Difference between revisions of "BIN-FUNC-Concepts"
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== Abstract == | == Abstract == | ||
<section begin=abstract /> | <section begin=abstract /> | ||
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Function is a ''concept'', not an observation and it is not trivial how we categorize and arrange observed activities to "functions". Once defined, functions need to be represented in the computer, associated with biomolecules through annotation, and used in prediction to complement experimentation. | Function is a ''concept'', not an observation and it is not trivial how we categorize and arrange observed activities to "functions". Once defined, functions need to be represented in the computer, associated with biomolecules through annotation, and used in prediction to complement experimentation. | ||
<section end=abstract /> | <section end=abstract /> | ||
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== This unit ... == | == This unit ... == | ||
=== Prerequisites === | === Prerequisites === | ||
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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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*<b>Biomolecules</b>: The molecules of life; nucleic acids and amino acids; the genetic code; protein folding; post-translational modifications and protein biochemistry; membrane proteins; biological function. | *<b>Biomolecules</b>: The molecules of life; nucleic acids and amino acids; the genetic code; protein folding; post-translational modifications and protein biochemistry; membrane proteins; biological function. | ||
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*<b>Metabolism</b>: Enzymatic catalysis and control; reaction sequences and pathways; chemiosmotic coupling; catabolic- and anabolic pathways. | *<b>Metabolism</b>: Enzymatic catalysis and control; reaction sequences and pathways; chemiosmotic coupling; catabolic- and anabolic pathways. | ||
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*<b>Organelles</b>: Compartmentalization, organelles and structures of the cell; the extracellular matrix. | *<b>Organelles</b>: Compartmentalization, organelles and structures of the cell; the extracellular matrix. | ||
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You need to complete the following units before beginning this one: | You need to complete the following units before beginning this one: | ||
*[[BIN-Abstractions|BIN-Abstractions (Abstractions for Bioinformatics)]] | *[[BIN-Abstractions|BIN-Abstractions (Abstractions for Bioinformatics)]] | ||
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=== Objectives === | === Objectives === | ||
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This unit will ... | This unit will ... | ||
* Introduce the meaning of "function" and issues that arise from it being a concept, not an observable; | * Introduce the meaning of "function" and issues that arise from it being a concept, not an observable; | ||
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=== Outcomes === | === Outcomes === | ||
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After working through this unit you ... | After working through this unit you ... | ||
* understand how observed activities are conceptualized as "functions" on various levels; | * understand how observed activities are conceptualized as "functions" on various levels; | ||
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=== Deliverables === | === Deliverables === | ||
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*<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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*<b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these. | *<b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these. | ||
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*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]]. | *<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]]. | ||
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<div id="BIO"> | <div id="BIO"> | ||
== Contents == | == Contents == | ||
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{{Task|1= | {{Task|1= | ||
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== Notes == | == Notes == | ||
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<references /> | <references /> | ||
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<div id="ABC-unit-framework"> | <div id="ABC-unit-framework"> | ||
== Self-evaluation == | == Self-evaluation == | ||
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=== Question 1=== | === Question 1=== | ||
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[[Category:ABC-units]] | [[Category:ABC-units]] | ||
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{{CC-BY}} | {{CC-BY}} | ||
Revision as of 01:24, 6 January 2018
Biomolecular Function Concepts
Keywords: The concept of function, representation of function, annotation, and prediction.
Contents
Abstract
Function is a concept, not an observation and it is not trivial how we categorize and arrange observed activities to "functions". Once defined, functions need to be represented in the computer, associated with biomolecules through annotation, and used in prediction to complement experimentation.
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:
- Biomolecules: The molecules of life; nucleic acids and amino acids; the genetic code; protein folding; post-translational modifications and protein biochemistry; membrane proteins; biological function.
- Metabolism: Enzymatic catalysis and control; reaction sequences and pathways; chemiosmotic coupling; catabolic- and anabolic pathways.
- Organelles: Compartmentalization, organelles and structures of the cell; the extracellular matrix.
You need to complete the following units before beginning this one:
Objectives
This unit will ...
- Introduce the meaning of "function" and issues that arise from it being a concept, not an observable;
- Introduce principles of representation, annotation and prediction of biomolecular function.
Outcomes
After working through this unit you ...
- understand how observed activities are conceptualized as "functions" on various levels;
- know about three common resources for function representation: E.C. codes, pathway collections, and above all, the Gene Ontology project;
- can name the three fundamental strategies for function prediction and give one example for each.
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.
Contents
Task:
- Read the introductory notes on the concepts and abstractions for annotating gene function.
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:
- 2017-09-16
Version:
- 1.0
Version history:
- 1.0 First final 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.
