Difference between revisions of "User:Boris/Temp/APB"
< User:Boris | Temp
Jump to navigation
Jump to search
m (moved User:Boris\Temp to User:Boris/Temp) |
m |
||
| Line 8: | Line 8: | ||
| − | <table | + | <table> |
| − | <tr class=" | + | <tr class="CSB_t"> |
| − | <td colspan="5">'''I n t r o d u c t i o n'''</td> | + | <td colspan="5" class="CSB">'''I n t r o d u c t i o n'''</td> |
</tr> | </tr> | ||
| − | <tr class=" | + | <tr class="CSB_h"> |
| − | <td>'''Week'''</td> | + | <td class="CSB">'''Week'''</td> |
| − | <td>'''Date'''</td> | + | <td class="CSB">'''Date'''</td> |
| − | <td>'''Lecturer'''</td> | + | <td class="CSB">'''Lecturer'''</td> |
| − | <td>'''Contents'''</td> | + | <td class="CSB">'''Contents'''</td> |
| − | <td>'''Activities'''</td> | + | <td class="CSB">'''Activities'''</td> |
</tr> | </tr> | ||
| − | <tr class=" | + | <tr class="CSB_1"> |
| − | <td>1</td> | + | <td class="CSB">1</td> |
| − | <td>Jan. 9 - 14</td> | + | <td class="CSB">Jan. 9 - 14</td> |
| − | <td>Steipe</td> | + | <td class="CSB">Steipe</td> |
| − | <td> | + | <td class="CSB"> |
* [[CSB_Introduction|Introduction to Computational Systems Biology]] | * [[CSB_Introduction|Introduction to Computational Systems Biology]] | ||
* [[CSB_Web_tools|CSB on the Web: Databases and services]] | * [[CSB_Web_tools|CSB on the Web: Databases and services]] | ||
* Course Organisation | * Course Organisation | ||
</td> | </td> | ||
| − | <td>—</td> | + | <td class="CSB">—</td> |
</tr> | </tr> | ||
<!-- =================== TOPIC =================== --> | <!-- =================== TOPIC =================== --> | ||
| − | <tr | + | <tr><td colspan="5" style="height: 10px;"> </td></tr> |
| − | <tr class=" | + | <tr class="CSB_t"> |
| − | <td colspan="5">'''F u n c t i o n a l A n n o t a t i o n'''</td> | + | <td colspan="5" class="CSB">'''F u n c t i o n a l A n n o t a t i o n'''</td> |
</tr> | </tr> | ||
| − | + | <tr class="CSB_h"> | |
| − | <tr class=" | + | <td class="CSB">'''Week'''</td> |
| − | <td>'''Week'''</td> | + | <td class="CSB">'''Date'''</td> |
| − | <td>'''Date'''</td> | + | <td class="CSB">'''Lecturer'''</td> |
| − | <td>'''Lecturer'''</td> | + | <td class="CSB">'''Contents'''</td> |
| − | <td>'''Contents'''</td> | + | <td class="CSB">'''Activities'''</td> |
| − | <td>'''Activities'''</td> | ||
</tr> | </tr> | ||
| − | |||
| − | |||
<!-- =================== /TOPIC =================== --> | <!-- =================== /TOPIC =================== --> | ||
| − | <tr class=" | + | <tr class="CSB_1"> |
| − | <td>2</td> | + | <td class="CSB">2</td> |
| − | <td>Jan. 16 - 21</td> | + | <td class="CSB">Jan. 16 - 21</td> |
| − | <td>Steipe</td> | + | <td class="CSB">Steipe</td> |
| − | <td> | + | <td class="CSB"> |
* [[CSB_Databases|GO, OMIM and other phenotype databases]] | * [[CSB_Databases|GO, OMIM and other phenotype databases]] | ||
* [[Data_mining|Data mining]] | * [[Data_mining|Data mining]] | ||
| Line 61: | Line 58: | ||
* [[Function_prediction|Prediction of function]] | * [[Function_prediction|Prediction of function]] | ||
</td> | </td> | ||
| − | <td>Quiz 1</td> | + | <td class="CSB">Quiz 1</td> |
</tr> | </tr> | ||
<!-- =================== TOPIC =================== --> | <!-- =================== TOPIC =================== --> | ||
| − | <tr | + | <tr><td colspan="5" style="height: 10px;"> </td></tr> |
| − | <tr class=" | + | <tr class="CSB_t"> |
| − | <td colspan="5">'''''"-omics"'''''</td> | + | <td colspan="5" class="CSB">'''''"-omics"'''''</td> |
</tr> | </tr> | ||
| − | <tr class=" | + | <tr class="CSB_h"> |
| − | <td>'''Week'''</td> | + | <td class="CSB">'''Week'''</td> |
| − | <td>'''Date'''</td> | + | <td class="CSB">'''Date'''</td> |
| − | <td>'''Lecturer'''</td> | + | <td class="CSB">'''Lecturer'''</td> |
| − | <td>'''Contents'''</td> | + | <td class="CSB">'''Contents'''</td> |
| − | <td>'''Activities'''</td> | + | <td class="CSB">'''Activities'''</td> |
</tr> | </tr> | ||
| − | |||
| − | |||
<!-- =================== /TOPIC =================== --> | <!-- =================== /TOPIC =================== --> | ||
| − | <tr class=" | + | <tr class="CSB_2"> |
| − | <td>3</td> | + | <td class="CSB">3</td> |
| − | <td>Jan. 23 - 28</td> | + | <td class="CSB">Jan. 23 - 28</td> |
| − | <td>Steipe</td> | + | <td class="CSB">Steipe</td> |
| − | <td> | + | <td class="CSB"> |
* Working with -ome scale data | * Working with -ome scale data | ||
** [[R_and_Bioconductor|R and Bioconductor]] | ** [[R_and_Bioconductor|R and Bioconductor]] | ||
| Line 93: | Line 88: | ||
** [[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="CSB">Quiz 2, project concept due</td> |
</tr> | </tr> | ||
| − | <tr class=" | + | <tr class="CSB_1"> |
| − | <td>4</td> | + | <td class="CSB">4</td> |
| − | <td>Jan. 30 - Feb. 3</td> | + | <td class="CSB">Jan. 30 - Feb. 3</td> |
| − | <td>Steipe</td> | + | <td class="CSB">Steipe</td> |
| − | <td> | + | <td class="CSB"> |
* [[Genomics|Genomics]] | * [[Genomics|Genomics]] | ||
* [[Transcriptome|The transcriptome]] | * [[Transcriptome|The transcriptome]] | ||
</td> | </td> | ||
| − | <td>Quiz 3</td> | + | <td class="CSB">Quiz 3</td> |
</tr> | </tr> | ||
| − | <tr class=" | + | <tr class="CSB_2"> |
| − | <td>5</td> | + | <td class="CSB">5</td> |
| − | <td>Feb. 6 - 10</td> | + | <td class="CSB">Feb. 6 - 10</td> |
| − | <td>Steipe</td> | + | <td class="CSB">Steipe</td> |
| − | <td> | + | <td class="CSB"> |
* [[Proteome|Proteome]] | * [[Proteome|Proteome]] | ||
* [[Interactome|Interactome]] | * [[Interactome|Interactome]] | ||
| Line 118: | Line 113: | ||
* [[Lipidome|Lipidome]] | * [[Lipidome|Lipidome]] | ||
</td> | </td> | ||
| − | <td>Quiz 4, project outline due</td> | + | <td class="CSB">Quiz 4, project outline due</td> |
</tr> | </tr> | ||
<!-- =================== TOPIC =================== --> | <!-- =================== TOPIC =================== --> | ||
| − | <tr | + | <tr><td colspan="5" style="height: 10px;"> </td></tr> |
| − | <tr class=" | + | <tr class="CSB_t"> |
| − | <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> | + | <td colspan="5" class="CSB">'''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> |
</tr> | </tr> | ||
| − | <tr class=" | + | <tr class="CSB_h"> |
| − | <td>'''Week'''</td> | + | <td class="CSB">'''Week'''</td> |
| − | <td>'''Date'''</td> | + | <td class="CSB">'''Date'''</td> |
| − | <td>'''Lecturer'''</td> | + | <td class="CSB">'''Lecturer'''</td> |
| − | <td>'''Contents'''</td> | + | <td class="CSB">'''Contents'''</td> |
| − | <td>'''Activities'''</td> | + | <td class="CSB">'''Activities'''</td> |
</tr> | </tr> | ||
| − | |||
| − | |||
<!-- =================== /TOPIC =================== --> | <!-- =================== /TOPIC =================== --> | ||
| − | <tr class=" | + | <tr class="CSB_1"> |
| − | <td>6</td> | + | <td class="CSB">6</td> |
| − | <td>Feb. 13 - 17</td> | + | <td class="CSB">Feb. 13 - 17</td> |
| − | <td>Steipe</td> | + | <td class="CSB">Steipe</td> |
| − | <td> | + | <td class="CSB"> |
* [[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="CSB">Quiz 5</td> |
</tr> | </tr> | ||
| − | <tr class=" | + | <tr class="CSB_2"> |
| − | <td> </td> | + | <td class="CSB"> </td> |
| − | <td>Feb. 20 - 24</td> | + | <td class="CSB">Feb. 20 - 24</td> |
<td colspan="3">''Reading Week - School closed''</td> | <td colspan="3">''Reading Week - School closed''</td> | ||
</tr> | </tr> | ||
| − | <tr class=" | + | <tr class="CSB_1"> |
| − | <td>7</td> | + | <td class="CSB">7</td> |
| − | <td>Feb. 27 - Mar. 2</td> | + | <td class="CSB">Feb. 27 - Mar. 2</td> |
| − | <td>Steipe</td> | + | <td class="CSB">Steipe</td> |
| − | <td> | + | <td class="CSB"> |
* [[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="CSB">Quiz 6</td> |
</tr> | </tr> | ||
<!-- =================== TOPIC =================== --> | <!-- =================== TOPIC =================== --> | ||
| − | <tr | + | <tr><td colspan="5" style="height: 10px;"> </td></tr> |
| − | <tr class=" | + | <tr class="CSB_t"> |
| − | <td colspan="5">'''S y s t e m s'''</td> | + | <td colspan="5" class="CSB">'''S y s t e m s'''</td> |
</tr> | </tr> | ||
| − | <tr class=" | + | <tr class="CSB_h"> |
| − | <td>'''Week'''</td> | + | <td class="CSB">'''Week'''</td> |
| − | <td>'''Date'''</td> | + | <td class="CSB">'''Date'''</td> |
| − | <td>'''Lecturer'''</td> | + | <td class="CSB">'''Lecturer'''</td> |
| − | <td>'''Contents'''</td> | + | <td class="CSB">'''Contents'''</td> |
| − | <td>'''Activities'''</td> | + | <td class="CSB">'''Activities'''</td> |
</tr> | </tr> | ||
| − | |||
| − | |||
<!-- =================== /TOPIC =================== --> | <!-- =================== /TOPIC =================== --> | ||
| − | <tr class=" | + | <tr class="CSB_2"> |
| − | <td>8</td> | + | <td class="CSB">8</td> |
| − | <td>Mar. 5 - 9</td> | + | <td class="CSB">Mar. 5 - 9</td> |
| − | <td>Steipe</td> | + | <td class="CSB">Steipe</td> |
| − | <td> | + | <td class="CSB"> |
* [[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 194: | Line 185: | ||
* [[KEGG]], [[BioCYC]] | * [[KEGG]], [[BioCYC]] | ||
</td> | </td> | ||
| − | <td>Quiz 7</td> | + | <td class="CSB">Quiz 7</td> |
</tr> | </tr> | ||
| − | <tr class=" | + | <tr class="CSB_1"> |
| − | <td>9</td> | + | <td class="CSB">9</td> |
| − | <td>Mar. 12 - 16</td> | + | <td class="CSB">Mar. 12 - 16</td> |
| − | <td>Steipe</td> | + | <td class="CSB">Steipe</td> |
| − | <td> | + | <td class="CSB"> |
* [[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="CSB">Quiz 8</td> |
</tr> | </tr> | ||
| − | <tr class=" | + | <tr class="CSB_2"> |
| − | <td>10</td> | + | <td class="CSB">10</td> |
| − | <td>Mar. 19 - 23</td> | + | <td class="CSB">Mar. 19 - 23</td> |
| − | <td>Steipe</td> | + | <td class="CSB">Steipe</td> |
| − | <td> | + | <td class="CSB"> |
* [[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="CSB">Quiz 9, project final submission due</td> |
</tr> | </tr> | ||
<!-- =================== TOPIC =================== --> | <!-- =================== TOPIC =================== --> | ||
| − | <tr | + | <tr><td colspan="5" style="height: 10px;"> </td></tr> |
| − | <tr class=" | + | <tr class="CSB_t"> |
| − | <td colspan="5">'''M o d e l s'''</td> | + | <td colspan="5" class="CSB">'''M o d e l s'''</td> |
</tr> | </tr> | ||
| − | <tr class=" | + | <tr class="CSB_h"> |
| − | <td>'''Week'''</td> | + | <td class="CSB">'''Week'''</td> |
| − | <td>'''Date'''</td> | + | <td class="CSB">'''Date'''</td> |
| − | <td>'''Lecturer'''</td> | + | <td class="CSB">'''Lecturer'''</td> |
| − | <td>'''Contents'''</td> | + | <td class="CSB">'''Contents'''</td> |
| − | <td>'''Activities'''</td> | + | <td class="CSB">'''Activities'''</td> |
</tr> | </tr> | ||
| − | |||
| − | |||
<!-- =================== /TOPIC =================== --> | <!-- =================== /TOPIC =================== --> | ||
| − | <tr class=" | + | <tr class="CSB_1"> |
| − | <td>11</td> | + | <td class="CSB">11</td> |
| − | <td>Mar. 26 - 30</td> | + | <td class="CSB">Mar. 26 - 30</td> |
| − | <td>Steipe</td> | + | <td class="CSB">Steipe</td> |
| − | <td> | + | <td class="CSB"> |
* [[CSB_modelling methods|Modelling methods]]: | * [[CSB_modelling methods|Modelling methods]]: | ||
** ODEs, PDEs and their stochastic counterparts | ** ODEs, PDEs and their stochastic counterparts | ||
| Line 249: | Line 238: | ||
* [[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="CSB">—</td> |
</tr> | </tr> | ||
| − | <tr class=" | + | <tr class="CSB_2"> |
| − | <td>12</td> | + | <td class="CSB">12</td> |
| − | <td>Apr. 2 - 6</td> | + | <td class="CSB">Apr. 2 - 6</td> |
| − | <td>Steipe</td> | + | <td class="CSB">Steipe</td> |
| − | <td> | + | <td class="CSB"> |
* [[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="CSB">—</td> |
</tr> | </tr> | ||
</table> | </table> | ||
Revision as of 22:43, 4 January 2012
Timetable and syllabus
| I n t r o d u c t i o n | ||||
| Week | Date | Lecturer | Contents | Activities |
| 1 | Jan. 9 - 14 | Steipe |
|
— |
| F u n c t i o n a l A n n o t a t i o n | ||||
| Week | Date | Lecturer | Contents | Activities |
| 2 | Jan. 16 - 21 | Steipe | Quiz 1 | |
| "-omics" | ||||
| Week | Date | Lecturer | Contents | Activities |
| 3 | Jan. 23 - 28 | Steipe |
|
Quiz 2, project concept due |
| 4 | Jan. 30 - Feb. 3 | Steipe | Quiz 3 | |
| 5 | Feb. 6 - 10 | Steipe | Quiz 4, project outline due | |
| 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 | Lecturer | Contents | Activities |
| 6 | Feb. 13 - 17 | Steipe |
|
Quiz 5 |
| Feb. 20 - 24 | Reading Week - School closed | |||
| 7 | Feb. 27 - Mar. 2 | Steipe |
|
Quiz 6 |
| S y s t e m s | ||||
| Week | Date | Lecturer | Contents | Activities |
| 8 | Mar. 5 - 9 | Steipe | Quiz 7 | |
| 9 | Mar. 12 - 16 | Steipe | Quiz 8 | |
| 10 | Mar. 19 - 23 | Steipe | Quiz 9, project final submission due | |
| M o d e l s | ||||
| Week | Date | Lecturer | Contents | Activities |
| 11 | Mar. 26 - 30 | Steipe |
|
— |
| 12 | Apr. 2 - 6 | Steipe | — | |
