identifying proteins with similar sequences and known structures. Fold recognition and threading can be used when there are no homologs, to identify proteins with the same overall fold but different sequences. Ab initio modeling uses physics-based modeling and protein fragments to predict structure from sequence alone, and has challenges due to the vast number of possible conformations.
Homology modeling is a computational technique for predicting the structure of a protein target based on its sequence similarity to proteins with known structures, and it involves finding a suitable template, aligning the target and template sequences, building a 3D model of the target, and evaluating the model quality. While experimental methods like X-ray crystallography and NMR can determine protein structures, they have limitations in terms of which proteins can be studied, so computational methods like homology modeling are needed to predict structures for the many proteins whose structures remain unknown.
The document discusses function prediction for unknown proteins. It begins with an overview of common methods for function prediction, including sequence and structure similarity, domains and motifs, gene expression, and interactions. It then uses a protein called Msa as a case study, analyzing it with various tools and finding evidence it may function as a signal transducer in bacterial response to environment. Finally, it briefly discusses another protein M46 and challenges in evaluating prediction accuracy.
Este documento presenta un artículo de la revista "Los Cuadernos de HACK X CRACK" que trata sobre los rootkits y su impacto en la seguridad informática. El artículo comienza con una introducción sobre los rootkits y su capacidad de ocultar su presencia en un sistema comprometido, lo que representa una pesadilla para los administradores. Además, incluye secciones sobre aprender a compilar programas, explotar vulnerabilidades de NetBIOS y otras técnicas de hacking.
Global Medical Cures™ | New York Cancer Incidence Rates
DISCLAIMER-
Global Medical Cures™ does not offer any medical advice, diagnosis, treatment or recommendations. Only your healthcare provider/physician can offer you information and recommendations for you to decide about your healthcare choices.
Resumo em evento. Citação:
GONÇALVES, P. A. S.;BOFF, P. PREPARADOS HOMEOPÁTICOS NO MANEJO FITOSSANITÁRIO E RENDIMENTO DE CEBOLA EM SISTEMA ORGÂNICO . In: SIMPÓSIO INTERNACIONAL CIÊNCIA, SAÚDE E TERRITÓRIO, 4, 2017, Lages. Anais... Lages: UNIPLAC, 2017. p. 442-448.
Solving Cross-Domain Issues When Building Mashupsmehmetakin
When building Mashups, you need to consider different techniques to solve the cross-domain issue that is caused by the browser's Same Origin Policy. This session gives you an overview of possible techniques to overcome that problem. Starting with client-side solutions including JSONP, iframes and usage of the browser window object, server-side solutions like Apache’s mod_rewrite module or IBM’s Ajax Proxy as well as proprietary solutions including browser plug-ins, applets, signed scripts and Internet Explorer 8’s XDomainRequest are explored. The session will also cover cross-document messaging that was added in HTML 5 and give an overview of other cross-domain access proposals.
Here are the steps to visualize a potential indel region after realignment:
1. Run GATK IndelRealigner on the target list:
java -jar $EBROOTGATK/GenomeAnalysisTK.jar -T IndelRealigner -R ../human_g1k_v37.fasta -I sample.dedup.bam -targetIntervals sample.intervals -o sample.realigned.bam
2. Index the realigned BAM:
samtools index sample.realigned.bam
3. Load the realigned BAM into IGV and navigate to a region of interest from the target list (sample.intervals).
4. In I
This document discusses phylogenetic analysis and tree building. It introduces the Bioinformatics and Computational Biology Branch (BCBB) group and their work analyzing biological sequences and constructing phylogenetic trees. The document explains why biological sequences are important to analyze and compares sequences to understand relatedness and evolution. It also covers multiple sequence alignment, substitution models, and algorithms for building trees, including neighbor-joining.
The webinar covered new features and updates to the Nephele 2.0 bioinformatics analysis platform. Key updates included a new website interface, improved performance through a new infrastructure framework, the ability to resubmit jobs by ID, and interactive mapping file submission. New pipelines for 16S analysis using DADA2 and quality control preprocessing were introduced, and the existing 16S mothur pipeline was updated. The quality control pipeline provides tools to assess data quality before running microbiome analyses through FastQC, primer/adapter trimming with cutadapt, and additional quality filtering options. The webinar emphasized the importance of data quality checks and highlighted troubleshooting tips such as examining the log file for error messages when jobs fail.
1) METAGENOTE is a new web-based tool for annotating genomic samples and submitting metadata and sequencing files to the Sequence Read Archive (SRA) at the National Center for Biotechnology Information (NCBI).
2) It provides templates and controlled vocabularies to streamline sample metadata annotation using existing ontologies and standards. This allows for easier cross-study comparisons.
3) The demonstration showed how to use METAGENOTE's interface to annotate a mouse ear skin sample with terms from relevant ontologies, import additional annotations in batch, and submit the metadata and files to NCBI SRA through a 5-step wizard.
This document provides an introduction to homology modeling using computational tools like I-TASSER and Phyre2. It discusses how homology modeling can be used to generate 3D structural models of proteins when an experimental structure is not available. The document addresses common questions from users and outlines the I-TASSER modeling pipeline. Hands-on exercises are provided to allow users to run homology modeling tools and examine the resulting models.
This document summarizes different computational methods for protein structure prediction, including homology modeling, fold recognition, threading, and ab initio modeling. Homology modeling relies on identifying proteins with similar sequences and known structures. Fold recognition and threading can be used when there are no homologs, to identify proteins with the same overall fold but different sequences. Ab initio modeling uses physics-based modeling and protein fragments to predict structure from sequence alone, and has challenges due to the vast number of possible conformations.
Homology modeling is a computational technique for predicting the structure of a protein target based on its sequence similarity to proteins with known structures, and it involves finding a suitable template, aligning the target and template sequences, building a 3D model of the target, and evaluating the model quality. While experimental methods like X-ray crystallography and NMR can determine protein structures, they have limitations in terms of which proteins can be studied, so computational methods like homology modeling are needed to predict structures for the many proteins whose structures remain unknown.
The document discusses function prediction for unknown proteins. It begins with an overview of common methods for function prediction, including sequence and structure similarity, domains and motifs, gene expression, and interactions. It then uses a protein called Msa as a case study, analyzing it with various tools and finding evidence it may function as a signal transducer in bacterial response to environment. Finally, it briefly discusses another protein M46 and challenges in evaluating prediction accuracy.
This presentation discusses protein structure prediction using Rosetta. It begins with an overview of the Critical Assessment of Protein Structure Prediction (CASP) experiments and notes that Rosetta is one of the top performing free-modeling servers. The presentation then describes the basic ab initio protocol used by Rosetta, which involves fragment insertion, scoring, and refinement. It also discusses limitations and success rates. Key aspects of the Rosetta energy functions and sampling algorithms are presented. Examples of specific Rosetta applications including low-resolution modeling and refinement are provided.
This document provides an outline for a presentation on biological networks, including introducing biological networks, describing their basic components and types, methods for predicting and building networks, sources of interaction data, tools for network visualization and analysis, and a demonstration of building, visualizing and analyzing biological networks using Cytoscape. The presentation covers topics like nodes and edges in networks, features used to analyze networks, methods for predicting networks from sequences and omics data, integrated databases for interaction data, and popular tools for searching, visualizing and performing network analysis.
This document provides an overview and introduction to using the command line interface and submitting jobs to the NIAID High Performance Computing (HPC) Cluster. The objectives are to learn basic Unix commands, practice file manipulation from the command line, and submit a job to the HPC cluster. The document covers topics such as the anatomy of the terminal, navigating directories, common commands, tips for using the command line more efficiently, accessing and mounting drives on the HPC cluster, and an overview of the cluster queue system.
This document provides an overview of statistical analyses that can be performed in PRISM. It discusses how to perform common statistical tests like t-tests, ANOVA, linear regression, and summarizes the appropriate tests to address different research questions. Examples are given of how to analyze pre-post treatment data using paired t-tests and compare groups using independent t-tests or ANOVA. Guidance is also provided on interpreting results and checking assumptions.
1) JMP is statistical software that allows for easy import, organization, and analysis of data. It features spreadsheet-like data tables, powerful statistical modeling capabilities, and customizable graphics.
2) The document reviews various features of JMP including importing data, organizing data tables, performing statistical analyses through platforms like distribution and fit model, and creating graphs and reports.
3) Assistance is available for using JMP through free training, support contacts, and detailed help menus within the software. JMP allows for both simple and advanced statistical analysis of data.
This document discusses methods for analyzing categorical data and response variables, including contingency tables, chi-square tests, Fisher's exact test, odds ratios, logistic regression, and generalized linear models. Contingency tables are used to display relationships between categorical variables and tests of independence. Fisher's exact test and chi-square tests determine if a relationship is statistically significant. Odds ratios and relative risk indicate the magnitude of relationships. Logistic regression models relationships between continuous predictors and categorical responses. Generalized linear models extend these methods.
This document provides a training manual on better graphics in R. It begins with an overview of R and BioConductor and reviews basic R functions. It then covers creating simple and customized graphics, multi-step graphics with legends, and multi-panel layouts. The manual aims to help researchers learn visualization techniques to improve the communication of their data and results.
This document describes two web tools that were created using R to automate biostatistics workflows: HDX NAME and DRAP. HDX NAME analyzes hydrogen-deuterium exchange mass spectrometry data to estimate protein flexibility. It computes protection factors, compares groups, and maps results to protein structures. DRAP fits logistic dose-response curves to drug screening data from multiple plates. It automates curve fitting, compares results, and exports summaries. Both tools were created with R on the backend for analysis and web interfaces for usability. This allows researchers to perform complex analyses without programming expertise.
This document discusses several common problems with data handling and quality including building and testing models with the same data, confusion between biological and technical replicates, and identification and handling of outliers. It provides examples and explanations of key concepts such as experimental and sampling units, pseudo-replication, outliers versus high influence points, and leverage plots. The importance of proper data handling techniques like dividing data into training, test, and confirmation sets and using cross-validation is emphasized to avoid overfitting models and generating spurious findings.
The document provides an overview of statistical testing, including:
- When to use parametric vs. nonparametric tests
- When large sample tests or exact tests are needed
- When adjustments for multiple testing are required
It discusses key concepts like null and alternative hypotheses, test statistics, p-values, and type I and II errors. Examples of the Student's t-test and Wilcoxon rank sum test are provided.
This document summarizes a presentation on curve fitting using GraphPad Prism. It discusses nonlinear regression techniques for analyzing dose-response and binding curve data commonly used by biologists. Specific nonlinear regression models like sigmoidal dose-response curves are described. The document provides guidance on choosing and fitting appropriate models, evaluating model fit, and improving model fit if needed.
This document provides solutions to sample problems using various datasets. It demonstrates how to use R functions like bargraph.CI(), boxplot(), hist(), and table() to analyze and visualize data. For example, it shows how to create bar charts comparing mean BMI by gender and mean AFP difference by drug concentration using the bargraph.CI() function from the sciplot package. It also provides solutions for manipulating datasets, such as recoding a variable or sorting and subsetting data.
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