Category:CACAO - Revision history

Bmcintosh: Replaced content with ''''For more information, please see [http://gowiki.tamu.edu/wiki/index.php/Category:CACAO CACAO on GONUTS]'''. Category:Education'

2011-07-13T16:50:21Z

Replaced content with ''''For more information, please see [http://gowiki.tamu.edu/wiki/index.php/Category:CACAO CACAO on GONUTS]'''. Category:Education'

← Older revision		Revision as of 16:50, 13 July 2011
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	[~~[File~~:~~Cacao card front~~.~~png\|thumb\|200px\|right]~~]		'''For more information, please see [http://gowiki.tamu.edu/wiki/index.php/Category:CACAO CACAO on GONUTS]'''.
	~~The '''Community Assessment of Community Annotation with Ontologies (CACAO)~~''' ~~is a competition for teams of undergrads around the world to improve the functional annotation of genes~~.

	The rapid advances in genomics technology mean that we are discovering genes faster than we can figure out what they do. For most new sequences, gene function will be inferred by comparison with well-studied model systems such as E. coli. This means that the quality of functional annotation for these models is very important for the future of biology.

	We ran a pilot competition in the Spring of 2010 with 20 volunteer undergraduates from Texas A&M University. The competition was then set up as a multi-national competition in the Fall of 2010 with the addition of teams from University College London. We completed a new competition in Spring 2011 with teams from TAMU, UNT, Miami Univ (Ohio), Penn State & Michigan State using [http://gowiki.tamu.edu/wiki/index.php/Main_Page GONUTS]. If you are interested in participating, please email us at {{Email}} or email [mailto:brenleymcintosh@gmail.com Brenley] or [mailto:jimhu@gmail.com Jim].

	~~<div style="float:none;">[[File:CourseDesign.jpg\|thumb\|500px]]</div>~~
	~~This image to the right illustrates the general logic behind the CACAO activity.~~

	~~===Over-reaching Learning Objective===~~
	~~The over-reaching learning objective is to help students understand:~~
	~~# Where does our knowledge come from?~~
	~~# How did the authors of textbooks or review papers know that certain gene products (proteins or RNAs) did the specific things they describe?~~
	~~# What techniques did scientists use to characterize them?~~

	~~===CACAO Course Learning Objectives===~~
	~~# <span style="color:blue;">'''To critically analyze scientific papers and identify evidence for functional annotations.'''</span>~~
	~~# seek information from online resources and add annotations to GONUTS.~~
	~~# formulate annotations using GO terminology while working effectively in a group.~~
	~~# evaluate peer-contributed annotations, construct challenges and prepare appropriate defenses.~~

	~~==CACAO Fall 2011==~~
	* We will be using [http://gowiki.tamu.edu/wiki/index.php/Main_Page GONUTS] again for our competition meaning students can again choose to annotate any protein in [http://www.uniprot.org/ UniProt].

	~~==='''Multi-Institutional Competition'''===~~
	* we are looking forward to another semester of heated biocuration competition
	* if you are interested in more information or joining, please email [mailto:brenleymcintosh@gmail.com Brenley] or [mailto:jimhu@gmail.com Jim].

	~~==='''The Setup'''===~~
	* we will be running 5 rounds and instructors can choose any or all rounds of the open competition to participate in. Additionally, instructors can choose to run their own round with support from us.

	~~==='''Advanced Biocuration Course for Undergraduates'''===~~
	* this fall, we are adding to our courses with an advanced biocuration course at TAMU. The course requires previous enrollment/volunteering in CACAO and is meant to train undergraduates to become judges and assessors of the annotations contributed by students participating in CACAO. We feel this is the next step in the evolution of CACAO and offers students further advancement and training in functional annotation.

	~~===Course Materials===~~
	* syllabus for CACAO
	* syllabus for Advanced Biocuration

	~~==CACAO Spring 2011==~~
	~~==='''Multi-Institutional Competition'''===~~
	* Spring 2011 - teams from Texas A&M, UNT, Miami Univ (Ohio), Penn State & Michigan State
	* TAMU, UNT & MU teams participated in all 5 rounds this semester
	* Penn State teams participated in an internal competition before joining the World Series (The fifth & final round)
	* all 5 universities participated in the World Series round with more than 100 students

	~~===Scoreboards===~~
	* We operated this semester's competition on [http://gowiki.tamu.edu/wiki/index.php/Main_Page GONUTS] and gave students the opportunity to annotate literature on any protein that has a [http://www.uniprot.org/ UniProt] record
	* ''E. coli'' was the most commonly annotated species, though

	* [http://gowiki.tamu.edu/wiki/index.php/Category:World_Series_2011_CACAO World Series Scoreboard]
	* [http://gowiki.tamu.edu/wiki/index.php/Category:Penn_State_CACAO Penn State Internal Competition Scoreboard]
	* [http://gowiki.tamu.edu/wiki/index.php/Category:CACAO_Spring_2011 Spring 2011 rounds 1-4 Scoreboard]

	~~==CACAO for Fall 2010==~~
	~~===Course Design & Syllabus===~~
	* Below is the syllabus for the CACAO competition at Texas A&M University for Fall 2010. Students are taking this class for 1 hour of directed studies credit or are volunteering for no credit.
	** [[File:BICH_485_syllabus.pdf]]

	~~===Scoreboard===~~
	* [http://gowiki.tamu.edu/wiki/index.php/Category:CACAO_Fall_2010 Fall 2010 scoreboard]

	~~==='''Multi-Institutional & Multi-National Competition'''===~~
	* Fall 2010 - 6 teams from Texas A&M and 2 teams from University College London
	* All teams participated in 4 rounds over the course of the semester

	~~===Annotations on GONUTS===~~
	* We operated the Fall 2010 competition on [http://gowiki.tamu.edu/wiki/index.php/Main_Page GONUTS] and gave students the opportunity to annotate literature on any protein that has a [http://www.uniprot.org/ UniProt] record

	~~==Course Materials Available for Download==~~
	* [[:File:CACAORubrics-2011.pdf\|CACAO_Rubrics_2011.pdf]]
	* [[:File:syllabus.pdf\|Syllabus.pdf]]

	~~=='''Links and Other resources'''==~~
	* [http://www.genomeweb.com//node/955722?hq_e=el&hq_m=872198&hq_l=1&hq_v=94de8d9dfb The Daily Scan Genome Web report on CACAO]
	* [http://gowiki.tamu.edu/wiki/index.php/Category:CACAO_Fall_2010 CACAO Fall 2010]
	* [http://www.ucl.ac.uk/cardiovasculargeneontology/Community_Annotation/Community_annotator CACAO on UCL]

	[[Category:Education]]		[[Category:Education]]

Bmcintosh at 16:58, 28 June 2011

2011-06-28T16:58:52Z

← Older revision		Revision as of 16:58, 28 June 2011
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	The rapid advances in genomics technology mean that we are discovering genes faster than we can figure out what they do. For most new sequences, gene function will be inferred by comparison with well-studied model systems such as E. coli. This means that the quality of functional annotation for these models is very important for the future of biology.		The rapid advances in genomics technology mean that we are discovering genes faster than we can figure out what they do. For most new sequences, gene function will be inferred by comparison with well-studied model systems such as E. coli. This means that the quality of functional annotation for these models is very important for the future of biology.

	We ran a pilot competition in the Spring of 2010 with 20 volunteer undergraduates from Texas A&M University. The competition was then set up as a multi-national competition in the Fall of 2010 with the addition of teams from University College London. We completed a new competition in Spring 2011 with teams from TAMU, UNT, Miami Univ (Ohio), Penn State & Michigan State using [http://gowiki.tamu.edu/wiki/index.php/Main_Page GONUTS]. If you are interested in participating, please email us at {{Email}}.		We ran a pilot competition in the Spring of 2010 with 20 volunteer undergraduates from Texas A&M University. The competition was then set up as a multi-national competition in the Fall of 2010 with the addition of teams from University College London. We completed a new competition in Spring 2011 with teams from TAMU, UNT, Miami Univ (Ohio), Penn State & Michigan State using [http://gowiki.tamu.edu/wiki/index.php/Main_Page GONUTS]. If you are interested in participating, please email us at {{Email}} or email [mailto:brenleymcintosh@gmail.com Brenley] or [mailto:jimhu@gmail.com Jim].

	<div style="float:none;">[[File:CourseDesign.jpg\|thumb\|500px]]</div>		<div style="float:none;">[[File:CourseDesign.jpg\|thumb\|500px]]</div>

Bmcintosh: /* CACAO Fall 2011 */

2011-06-28T16:56:52Z

CACAO Fall 2011

← Older revision		Revision as of 16:56, 28 June 2011
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	==CACAO Fall 2011==		==CACAO Fall 2011==
	* We will be using [http://gowiki.tamu.edu/wiki/index.php/Main_Page GONUTS] again for our competition meaning students can again choose to annotate any protein in [http://www.uniprot.org/ UniProt].		* We will be using [http://gowiki.tamu.edu/wiki/index.php/Main_Page GONUTS] again for our competition meaning students can again choose to annotate any protein in [http://www.uniprot.org/ UniProt].


	==='''Multi-Institutional Competition'''===		==='''Multi-Institutional Competition'''===

Bmcintosh: /* CACAO Fall 2011 */

2011-06-28T16:56:35Z

CACAO Fall 2011

← Older revision		Revision as of 16:56, 28 June 2011
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	==CACAO Fall 2011==		==CACAO Fall 2011==
			* We will be using [http://gowiki.tamu.edu/wiki/index.php/Main_Page GONUTS] again for our competition meaning students can again choose to annotate any protein in [http://www.uniprot.org/ UniProt].


	==='''Multi-Institutional Competition'''===		==='''Multi-Institutional Competition'''===
	* we are looking forward to another semester of heated biocuration competition		* we are looking forward to another semester of heated biocuration competition

Bmcintosh: /* CACAO Fall 2011 */

2011-06-28T16:54:30Z

CACAO Fall 2011

← Older revision		Revision as of 16:54, 28 June 2011
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	==='''The Setup'''===		==='''The Setup'''===
	* we will be running 5 rounds and instructors can choose any or all rounds of the open competition to participate in. Additionally, instructors can choose to run their own round with support from us.		* we will be running 5 rounds and instructors can choose any or all rounds of the open competition to participate in. Additionally, instructors can choose to run their own round with support from us.


	==='''Advanced Biocuration Course for Undergraduates'''===		==='''Advanced Biocuration Course for Undergraduates'''===
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	* syllabus for CACAO		* syllabus for CACAO
	* syllabus for Advanced Biocuration		* syllabus for Advanced Biocuration



	==CACAO Spring 2011==		==CACAO Spring 2011==

Bmcintosh: /* CACAO Spring 2011 */

2011-06-28T16:54:13Z

CACAO Spring 2011

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 # formulate annotations using GO terminology while working effectively in a group.
 # evaluate peer-contributed annotations, construct challenges and prepare appropriate defenses.
 ==CACAO Spring 2011==

Bmcintosh: /* Links and Other resources */

2011-06-28T16:45:13Z

Links and Other resources

← Older revision		Revision as of 16:45, 28 June 2011
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	=='''Links and Other resources'''==		=='''Links and Other resources'''==
	* [http://www.genomeweb.com//node/955722?hq_e=el&hq_m=872198&hq_l=1&hq_v=94de8d9dfb The Daily Scan Genome Web report on CACAO]		* [http://www.genomeweb.com//node/955722?hq_e=el&hq_m=872198&hq_l=1&hq_v=94de8d9dfb The Daily Scan Genome Web report on CACAO]
	* [http://gowiki.tamu.edu/wiki/index.php/~~Special~~:~~Cacao~~ CACAO Fall 2010]		* [http://gowiki.tamu.edu/wiki/index.php/Category:CACAO_Fall_2010 CACAO Fall 2010]
	* [http://www.ucl.ac.uk/cardiovasculargeneontology/Community_Annotation/Community_annotator CACAO on UCL]		* [http://www.ucl.ac.uk/cardiovasculargeneontology/Community_Annotation/Community_annotator CACAO on UCL]

	[[Category:Education]]		[[Category:Education]]

Bmcintosh: /* Scoreboard */

2011-06-28T16:44:56Z

Scoreboard

← Older revision		Revision as of 16:44, 28 June 2011
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	===Scoreboard===		===Scoreboard===
	* [http://gowiki.tamu.edu/wiki/index.php/~~Special~~:~~Cacao~~ Fall 2010 scoreboard]		* [http://gowiki.tamu.edu/wiki/index.php/Category:CACAO_Fall_2010 Fall 2010 scoreboard]

	==='''Multi-Institutional & Multi-National Competition'''===		==='''Multi-Institutional & Multi-National Competition'''===

Bmcintosh: /* CACAO Course Learning Objectives */

2011-06-28T16:42:23Z

CACAO Course Learning Objectives

← Older revision		Revision as of 16:42, 28 June 2011
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	===CACAO Course Learning Objectives===		===CACAO Course Learning Objectives===
	~~'''CACAO Course Learning Objectives:'''~~
	# <span style="color:blue;">'''To critically analyze scientific papers and identify evidence for functional annotations.'''</span>		# <span style="color:blue;">'''To critically analyze scientific papers and identify evidence for functional annotations.'''</span>
	# seek information from online resources and add annotations to GONUTS.		# seek information from online resources and add annotations to GONUTS.
	# formulate annotations using GO terminology while working effectively in a group.		# formulate annotations using GO terminology while working effectively in a group.
	# evaluate peer-contributed annotations, construct challenges and prepare appropriate defenses.		# evaluate peer-contributed annotations, construct challenges and prepare appropriate defenses.


	==CACAO Spring 2011==		==CACAO Spring 2011==

Bmcintosh at 16:40, 28 June 2011

2011-06-28T16:40:55Z

@@ Line 7: / Line 7: @@
 <div style="float:none;">[[File:CourseDesign.jpg|thumb|500px]]</div>
 This image to the right illustrates the general logic behind the CACAO activity.
@@ Line 23: / Line 22: @@
 # evaluate peer-contributed annotations, construct challenges and prepare appropriate defenses.
 ==CACAO Spring 2011==
@@ Line 51: / Line 37: @@
 * [http://gowiki.tamu.edu/wiki/index.php/Category:Penn_State_CACAO Penn State Internal Competition Scoreboard]
 * [http://gowiki.tamu.edu/wiki/index.php/Category:CACAO_Spring_2011 Spring 2011 rounds 1-4 Scoreboard]
 ==Course Materials Available for Download==