Difference between revisions of "User:Boris/Temp/APB"
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| Line 11: | Line 11: | ||
<tr class="sh"> | <tr class="sh"> | ||
| − | <td>'''Week'''</td> | + | <td class="sc">'''Week'''</td> |
| − | <td>'''Date'''</td> | + | <td class="sc">'''Date'''</td> |
| − | <td>'''Contents'''</td> | + | <td class="sc">'''Contents'''</td> |
| − | <td>'''Activities'''</td> | + | <td class="sc">'''Activities'''</td> |
| − | <td>'''Assignment'''</td> | + | <td class="sc">'''Assignment'''</td> |
</tr> | </tr> | ||
<tr class="s1"> | <tr class="s1"> | ||
| − | <td>1</td> | + | <td class="sc">1</td> |
| − | <td>Jan. 9 - 14</td> | + | <td class="sc">Jan. 9 - 14</td> |
| − | <td> | + | <td class="sc"> |
* [[CSB_Introduction|Introduction to Computational Systems Biology]] | * [[CSB_Introduction|Introduction to Computational Systems Biology]] | ||
* Course Organisation | * Course Organisation | ||
</td> | </td> | ||
| − | <td>—</td> | + | <td class="sc">—</td> |
| − | <td>[[CSB_Assignment_Week_1|Assignment 1]]</td> | + | <td class="sc">[[CSB_Assignment_Week_1|Assignment 1]]</td> |
</tr> | </tr> | ||
| Line 35: | Line 35: | ||
</tr> | </tr> | ||
<tr class="sh"> | <tr class="sh"> | ||
| − | <td>'''Week'''</td> | + | <td class="sc">'''Week'''</td> |
| − | <td>'''Date'''</td> | + | <td class="sc">'''Date'''</td> |
| − | <td>'''Contents'''</td> | + | <td class="sc">'''Contents'''</td> |
| − | <td>'''Activities'''</td> | + | <td class="sc">'''Activities'''</td> |
| − | <td>'''Assignment'''</td> | + | <td class="sc">'''Assignment'''</td> |
</tr> | </tr> | ||
<!-- =================== /TOPIC =================== --> | <!-- =================== /TOPIC =================== --> | ||
<tr class="s1"> | <tr class="s1"> | ||
| − | <td>2</td> | + | <td class="sc">2</td> |
| − | <td>Jan. 16 - 21</td> | + | <td class="sc">Jan. 16 - 21</td> |
| − | <td> | + | <td class="sc"> |
* Databases and tools | * Databases and tools | ||
** [[CSB_Web_tools|CSB on the Web: Databases and services]] | ** [[CSB_Web_tools|CSB on the Web: Databases and services]] | ||
| Line 53: | Line 53: | ||
** [[Function_prediction|Prediction of function]] | ** [[Function_prediction|Prediction of function]] | ||
</td> | </td> | ||
| − | <td>Quiz 1</td> | + | <td class="sc">Quiz 1</td> |
| − | <td>[[CSB_Assignment_Week_2|Assignment 2]]</td> | + | <td class="sc">[[CSB_Assignment_Week_2|Assignment 2]]</td> |
</tr> | </tr> | ||
<tr class="s1"> | <tr class="s1"> | ||
| − | <td>3</td> | + | <td class="sc">3</td> |
| − | <td>Jan. 23 - 28</td> | + | <td class="sc">Jan. 23 - 28</td> |
| − | <td> | + | <td class="sc"> |
* Working with -ome scale data | * Working with -ome scale data | ||
** [[R_and_Bioconductor|R and Bioconductor]] | ** [[R_and_Bioconductor|R and Bioconductor]] | ||
| Line 69: | Line 69: | ||
** [[IDE|IDE - Komodo]], [http://en.wikipedia.org/wiki/KDevelop KDevelop] (also Eclipse, except no Perl) | ** [[IDE|IDE - Komodo]], [http://en.wikipedia.org/wiki/KDevelop KDevelop] (also Eclipse, except no Perl) | ||
</td> | </td> | ||
| − | <td>Quiz 2, project concept due</td> | + | <td class="sc">Quiz 2, project concept due</td> |
| − | <td>[[CSB_Assignment_Week_3|Assignment 3]]</td> | + | <td class="sc">[[CSB_Assignment_Week_3|Assignment 3]]</td> |
</tr> | </tr> | ||
| Line 81: | Line 81: | ||
<tr class="sh"> | <tr class="sh"> | ||
| − | <td>'''Week'''</td> | + | <td class="sc">'''Week'''</td> |
| − | <td>'''Date'''</td> | + | <td class="sc">'''Date'''</td> |
| − | <td>'''Contents'''</td> | + | <td class="sc">'''Contents'''</td> |
| − | <td>'''Activities'''</td> | + | <td class="sc">'''Activities'''</td> |
| − | <td>'''Assignment'''</td> | + | <td class="sc">'''Assignment'''</td> |
</tr> | </tr> | ||
<!-- =================== /TOPIC =================== --> | <!-- =================== /TOPIC =================== --> | ||
<tr class="s2"> | <tr class="s2"> | ||
| − | <td>4</td> | + | <td class="sc">4</td> |
| − | <td>Jan. 30 - Feb. 3</td> | + | <td class="sc">Jan. 30 - Feb. 3</td> |
| − | <td> | + | <td class="sc"> |
* [[Genomics|Genomics]] | * [[Genomics|Genomics]] | ||
* [[Transcriptome|The transcriptome]] | * [[Transcriptome|The transcriptome]] | ||
</td> | </td> | ||
| − | <td>Quiz 3</td> | + | <td class="sc">Quiz 3</td> |
| − | <td>[[CSB_Assignment_Week_4|Assignment 4]]</td> | + | <td class="sc">[[CSB_Assignment_Week_4|Assignment 4]]</td> |
</tr> | </tr> | ||
<tr class="s1"> | <tr class="s1"> | ||
| − | <td>5</td> | + | <td class="sc">5</td> |
| − | <td>Feb. 6 - 10</td> | + | <td class="sc">Feb. 6 - 10</td> |
| − | <td> | + | <td class="sc"> |
* [[Proteome|Proteome]] | * [[Proteome|Proteome]] | ||
* [[Interactome|Interactome]] | * [[Interactome|Interactome]] | ||
| Line 110: | Line 110: | ||
* [[Lipidome|Lipidome]] | * [[Lipidome|Lipidome]] | ||
</td> | </td> | ||
| − | <td>Quiz 4, project outline due</td> | + | <td class="sc">Quiz 4, project outline due</td> |
| − | <td>[[CSB_Assignment_Week_5|Assignment 5]]</td> | + | <td class="sc">[[CSB_Assignment_Week_5|Assignment 5]]</td> |
</tr> | </tr> | ||
| Line 121: | Line 121: | ||
<tr class="sh"> | <tr class="sh"> | ||
| − | <td>'''Week'''</td> | + | <td class="sc">'''Week'''</td> |
| − | <td>'''Date'''</td> | + | <td class="sc">'''Date'''</td> |
| − | <td>'''Contents'''</td> | + | <td class="sc">'''Contents'''</td> |
| − | <td>'''Activities'''</td> | + | <td class="sc">'''Activities'''</td> |
| − | <td>'''Assignment'''</td> | + | <td class="sc">'''Assignment'''</td> |
</tr> | </tr> | ||
<!-- =================== /TOPIC =================== --> | <!-- =================== /TOPIC =================== --> | ||
<tr class="s1"> | <tr class="s1"> | ||
| − | <td>6</td> | + | <td class="sc">6</td> |
| − | <td>Feb. 13 - 17</td> | + | <td class="sc">Feb. 13 - 17</td> |
| − | <td> | + | <td class="sc"> |
* [[Cytoscape|Cytoscape]] | * [[Cytoscape|Cytoscape]] | ||
* [[Graph_theory|Graph theory]], graph types and metrics; small-world or random-geometric, date-hubs and party-hubs | * [[Graph_theory|Graph theory]], graph types and metrics; small-world or random-geometric, date-hubs and party-hubs | ||
</td> | </td> | ||
| − | <td>Quiz 5</td> | + | <td class="sc">Quiz 5</td> |
| − | <td>[[CSB_Assignment_Week_6|Assignment 6]]</td> | + | <td class="sc">[[CSB_Assignment_Week_6|Assignment 6]]</td> |
</tr> | </tr> | ||
<tr class="s2"> | <tr class="s2"> | ||
| − | <td> </td> | + | <td class="sc"> </td> |
| − | <td>Feb. 20 - 24</td> | + | <td class="sc">Feb. 20 - 24</td> |
<td colspan="3">''Reading Week - School closed''</td> | <td colspan="3">''Reading Week - School closed''</td> | ||
</tr> | </tr> | ||
<tr class="s1"> | <tr class="s1"> | ||
| − | <td>7</td> | + | <td class="sc">7</td> |
| − | <td>Feb. 27 - Mar. 2</td> | + | <td class="sc">Feb. 27 - Mar. 2</td> |
| − | <td> | + | <td class="sc"> |
* [[PPI|The biology of protein-protein interactions]]; physical vs. genetic interactions | * [[PPI|The biology of protein-protein interactions]]; physical vs. genetic interactions | ||
* [[Interaction_databases|Interaction databases]] | * [[Interaction_databases|Interaction databases]] | ||
* [[Interaction_prediction|Interaction prediction]], Interologs | * [[Interaction_prediction|Interaction prediction]], Interologs | ||
</td> | </td> | ||
| − | <td>Quiz 6</td> | + | <td class="sc">Quiz 6</td> |
| − | <td>[[CSB_Assignment_Week_7|Assignment 7]]</td> | + | <td class="sc">[[CSB_Assignment_Week_7|Assignment 7]]</td> |
</tr> | </tr> | ||
| Line 165: | Line 165: | ||
<tr class="sh"> | <tr class="sh"> | ||
| − | <td>'''Week'''</td> | + | <td class="sc">'''Week'''</td> |
| − | <td>'''Date'''</td> | + | <td class="sc">'''Date'''</td> |
| − | <td>'''Contents'''</td> | + | <td class="sc">'''Contents'''</td> |
| − | <td>'''Activities'''</td> | + | <td class="sc">'''Activities'''</td> |
| − | <td>'''Assignment'''</td> | + | <td class="sc">'''Assignment'''</td> |
</tr> | </tr> | ||
<!-- =================== /TOPIC =================== --> | <!-- =================== /TOPIC =================== --> | ||
<tr class="s1"> | <tr class="s1"> | ||
| − | <td>8</td> | + | <td class="sc">8</td> |
| − | <td>Mar. 5 - 9</td> | + | <td class="sc">Mar. 5 - 9</td> |
| − | <td> | + | <td class="sc"> |
* [[Gene_regulatory_networks|Gene regulatory networks]] | * [[Gene_regulatory_networks|Gene regulatory networks]] | ||
* [[Signal_transduction_networks|Signal transduction networks]] | * [[Signal_transduction_networks|Signal transduction networks]] | ||
| Line 182: | Line 182: | ||
* [[KEGG]], [[BioCYC]] | * [[KEGG]], [[BioCYC]] | ||
</td> | </td> | ||
| − | <td>Quiz 7</td> | + | <td class="sc">Quiz 7</td> |
| − | <td>[[CSB_Assignment_Week_8|Assignment 8]]</td> | + | <td class="sc">[[CSB_Assignment_Week_8|Assignment 8]]</td> |
</tr> | </tr> | ||
<tr class="s2"> | <tr class="s2"> | ||
| − | <td>9</td> | + | <td class="sc">9</td> |
| − | <td>Mar. 12 - 16</td> | + | <td class="sc">Mar. 12 - 16</td> |
| − | <td> | + | <td class="sc"> |
* [[CSB_Regulatory_network_extraction|Extracting regulatory networks from gene expression data]] | * [[CSB_Regulatory_network_extraction|Extracting regulatory networks from gene expression data]] | ||
* [[CSB_Mutual information|Extracting systems from -omics datasets through mutual information]] | * [[CSB_Mutual information|Extracting systems from -omics datasets through mutual information]] | ||
</td> | </td> | ||
| − | <td>Quiz 8</td> | + | <td class="sc">Quiz 8</td> |
| − | <td>[[CSB_Assignment_Week_9|Assignment 9]]</td> | + | <td class="sc">[[CSB_Assignment_Week_9|Assignment 9]]</td> |
</tr> | </tr> | ||
<tr class="s1"> | <tr class="s1"> | ||
| − | <td>10</td> | + | <td class="sc">10</td> |
| − | <td>Mar. 19 - 23</td> | + | <td class="sc">Mar. 19 - 23</td> |
| − | <td> | + | <td class="sc"> |
* [[CSB_Structural_network_analysis|Structural network analysis]] http://www.csb.ethz.ch/research/structural | * [[CSB_Structural_network_analysis|Structural network analysis]] http://www.csb.ethz.ch/research/structural | ||
* [[Systems dynamics|Systems dynamics]] http://www.csb.ethz.ch/research/dynamic | * [[Systems dynamics|Systems dynamics]] http://www.csb.ethz.ch/research/dynamic | ||
</td> | </td> | ||
| − | <td>Quiz 9, project final submission due</td> | + | <td class="sc">Quiz 9, project final submission due</td> |
| − | <td>[[CSB_Assignment_Week_10|Assignment 10]]</td> | + | <td class="sc">[[CSB_Assignment_Week_10|Assignment 10]]</td> |
</tr> | </tr> | ||
| Line 215: | Line 215: | ||
<tr class="sh"> | <tr class="sh"> | ||
| − | <td>'''Week'''</td> | + | <td class="sc">'''Week'''</td> |
| − | <td>'''Date'''</td> | + | <td class="sc">'''Date'''</td> |
| − | <td>'''Contents'''</td> | + | <td class="sc">'''Contents'''</td> |
| − | <td>'''Activities'''</td> | + | <td class="sc">'''Activities'''</td> |
| − | <td>'''Assignment'''</td> | + | <td class="sc">'''Assignment'''</td> |
</tr> | </tr> | ||
<!-- =================== /TOPIC =================== --> | <!-- =================== /TOPIC =================== --> | ||
<tr class="s1"> | <tr class="s1"> | ||
| − | <td>11</td> | + | <td class="sc">11</td> |
| − | <td>Mar. 26 - 30</td> | + | <td class="sc">Mar. 26 - 30</td> |
| − | <td> | + | <td class="sc"> |
* [[CSB_modelling methods|Modelling methods]]: | * [[CSB_modelling methods|Modelling methods]]: | ||
** ODEs, PDEs and their stochastic counterparts | ** ODEs, PDEs and their stochastic counterparts | ||
| Line 235: | Line 235: | ||
* [[CSB_Modelling|Modelling examples]](E-Cell, M-Cell, Virtual Cell) | * [[CSB_Modelling|Modelling examples]](E-Cell, M-Cell, Virtual Cell) | ||
</td> | </td> | ||
| − | <td>—</td> | + | <td class="sc">—</td> |
| − | <td>[[CSB_Assignment_Week_11|Assignment 11]]</td> | + | <td class="sc">[[CSB_Assignment_Week_11|Assignment 11]]</td> |
</tr> | </tr> | ||
<tr class="s2"> | <tr class="s2"> | ||
| − | <td>12</td> | + | <td class="sc">12</td> |
| − | <td>Apr. 2 - 6</td> | + | <td class="sc">Apr. 2 - 6</td> |
| − | <td> | + | <td class="sc"> |
* [[Constraint based modelling]], [[Flux balance analysis]] | * [[Constraint based modelling]], [[Flux balance analysis]] | ||
* [[Computational Synthetic Biology]] http://www.csb.ethz.ch/research/synthetic | * [[Computational Synthetic Biology]] http://www.csb.ethz.ch/research/synthetic | ||
</td> | </td> | ||
| − | <td>—</td> | + | <td class="sc">—</td> |
| − | <td>[[CSB_Assignment_Week_12|Assignment 12]]</td> | + | <td class="sc">[[CSB_Assignment_Week_12|Assignment 12]]</td> |
</tr> | </tr> | ||
Revision as of 17:17, 15 January 2012
Timetable and syllabus
| I n t r o d u c t i o n | ||||
| Week | Date | Contents | Activities | Assignment |
| 1 | Jan. 9 - 14 |
|
— | Assignment 1 |
| D a t a | ||||
| Week | Date | Contents | Activities | Assignment |
| 2 | Jan. 16 - 21 | Quiz 1 | Assignment 2 | |
| 3 | Jan. 23 - 28 |
|
Quiz 2, project concept due | Assignment 3 |
| "-omics" | ||||
| Week | Date | Contents | Activities | Assignment |
| 4 | Jan. 30 - Feb. 3 | Quiz 3 | Assignment 4 | |
| 5 | Feb. 6 - 10 | Quiz 4, project outline due | Assignment 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 | ||||
| Week | Date | Contents | Activities | Assignment |
| 6 | Feb. 13 - 17 |
|
Quiz 5 | Assignment 6 |
| Feb. 20 - 24 | Reading Week - School closed | |||
| 7 | Feb. 27 - Mar. 2 |
|
Quiz 6 | Assignment 7 |
| S y s t e m s | ||||
| Week | Date | Contents | Activities | Assignment |
| 8 | Mar. 5 - 9 | Quiz 7 | Assignment 8 | |
| 9 | Mar. 12 - 16 | Quiz 8 | Assignment 9 | |
| 10 | Mar. 19 - 23 | Quiz 9, project final submission due | Assignment 10 | |
| M o d e l s | ||||
| Week | Date | Contents | Activities | Assignment |
| 11 | Mar. 26 - 30 |
|
— | Assignment 11 |
| 12 | Apr. 2 - 6 | — | Assignment 12 | |
