Difference between revisions of "BIN-SYS-Concepts"
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<!-- included from "../components/BIN-SYS-Concepts.components.wtxt", section: "abstract" --> | <!-- included from "../components/BIN-SYS-Concepts.components.wtxt", section: "abstract" --> | ||
| − | . | + | The functional composition of individual biomolecules to "systems" faces challenges from incomplete data for "bottom up" approaches, and incomplete knowledge for "top down" approaches. This unit discusses the issues, explains the concept of reverse engineering higher order functions from basic components and demonstrates stratgeies for architectural modelling of systems. |
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=== Objectives === | === Objectives === | ||
<!-- included from "../components/BIN-SYS-Concepts.components.wtxt", section: "objectives" --> | <!-- included from "../components/BIN-SYS-Concepts.components.wtxt", section: "objectives" --> | ||
| − | ... | + | This unit will ... |
| + | * ... introduce a definition of biological '''systems'''; | ||
| + | * ... review facts and concepts of the yeast G1/S cell cycle switch to illustrate the building blocks of a functional architecture of this system; | ||
| + | * ... present examples of how this system is presented in different databases; | ||
| + | * ... teach how to apply reverse engineering principles, guided by the concept of a "system architecture", to categorize system components, define their functional relationships, and illustrate categories and functions in an informative diagram; | ||
{{Vspace}} | {{Vspace}} | ||
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=== Outcomes === | === Outcomes === | ||
<!-- included from "../components/BIN-SYS-Concepts.components.wtxt", section: "outcomes" --> | <!-- included from "../components/BIN-SYS-Concepts.components.wtxt", section: "outcomes" --> | ||
| − | ... | + | After working through this unit you ... |
| + | * ... can identify key components of the yeast G1/S cell cycle switch by name and role; | ||
| + | * ... are familar with concepts of systems modelling; | ||
| + | * ... can abstract and organize factual knowledge to a sytems architecture diagram. | ||
{{Vspace}} | {{Vspace}} | ||
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{{Task|1= | {{Task|1= | ||
| − | * Read the introductory notes on {{ABC-PDF|BIN-SYS-Concepts| | + | * Read the introductory notes on {{ABC-PDF|BIN-SYS-Concepts|Concepts of systems modelling}} |
| + | }} | ||
| + | |||
| + | {{Vspace}} | ||
| + | |||
| + | {{Task|1= | ||
| + | <table cellpadding="10"> | ||
| + | <tr> | ||
| + | <td> | ||
| + | Draw a system architecture diagram to represent the function of either | ||
| + | * a water canister (cf. the image at the side); | ||
| + | * a bicycle; | ||
| + | * an anteater; | ||
| + | * a hockey puck; | ||
| + | * F1/FO-ATPase; | ||
| + | * a desk-lamp; or | ||
| + | * a cookbook<ref>Some of these were an in-class quiz in 2016, with an alloted time of 15 minutes. Try hard not to take longer.</ref>. | ||
| + | |||
| + | Prepare your diagram by clearly defining and listing purpose, input, output and interfaces, feedback control and other structural and behavioural elements. Draw a draft on a separate piece of paper first, then prepare a legible sketch of your diagram. Don't overcomplicate your diagram: 10 to 15 elements will be plenty. | ||
| + | </td> | ||
| + | <td>[[Media:Water_canister.jpg]]</td> | ||
| + | </tr> | ||
| + | </table> | ||
| + | |||
}} | }} | ||
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:2017-08-05 | :2017-08-05 | ||
<b>Modified:</b><br /> | <b>Modified:</b><br /> | ||
| − | :2017-08 | + | :2017-11-08 |
<b>Version:</b><br /> | <b>Version:</b><br /> | ||
| − | :0 | + | :1,0 |
<b>Version history:</b><br /> | <b>Version history:</b><br /> | ||
| + | *1.0 First live version | ||
*0.1 First stub | *0.1 First stub | ||
</div> | </div> | ||
Revision as of 04:04, 9 November 2017
Systems Models
Keywords: Systems Models
Contents
This unit is under development. There is some contents here but it is incomplete and/or may change significantly: links may lead to nowhere, the contents is likely going to be rearranged, and objectives, deliverables etc. may be incomplete or missing. Do not work with this material until it is updated to "live" status.
Abstract
The functional composition of individual biomolecules to "systems" faces challenges from incomplete data for "bottom up" approaches, and incomplete knowledge for "top down" approaches. This unit discusses the issues, explains the concept of reverse engineering higher order functions from basic components and demonstrates stratgeies for architectural modelling of systems.
This unit ...
Prerequisites
You need the following preparation before beginning this unit. If you are not familiar with this material from courses you took previously, you need to prepare yourself from other information sources:
- Metabolism: Enzymatic catalysis and control; reaction sequences and pathways; chemiosmotic coupling; catabolic- and anabolic pathways.
- Cell cycle: Replication control and mechanism; phases of the cell-cycle; checkpoints and apoptosis.
You need to complete the following units before beginning this one:
Objectives
This unit will ...
- ... introduce a definition of biological systems;
- ... review facts and concepts of the yeast G1/S cell cycle switch to illustrate the building blocks of a functional architecture of this system;
- ... present examples of how this system is presented in different databases;
- ... teach how to apply reverse engineering principles, guided by the concept of a "system architecture", to categorize system components, define their functional relationships, and illustrate categories and functions in an informative diagram;
Outcomes
After working through this unit you ...
- ... can identify key components of the yeast G1/S cell cycle switch by name and role;
- ... are familar with concepts of systems modelling;
- ... can abstract and organize factual knowledge to a sytems architecture diagram.
Deliverables
- Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
- Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don't overlook these.
- Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.
Evaluation
Evaluation: NA
- This unit is not evaluated for course marks.
Contents
Task:
- Read the introductory notes on Concepts of systems modelling
Task:
|
Draw a system architecture diagram to represent the function of either
Prepare your diagram by clearly defining and listing purpose, input, output and interfaces, feedback control and other structural and behavioural elements. Draw a draft on a separate piece of paper first, then prepare a legible sketch of your diagram. Don't overcomplicate your diagram: 10 to 15 elements will be plenty. |
Media:Water_canister.jpg |
Further reading, links and resources
Notes
- ↑ Some of these were an in-class quiz in 2016, with an alloted time of 15 minutes. Try hard not to take longer.
Self-evaluation
If in doubt, ask! If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.
About ...
Author:
- Boris Steipe <boris.steipe@utoronto.ca>
Created:
- 2017-08-05
Modified:
- 2017-11-08
Version:
- 1,0
Version history:
- 1.0 First live version
- 0.1 First stub
This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.
