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SYSTEMS BIOLOGY MARKUP LANGUAGE (SBML), How is SBML is used?, Some important SBML constructs, SBML “rules”, Levels of SBML
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Histotypic culture
Histotypic culture involves growing cell lines in a three-dimensional matrix at high density to form tissue-like structures. Common techniques include using gels, sponges, hollow fibers, spheroids, and rotating chambers to provide a 3D environment that allows cells to organize similarly to how they would in tissues. This allows for the study of processes like drug penetration and cell differentiation that are not possible with traditional 2D cultures. While histotypic cultures provide a model for certain tissue functions, they also face challenges like loss of cell differentiation over time.
NEXT GENERATION SEQUENCING
Deciphering DNA sequences is essential for virtually all branches of biological research. With the
advent of capillary electrophoresis (CE)-based Sanger sequencing, scientists gained the ability to
elucidate genetic information from any given biological system. This technology has become widely
adopted in laboratories around the world, yet has always been hampered by inherent limitations in
throughput, scalability, speed, and resolution that often preclude scientists from obtaining the essential
information they need for their course of study. To overcome these barriers, an entirely new technology
was required—Next-Generation Sequencing (NGS), a fundamentally different approach to sequencing
that triggered numerous ground-breaking discoveries and ignited a revolution in genomic science.
SAGE (Serial analysis of Gene Expression)
SAGE (Serial Analysis of Gene Expression) is a technique that allows for the rapid and comprehensive analysis of gene expression patterns in a given cell population. It works by isolating mRNA, synthesizing cDNA, ligating short sequence tags to the cDNA, and then counting the number of times each tag is observed to quantify gene expression levels. The tags are concatenated and sequenced to generate vast amounts of data that must be analyzed computationally to identify which genes particular tags correspond to and to compare expression profiles between cell types. SAGE provides an overview of a cell's complete transcriptional activity and has been applied to study differences in cancer vs normal cells and to identify targets of oncogenes and tumor suppressor genes.
Next Generation Sequencing (NGS)
Next Generation Sequencing (NGS) Is A Modern And Cost Effective Sequencing Technology Which Enables Scientists To Sequence Nucleic Acids At Much Faster Rate. In This Presentation, You Will Learn About What is NGS, Idea Behind NGS, Methodology And Protocol, Widely Adapted NGS Protocols, Applications And References For Further Study.
Next Generation Sequencing of DNA
Next generation sequencing (NGS) refers to modern DNA sequencing technologies that allow for high-speed, low-cost sequencing of entire genomes. NGS works by massively parallel sequencing of millions of DNA fragments. The Illumina sequencing by synthesis method is the most commonly used NGS approach. It involves library preparation, cluster generation on a flow cell, sequencing via reversible dye-terminator chemistry, and computational analysis of sequenced reads. Key advantages of NGS include its scalability, unlimited dynamic range, tunable coverage levels, and ability to multiplex many samples simultaneously in a single run.
Comparative genomic hybridization
Comparative genomic hybridization (CGH) is a molecular cytogenetic technique that allows detection of copy number variations between a test and reference DNA sample without cell culturing. CGH involves labeling and hybridizing test and reference DNA to normal metaphase chromosomes before visualizing differences in fluorescence to identify regions of gains or losses. While CGH was originally used for cancer research, it can also detect chromosomal abnormalities associated with genetic disorders and has improved resolution over traditional cytogenetic methods. The main limitations of CGH are its inability to detect structural aberrations without copy number changes and resolutions above 5-10 megabases.
Molecular hybridization
Molecular hybridization is the process by which two complementary strands of DNA or RNA bind together via hydrogen bonding between bases. It is used in techniques like cloning, PCR, and diagnostic tests involving nucleic acid probes. The document describes the process of hybridization, factors that affect binding strength, and techniques that utilize molecular hybridization like Southern blotting, dot/slot blotting, microarrays, and in situ hybridization.
Elispot
ELISPOT assays are the most sensitive technology for detecting immune cells that secrete proteins like cytokines. They directly capture the analyte secreted by each individual cell, preventing dilution or degradation, making ELISPOT more sensitive than other methods like ELISA or flow cytometry. ELISPOT assays can detect rare antigen-specific immune cells and characterize both the quantity and effector classes of the antigen-specific immune response.
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Histotypic culture
Histotypic culture involves growing cell lines in a three-dimensional matrix at high density to form tissue-like structures. Common techniques include using gels, sponges, hollow fibers, spheroids, and rotating chambers to provide a 3D environment that allows cells to organize similarly to how they would in tissues. This allows for the study of processes like drug penetration and cell differentiation that are not possible with traditional 2D cultures. While histotypic cultures provide a model for certain tissue functions, they also face challenges like loss of cell differentiation over time.
NEXT GENERATION SEQUENCING
Deciphering DNA sequences is essential for virtually all branches of biological research. With the
advent of capillary electrophoresis (CE)-based Sanger sequencing, scientists gained the ability to
elucidate genetic information from any given biological system. This technology has become widely
adopted in laboratories around the world, yet has always been hampered by inherent limitations in
throughput, scalability, speed, and resolution that often preclude scientists from obtaining the essential
information they need for their course of study. To overcome these barriers, an entirely new technology
was required—Next-Generation Sequencing (NGS), a fundamentally different approach to sequencing
that triggered numerous ground-breaking discoveries and ignited a revolution in genomic science.
SAGE (Serial analysis of Gene Expression)
SAGE (Serial Analysis of Gene Expression) is a technique that allows for the rapid and comprehensive analysis of gene expression patterns in a given cell population. It works by isolating mRNA, synthesizing cDNA, ligating short sequence tags to the cDNA, and then counting the number of times each tag is observed to quantify gene expression levels. The tags are concatenated and sequenced to generate vast amounts of data that must be analyzed computationally to identify which genes particular tags correspond to and to compare expression profiles between cell types. SAGE provides an overview of a cell's complete transcriptional activity and has been applied to study differences in cancer vs normal cells and to identify targets of oncogenes and tumor suppressor genes.
Next Generation Sequencing (NGS)
Next Generation Sequencing (NGS) Is A Modern And Cost Effective Sequencing Technology Which Enables Scientists To Sequence Nucleic Acids At Much Faster Rate. In This Presentation, You Will Learn About What is NGS, Idea Behind NGS, Methodology And Protocol, Widely Adapted NGS Protocols, Applications And References For Further Study.
Next Generation Sequencing of DNA
Next generation sequencing (NGS) refers to modern DNA sequencing technologies that allow for high-speed, low-cost sequencing of entire genomes. NGS works by massively parallel sequencing of millions of DNA fragments. The Illumina sequencing by synthesis method is the most commonly used NGS approach. It involves library preparation, cluster generation on a flow cell, sequencing via reversible dye-terminator chemistry, and computational analysis of sequenced reads. Key advantages of NGS include its scalability, unlimited dynamic range, tunable coverage levels, and ability to multiplex many samples simultaneously in a single run.
Comparative genomic hybridization
Comparative genomic hybridization (CGH) is a molecular cytogenetic technique that allows detection of copy number variations between a test and reference DNA sample without cell culturing. CGH involves labeling and hybridizing test and reference DNA to normal metaphase chromosomes before visualizing differences in fluorescence to identify regions of gains or losses. While CGH was originally used for cancer research, it can also detect chromosomal abnormalities associated with genetic disorders and has improved resolution over traditional cytogenetic methods. The main limitations of CGH are its inability to detect structural aberrations without copy number changes and resolutions above 5-10 megabases.
Molecular hybridization
Molecular hybridization is the process by which two complementary strands of DNA or RNA bind together via hydrogen bonding between bases. It is used in techniques like cloning, PCR, and diagnostic tests involving nucleic acid probes. The document describes the process of hybridization, factors that affect binding strength, and techniques that utilize molecular hybridization like Southern blotting, dot/slot blotting, microarrays, and in situ hybridization.
Elispot
ELISPOT assays are the most sensitive technology for detecting immune cells that secrete proteins like cytokines. They directly capture the analyte secreted by each individual cell, preventing dilution or degradation, making ELISPOT more sensitive than other methods like ELISA or flow cytometry. ELISPOT assays can detect rare antigen-specific immune cells and characterize both the quantity and effector classes of the antigen-specific immune response.
Maldi tof
Mass spectrometry is an analytical technique that ionizes samples and measures the mass-to-charge ratio of ions to determine molecular masses. It requires charged gaseous molecules for analysis. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry uses a laser to ionize analyte molecules embedded in a matrix, which are then accelerated through a flight tube based on their mass-to-charge ratios. MALDI-TOF is commonly used to analyze biomolecules like proteins and is applied in fields like proteomics, metabolomics, environmental analysis, and forensics.
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Cloning and expression vectors
Cloning and Expression Vectors document discusses:
1) Cloning a gene of interest involves inserting it into a vector that can be replicated in host cells, producing recombinant DNA molecules.
2) Vectors contain features like replication origins, antibiotic resistance genes, and unique restriction sites to facilitate cloning and isolation.
3) Early cloning experiments demonstrated that recombinant plasmids containing both prokaryotic and eukaryotic DNA could replicate stably in bacteria, allowing genetic engineering.
Sage
SAGE is a technique that allows for the digital analysis of overall gene expression patterns through the use of short sequence tags to uniquely identify transcripts without requiring preexisting clones. It works by linking these tags together into long serial molecules that can then be cloned and sequenced, with the number of times a particular tag is observed providing the expression level of the corresponding transcript. This allows for rapid sequencing analysis of multiple transcripts from a single sequencing event. SAGE is useful for comparative expression studies to identify differences in gene expression between tissues.
Transcriptomics
Transcriptomics is the study of RNA in cells and tissues. The transcriptome refers to the complete set of transcripts in a cell under a specific condition. Understanding the transcriptome reveals the functional elements of the genome and molecular constituents of cells. Techniques for studying the transcriptome include microarray analysis and RNA sequencing. Microarrays measure gene expression levels using fluorescently-labeled cDNA hybridized to probes on an array. RNA sequencing determines expression levels by sequencing individual cDNAs produced from target RNA. Transcriptomics provides insights into development, disease, and varying gene expression under different environmental conditions.
Emulsion pcr
Emulsion PCR is a technique used in next-generation sequencing to amplify DNA sequences attached to beads. It involves compartmentalizing DNA fragments with primer-coated beads into water-in-oil emulsion droplets, with each droplet containing one fragment. The droplets then act as individual PCR reactors to amplify each fragment clonally onto a single bead. After thermal cycling, millions of copies of the DNA fragment are attached to each bead for downstream sequencing applications.
Basic Steps of the NGS Method
Next generation sequencing (NGS) involves chemical assays other than traditional Sanger sequencing to sequence DNA. The basic steps of NGS are: 1) library preparation where DNA is fragmented and adapters are ligated, 2) clonal amplification where fragments are amplified, and 3) sequencing reactions using techniques like pyrosequencing or reversible dye terminators to determine the sequence. The sequenced fragments are then analyzed bioinformatically to map reads and assemble sequences.
Derivatives of pBR322
The document discusses the plasmid vector pBR322, which was constructed in 1977 and is one of the most commonly used cloning vectors. It describes the origins and components of pBR322, including two antibiotic resistance genes, the origin of replication, and restriction enzyme cleavage sites. The document also summarizes the construction of several derivatives of pBR322, including pBR327, pUC18, and pBR118/119, and notes their applications and advantages over the original pBR322 vector.
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Flow cytometry works by passing cells in a fluid stream through a laser beam, which causes light scattering and fluorescence that is detected and analyzed. Cells are labeled with fluorescent markers and passed through the flow cell in a hydrodynamically focused stream. A laser excites the fluorescent molecules, which emit light at different wavelengths. Forward scatter detects cell size, side scatter detects internal complexity. Detectors convert light signals to digital data, which is analyzed through gating and dot plots to identify cell populations and properties. Flow cytometry allows rapid multi-parameter analysis of individual cells.
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Sequencing is one of the major technological advancement that has taken shape in the last two or three decade. Starting from Sanger and Maxam-Gilbert sequencing methods to the latest high-throughput methods, sequencing technologies has changed the the landscape of biological sciences.
This slide takes a look a the major sequencing methods over time.
Note: Several images included here have been sourced from GOOGLE IMAGES. The content has been extracted from several SCIENTIFIC PAPERS and WEBSITES.
PLEASE DO CONTACT THE AUTHOR DIRECTLY IF ANY COPYRIGHT ISSUE ARISES.
Homology modeling
Homology modeling is a technique used to predict the 3D structure of a protein based on the alignment of its amino acid sequence to known protein structures. It relies on the observation that structure is more conserved than sequence during evolution. The key steps in homology modeling include: 1) identifying a template structure through sequence alignment tools like BLAST, 2) correcting any errors in the initial alignment, 3) generating the protein backbone based on the template structure, 4) modeling any loops or missing regions, 5) adding side chains, 6) optimizing the model structure energetically, and 7) validating that the final model matches the template structure and has correct stereochemistry. Homology modeling is useful for applications like structure-based drug design
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This document provides an overview of cancer immunology, including how tumors are able to evade and enhance immune responses. It discusses the types of tumors of the immune system, such as lymphomas and leukemias, and how tumors enhance their growth by modulating antigens, expressing low levels of MHC molecules, and lacking costimulatory signals. It also describes tumor antigens, how the immune system responds to tumors through cells like NK cells and macrophages, and immunotherapy approaches to boost anti-tumor immunity.
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Overview
Reductionist approach
Holistic approach
What is systems biology?
○ Advantages of Systems Biology
Tools of holistic approach
○ Proteomics, Transcriptomics and Metabolomics
Conclusion
References
Maxam–Gilbert sequencing
This document discusses DNA sequencing methods. It describes the Maxam-Gilbert sequencing method developed in 1976-1977 which uses chemical modification and cleavage of DNA at specific bases, followed by electrophoresis to separate fragments by size. It also mentions the popular Sanger sequencing method. The procedure for Maxam-Gilbert sequencing involves labeling DNA, cleaving it with chemicals, running the fragments on a gel, and analyzing the results to deduce the DNA sequence. Advantages include no premature termination and ability to sequence stretches not possible with enzymatic methods, while disadvantages include use of radioactivity and toxic chemicals.
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This document discusses SBML (Systems Biology Markup Language), SBGN (Systems Biology Graphical Notation), and BioModels.net. SBML is a standard format for representing computational models of biochemical networks that allows models to be exchanged between software tools and researchers. Over 100 software tools now support SBML. SBGN is a project to develop a standard notation for diagrams of cellular networks. BioModels.net is a database of models encoded in SBML that has been made possible by the adoption of SBML as a common exchange format.
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Mass spectrometry is an analytical technique that ionizes samples and measures the mass-to-charge ratio of ions to determine molecular masses. It requires charged gaseous molecules for analysis. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry uses a laser to ionize analyte molecules embedded in a matrix, which are then accelerated through a flight tube based on their mass-to-charge ratios. MALDI-TOF is commonly used to analyze biomolecules like proteins and is applied in fields like proteomics, metabolomics, environmental analysis, and forensics.
LAMP (Loop Mediated Isothermal Amplification)
Njiru, 2012 has described that " Lack of effective point of care diagnostic tests applicable in resource-poor endemic areas is a critical barrier to effective treatment and control of infectious diseases.” Therefore, Innovations in biotechnology that combine molecular biology, microfabrication and bioinformatics are moving nucleic acid technologies from futuristic possibilities to common laboratory techniques and modes for diagnoses. In this context, LAMP (Loop Mediated Isothermal Amplification) is a highly sensitive and specific DNA/RNA amplification method. Advantage of LAMP is isothermal reaction condition and therefore, LAMP is affordable because of no need to have expensive thermal cycler.
MICROARRAY
Microarray technology allows researchers to analyze the expression levels of thousands of genes simultaneously using DNA probes attached to a solid surface. There are two main types of microarrays: glass cDNA microarrays which involve spotting pre-fabricated cDNA fragments on glass slides; and high-density oligonucleotide arrays which involve the in situ synthesis of oligonucleotides on a chip. The key steps in a microarray experiment are sample preparation and labeling, hybridization of labeled cDNA to the probes, washing, and image analysis to quantify gene expression levels. Microarrays have numerous applications including gene expression profiling, comparative genomics, disease diagnosis, drug discovery, and toxicology research.
Msa
This document provides an overview of multiple sequence alignment (MSA). MSA is used to align biological sequences, such as DNA, RNA, or proteins, to find similarities and differences between sequences. The document outlines the goal of MSA as finding structural, functional, and evolutionary relationships. It describes the general considerations and steps of MSA, including pairwise comparison of sequences, cluster analysis to generate a hierarchy, and progressive alignment. Common MSA software and applications are also summarized.
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Q pcr
Q-PCR allows for quantitative analysis of DNA amplification in real-time using fluorescence detection. It monitors accumulation of fluorescent signals during each PCR cycle, allowing quantification of starting DNA template. Common probe-based methods include TaqMan probes with a fluorophore-quencher pair and molecular beacons which become fluorescent upon target binding. SYBR Green also detects amplification nonspecifically by binding double-stranded DNA. Q-PCR provides advantages over conventional PCR such as greater precision, sensitivity, and ability to quantify initial template amounts.
Cloning and expression vectors
Cloning and Expression Vectors document discusses:
1) Cloning a gene of interest involves inserting it into a vector that can be replicated in host cells, producing recombinant DNA molecules.
2) Vectors contain features like replication origins, antibiotic resistance genes, and unique restriction sites to facilitate cloning and isolation.
3) Early cloning experiments demonstrated that recombinant plasmids containing both prokaryotic and eukaryotic DNA could replicate stably in bacteria, allowing genetic engineering.
Sage
SAGE is a technique that allows for the digital analysis of overall gene expression patterns through the use of short sequence tags to uniquely identify transcripts without requiring preexisting clones. It works by linking these tags together into long serial molecules that can then be cloned and sequenced, with the number of times a particular tag is observed providing the expression level of the corresponding transcript. This allows for rapid sequencing analysis of multiple transcripts from a single sequencing event. SAGE is useful for comparative expression studies to identify differences in gene expression between tissues.
Transcriptomics
Transcriptomics is the study of RNA in cells and tissues. The transcriptome refers to the complete set of transcripts in a cell under a specific condition. Understanding the transcriptome reveals the functional elements of the genome and molecular constituents of cells. Techniques for studying the transcriptome include microarray analysis and RNA sequencing. Microarrays measure gene expression levels using fluorescently-labeled cDNA hybridized to probes on an array. RNA sequencing determines expression levels by sequencing individual cDNAs produced from target RNA. Transcriptomics provides insights into development, disease, and varying gene expression under different environmental conditions.
Emulsion pcr
Emulsion PCR is a technique used in next-generation sequencing to amplify DNA sequences attached to beads. It involves compartmentalizing DNA fragments with primer-coated beads into water-in-oil emulsion droplets, with each droplet containing one fragment. The droplets then act as individual PCR reactors to amplify each fragment clonally onto a single bead. After thermal cycling, millions of copies of the DNA fragment are attached to each bead for downstream sequencing applications.
Basic Steps of the NGS Method
Next generation sequencing (NGS) involves chemical assays other than traditional Sanger sequencing to sequence DNA. The basic steps of NGS are: 1) library preparation where DNA is fragmented and adapters are ligated, 2) clonal amplification where fragments are amplified, and 3) sequencing reactions using techniques like pyrosequencing or reversible dye terminators to determine the sequence. The sequenced fragments are then analyzed bioinformatically to map reads and assemble sequences.
Derivatives of pBR322
The document discusses the plasmid vector pBR322, which was constructed in 1977 and is one of the most commonly used cloning vectors. It describes the origins and components of pBR322, including two antibiotic resistance genes, the origin of replication, and restriction enzyme cleavage sites. The document also summarizes the construction of several derivatives of pBR322, including pBR327, pUC18, and pBR118/119, and notes their applications and advantages over the original pBR322 vector.
Conventional and next generation sequencing ppt
This presentation is all about the basic principle behind conventional and next generation sequencing.
Flow cytometry
Flow cytometry works by passing cells in a fluid stream through a laser beam, which causes light scattering and fluorescence that is detected and analyzed. Cells are labeled with fluorescent markers and passed through the flow cell in a hydrodynamically focused stream. A laser excites the fluorescent molecules, which emit light at different wavelengths. Forward scatter detects cell size, side scatter detects internal complexity. Detectors convert light signals to digital data, which is analyzed through gating and dot plots to identify cell populations and properties. Flow cytometry allows rapid multi-parameter analysis of individual cells.
Systems biology & Approaches of genomics and proteomics
This presentation provides the basic understanding of varous genomics and proteomics techniques.Systems biology studies life as a system .It includes the study of living system using various omic technologies .
Next Generation Sequencing
Sequencing is one of the major technological advancement that has taken shape in the last two or three decade. Starting from Sanger and Maxam-Gilbert sequencing methods to the latest high-throughput methods, sequencing technologies has changed the the landscape of biological sciences.
This slide takes a look a the major sequencing methods over time.
Note: Several images included here have been sourced from GOOGLE IMAGES. The content has been extracted from several SCIENTIFIC PAPERS and WEBSITES.
PLEASE DO CONTACT THE AUTHOR DIRECTLY IF ANY COPYRIGHT ISSUE ARISES.
Homology modeling
Homology modeling is a technique used to predict the 3D structure of a protein based on the alignment of its amino acid sequence to known protein structures. It relies on the observation that structure is more conserved than sequence during evolution. The key steps in homology modeling include: 1) identifying a template structure through sequence alignment tools like BLAST, 2) correcting any errors in the initial alignment, 3) generating the protein backbone based on the template structure, 4) modeling any loops or missing regions, 5) adding side chains, 6) optimizing the model structure energetically, and 7) validating that the final model matches the template structure and has correct stereochemistry. Homology modeling is useful for applications like structure-based drug design
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This document provides an overview of cancer immunology, including how tumors are able to evade and enhance immune responses. It discusses the types of tumors of the immune system, such as lymphomas and leukemias, and how tumors enhance their growth by modulating antigens, expressing low levels of MHC molecules, and lacking costimulatory signals. It also describes tumor antigens, how the immune system responds to tumors through cells like NK cells and macrophages, and immunotherapy approaches to boost anti-tumor immunity.
Systems biology
Introduction
Overview
Reductionist approach
Holistic approach
What is systems biology?
○ Advantages of Systems Biology
Tools of holistic approach
○ Proteomics, Transcriptomics and Metabolomics
Conclusion
References
Maxam–Gilbert sequencing
This document discusses DNA sequencing methods. It describes the Maxam-Gilbert sequencing method developed in 1976-1977 which uses chemical modification and cleavage of DNA at specific bases, followed by electrophoresis to separate fragments by size. It also mentions the popular Sanger sequencing method. The procedure for Maxam-Gilbert sequencing involves labeling DNA, cleaving it with chemicals, running the fragments on a gel, and analyzing the results to deduce the DNA sequence. Advantages include no premature termination and ability to sequence stretches not possible with enzymatic methods, while disadvantages include use of radioactivity and toxic chemicals.
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This document compares model-oriented and process algebra approaches to formal specification languages. It discusses key formal specification styles including model-oriented, algebraic, transition-based, process algebra, logic-based, and reactive approaches. It then evaluates several model-oriented languages (Z, VDM, B) and process algebra languages (CSP, CCS) based on criteria like abstraction, ambiguity, consistency, concurrency, readability and reusability. Finally, it discusses the B method and Event-B modeling language and related formal techniques, and notes that the Rodin platform provides effective tool support for modeling and proving in Event-B.
Uml
The document discusses UML (Unified Modeling Language) and object-oriented software development. It describes the software development life cycle and various modeling techniques used in UML, including use case diagrams, class diagrams, sequence diagrams, and collaboration diagrams. It explains key UML concepts such as classes, objects, attributes, operations, actors, and relationships. The benefits of visual modeling and UML are also summarized.
[RPL2] Pertemuan 3 - UML dan USECASE VIEW
Materi yang ada pada slide ini berisi :
Pengenalan UML Sebagai Alat Bantu Pemodelan Pada Pembangunan Perangkat Lunak Menggunakan Pendekatan Analisis dan Desain Berorientasi Objek
Notasi, Semantik, dan Stereotype Pada UML
Komponen pada UML (Use Case View, Logical View, Physical View, dan Process View)
Pengenalan Use Case Diagram sebagai Use Case View Pada UML
Penjelasan Aktor, Generalisasi Aktor, dan Use Case
Penjelasan Use Case Scenario
Use Case Refinement (Relasi Include, Extends, dan Generalisasi Use Case)
----------------------------------------------------------------------
Keep in touch with me in :
Twitter : https://twitter.com/rizkiadam_1991
Email : rizkiadamunikom@gmail.com
IG : @rizkiadamkurniawan
Module 2 17CS45
System modeling involves developing abstract models of a system from different perspectives using notations like UML. Models are used during requirements, design, and documentation. Common model types include context models, interaction models using use cases and sequence diagrams, structural class diagrams, and behavioral state diagrams. Model-driven engineering aims to generate implementations automatically from models. Key aspects of software design include understanding interactions, architectural design, identifying objects, developing design models, and specifying interfaces. Design patterns provide reusable solutions to common problems.
UML Diagrams, examples, descriptions and tutorials
UML is a modeling language used to create visual models of object-oriented software systems. It was developed in the early 1990s to standardize the various object-oriented modeling notations in use at the time. UML uses different types of diagrams to represent different views of a system, including use case diagrams, class diagrams, sequence diagrams, and state machine diagrams. The language provides a standardized way to visualize the various components of an object-oriented system.
Unified Modeling Language
The document provides an introduction to the Unified Modeling Language (UML). It discusses the key principles of modeling and an overview of UML. The UML is a standard language for writing software blueprints and can be used to visualize, specify, construct, and document software systems. The UML has building blocks like classes, objects, use cases and relationships. It consists of diagrams like class diagrams, sequence diagrams, and state machine diagrams. The UML addresses multiple views of a system including use case, design, interaction and implementation views.
SE Complete notes mod 4 &5.pdf
This document discusses various system modeling techniques, including context models, interaction models, structural models, and behavioral models. It provides examples of each type of model using the Unified Modeling Language (UML). Context models show the system and its relationships to other external systems. Interaction models include use case diagrams and sequence diagrams. Structural models include class diagrams, which depict classes and relationships. Behavioral models show how a system responds to events. The document also discusses object-oriented design, implementation issues, and open source development.
UML Design
This document discusses various UML diagrams including class diagrams, use case diagrams, and their advantages and disadvantages. It provides an example class diagram for the abstract factory design pattern. Use case diagrams are used to gather system requirements and show interactions between actors and use cases. They provide an outside view of a system and can be used in both forward and reverse engineering. While useful for requirements analysis, use case diagrams do not describe implementation details.
SE - System Models
The document discusses system modeling and different types of models used during requirements engineering including context models, data flow diagrams, state machine models, semantic data models, object models, and sequence diagrams. It also introduces the Unified Modeling Language (UML) notation and explains how analysis workbenches can support system modeling.
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7.
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- 1. SYSTEMS BIOLOGY MARKUP LANGUAGE 1 PRESENTED BY S. R.BHARATHKUMAAR, II M.Sc., BIOTECHNOLOGY 2019-2021 BHARATHIAR UNIVERSITY
- 2. SYSTEMS BIOLOGY MARKUP LANGUAGE (SBML) SBML is a machine-readable language, based on XML, free and open interchange format for representing models of biological processes. It can represent metabolic networks, cell-signaling pathways, regulatory networks and many other kinds of systems. SBML as an input and output format, different software tools can operate on the same representation of a model, removing chances for errors in translation and assuring a common starting point for analyses and simulations SBML can encode models consisting of entities (for example, molecular species) linked and modified by processes (for example, biochemical reactions). Here is an artificial example of a small set of biochemical reactions The symbols in square brackets (e.g., S1) represent concentrations of molecular species, the arrows represent reactions, and the formulas above the arrows represent the rates at which the reactions take place. Broken down into its constituents, this model contains a number of components: reactant species, product species, reactions, reaction rates, and parameters in the rate expressions. 2
- 3. Two important principles in SBML are that Models are decomposed into explicitly-labeled constituent elements, and The representation deliberately does not cast the model directly into a set of differential equations or other specific interpretation of the model. This makes it easier for a software tool to interpret the model and translate the SBML form into whatever internal form the tool actually uses How is SBML is used? • Meant to provide an exchange language for software tools • Don’t write SBML by hand, a software can do it • Software tools that “speak” SBML provides a higher-level interface • Applications usually have their own native format. • Import/export SBML rather than natively save as SBML. Some important SBML constructs Basic elements Species Compartment Parameter Reaction 3 Additional useful elements Unit definition Rule Function definition Event Initial assignment Constraint
- 4. SBML “rules” Rules in SBML define extra mathematical expressions E.g., If need to express additional mathematical relationships beyond what is implied by the system of reactions. 3 subtypes: Rules that defines relationship that hold at all times 4 Rules in the context of the overall model Equation derived from reaction definitions Algebraic rules Assignment rules Rate rules
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- 16. Some practical details useful to know about SBML 16
- 17. F 17
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Editor's Notes
- (And while this example uses concentrations, it could equally have used other measures, such as the number of molecules of each chemical species.)
- Accepted by dozens of journals 100’s of software tools available today Libraries: libSBML, JSBML 260+ listed in SBML software guide 1000’s of model available In public databases eg., Bio-Models database, Reactome As supplementary data to papers In private repositories
- Level 3 packages add constructs on top of sbml level 3 core