ERASysAPP

A platform for the exchange of educational material on systems biology.

ERASysAPP https://tess.elixir-europe.org/content_providers/erasys-app A platform for the exchange of educational material on systems biology. /system/content_providers/images/000/000/043/original/erasysapp.PNG?1469458222
Showing 29 materials.

Erasmus Intensive Program "MoSyB 2013" "Modeling in systems biology and synthetic biology" video lectures.

Keywords: Synthetic biology, Standards

MoSyB 2013 - Synthetic Biology Standards https://tess.elixir-europe.org/materials/mosyb-2013-synthetic-biology-standards Erasmus Intensive Program "MoSyB 2013" "Modeling in systems biology and synthetic biology" video lectures. Synthetic biology, Standards 2015-02-26 2017-10-09

Structural or qualitative (parameter-free) models relying solely on the often well-known network structure provide an alternative approach still are capable to gain useful insights in the functioning of these networks (Klamt et al.,, 2007, BMC Systems Biology). Structures of networks can be...

Scientific topics: Pathway or network analysis

Keywords: Metabolic network, Structural analysis, Network analysis

Structural network analysis (graph theoretic algorithms) https://tess.elixir-europe.org/materials/structural-network-analysis-graph-theoretic-algorithms Structural or qualitative (parameter-free) models relying solely on the often well-known network structure provide an alternative approach still are capable to gain useful insights in the functioning of these networks (Klamt et al.,, 2007, BMC Systems Biology). Structures of networks can be analysed to find out its graph-theoretic tasks as cycle analysis, network diameter, determination of incidence matrix, adjacency matrix, distance matrix and others. Pathway or network analysis Metabolic network, Structural analysis, Network analysis 2014-01-22 2017-10-09

Genomics pioneer Craig Venter takes a break from his epic round-the-world expedition to talk about the millions of genes his team has discovered so far in its quest to map the ocean’s biodiversity.

Scientific topics: DNA

Keywords: Sampling, DNA

Craig Venter: Sampling the ocean's DNA https://tess.elixir-europe.org/materials/craig-venter-sampling-the-ocean-s-dna Genomics pioneer Craig Venter takes a break from his epic round-the-world expedition to talk about the millions of genes his team has discovered so far in its quest to map the ocean’s biodiversity. DNA Sampling, DNA 2015-02-26 2017-10-09

Virtually all methods of learning dynamic systems from data start from the same basic assumption: that the learning algorithm will be provided with a sequence, or trajectory, of data generated from the dynamic system. In this paper we consider the case where the data is not sequenced. The...

Scientific topics: Sequencing

Keywords: Sequencing

Learning Linear Dynamical Systems without Sequence Information https://tess.elixir-europe.org/materials/learning-linear-dynamical-systems-without-sequence-information Virtually all methods of learning dynamic systems from data start from the same basic assumption: that the learning algorithm will be provided with a sequence, or trajectory, of data generated from the dynamic system. In this paper we consider the case where the data is not sequenced. The learning algorithm is presented a set of data points from the system's operation but with no temporal ordering. The data are simply drawn as individual disconnected points. Sequencing Sequencing 2014-01-22 2017-10-09

Chromatography is a physical method based on separation of the components by distribution between two phases, one of which is stationary (stationary phase) while the other (the mobile phase) moves in a definite direction. Quantitative chromatography is used to determine the concentration of...

Keywords: Gas chromatograph, Chromotography

Quantitative chromatography methods (LC, GC, CE) https://tess.elixir-europe.org/materials/quantitative-chromatography-methods-lc-gc-ce Chromatography is a physical method based on separation of the components by distribution between two phases, one of which is stationary (stationary phase) while the other (the mobile phase) moves in a definite direction. Quantitative chromatography is used to determine the concentration of analytes in a sample. The components is identified by its retention time and concentration calculated from intensity of detector signal. (In optimal system the signal is proportional to the concentration of the specific analyte separated). Gas chromatograph, Chromotography 2014-01-26 2017-10-09

Forget the microscopes. Gene sequencers, microarrays and mass spectrometers are the tools of the trade for today's biologists. Huge advances in technology and computing have revolutionized the field, and instead of breaking living things down into smaller and smaller parts, biologists are looking...

Scientific topics: Systems biology

Keywords: Systems biology

A New Frontier: Systems Biology https://tess.elixir-europe.org/materials/a-new-frontier-systems-biology Forget the microscopes. Gene sequencers, microarrays and mass spectrometers are the tools of the trade for today's biologists. Huge advances in technology and computing have revolutionized the field, and instead of breaking living things down into smaller and smaller parts, biologists are looking at the systems that make up living things, reaching out to other disciplines, and trying to get a grip on the eternal mystery: what, exactly, is life? There's been a paradigm shift in the science of life, and it's called systems biology. Systems biology Systems biology 2014-03-20 2017-10-09

Medical animator David Bolinsky presents 3 minutes of stunning animation that show the bustling life inside a cell.

Keywords: Cell, Cellular Processes

David Bolinsky: Visualizing the wonder of a living cell https://tess.elixir-europe.org/materials/david-bolinsky-visualizing-the-wonder-of-a-living-cell Medical animator David Bolinsky presents 3 minutes of stunning animation that show the bustling life inside a cell. Cell, Cellular Processes 2015-02-26 2017-10-09

Found historical video from 2010 on TED talks:

Scientific topics: DNA

Keywords: DNA, Cell, Cellular Processes, Synthetic biology

Craig Venter: Watch me unveil "synthetic life" https://tess.elixir-europe.org/materials/craig-venter-watch-me-unveil-synthetic-life Found historical video from 2010 on TED talks: DNA DNA, Cell, Cellular Processes, Synthetic biology 2015-02-26 2017-10-09

Erasmus Intensive Program "MoSyB 2013" "Modeling in systems biology and synthetic biology" video lectures.

Keywords: Annotations, Synthetic biology, Modeling

MoSyB 2013 - how can annotations be used in model driven design for SynBio https://tess.elixir-europe.org/materials/mosyb-2013-how-can-annotations-be-used-in-model-driven-design-for-synbio Erasmus Intensive Program "MoSyB 2013" "Modeling in systems biology and synthetic biology" video lectures. Annotations, Synthetic biology, Modeling 2015-02-26 2017-10-09

Quantitative mass spectroscopy (MS) is a technology that allows to quantitate the number of specific protein molecules in studied samples.

Keywords: Mass Spectroscopy

Quantitative mass spectroscopy https://tess.elixir-europe.org/materials/quantitative-mass-spectroscopy Quantitative mass spectroscopy (MS) is a technology that allows to quantitate the number of specific protein molecules in studied samples. Mass Spectroscopy 2014-01-26 2017-10-09

Technical and biological systems: how different they are?

Keywords: Biological systems

Systemic differences between biological and technical systems https://tess.elixir-europe.org/materials/systemic-differences-between-biological-and-technical-systems Technical and biological systems: how different they are? Biological systems 2014-03-17 2017-05-09

COPASI tool tutorial videos are from COPASI YouTube channel (CopasiTutorials) and describe specific functions of COPASI

Keywords: Model, Kinetic modeling, COPASI, Biomodelling, Modeling, Tutorial

COPASI tutorial https://tess.elixir-europe.org/materials/copasi-tutorial COPASI tool tutorial videos are from COPASI YouTube channel (CopasiTutorials) and describe specific functions of COPASI Model, Kinetic modeling, COPASI, Biomodelling, Modeling, Tutorial 2015-05-05 2017-10-09

Isotopic labeling is a technique for tracking the passage of a sample of substance through a system. The substance is 'labeled' by including unusual isotopes in its chemical composition. One or more of the atoms of the molecule of interest is substituted for an atom of the same chemical element,...

Keywords: Isotopic lebeling

Metabolic isotopes https://tess.elixir-europe.org/materials/metabolic-isotopes Isotopic labeling is a technique for tracking the passage of a sample of substance through a system. The substance is 'labeled' by including unusual isotopes in its chemical composition. One or more of the atoms of the molecule of interest is substituted for an atom of the same chemical element, but of a different isotope. Isotopic lebeling 2014-01-26 2017-10-09

DNA sequencing is an important method for system biology studies. There are different technologies that allow determination of nucleotide sequence in DNA molecules. Traditionally, the sequence of genomes is determined with so called Sanger sequencing technology. In recent years, new 2nd and 3rd...

Scientific topics: Sequencing

Keywords: Sequencing, Genome Sequencing

Sequencing Methods https://tess.elixir-europe.org/materials/sequencing-methods DNA sequencing is an important method for system biology studies. There are different technologies that allow determination of nucleotide sequence in DNA molecules. Traditionally, the sequence of genomes is determined with so called Sanger sequencing technology. In recent years, new 2nd and 3rd generation technologies have appeared that allow much faster and higher throughput. Sequencing Sequencing, Genome Sequencing 2014-01-26 2017-10-09

Two-dimensional electrophoresis is a well known method for protein separation which is extremely useful in the field of proteomics. The basic idea is to separate proteins contained in a sample using two independent properties such isoelectric point and mass. In the gel, each spot represents a...

Keywords: Electrophoresis

2D gel electrophoreses (DIGE) https://tess.elixir-europe.org/materials/2d-gel-electrophoreses-dige Two-dimensional electrophoresis is a well known method for protein separation which is extremely useful in the field of proteomics. The basic idea is to separate proteins contained in a sample using two independent properties such isoelectric point and mass. In the gel, each spot represents a protein accumulation and its size depends on the amount of protein present in the sample. Electrophoresis 2014-01-26 2017-10-09

Erasmus Intensive Program "MoSyB 2013" "Modeling in systems biology and synthetic biology" video lectures.

Keywords: Metabolic flux analysis, Modeling

MoSyB 2013 - FAME, the Flux Analysis and Modeling Environment https://tess.elixir-europe.org/materials/mosyb-2013-fame-the-flux-analysis-and-modeling-environment Erasmus Intensive Program "MoSyB 2013" "Modeling in systems biology and synthetic biology" video lectures. Metabolic flux analysis, Modeling 2015-02-26 2017-10-09

Erasmus Intensive Program "MoSyB 2013" "Modeling in systems biology and synthetic biology" video lectures.

Keywords: Biomodelling, Modeling

MoSyB 2013 - FiJo: a tool for assisted model construction https://tess.elixir-europe.org/materials/mosyb-2013-fijo-a-tool-for-assisted-model-construction Erasmus Intensive Program "MoSyB 2013" "Modeling in systems biology and synthetic biology" video lectures. Biomodelling, Modeling 2015-02-26 2017-10-09

Erasmus Intensive Program "MoSyB 2013" "Modeling in systems biology and synthetic biology" video lectures.

Keywords: Control, Biomodelling, Modeling

MoSyB 2013 - Modelling as a precondition of control development https://tess.elixir-europe.org/materials/mosyb-2013-modelling-as-a-precondition-of-control-development Erasmus Intensive Program "MoSyB 2013" "Modeling in systems biology and synthetic biology" video lectures. Control, Biomodelling, Modeling 2015-02-26 2017-10-09

Erasmus Intensive Program "MoSyB 2013" "Modeling in systems biology and synthetic biology" video lectures.

Scientific topics: Systems biology

Keywords: Systems biology, Synthetic biology, Biomodelling, Modeling

MoSyB 2013 - BioModel Engineering for Systems and Synthetic Biology https://tess.elixir-europe.org/materials/mosyb-2013-biomodel-engineering-for-systems-and-synthetic-biology Erasmus Intensive Program "MoSyB 2013" "Modeling in systems biology and synthetic biology" video lectures. Systems biology Systems biology, Synthetic biology, Biomodelling, Modeling 2015-02-26 2017-10-09

Synthetic life, defined as life that did not arise from preexisting life, spontaneously emerged when the first cell-like structures assembled from mixtures of organic molecules on the early Earth. These structures, referred to as protocells, exhibited certain properties of living systems and...

Scientific topics: Systems biology

Keywords: Systems biology, Synthetic biology

Systems biology, synthetic biology and the origin of life https://tess.elixir-europe.org/materials/systems-biology-synthetic-biology-and-the-origin-of-life Synthetic life, defined as life that did not arise from preexisting life, spontaneously emerged when the first cell-like structures assembled from mixtures of organic molecules on the early Earth. These structures, referred to as protocells, exhibited certain properties of living systems and represented evolutionary steps toward the first forms of cellular life.  Systems biology Systems biology, Synthetic biology 2014-03-20 2017-10-09

DNA microarrays (DNA chips) are widely used to perform a large number of DNA hybridization experiments in parallel. Current microarrays allow studying up to 1 million different locations in human genome at the same time - in one experiment. Microarrays are widely used in studying mRNA...

Keywords: DNA Microarray

Chip technology (transcriptome, proteome) https://tess.elixir-europe.org/materials/chip-technology-transcriptome-proteome DNA microarrays (DNA chips) are widely used to perform a large number of DNA hybridization experiments in parallel. Current microarrays allow studying up to 1 million different locations in human genome at the same time - in one experiment. Microarrays are widely used in studying mRNA (transcriptome), genomic DNA (genome), protein-DNA interactions (interactome) and for many other large scale studies. DNA Microarray 2014-01-26 2017-10-09

The quantitative immunoblot is a similar approach to ELISA. It uses the same principles as the ELISA, a reliance on the highly specific antibody antigen interaction to measure the amount of a given protein in a complex mixture. The major distinguishing feature of this method is the inclusion of a...

Keywords: Quantitative Immunoblot

Quantitative immunoblotting https://tess.elixir-europe.org/materials/quantitative-immunoblotting The quantitative immunoblot is a similar approach to ELISA. It uses the same principles as the ELISA, a reliance on the highly specific antibody antigen interaction to measure the amount of a given protein in a complex mixture. The major distinguishing feature of this method is the inclusion of a step to electrophoretically separate the proteins in the sample according to their molecular weights. Thus, all samples can be solubilized using a standardized procedure and analyzed concurrently for a number of interesting proteins. Quantitative Immunoblot 2014-01-26 2017-10-09

Reporter genes are genes that will be attached to a specific gene under investigation. It is used to verify if a certain gene was taken up by an organism of interest or if it was expressed in a cell. Reporter genes are easier detectable through the characteristics they confer to the host...

Keywords: Reporter genes, Genes

Reporter genes https://tess.elixir-europe.org/materials/reporter-genes Reporter genes are genes that will be attached to a specific gene under investigation. It is used to verify if a certain gene was taken up by an organism of interest or if it was expressed in a cell. Reporter genes are easier detectable through the characteristics they confer to the host organism. Typical reporter genes are those that encode fluorescent and luminescent proteins like GFP (green fluorescent protein). These proteins are visually detectable. A reporter gene is usually transplanted together with the gene of interest in a so called DNA construct (generally a plasmid) into the cell. Reporter genes, Genes 2014-01-26 2017-10-09

Real-time PCR (RT-PCR) is a technology that allows to quantitate the number of specific DNA or RNA molecules in studied samples. It is a sensitive (up to single molecule detection) and robust (linear in wide range of concentrations) method. It requires specific instrument, which costs about 50...

Keywords: Sampling, Polymerase

Real-time polymerase chain reaction (RT-PCR) https://tess.elixir-europe.org/materials/real-time-polymerase-chain-reaction-rt-pcr Real-time PCR (RT-PCR) is a technology that allows to quantitate the number of specific DNA or RNA molecules in studied samples. It is a sensitive (up to single molecule detection) and robust (linear in wide range of concentrations) method. It requires specific instrument, which costs about 50 000 EUR. One experiment (100-400 samples in parallel) takes about half a day to perform. Sampling, Polymerase 2014-01-26 2017-10-09

Biosynthesis is a phenomenon wherein chemical compounds are produced from simpler reagents. Biosynthesis, unlike chemosynthesis, takes place within living organisms and is generally catalyzed by enzymes. The process is a vital part of metabolism.

Scientific topics: Endocrinology and metabolism

Keywords: Metabolic network, Biosynthesis, Metabolic pathway, Metabolism

Diverse biosynthesis pathways and secondary metabolism https://tess.elixir-europe.org/materials/diverse-biosynthesis-pathways-and-secondary-metabolism Biosynthesis is a phenomenon wherein chemical compounds are produced from simpler reagents. Biosynthesis, unlike chemosynthesis, takes place within living organisms and is generally catalyzed by enzymes. The process is a vital part of metabolism. Endocrinology and metabolism Metabolic network, Biosynthesis, Metabolic pathway, Metabolism 2014-01-22 2017-10-09

Metabolism of living cells is a complex network of chemical reactions to extract, convert and store energy from nutrients that can be analyzed in self-contained parts called pathways. Metabolic pathways contribute to catabolism - the oxidative degradation of complex molecules to simpler...

Scientific topics: Endocrinology and metabolism

Keywords: Metabolic pathway, Metabolic energetics, Metabolism

Energetic view of metabolic pathways https://tess.elixir-europe.org/materials/energetic-view-of-metabolic-pathways Metabolism of living cells is a complex network of chemical reactions to extract, convert and store energy from nutrients that can be analyzed in self-contained parts called pathways. Metabolic pathways contribute to catabolism - the oxidative degradation of complex molecules to simpler compounds, and - the reductive synthesis of complicated molecules from simpler ones. Catabolic pathways release free energy some of which is conserved in the formation of adenosine triphosphate (ATP) and reduced pyridine nucleotides (NADH, NADPH). Endocrinology and metabolism Metabolic pathway, Metabolic energetics, Metabolism 2014-01-22 2017-10-09

Erasmus Intensive Program "MoSyB 2013" "Modeling in systems biology and synthetic biology" video lectures.

Keywords: Synthetic biology, Modeling

MoSyB 2013 - Synthetic Biology modelling: from model-based design to reality https://tess.elixir-europe.org/materials/mosyb-2013-synthetic-biology-modelling-from-model-based-design-to-reality Erasmus Intensive Program "MoSyB 2013" "Modeling in systems biology and synthetic biology" video lectures. Synthetic biology, Modeling 2015-02-26 2017-10-09

In 2007, Paul Rothemund gave TED a short summary of his specialty, DNA folding. Now he lays out in clear, abundant detail the immense promise of this field — to create tiny machines that assemble themselves.

Scientific topics: DNA

Keywords: DNA, Synthetic biology

Paul Rothemund - DNA folding https://tess.elixir-europe.org/materials/paul-rothemund-dna-folding In 2007, Paul Rothemund gave TED a short summary of his specialty, DNA folding. Now he lays out in clear, abundant detail the immense promise of this field — to create tiny machines that assemble themselves. DNA DNA, Synthetic biology 2015-02-26 2017-10-09

Nobel laureate James Watson opens TED2005 with the frank and funny story of how he and his research partner, Francis Crick, discovered the structure of DNA.

Scientific topics: Genetics, DNA

Keywords: DNA, Genetic engineering, Genetics

James Watson: How we discovered DNA https://tess.elixir-europe.org/materials/james-watson-how-we-discovered-dna Nobel laureate James Watson opens TED2005 with the frank and funny story of how he and his research partner, Francis Crick, discovered the structure of DNA. Genetics DNA DNA, Genetic engineering, Genetics 2015-02-26 2017-10-09
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