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| − |
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| − | == Timetable and syllabus ==
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| − | <table>
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| − | <tr class="st">
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| − | <td colspan="5">'''I n t r o d u c t i o n'''</td>
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| − | </tr>
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| − |
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| − | <tr class="sh">
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| − | <td class="sc">'''Week'''</td>
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| − | <td class="sc">'''Date'''</td>
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| − | <td class="sc">'''Topics'''</td>
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| − | <td class="sc">'''Activities'''</td>
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| − | <td class="sc">'''Assignment'''</td>
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| − | </tr>
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| − | <tr class="s1">
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| − | <td class="sc">1</td>
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| − | <td class="sc">Jan. 9 - 14</td>
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| − | <td class="sc">
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| − | <div class="table-intro-text">Computational Biology aims to bring biology from its descriptive beginnings to a truly predictive science, based on consistent and well understood principles. In the systems biology field of computational biology, we deal primarily with large-scale, cross-sectional data, its relationships and hierarchies.</div>
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| − | * Course Organisation
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| − | * [[CSB_Introduction|Introduction to Computational Systems Biology]]
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| − | </td>
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| − | <td class="sc">—</td>
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| − | <td class="sc">[[CSB_Assignment_Week_1|Assignment 1]]</td>
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| − | </tr>
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| − |
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| − | <!-- =================== THEME =================== -->
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| − | <tr><td colspan="5" class="sp"> </td></tr>
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| − | <tr class="st">
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| − | <td colspan="5">'''D a t a'''</td>
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| − | </tr>
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| − | <tr class="sh">
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| − | <td class="sc">'''Week'''</td>
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| − | <td class="sc">'''Date'''</td>
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| − | <td class="sc">'''Topics'''</td>
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| − | <td class="sc">'''Activities'''</td>
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| − | <td class="sc">'''Assignment'''</td>
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| − | </tr>
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| − | <!-- =================== /THEME =================== -->
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| − |
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| − | <tr class="s1">
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| − | <td class="sc">2</td>
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| − | <td class="sc">Jan. 16 - 21</td>
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| − | <td class="sc">
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| − | <div class="table-intro-text">In principle, most of the data of interest to us is freely available on the Web, in public repositories. However, the number of databases and associated Web services is large and in constant flux and integrating the data has its own issues. The most important issue is the question of how to define ''function'' and make this concept computable; from this arises the central role that ontologies play in the field.</div>
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| − | * [[CSB_Web_tools|CSB on the Web: Databases and services]]
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| − | * [[Data_integration|Data integration]]
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| − | * [[CSB_Ontologies|Ontologies and phenotypes]]
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| − | * [[Function_prediction|Prediction of function]]
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| − | </td>
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| − | <td class="sc">Quiz 1</td>
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| − | <td class="sc">[[CSB_Assignment_Week_2|Assignment 2]]</td>
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| − | </tr>
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| − |
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| − | <tr class="s1">
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| − | <td class="sc">3</td>
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| − | <td class="sc">Jan. 23 - 28</td>
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| − | <td class="sc">
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| − | <div class="table-intro-text">The large volume of data in any given systems biology experiment basically precludes the manual, gene-by-gene analysis of results. Questions arise regarding computational strategies for ''gene lists'', especially the statistical tools and strategies we have at our disposal, and a minimum set of programming and automation skills.</div>
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| − | * Lists of genes - a common outcome of high-throughput experiments
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| − | ** [[CSB Gene lists|Gene lists]]
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| − | ** [[Enrichment|Enrichment analysis]]
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| − | ** [[GSEA|The GSEA approach]]
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| − | * Statistics
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| − | ** [[Statistics|Principles of Statistics in molecular biology]]
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| − | ** [[R]]
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| − | ** [[Bioconductor]]
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| − | ** [[Clustering|Clustering and Classification]]
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| − | ** [[EDA|Exploratory Data Analysis]]
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| − | ** [[Data_mining|Data mining]]
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| − | * Programming
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| − | ** [[Informal_programming|Informal programming]]
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| − | ** [[IDE|Using an IDE (Integrated Development Environments)]]
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| − | </td>
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| − | <td class="sc">Quiz 2, project concept due</td>
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| − | <td class="sc">[[CSB_Assignment_Week_3|Assignment 3]]</td>
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| − | </tr>
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| − |
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| − |
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| − | <!-- =================== THEME =================== -->
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| − | <tr><td colspan="5" class="sp"> </td></tr>
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| − | <tr class="st">
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| − | <td colspan="5">'''''"-omics"'''''</td>
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| − | </tr>
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| − |
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| − | <tr class="sh">
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| − | <td class="sc">'''Week'''</td>
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| − | <td class="sc">'''Date'''</td>
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| − | <td class="sc">'''Topics'''</td>
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| − | <td class="sc">'''Activities'''</td>
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| − | <td class="sc">'''Assignment'''</td>
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| − | </tr>
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| − | <!-- =================== /THEME =================== -->
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| − |
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| − | <tr class="s2">
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| − | <td class="sc">4</td>
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| − | <td class="sc">Jan. 30 - Feb. 3</td>
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| − | <td class="sc">
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| − | <div class="table-intro-text">Genome sequencing brought the first complete overview of the information underlying life; the associated concept of the ''transcriptome'' - a description of which portion of the genome is expressed at what time - is the most basic ''functional'' description of this information.</div>
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| − | * [[Genome|Genome]]
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| − | * [[Transcriptome|Transcriptome]]
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| − | </td>
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| − | <td class="sc">Quiz 3</td>
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| − | <td class="sc">[[CSB_Assignment_Week_4|Assignment 4]]</td>
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| − | </tr>
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| − |
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| − | <tr class="s1">
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| − | <td class="sc">5</td>
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| − | <td class="sc">Feb. 6 - 10</td>
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| − | <td class="sc">
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| − | <div class="table-intro-text">Many more holistic, or cross-sectional descriptions of the molecular composition and assembly of the cell are being worked on.</div>
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| − | * [[Proteome|Proteome]]
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| − | * [[Metabolome|Metabolome]]
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| − | * [[Glycome|Glycome]]
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| − | * [[Lipidome|Lipidome]]
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| − | </td>
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| − | <td class="sc">Quiz 4, project outline due</td>
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| − | <td class="sc">[[CSB_Assignment_Week_5|Assignment 5]]</td>
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| − | </tr>
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| − |
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| − | <!-- =================== THEME =================== -->
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| − | <tr><td colspan="5" class="sp"> </td></tr>
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| − | <tr class="st">
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| − | <td colspan="5">'''I n t e r a c t i o n s , P a t h w a y s a n d N e t w o r k s'''</td>
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| − | </tr>
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| − |
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| − | <tr class="sh">
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| − | <td class="sc">'''Week'''</td>
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| − | <td class="sc">'''Date'''</td>
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| − | <td class="sc">'''Theme'''</td>
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| − | <td class="sc">'''Activities'''</td>
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| − | <td class="sc">'''Assignment'''</td>
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| − | </tr>
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| − | <!-- =================== /THEME =================== -->
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| − |
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| − | <tr class="s1">
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| − | <td class="sc">6</td>
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| − | <td class="sc">Feb. 13 - 17</td>
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| − | <td class="sc">
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| − | <div class="table-intro-text">Fundamentally, ''-omics'' descriptions provide us with lists of components. However, to understand how things work, we need to address the ''relationships'' of the components - how things are put together: the molecular blueprints. At its most basic level, this is the question of molecular interactions in the cell. A quantitative description of molecular interactions relies heavily on the mathematical discipline of ''graph theory''. ''Cytoscape'' is a visualization and analysis platform for molecular interactions. </div>
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| − | * [[Graph_theory|Graph theory]]
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| − | * [[Cytoscape|Cytoscape]]
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| − | </td>
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| − | <td class="sc">Quiz 5</td>
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| − | <td class="sc">[[CSB_Assignment_Week_6|Assignment 6]]</td>
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| − | </tr>
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| − | <tr class="s2">
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| − | <td class="sc"> </td>
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| − | <td class="sc">Feb. 20 - 24</td>
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| − | <td colspan="3">''Reading Week - School closed''</td>
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| − | </tr>
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| − | <tr class="s1">
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| − | <td class="sc">7</td>
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| − | <td class="sc">Feb. 27 - Mar. 2</td>
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| − | <td class="sc">
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| − | <div class="table-intro-text">Here we focus on the biological objects of "Interaction Science".</div>
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| − | * [[Interactome|The Interactome]]
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| − | * [[Interaction_databases|Interaction databases]]
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| − | * [[Pathways_and_Networks|Pathways and Networks]]
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| − | * [[Interaction_prediction|Interaction prediction]]
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| − | </td>
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| − | <td class="sc">Quiz 6</td>
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| − | <td class="sc">[[CSB_Assignment_Week_7|Assignment 7]]</td>
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| − | </tr>
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| − |
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| − | <!-- =================== THEME =================== -->
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| − | <tr><td colspan="5" class="sp"> </td></tr>
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| − | <tr class="st">
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| − | <td colspan="5">'''S y s t e m s'''</td>
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| − | </tr>
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| − |
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| − | <tr class="sh">
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| − | <td class="sc">'''Week'''</td>
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| − | <td class="sc">'''Date'''</td>
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| − | <td class="sc">'''Topics'''</td>
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| − | <td class="sc">'''Activities'''</td>
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| − | <td class="sc">'''Assignment'''</td>
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| − | </tr>
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| − | <!-- =================== /THEME =================== -->
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| − |
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| − | <tr class="s1">
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| − | <td class="sc">8</td>
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| − | <td class="sc">Mar. 5 - 9</td>
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| − | <td class="sc">
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| − | <div class="table-intro-text">Several key networked systems exist in the cell. Here we discuss their paradigms, how they are constructed from experimental data and examples of how they can be organized in databases.</div>
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| − | * [[Gene_regulatory_networks|Gene regulatory networks]]
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| − | * [[Metabolic_networks|Metabolic networks]]
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| − | * [[Signaling_networks|Signaling networks]]
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| − | * [[Developmental_networks|Developmental networks]]
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| − | * [[Pathway databases|Pathway and network databases]]
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| − | ** [[KEGG]]
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| − | ** [[BioCyc]]
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| − | </td>
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| − | <td class="sc">Quiz 7</td>
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| − | <td class="sc">[[CSB_Assignment_Week_8|Assignment 8]]</td>
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| − | </tr>
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| − | <tr class="s2">
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| − | <td class="sc">9</td>
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| − | <td class="sc">Mar. 12 - 16</td>
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| − | <td class="sc">
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| − | <div class="table-intro-text">Information theory has proven to be one of the cornerstones of biological analysis. A good example of its power and utility is the definition of systems in large-scale biological datasets.</div>
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| − | * [[CSB_Mutual information|Extracting systems from ''-omics'' datasets through mutual information]]
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| − | </td>
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| − | <td class="sc">Quiz 8</td>
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| − | <td class="sc">[[CSB_Assignment_Week_9|Assignment 9]]</td>
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| − | </tr>
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| − | <tr class="s1">
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| − | <td class="sc">10</td>
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| − | <td class="sc">Mar. 19 - 23</td>
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| − | <td class="sc">
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| − | <div class="table-intro-text">Life is not static, only death is. Yet, the dynamic nature of biological systems is often overlooked.</div>
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| − | * [[Systems dynamics|Systems dynamics]]
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| − | </td>
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| − | <td class="sc">Quiz 9, project final submission due</td>
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| − | <td class="sc">[[CSB_Assignment_Week_10|Assignment 10]]</td>
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| − | </tr>
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| − |
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| − | <!-- =================== THEME =================== -->
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| − | <tr><td colspan="5" class="sp"> </td></tr>
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| − | <tr class="st">
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| − | <td colspan="5">'''M o d e l s'''</td>
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| − | </tr>
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| − |
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| − | <tr class="sh">
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| − | <td class="sc">'''Week'''</td>
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| − | <td class="sc">'''Date'''</td>
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| − | <td class="sc">'''Theme'''</td>
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| − | <td class="sc">'''Activities'''</td>
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| − | <td class="sc">'''Assignment'''</td>
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| − | </tr>
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| − | <!-- =================== /THEME =================== -->
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| − |
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| − | <tr class="s1">
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| − | <td class="sc">11</td>
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| − | <td class="sc">Mar. 26 - 30</td>
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| − | <td class="sc">
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| − | <div class="table-intro-text">The notion that computational biology will at some time become predictive is tied to the idea that we will be able to model the cell's systems. Many approaches exist, each with its own strengths and weaknesses; how to integrate such models - preferrably across multiple scales - is a question of its own.</div>
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| − | * [[CSB_modelling_principles|Modelling principles]]
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| − | * [[CSB_model_representations|Model representations]]
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| − | * [[CSB_modelling_methods|Modelling methods]]
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| − | * [[CSB_modelling_examples|Modelling examples]]
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| − | </td>
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| − | <td class="sc">—</td>
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| − | <td class="sc">[[CSB_Assignment_Week_11|Assignment 11]]</td>
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| − | </tr>
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| − |
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| − | <tr class="s2">
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| − | <td class="sc">12</td>
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| − | <td class="sc">Apr. 2 - 6</td>
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| − | <td class="sc">
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| − | <div class="table-intro-text">Do we really ''understand'' systems biology? Computational Synthetic Biology is the ultimate test.</div>
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| − | * [[Computational Synthetic Biology]]
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| − | </td>
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| − | <td class="sc">—</td>
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| − | <td class="sc">[[CSB_Assignment_Week_12|Assignment 12]]</td>
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| − | </tr>
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| − |
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| − | </table>
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| | </div> | | </div> |
