Bioinformatics
•
0 likes•128 views
Bioinformatics applies statistics and computer science to molecular biology, mapping and analyzing DNA and protein sequences and comparing sequences between organisms. The workshop taught how bioinformatics is used in scientific investigations by allowing easy access to known data. Participants practiced using bioinformatics databases to find DNA sequences for fibrinogen alpha chains across species, translate DNA to protein sequences, and compare protein sequences between species to understand how bioinformatics works.
Report
Share
Report
Share
Download to read offline
Recommended
Sage
serial analysis gene expression is a transcriptomic technique used by molecular biologists to produce a snapshot of the messenger RNA population in a sample of interest in the form of small tags that correspond to fragments of those transcripts.
Samir Rahman updated Cover Letter
Samir Rahman is currently seeking a research associate position in the biotechnology industry. He has extensive experience using molecular genetics techniques and single molecule resolution microscopy to study gene expression regulation in eukaryotes. For his PhD, Samir investigated the role of long non-coding RNAs in eukaryotic gene transcription using single molecule microscopy and computational tools. One project showed that antisense transcription of an RNA led to complete repression of a gene in yeast. A second paper revealed insights into enhancer RNAs in breast cancer cells and showed that eRNAs are nuclear and rarely co-transcribed with target genes. Samir was awarded a prize for this work and is looking to apply his skills in industry.
Future Computing
This document discusses future computing technologies including DNA computing, membrane computing, and carbon nanotube computing. DNA computing uses DNA molecules to store and process information, using enzymes as software. Membrane computing models biological cells and membranes to develop novel parallel and distributed computing models called P-systems. Carbon nanotube computing could allow for much smaller transistors than silicon, potentially enabling faster and more energy efficient computing through approaches like building nanotube transistors.
Bioinformatics Applications in Biotechnology
This document discusses the role of bioinformatics in biotechnology applications. It summarizes that bioinformatics has become essential for analyzing the vast amounts of genomic data generated from sequencing projects. It provides examples of how bioinformatics tools can be applied to microbial genome analysis, molecular medicine, drug development, next generation sequencing, and more. The document also outlines two major fields of bioinformatics - developing computational tools and databases, and generating biological knowledge to understand living systems.
Introduction to Apollo: A webinar for the i5K Research Community
This document provides an introduction and outline for a webinar on using the Apollo genome annotation editing tool. It was presented by Monica Munoz-Torres of BBOP to the i5K Research Community. The webinar aimed to help participants better understand genome curation in the context of automated and manual annotation. It also aimed to familiarize participants with Apollo's functionality and how to identify homologs of known genes, corroborate gene models using evidence, and modify automated annotations in Apollo. The document includes sections on genome sequencing projects, the objectives and uses of genome annotation, and a biological refresher on concepts relevant to manual annotation like genes, transcription, translation, and genome curation steps.
BiPday 2014 -- Tulipano Angelica
This document summarizes an ncRNA analysis pipeline called nc-aReNA. It describes how nc-aReNA can be used to classify and analyze small non-coding RNAs from deep RNA sequencing data. The pipeline performs tasks such as adapter removal, quality control checks, mapping reads to reference databases to identify known ncRNA classes, filtering of rRNA sequences, quantification of ncRNA expression, differential expression analysis, and identification of isomiRs. Two test cases demonstrating ncRNA classification and differential expression analysis using nc-aReNA on mouse datasets are also described.
Introduction to Apollo: i5K E affinis
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
The i5K, an initiative to sequence the genomes of 5,000 insect and related arthropod species, is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process, and Apollo is serving as the platform to empower this community.
This presentation is an introduction to Apollo for the members of the i5K Pilot Project on Eurytemora affinis
ELIXIR Node poster Italy
The Italian node of ELIXIR, called Elixir-ITA, coordinates existing national bioinformatics services and provides key services to ELIXIR. Led by the National Research Council of Italy, Elixir-ITA includes 12 partners such as universities and high-performance computing groups. It establishes procedures for additional participants to contribute relevant resources through open calls and peer review. Services provided include databases for alternative splicing, untranslated mRNA regions, immunoglobulin sequences, and fungal ribosomal RNA, as well as tools for modeling splicing isoforms and predicting protein disorder.
Recommended
Sage
serial analysis gene expression is a transcriptomic technique used by molecular biologists to produce a snapshot of the messenger RNA population in a sample of interest in the form of small tags that correspond to fragments of those transcripts.
Samir Rahman updated Cover Letter
Samir Rahman is currently seeking a research associate position in the biotechnology industry. He has extensive experience using molecular genetics techniques and single molecule resolution microscopy to study gene expression regulation in eukaryotes. For his PhD, Samir investigated the role of long non-coding RNAs in eukaryotic gene transcription using single molecule microscopy and computational tools. One project showed that antisense transcription of an RNA led to complete repression of a gene in yeast. A second paper revealed insights into enhancer RNAs in breast cancer cells and showed that eRNAs are nuclear and rarely co-transcribed with target genes. Samir was awarded a prize for this work and is looking to apply his skills in industry.
Future Computing
This document discusses future computing technologies including DNA computing, membrane computing, and carbon nanotube computing. DNA computing uses DNA molecules to store and process information, using enzymes as software. Membrane computing models biological cells and membranes to develop novel parallel and distributed computing models called P-systems. Carbon nanotube computing could allow for much smaller transistors than silicon, potentially enabling faster and more energy efficient computing through approaches like building nanotube transistors.
Bioinformatics Applications in Biotechnology
This document discusses the role of bioinformatics in biotechnology applications. It summarizes that bioinformatics has become essential for analyzing the vast amounts of genomic data generated from sequencing projects. It provides examples of how bioinformatics tools can be applied to microbial genome analysis, molecular medicine, drug development, next generation sequencing, and more. The document also outlines two major fields of bioinformatics - developing computational tools and databases, and generating biological knowledge to understand living systems.
Introduction to Apollo: A webinar for the i5K Research Community
This document provides an introduction and outline for a webinar on using the Apollo genome annotation editing tool. It was presented by Monica Munoz-Torres of BBOP to the i5K Research Community. The webinar aimed to help participants better understand genome curation in the context of automated and manual annotation. It also aimed to familiarize participants with Apollo's functionality and how to identify homologs of known genes, corroborate gene models using evidence, and modify automated annotations in Apollo. The document includes sections on genome sequencing projects, the objectives and uses of genome annotation, and a biological refresher on concepts relevant to manual annotation like genes, transcription, translation, and genome curation steps.
BiPday 2014 -- Tulipano Angelica
This document summarizes an ncRNA analysis pipeline called nc-aReNA. It describes how nc-aReNA can be used to classify and analyze small non-coding RNAs from deep RNA sequencing data. The pipeline performs tasks such as adapter removal, quality control checks, mapping reads to reference databases to identify known ncRNA classes, filtering of rRNA sequences, quantification of ncRNA expression, differential expression analysis, and identification of isomiRs. Two test cases demonstrating ncRNA classification and differential expression analysis using nc-aReNA on mouse datasets are also described.
Introduction to Apollo: i5K E affinis
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
The i5K, an initiative to sequence the genomes of 5,000 insect and related arthropod species, is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process, and Apollo is serving as the platform to empower this community.
This presentation is an introduction to Apollo for the members of the i5K Pilot Project on Eurytemora affinis
ELIXIR Node poster Italy
The Italian node of ELIXIR, called Elixir-ITA, coordinates existing national bioinformatics services and provides key services to ELIXIR. Led by the National Research Council of Italy, Elixir-ITA includes 12 partners such as universities and high-performance computing groups. It establishes procedures for additional participants to contribute relevant resources through open calls and peer review. Services provided include databases for alternative splicing, untranslated mRNA regions, immunoglobulin sequences, and fungal ribosomal RNA, as well as tools for modeling splicing isoforms and predicting protein disorder.
Genome Curation using Apollo - Workshop at UTK
Comparative genome analysis requires high quality annotations of all genomic elements. Today’s sequencing projects face numerous challenges including lower coverage, more frequent assembly errors, and the lack of closely related species with well-annotated genomes. Precise elucidation of the many different biological features encoded in any genome requires careful examination and review. We need genome annotation editing tools to modify and refine the location and structure of the genome elements that predictive algorithms cannot yet resolve automatically. During the manual annotation process, curators identify elements that best represent the underlying biology and eliminate elements that reflect systemic errors of automated analyses.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, analogous to Google Docs, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Researchers from nearly one hundred institutions worldwide are currently using Apollo for distributed curation efforts in over sixty genome projects across the tree of life: from plants to arthropods, to fungi, to species of fish and other vertebrates including human, cattle (bovine), and dog.
Introduction to Apollo for i5k
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
The i5K, an initiative to sequence the genomes of 5,000 insect and related arthropod species, is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process, and Apollo is serving as the platform to empower this community.
This presentation is an introduction to Apollo for the members of the i5K Pilot Project working on species of the order Hemiptera.
Mauricio carrillo tripp
This document discusses computational biophysics, including current trends, needs, and challenges regarding high-performance computing (HPC). Computational biophysics uses physics-based modeling and simulation to study biological processes at the molecular level. Simulation sizes have increased from 20,000 atoms in 2000 to over 3 million atoms currently. Emerging needs include faster CPUs, solid state storage, and GPUs to analyze large simulation data in real time. Connectivity and infrastructure also need improvements to enable larger multicenter simulations. Overall, computational biophysics provides insights into cellular functions and mechanisms of life through increasingly detailed molecular simulations.
conventional Vs. tactile computing
This document compares conventional computers to tactile and biomolecular computing. Conventional computers follow a set of instructions to process data symbolically, while tactile computers recognize patterns physically through molecular interactions. Biomolecular computing uses molecules like DNA as the medium for computation, with the program encoded in the molecules themselves. Some advantages of molecular computing include smaller size, 3D structures, high density, and low power needs compared to silicon-based technologies. Challenges include reliability, efficiency, and scalability in controlling molecular interactions for computation.
Genome Curation using Apollo
Comparative genome analysis requires high quality annotations of all genomic elements. Today’s sequencing projects face numerous challenges including lower coverage, more frequent assembly errors, and the lack of closely related species with well-annotated genomes. Precise elucidation of the many different biological features encoded in any genome requires careful examination and review. We need genome annotation editing tools to modify and refine the location and structure of the genome elements that predictive algorithms cannot yet resolve automatically. During the manual annotation process, curators identify elements that best represent the underlying biology and eliminate elements that reflect systemic errors of automated analyses.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, analogous to Google Docs, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Researchers from nearly one hundred institutions worldwide are currently using Apollo for distributed curation efforts in over sixty genome projects across the tree of life: from plants to arthropods, to fungi, to species of fish and other vertebrates including human, cattle (bovine), and dog.
BiPday 2014 -- Ceci Michelangelo
The document describes a new database called ComiRNet that uses an integrative data-mining approach to discover microRNA-gene regulatory networks. It uses a semi-supervised learning method called HOCCLUS2 to extract overlapping biclusters from predicted and validated miRNA-mRNA interactions. These biclusters represent potential regulatory networks. The database contains over 5 million predicted interactions between miRNAs and mRNAs organized into 15 hierarchical levels of biclusters. ComiRNet aims to help elucidate miRNA functional roles and mechanisms in biological processes.
International Journal of Engineering Research and Development
This document discusses using artificial neural networks (ANN) and adaptive neuro-fuzzy inference systems (ANFIS) to predict promoter regions in genomic DNA sequences. It analyzes 106 DNA sequences from E. coli, each 57 nucleotides long, labeled as having a promoter region (+ label) or not (- label). ANN and ANFIS classifiers are trained on most of the data and tested on the remaining data using 5-fold cross-validation. The classifiers are evaluated based on accuracy, Matthews correlation coefficient, sensitivity, and specificity metrics. The results show that ANN and ANFIS are promising approaches for identifying promoter regions that compete with existing techniques.
Apollo Introduction for i5K Groups 2015-10-07
This is an introduction to conducting manual annotation efforts using Apollo. This webinar was offered to members of the i5K Research community on 2015-10-07.
Genome annotation 2013
Genome annotation, NGS sequence data, decoding sequence information, The genome contains all the biological information required to build and maintain any given living organism.
Apollo : A workshop for the Manakin Research Coordination Network
Apollo is a web-based, collaborative genomic annotation editing platform. We need annotation editing tools to modify and refine precise location and structure of the genome elements that predictive algorithms cannot yet resolve automatically.
This presentation is an introduction to how the manual annotation process takes place using Apollo. It is addressed to the members of the Manakin Genomics research community.
What Is Bioinformatics?
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. It involves the analysis of genome sequences, gene expression, protein structures, and molecular interactions. The goal of bioinformatics is to collect and analyze complex biological data to better understand organisms on the molecular level, such as genes, proteins, tissues, cells, and intracellular signaling pathways. Current areas of bioinformatics research include genome sequencing, gene regulation, protein function, molecular interactions, and evolutionary studies.
Bioinformatics Software
Bioinformatics is an interdisciplinary field that combines computer science, statistics, mathematics and engineering to study and process biological data, such as DNA sequences, in order to better understand biology. It involves developing methods and software tools to analyze large amounts of biological data, including sequencing genomes to understand what makes different organisms function. As data sets have grown enormously in size, bioinformatics relies on high-performance computing to make sense of it all and gain insights into normal cellular processes and how they are altered in disease states.
Paper2
1. The document proposes a system for secure user authentication and access control for encrypted data stored in the cloud. It aims to address issues with centralized access control and storing data in plaintext.
2. The proposed system uses a key distribution center to generate public, private, and access keys for authentication at different levels. Data is encrypted before being fragmented and distributed across multiple servers.
3. Only authorized users with proper keys can decrypt the data. Access policies set by data creators restrict which users can access files. Storing encrypted and distributed data along with key-based authentication aims to improve security over existing cloud storage systems.
2015 03 13_puurs_v_public
The document discusses a lab for bioinformatics and computational genomics at Ghent University. The lab has 10 "genome hackers" who are mostly engineers and 42 scientists, technicians, geneticists and clinicians. The lab focuses on bioinformatics, epigenetics, personal genomics and 3D printing. Bioinformatics is defined as the application of information technology to biological information, facilitated by computers. The document then discusses various topics related to genetics, genomics and personalized medicine.
Bioinformatics A Biased Overview
The document provides an overview of bioinformatics and examples of how it is used at different biological scales and levels of complexity, from genomics to proteomics to biological networks and systems biology. It discusses how bioinformatics integrates biological data from different sources and scales to offer new biological insights. Examples are given of how bioinformatics is applied to analyze genomic, metagenomic, and proteomic data as well as protein structures and interactions.
Bioinformatics principles and applications
Bioinformatics principles and applicationsSouth African National Bioinformatics Institute at the University of the Western Cape
This document provides an overview of bioinformatics and bioinformatics databases. It defines bioinformatics as the application of information technology to molecular biology to analyze and interpret biological data. This includes tasks like mapping and analyzing DNA and protein sequences. The document discusses how bioinformatics databases are used to store and manage the large amounts of biological data generated. It describes the characteristics of biological databases and how they are used for querying and retrieving sequence information. Key areas of bioinformatics research and important sequence databases are also summarized.Application of Bioinformatics in different fields of sciences
"The mathematical, statistical and computing methods that aim to solve biological problems using DNA and amino acid sequences and related information”
Bioinformatics
An Introduction to Bioinformatics
Drexel University INFO648-900-200915
A Presentation of Health Informatics Group 5
Cecilia Vernes
Joel Abueg
Kadodjomon Yeo
Sharon McDowell Hall
Terrence Hughes
Bioinfo
Bioinformatics is the application of statistics and computer science to biology. It is used for DNA sequencing and comparing genes and genomes between different or similar organisms. The document describes a bioinformatics workshop where students sequenced chicken and plant DNA using an NIH website to compare their genomes and answer questions. Bioinformatics is widely used in biology and genetics for sequencing DNA and comparing samples, as well as sequencing proteins and modeling protein structures.
Bioinformatics
This document provides an introduction to the field of bioinformatics. It defines bioinformatics as a branch of science that uses computer technology to analyze and integrate biological information that can be applied to gene-based drug discoveries. It discusses the emergence of bioinformatics due to the desire to understand how genetic structure affects traits. It also outlines some common applications of bioinformatics like drug design, gene therapy, and microbial genomic analysis. Finally, it provides examples of some bioinformatics tools, databases, and centers in India.
Introduction to bioinformatics
Bioinformatics is the use of computer science and statistical techniques to analyze and interpret biological data. It involves developing tools to access and manage biological data, analyzing sequences like DNA and proteins, and developing algorithms to understand relationships within large data sets. The main areas of bioinformatics are molecular, cellular, and organismal/community levels. It is used for tasks like gene finding, predicting protein structure and function, understanding evolutionary relationships, and aiding drug discovery.
Bioinformatics
This document provides an overview of bioinformatics. It begins by explaining how bioinformatics emerged from the need to analyze vast amounts of genetic sequence data produced by projects like the Human Genome Project. It then defines bioinformatics as the field that develops tools and methods for understanding biological data by combining computer science, statistics, and other disciplines. The document outlines several goals and applications of bioinformatics, such as identifying genes and their functions, modeling protein structures, comparing genomes, and its uses in medicine, microbial research, and more. It also provides a brief history of important developments in bioinformatics and DNA sequencing.
More Related Content
What's hot
Genome Curation using Apollo - Workshop at UTK
Comparative genome analysis requires high quality annotations of all genomic elements. Today’s sequencing projects face numerous challenges including lower coverage, more frequent assembly errors, and the lack of closely related species with well-annotated genomes. Precise elucidation of the many different biological features encoded in any genome requires careful examination and review. We need genome annotation editing tools to modify and refine the location and structure of the genome elements that predictive algorithms cannot yet resolve automatically. During the manual annotation process, curators identify elements that best represent the underlying biology and eliminate elements that reflect systemic errors of automated analyses.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, analogous to Google Docs, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Researchers from nearly one hundred institutions worldwide are currently using Apollo for distributed curation efforts in over sixty genome projects across the tree of life: from plants to arthropods, to fungi, to species of fish and other vertebrates including human, cattle (bovine), and dog.
Introduction to Apollo for i5k
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
The i5K, an initiative to sequence the genomes of 5,000 insect and related arthropod species, is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process, and Apollo is serving as the platform to empower this community.
This presentation is an introduction to Apollo for the members of the i5K Pilot Project working on species of the order Hemiptera.
Mauricio carrillo tripp
This document discusses computational biophysics, including current trends, needs, and challenges regarding high-performance computing (HPC). Computational biophysics uses physics-based modeling and simulation to study biological processes at the molecular level. Simulation sizes have increased from 20,000 atoms in 2000 to over 3 million atoms currently. Emerging needs include faster CPUs, solid state storage, and GPUs to analyze large simulation data in real time. Connectivity and infrastructure also need improvements to enable larger multicenter simulations. Overall, computational biophysics provides insights into cellular functions and mechanisms of life through increasingly detailed molecular simulations.
conventional Vs. tactile computing
This document compares conventional computers to tactile and biomolecular computing. Conventional computers follow a set of instructions to process data symbolically, while tactile computers recognize patterns physically through molecular interactions. Biomolecular computing uses molecules like DNA as the medium for computation, with the program encoded in the molecules themselves. Some advantages of molecular computing include smaller size, 3D structures, high density, and low power needs compared to silicon-based technologies. Challenges include reliability, efficiency, and scalability in controlling molecular interactions for computation.
Genome Curation using Apollo
Comparative genome analysis requires high quality annotations of all genomic elements. Today’s sequencing projects face numerous challenges including lower coverage, more frequent assembly errors, and the lack of closely related species with well-annotated genomes. Precise elucidation of the many different biological features encoded in any genome requires careful examination and review. We need genome annotation editing tools to modify and refine the location and structure of the genome elements that predictive algorithms cannot yet resolve automatically. During the manual annotation process, curators identify elements that best represent the underlying biology and eliminate elements that reflect systemic errors of automated analyses.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, analogous to Google Docs, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Researchers from nearly one hundred institutions worldwide are currently using Apollo for distributed curation efforts in over sixty genome projects across the tree of life: from plants to arthropods, to fungi, to species of fish and other vertebrates including human, cattle (bovine), and dog.
BiPday 2014 -- Ceci Michelangelo
The document describes a new database called ComiRNet that uses an integrative data-mining approach to discover microRNA-gene regulatory networks. It uses a semi-supervised learning method called HOCCLUS2 to extract overlapping biclusters from predicted and validated miRNA-mRNA interactions. These biclusters represent potential regulatory networks. The database contains over 5 million predicted interactions between miRNAs and mRNAs organized into 15 hierarchical levels of biclusters. ComiRNet aims to help elucidate miRNA functional roles and mechanisms in biological processes.
International Journal of Engineering Research and Development
This document discusses using artificial neural networks (ANN) and adaptive neuro-fuzzy inference systems (ANFIS) to predict promoter regions in genomic DNA sequences. It analyzes 106 DNA sequences from E. coli, each 57 nucleotides long, labeled as having a promoter region (+ label) or not (- label). ANN and ANFIS classifiers are trained on most of the data and tested on the remaining data using 5-fold cross-validation. The classifiers are evaluated based on accuracy, Matthews correlation coefficient, sensitivity, and specificity metrics. The results show that ANN and ANFIS are promising approaches for identifying promoter regions that compete with existing techniques.
Apollo Introduction for i5K Groups 2015-10-07
This is an introduction to conducting manual annotation efforts using Apollo. This webinar was offered to members of the i5K Research community on 2015-10-07.
Genome annotation 2013
Genome annotation, NGS sequence data, decoding sequence information, The genome contains all the biological information required to build and maintain any given living organism.
Apollo : A workshop for the Manakin Research Coordination Network
Apollo is a web-based, collaborative genomic annotation editing platform. We need annotation editing tools to modify and refine precise location and structure of the genome elements that predictive algorithms cannot yet resolve automatically.
This presentation is an introduction to how the manual annotation process takes place using Apollo. It is addressed to the members of the Manakin Genomics research community.
What's hot (10)
International Journal of Engineering Research and Development
International Journal of Engineering Research and Development
Apollo : A workshop for the Manakin Research Coordination Network
Apollo : A workshop for the Manakin Research Coordination Network
Viewers also liked
What Is Bioinformatics?
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. It involves the analysis of genome sequences, gene expression, protein structures, and molecular interactions. The goal of bioinformatics is to collect and analyze complex biological data to better understand organisms on the molecular level, such as genes, proteins, tissues, cells, and intracellular signaling pathways. Current areas of bioinformatics research include genome sequencing, gene regulation, protein function, molecular interactions, and evolutionary studies.
Bioinformatics Software
Bioinformatics is an interdisciplinary field that combines computer science, statistics, mathematics and engineering to study and process biological data, such as DNA sequences, in order to better understand biology. It involves developing methods and software tools to analyze large amounts of biological data, including sequencing genomes to understand what makes different organisms function. As data sets have grown enormously in size, bioinformatics relies on high-performance computing to make sense of it all and gain insights into normal cellular processes and how they are altered in disease states.
Paper2
1. The document proposes a system for secure user authentication and access control for encrypted data stored in the cloud. It aims to address issues with centralized access control and storing data in plaintext.
2. The proposed system uses a key distribution center to generate public, private, and access keys for authentication at different levels. Data is encrypted before being fragmented and distributed across multiple servers.
3. Only authorized users with proper keys can decrypt the data. Access policies set by data creators restrict which users can access files. Storing encrypted and distributed data along with key-based authentication aims to improve security over existing cloud storage systems.
2015 03 13_puurs_v_public
The document discusses a lab for bioinformatics and computational genomics at Ghent University. The lab has 10 "genome hackers" who are mostly engineers and 42 scientists, technicians, geneticists and clinicians. The lab focuses on bioinformatics, epigenetics, personal genomics and 3D printing. Bioinformatics is defined as the application of information technology to biological information, facilitated by computers. The document then discusses various topics related to genetics, genomics and personalized medicine.
Bioinformatics A Biased Overview
The document provides an overview of bioinformatics and examples of how it is used at different biological scales and levels of complexity, from genomics to proteomics to biological networks and systems biology. It discusses how bioinformatics integrates biological data from different sources and scales to offer new biological insights. Examples are given of how bioinformatics is applied to analyze genomic, metagenomic, and proteomic data as well as protein structures and interactions.
Bioinformatics principles and applications
Bioinformatics principles and applicationsSouth African National Bioinformatics Institute at the University of the Western Cape
This document provides an overview of bioinformatics and bioinformatics databases. It defines bioinformatics as the application of information technology to molecular biology to analyze and interpret biological data. This includes tasks like mapping and analyzing DNA and protein sequences. The document discusses how bioinformatics databases are used to store and manage the large amounts of biological data generated. It describes the characteristics of biological databases and how they are used for querying and retrieving sequence information. Key areas of bioinformatics research and important sequence databases are also summarized.Application of Bioinformatics in different fields of sciences
"The mathematical, statistical and computing methods that aim to solve biological problems using DNA and amino acid sequences and related information”
Bioinformatics
An Introduction to Bioinformatics
Drexel University INFO648-900-200915
A Presentation of Health Informatics Group 5
Cecilia Vernes
Joel Abueg
Kadodjomon Yeo
Sharon McDowell Hall
Terrence Hughes
Viewers also liked (8)
Application of Bioinformatics in different fields of sciences
Application of Bioinformatics in different fields of sciences
Similar to Bioinformatics
Bioinfo
Bioinformatics is the application of statistics and computer science to biology. It is used for DNA sequencing and comparing genes and genomes between different or similar organisms. The document describes a bioinformatics workshop where students sequenced chicken and plant DNA using an NIH website to compare their genomes and answer questions. Bioinformatics is widely used in biology and genetics for sequencing DNA and comparing samples, as well as sequencing proteins and modeling protein structures.
Bioinformatics
This document provides an introduction to the field of bioinformatics. It defines bioinformatics as a branch of science that uses computer technology to analyze and integrate biological information that can be applied to gene-based drug discoveries. It discusses the emergence of bioinformatics due to the desire to understand how genetic structure affects traits. It also outlines some common applications of bioinformatics like drug design, gene therapy, and microbial genomic analysis. Finally, it provides examples of some bioinformatics tools, databases, and centers in India.
Introduction to bioinformatics
Bioinformatics is the use of computer science and statistical techniques to analyze and interpret biological data. It involves developing tools to access and manage biological data, analyzing sequences like DNA and proteins, and developing algorithms to understand relationships within large data sets. The main areas of bioinformatics are molecular, cellular, and organismal/community levels. It is used for tasks like gene finding, predicting protein structure and function, understanding evolutionary relationships, and aiding drug discovery.
Bioinformatics
This document provides an overview of bioinformatics. It begins by explaining how bioinformatics emerged from the need to analyze vast amounts of genetic sequence data produced by projects like the Human Genome Project. It then defines bioinformatics as the field that develops tools and methods for understanding biological data by combining computer science, statistics, and other disciplines. The document outlines several goals and applications of bioinformatics, such as identifying genes and their functions, modeling protein structures, comparing genomes, and its uses in medicine, microbial research, and more. It also provides a brief history of important developments in bioinformatics and DNA sequencing.
Valeria laboratory 5lv
DNA profiling or fingerprinting uses DNA samples to distinguish between individuals of the same species, which involves preparing DNA samples with enzymes, digesting the samples, separating DNA pieces by size using electrophoresis, and visualizing and comparing bands to identify suspects at a crime scene. The laboratory also involved using bioinformatics databases from NCBI to search for species, check DNA sequences, and compare sequences to determine the most similar species, which is important for understanding diseases and identifying new targets for pharmaceuticals through genomic information.
LECTURE NOTES ON BIOINFORMATICS
introduction,history scope and applications of
relation to other fields , bioinformatics,biological databases,computers internet,sequence development, and
introduction to sequence development and alignment
Introduction to Bioinformatics-1.pdf
Bioinformatics is the application of computational tools and techniques to analyze and interpret biological data. It involves the development of these tools and databases, as well as their application to better understand biological systems and functions at the molecular level through analysis of genetic sequences, protein structures, and more. The goal is to gain a global understanding of cellular functions by analyzing genetic data as dictated by the central dogma of biology, and relating sequence information to protein functions and cellular processes.
Bio Informatics
This document discusses bioinformatics and some of its key techniques and uses. It introduces bioinformatics as a field that merges biology, computer science, and information technology to manage and analyze biological data using advanced computing. Some techniques discussed include phylogenetics, proteomics, sequence analysis, structure determination, and gene expression analysis. Recombinant DNA technology and cloning are also summarized, including the process of recombining DNA from different species and the various types of human cloning.
Bioinformatics Introduction and Use of BLAST Tool
Hi, I am Jesmin, studying MCSE. I think this file will help you if you want to know the basic information about Bioinformatics and the use of BLAST tool. The BLAST tool is the tool that matches the sequences of DNA,RNA and proteins.
BioInformatics Tools -Genomics , Proteomics and metablomics
This document discusses various bioinformatics tools used for genomics, proteomics, and metabolomics. It begins with an introduction to bioinformatics and defines key terms. It then describes several important databases for nucleotide and protein sequences including NCBI, GenBank, and KEGG. Important analytical tools like BLAST and Clustal are also mentioned. Subsequent chapters discuss genomics, proteomics, and metabolomics in more detail and provide examples of specific tools used for each including KNApSAcK, MetaboAnalyst, and PSI-PRED. The document aims to outline the key concepts and computational tools involved in these three areas of bioinformatics.
Introducción a la bioinformatica
The document introduces bioinformatics and discusses its goals and applications. Bioinformatics involves using computational tools and databases to analyze and understand biological data like DNA, RNA, and proteins. It has two main subfields - developing computational tools and databases, and applying these tools to generate biological knowledge and insights into living systems. Bioinformatics aims to better understand cells at the molecular level and how they function. It has applications in areas like drug design, forensics, agriculture, and medicine.
DNA Query Language DNAQL: A Novel Approach
This document describes a proposed DNA Query Language (DNAQL) that could allow researchers to query DNA databases in a more intuitive way compared to SQL. The DNAQL is presented as a novel approach that would introduce an abstraction layer between the user interface and database, translating queries in a familiar biochemical language into SQL understood by the database. This could help alleviate challenges biochemistry researchers face in accessing and analyzing protein data from databases. The document provides background on DNA computing and challenges in current databases, reviews related work on biological database querying, and describes the proposed methodology for DNA sequencing and DNAQL.
Bioinformatics-General_Intro
This document discusses bioinformatics and computational biology. It defines bioinformatics as conceptualizing biology in terms of molecules and applying informatics techniques like mathematics and computer science to understand and organize molecular information on a large scale. Computational biology refers to developing algorithms and statistical models to analyze biological data through computers. The document provides examples of areas studied in bioinformatics like sequence analysis, genome annotation, and regulation analysis. It also outlines some important applications of bioinformatics like gene therapy and personalized medicine.
introduction of Bioinformatics
This document discusses the field of bioinformatics. It begins by defining bioinformatics as the combination of biology, computer science, and information technology, and explains that it involves applying computational techniques to understand biological data. It distinguishes bioinformatics from computational biology. The document then outlines what tasks bioinformatics can perform, describes the components and levels of organization in bioinformatics, and discusses the main branches of genomics, proteomics, and transcriptomics.
biocomputing-190618135550.pdf
This document discusses biological computing, which uses biological components like DNA to store and manipulate data similar to processes in the human body. It can enable smaller, faster computing that operates accurately. Biocomputers use DNA as software and molecular biology parts as hardware to process inputs and outputs like a computer. DNA is well-suited for data storage and parallel processing. A DNA computer uses DNA strands and enzymes to solve problems with many possible solutions calculated at once. Biological computing has applications in DNA chips for genetic analysis and is more energy efficient than traditional computing. However, better control of molecules is needed to reduce errors and increase precision.
Biocomputing- biological computing
Bio computers use systems of biologically derived molecules—such as DNA and proteins—to perform computational calculations involving storing, retrieving, and processing data. The development of biocomputers has been made possible by the expanding new science of nanobiotechnology.
Bioinformatics
This document provides an overview of bioinformatics, including its history, major areas of research, databases, tools, and applications. Bioinformatics is defined as the use of computer science and information technology to analyze and interpret biological data. The document traces the history of bioinformatics from early genetics experiments in the 1860s to advances in computing and molecular biology in the 1970s that enabled the field. It outlines major research areas like sequence analysis, genome annotation, and computational evolutionary biology. It also discusses biological databases, common bioinformatics tools, and applications of bioinformatics in fields like medicine, agriculture, and comparative genomics.
Presentation.pptx
This document provides an introduction to bioinformatics databases. It defines bioinformatics as using computer programming in biological studies. The history and components of bioinformatics are discussed. There are three main types of biological databases - primary, secondary, and composite. Primary databases contain experimental data, secondary databases contain analyzed primary data, and composite databases merge and filter primary data. Databases are important for applications like sequencing, gene prediction, and phylogenetic analysis. Computational biology uses computer science to analyze large biological datasets and solve biological problems. It differs from bioinformatics in emphasizing theoretical methods and modeling over informatics.
MoM2010: Bioinformatics
Bioinformatics is an interdisciplinary field that combines biology, computer science, and information technology. It involves the electronic storage, retrieval, analysis, and correlation of biological data. The document outlines key concepts in bioinformatics including the central dogma of molecular biology, biological data representation, how computers can be useful for biology, challenges in the field, and examples of intelligent bioinformatics applications. It emphasizes that bioinformatics is an important and growing field at the intersection of biology and computer science.
Graziano Pesole - il progetto EPIGEN
The EPIGEN project aims to advance epigenetics research in Italy by creating centralized platforms providing researchers access to new technologies. It has established next generation sequencing, bioinformatics, and cell imaging platforms to overcome limitations in Italian research facilities. The project has over 70 participating labs organized into 8 subprojects. It has already produced over 1.5 trillion bases of sequencing data through its sequencing center and established databases and analysis pipelines through its bioinformatics platform to enable collaborative epigenomics research.
Similar to Bioinformatics (20)
BioInformatics Tools -Genomics , Proteomics and metablomics
BioInformatics Tools -Genomics , Proteomics and metablomics
More from Lester Rosario
Rise program makes new scientists
The RISE Program helps students become familiar with scientific research through hands-on experiences. It teaches students how to think creatively by proposing original research topics and defending proposals. It also teaches how to access and interpret scientific literature to inform research. Students learn important laboratory techniques that will help them perform research. The various courses and experiences of the RISE Program contribute to preparing new potential scientists and benefiting society through advancing scientific understanding.
Escrito proposal
This document proposes a study to determine if prenatal exposure to cell phone use causes attention-deficit/hyperactivity disorder (ADHD) in offspring. The study would have two phases: first, surveying pregnant women and mothers of 3-6 year olds about cell phone use during pregnancy and children's behavior; second, exposing pregnant hamsters to cell phone electromagnetic radiation at different frequencies and durations and observing offspring behavior. The goal is to raise awareness in pregnant women about cell phone use and further research effects of prenatal exposure on children's health and behavior.
Nano workshop 2010
This summary discusses a workshop on nanotechnology attended by the author. The workshop covered microfluidics and developing miniaturized technologies to integrate an entire laboratory onto a single chip, called a "lab on a chip". It also discussed photolithography techniques used to create chip patterns, including e-beam lithography and optical lithography. As an exercise, the author made a Jell-O chip in the shape of a frog to learn how real chips are produced using inexpensive materials.
Photo Workshop oct 7 9,2010
The document announces a nanotechnology workshop from October 7th to 9th organized by Ms. Ivonne Ferrer and Ms. Jesus Velazquez. The workshop will likely focus on nanotechnology topics over the three day period and is being run by the two individuals mentioned.
Aplicaciones del ADN en la nueva tecnologia
El documento describe varias aplicaciones del ADN en la tecnología moderna, incluyendo su uso para entender los mecanismos de la vida a través del estudio de genes y mutaciones, resolver crímenes y misterios mediante pruebas de identificación forense, y crear soluciones para la salud y nutrición como la insulina recombinante y los alimentos modificados genéticamente.
Reflective paragraph 3 summer
During the morning, the student took a biology class with Dr. Belinda Román where they discussed chemistry and reviewed material from high school. The class talked about evolution and its relation to chemistry. They finished at 10:30 pm so the student went to the library to work on assignments.
Reflective paragraph 3 summer
During the morning, the student took a biology class with Dr. Belinda Román where they discussed chemistry and reviewed material from high school. The class talked about evolution and its relation to chemistry. They finished at 10:30 pm so the student went to the library to work on assignments.
Reflective paragraph 1 summer
Lester Rosario attended his first workshop for the Rise Program 2010 where he learned how to create a blog, something he had never done before. The professor taught him how to include personal information and make the blog interesting by including details about the Rise Program. Creating a blog will make communication easier between Lester and his professor and allow him to document his experiences as a student and future professional.
ELISA
ELISA is a technique used to detect antibodies or antigens in a sample. It works by first adding antigens to wells which antibodies then bind to. Secondary antibodies with an enzyme are then added, and if the antigens and primary antibodies are present, the enzyme causes a color change reaction. This process allows ELISA to be used to test for conditions like HIV in patients by simulating the immune response in a lab setting.
Biofuel: Enzyme Kinetics
Enzymes accelerate biological reactions and their reaction rates depend on conditions like temperature and pH levels. The workshop explored how altering conditions affected catalysis and reaction rates using the enzyme p-nitrophenyl glucopyranoside. Experiments showed this enzyme works best at pH 5, where it hydrolyzes starch into glucose and p-nitrophenol, detected by its yellow color. Samples tested at different pH levels found only pH 5 turned yellow, and spectrometer readings confirmed more products formed at lower pH, demonstrating pH significantly impacts the enzyme's reaction rate.
Got protein?
The workshop tested the protein content of different types of milk using the Bradford Protein Assay. Samples of different milks were diluted and added to Coomassie blue dye, which binds to amino acids and changes color based on protein concentration. Known protein standards were also prepared. Absorbance measurements from a spectrophotometer were used to create a standard curve to calculate the exact protein concentration in mg/mL of the milk samples.
pGLO Bacterial Transformation and pGLO SDS Page Extension
Bacterial transformation involves inserting a gene from one organism into another using plasmids. Plasmids containing a gene of interest are introduced into bacteria, allowing the bacteria to express proteins from that gene. In this workshop, green fluorescent protein (GFP) was used as a marker to test if E. coli bacteria were transformed. E. coli cultures were grown, one containing a GFP plasmid. Under UV light, the plasmid-containing culture showed GFP expression, indicating transformation occurred. SDS-PAGE was used to separate and observe the transformed bacteria's proteins, revealing bands corresponding to GFP.
Nanotechnology
The workshop covered nanotechnology, which involves working with materials smaller than 100 nm. At this scale, materials exhibit different physical, chemical, and biological properties that can be exploited for various applications. For example, nanomaterials have more surface area, inducing more catalytic reactions and reactivity. The workshop demonstrated creating a hydrogen sensor using electrospun polyethylene oxide fibers coated with palladium and gold through sputtering to detect hydrogen concentrations.
Genetic Modification in Papaya and Fritos® Corn Chips
The document summarizes an experiment testing genetically modified organisms (GMOs) in papaya and Fritos corn chips. DNA was extracted from the samples and tested using PCR and gel electrophoresis. The results initially showed no GMO DNA sequences in the papaya or corn chips. However, the results were deemed unreliable due to DNA degradation. The experiment would need to be repeated to obtain more reliable conclusions about the presence of GMOs in the food samples.
Genetic Modification in Maize, Papaya, Fritos® Corn Chips, and Natura® Soymilk
This document summarizes an experiment to identify GMO genes in corn, soy milk, and papaya samples. DNA was extracted from the samples and amplified via PCR with primers for the 35S promoter, NOS terminator, and PSII genes. The resulting DNA fragments were run on an agarose gel during electrophoresis. Bands were observed at the expected sizes for the 35S and NOS genes in the corn and papaya samples, indicating they contain those GMO genes, but not in the soy milk sample. The results suggest the corn and papaya samples contain GMOs while the soy milk does not, but the experiment needs to be repeated to obtain reliable conclusions due to potential human errors.
Review Paper 1
This review paper summarizes research on the effects of cell phone electromagnetic radiation exposure on the brain. Several studies found associations between long-term cell phone use (>10 years) and brain tumor development, especially on the side of the head most used. Exposure has been shown to up-regulate cell death pathways in neurons and affect neural function in humans. It may also cause oxidative damage to neuronal mitochondrial DNA and alter blood-brain barrier permeability. Additionally, cell phone radiation was found to change the oxygen affinity and structure of hemoglobin as well as disrupt inter-hemispheric brain synchronization. While some studies found no effects, overall the review indicates that cell phone use may pose brain-related health risks.
Annotated bibliography #2
This study investigated whether exposure to cell phone radiation up-regulates (increases) genes related to apoptosis in primary cultures of neurons and astrocytes. The researchers exposed cultures of neurons and astrocytes to cell phone radiation for 2 hours. Gene expression analysis found increased expression of caspase-2, caspase-6, and Asc apoptosis genes in both neurons and astrocytes exposed to the radiation. The study concluded that even short-term exposure to cell phone radiation can increase expression of genes involved in apoptosis pathways and cause cell death in brain cells, with neurons appearing more sensitive than astrocytes.
Magnetic Resonance as a Tool for Structural Studies of Membrane Proteins
The document summarizes a seminar on using magnetic resonance techniques like NMR and EPR spectroscopy to study the structure and dynamics of membrane proteins like Sec14p. The presenter Mary Chely Quiñones discussed using EPR spectroscopy with spin-labeled lipids to investigate the local dynamics and electrostatic environment of lipids binding to Sec14p in order to better understand vitamin E disorders.
Seminar mary chely 2010
The document summarizes a seminar on using magnetic resonance techniques like NMR and EPR spectroscopy to study the structure and dynamics of membrane proteins like Sec14p. The presenter Mary Chely Quiñones discussed using EPR spectroscopy with spin-labeled lipids to study the local environment and dynamics of lipids binding to Sec14p in order to better understand vitamin E disorders.
Annotated bibliography #3
Seyed et al. investigated the effects of mobile phone radiofrequency electromagnetic fields (EMFs) at 910 MHz and 940 MHz on the structure and function of hemoglobin. They found that exposure to EMFs altered hemoglobin's oxygen affinity and tertiary structure by decreasing its ability to bind oxygen in the lungs and increasing its release of oxygen to tissues. The changes corresponded to the intensity and duration of EMF exposure, suggesting that EMFs could affect human respiration.
More from Lester Rosario (20)
pGLO Bacterial Transformation and pGLO SDS Page Extension
pGLO Bacterial Transformation and pGLO SDS Page Extension
Genetic Modification in Papaya and Fritos® Corn Chips
Genetic Modification in Papaya and Fritos® Corn Chips
Genetic Modification in Maize, Papaya, Fritos® Corn Chips, and Natura® Soymilk
Genetic Modification in Maize, Papaya, Fritos® Corn Chips, and Natura® Soymilk
Magnetic Resonance as a Tool for Structural Studies of Membrane Proteins
Magnetic Resonance as a Tool for Structural Studies of Membrane Proteins
Bioinformatics
- 1. Workshop: Bioinformatics By Belinda Román Bioinformatics is the application of statistics and computer science to the field of molecular biology. A few things that we can do with the usage of bioinformatics are mapping and analyzing DNA and protein sequences, and aligning different DNA and protein sequences to compare them . In this workshop, I learned where and how people are using this area of sciences, and how it is contributing to investigations, making it easy for scientists to access data that is already known. In order for me to understand how bioinformatics works, I made a practice using the following database website: www.ncbi.nlm.gov. Here I looked first for the DNA sequence of the fibrinogen alpha chain in different species of organisms. In this step, I varied the search by also using accession numbers. Then, we learned how to translate a DNA sequence into a protein. In order to do this, the database translates the sequence into an amino acid sequence and then into a protein. Another interesting thing I did was the comparison of two sequences from different species. At the end, I was able to interpret the results of each of the different techniques used for searching and comparing sequences.