Difference between revisions of "FND-MAT-Graphs and networks"
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<div id="BIO"> | <div id="BIO"> | ||
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| − | + | Graphs and Networks | |
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<div class="keywords"> | <div class="keywords"> | ||
<b>Keywords:</b> | <b>Keywords:</b> | ||
| − | + | Intoduction to graph theory and network science; iGraph | |
</div> | </div> | ||
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| − | {{ | + | {{DEV}} |
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<div id="ABC-unit-framework"> | <div id="ABC-unit-framework"> | ||
== Abstract == | == Abstract == | ||
| − | <!-- included from "../components/FND-MAT- | + | <!-- included from "../components/FND-MAT-Graphs_and_networks.components.wtxt", section: "abstract" --> |
... | ... | ||
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== This unit ... == | == This unit ... == | ||
=== Prerequisites === | === Prerequisites === | ||
| − | <!-- included from "../components/FND-MAT- | + | <!-- included from "../components/FND-MAT-Graphs_and_networks.components.wtxt", section: "prerequisites" --> |
<!-- included from "ABC-unit_components.wtxt", section: "notes-external_prerequisites" --> | <!-- included from "ABC-unit_components.wtxt", section: "notes-external_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: | 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: | ||
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<!-- included from "ABC-unit_components.wtxt", section: "notes-prerequisites" --> | <!-- included from "ABC-unit_components.wtxt", section: "notes-prerequisites" --> | ||
You need to complete the following units before beginning this one: | You need to complete the following units before beginning this one: | ||
| − | *[[ | + | *[[RPR-Introduction]] |
{{Vspace}} | {{Vspace}} | ||
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=== Objectives === | === Objectives === | ||
| − | <!-- included from "../components/FND-MAT- | + | <!-- included from "../components/FND-MAT-Graphs_and_networks.components.wtxt", section: "objectives" --> |
... | ... | ||
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=== Outcomes === | === Outcomes === | ||
| − | <!-- included from "../components/FND-MAT- | + | <!-- included from "../components/FND-MAT-Graphs_and_networks.components.wtxt", section: "outcomes" --> |
... | ... | ||
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=== Deliverables === | === Deliverables === | ||
| − | <!-- included from "../components/FND-MAT- | + | <!-- included from "../components/FND-MAT-Graphs_and_networks.components.wtxt", section: "deliverables" --> |
<!-- included from "ABC-unit_components.wtxt", section: "deliverables-time_management" --> | <!-- included from "ABC-unit_components.wtxt", section: "deliverables-time_management" --> | ||
*<b>Time management</b>: 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. | *<b>Time management</b>: 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. | ||
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=== Evaluation === | === Evaluation === | ||
| − | <!-- included from "../components/FND-MAT- | + | <!-- included from "../components/FND-MAT-Graphs_and_networks.components.wtxt", section: "evaluation" --> |
<!-- included from "ABC-unit_components.wtxt", section: "eval-none" --> | <!-- included from "ABC-unit_components.wtxt", section: "eval-none" --> | ||
<b>Evaluation: NA</b><br /> | <b>Evaluation: NA</b><br /> | ||
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<div id="BIO"> | <div id="BIO"> | ||
== Contents == | == Contents == | ||
| − | <!-- included from "../components/FND-MAT- | + | <!-- included from "../components/FND-MAT-Graphs_and_networks.components.wtxt", section: "contents" --> |
| − | ... | + | |
| + | {{Task|1= | ||
| + | * Read the introductory notes on {{ABC-PDF|FND-MAT-Graphs_and_networks|graph theory and network science}}. | ||
| + | }} | ||
| + | |||
| + | |||
| + | |||
| + | {{task|1= | ||
| + | |||
| + | * Carefully read the lecture notes for this unit <span class="PDFlink">[http://steipe.biochemistry.utoronto.ca/abc/CourseMaterials/BCH441/11-Interactions_LectureNotes.pdf Week 11: Annotated Notes <small>(PDF 12.2 MB)</small>]</span>. | ||
| + | |||
| + | * For a useful overview of graph-theory concepts you could additionally have a look at: | ||
| + | {{#pmid: 21527005}} | ||
| + | |||
| + | However, the concepts you need to know for this assignment should become clear from the notes. | ||
| + | |||
| + | }} | ||
| + | |||
| + | |||
{{Vspace}} | {{Vspace}} | ||
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== Notes == | == Notes == | ||
| − | <!-- included from "../components/FND-MAT- | + | <!-- included from "../components/FND-MAT-Graphs_and_networks.components.wtxt", section: "notes" --> |
<!-- included from "ABC-unit_components.wtxt", section: "notes" --> | <!-- included from "ABC-unit_components.wtxt", section: "notes" --> | ||
<references /> | <references /> | ||
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<div id="ABC-unit-framework"> | <div id="ABC-unit-framework"> | ||
== Self-evaluation == | == Self-evaluation == | ||
| − | <!-- included from "../components/FND-MAT- | + | <!-- included from "../components/FND-MAT-Graphs_and_networks.components.wtxt", section: "self-evaluation" --> |
<!-- | <!-- | ||
=== Question 1=== | === Question 1=== | ||
Revision as of 04:35, 31 August 2017
Graphs and Networks
Keywords: Intoduction to graph theory and network science; iGraph
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
...
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:
- Calculus: functions and equations; polynomial functions, logarithms, trigonometric functions; integrals and derivatives; theorem and proof.
You need to complete the following units before beginning this one:
Objectives
...
Outcomes
...
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.
- 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 graph theory and network science.
Task:
- Carefully read the lecture notes for this unit Week 11: Annotated Notes (PDF 12.2 MB).
- For a useful overview of graph-theory concepts you could additionally have a look at:
| Pavlopoulos et al. (2011) Using graph theory to analyze biological networks. BioData Min 4:10. (pmid: 21527005) |
|
[ PubMed ] [ DOI ] Understanding complex systems often requires a bottom-up analysis towards a systems biology approach. The need to investigate a system, not only as individual components but as a whole, emerges. This can be done by examining the elementary constituents individually and then how these are connected. The myriad components of a system and their interactions are best characterized as networks and they are mainly represented as graphs where thousands of nodes are connected with thousands of vertices. In this article we demonstrate approaches, models and methods from the graph theory universe and we discuss ways in which they can be used to reveal hidden properties and features of a network. This network profiling combined with knowledge extraction will help us to better understand the biological significance of the system. |
However, the concepts you need to know for this assignment should become clear from the notes.
Further reading, links and resources
Notes
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:
- 2017-08-05
Version:
- 0.1
Version history:
- 0.1 First stub
This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.
