Hhmi-gcat - Revision history

Matlada at 18:35, 11 September 2007

2007-09-11T18:35:41Z

← Older revision		Revision as of 18:35, 11 September 2007
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	Input from David:		Input from David:
	Microarray ~~and mass spectroscopy~~ will be used to assess the transcriptomes ~~and proteomes~~ of developing organisms in Biology 356, Developmental Biology lecture and lab. In the ~~early~~ phase ~~(change wording here...training phase is what I mean but doesn't sound right~~,) yeast will serve as a model for studying the regulation of cell cycle control genes. In the later phase of the grant, evolution of the neural crest will be explored through comparative gene expression patterns in various models such as the zebrafish and sequenced protochordates such as Ciona intestinalis and Oikopleaura. Students will also be able to visualize specific gene expression patterns with in situ hybridization and immunohistochemistry on frozen sections~~. This work will entail collaboration with and cooperation of labs working with these organisms and with extra slides to share~~.		Microarray will be used to assess the transcriptomes of developing organisms in Biology 356, Developmental Biology lecture and lab. In the developmental phase of this module, yeast will serve as a model for studying the regulation of cell cycle control genes. In the later phase of the grant, evolution of the neural crest will be explored through comparative gene expression patterns in various models such as the zebrafish and sequenced protochordates such as Ciona intestinalis and Oikopleaura. This work will entail collaboration with and cooperation of labs working with these organisms and with extra slides to share. Students will also be able to visualize specific gene expression patterns with in situ hybridization and immunohistochemistry on frozen sections.
	The yeast microarray data set generated by Biloogy 356 students will be used in a dry lab in Biology 112, Cells, Genes and Inheritance. In this exercise, students will use the data set in GenMAPP to explore strategies for working with huge data sets as well as for studying the central dogma.		The yeast microarray data set generated by Biloogy 356 students will be used in a dry lab in Biology 112, Cells, Genes and Inheritance. In this exercise, students will use the data set in GenMAPP to explore strategies for working with huge data sets as well as for studying the central dogma.
	(More on mass spec and proteomics as I learn more from Chemistry on capabilities, but I could see a similar dry lab/problem space for Cell Phys with emphasis on proteomics but also using the yeast microarray data set.)
	Biology 356 is an upper-level course with a typical enrollment of 12 to 18 students. Biology 121 is an introductory level course with a typical enrollment of eighty.		Biology 356 is an upper-level course with a typical enrollment of 12 to 18 students. Biology 121 is an introductory level course with a typical enrollment of eighty.
	Peter's plan:		Peter's plan:
	* In the near future we should generate a written synopsis of each particular program component. This mock 'executive summary' should include: 1) Brief summary, 2) Statement of (educational) outcomes, 3) Mode of assessment, 4) Timeframes, and 4) Preliminary budget.		* In the near future we should generate a written synopsis of each particular program component. This mock 'executive summary' should include: 1) Brief summary, 2) Statement of (educational) outcomes, 3) Mode of assessment, 4) Timeframes, and 4) Preliminary budget.

Blairpe at 20:01, 7 August 2007

2007-08-07T20:01:54Z

← Older revision		Revision as of 20:01, 7 August 2007
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			Input from Peter:

			Part IV: PRECOLLEGE AND OTHER OUTREACH

			A. Initiate an active membership and become scanning facility for the Genome Consortium for Active Teaching

			The Genome Consortium for Active Teaching (GCAT) is a success story for both the integration of and access to computational biology, bioinformatics and genomics within undergraduate education. Briefly, GCAT provides affordable microarray slides, off-site scanning services, free analytical software, faculty workshops, and technical support for interested undergraduate institutes (currently totaling 141 faculty on 134 campuses). In doing so, GCAT meets many of the goals of BIO2010. Under the supervision of founder Dr. Malcolm Campbell (Davidson College), the Consortium now has six years of supportive and positive assessment and a projection for continued growth (Campbell et al, Life Sciences Education 2007). In fact, member institutes have placed requests for 1,156 microarrays slides for the 2007-08 academic year correlating to a 30% increase from the prior year (Malcolm Campbell, personal communication). With great respect to the success to this program, and the need to sustain it for the future, Earlham College seeks to become an active member of this consortium.

			We propose to become the fourth scanning center, joining Davidson College, Pomona College, and Niagara University, to assist in managing the increased GCAT scanning needs. Dr. Peter Blair, who has experience with microarray technology, including RNA preparation, and analysis (see CV publications), is committed to become the program director. He will supervise two undergraduate â€˜work studyâ€™ students per semester in the scheduling, scanning, and maintenance of the facility. Students that have completed the Bridge to Excellence Program, thus exposed to microarray technologies and experimentation, will be the target group for these student positions. The receiving of hybridized glass slides, scanning, and the dissemination of data to GCAT participating institutes will be governed through the established GCAT methodologies (http://www.bio.davidson.edu/projects/gcat/GCAT.html#mission). Dr. Charlie Peck (perhaps?) will oversee the management of the ISB FTP server for data delivery.

			We feel Earlham is an attractive addition to the team of GCAT scanning facilities. Currently, the existing facilities are geographically located on either the east or west coasts. We would provide proximal access to institutes in the Midwest region (approximately 40 colleges/universities) and become only the second institute in Indiana to gain GCAT membership. What are the advantages of having a facility in closer location? First, less time for postal handling lends itself to rewarding and successful experimentation. Furthermore, similar to the Earlham College mission to provide full hands-on research, in which students conduct research from initial hypothesis to analysis, we offer this same opportunity to our GCAT neighbors. Upon a funded HHMI proposal, Dr. Blair would communicate to regional institutes (including both GCAT members and non-members) to encourage active GCAT participation at our facility. Students and instructors could visit the facility and run samples firsthand. To our knowledge, Earlham would become the sole microarray scanning facility in Eastern Indiana.


			Input from David:
	Microarray and mass spectroscopy will be used to assess the transcriptomes and proteomes of developing organisms in Biology 356, Developmental Biology lecture and lab. In the early phase (change wording here...training phase is what I mean but doesn't sound right,) yeast will serve as a model for studying the regulation of cell cycle control genes. In the later phase of the grant, evolution of the neural crest will be explored through comparative gene expression patterns in various models such as the zebrafish and sequenced protochordates such as Ciona intestinalis and Oikopleaura. Students will also be able to visualize specific gene expression patterns with in situ hybridization and immunohistochemistry on frozen sections. This work will entail collaboration with and cooperation of labs working with these organisms and with extra slides to share.		Microarray and mass spectroscopy will be used to assess the transcriptomes and proteomes of developing organisms in Biology 356, Developmental Biology lecture and lab. In the early phase (change wording here...training phase is what I mean but doesn't sound right,) yeast will serve as a model for studying the regulation of cell cycle control genes. In the later phase of the grant, evolution of the neural crest will be explored through comparative gene expression patterns in various models such as the zebrafish and sequenced protochordates such as Ciona intestinalis and Oikopleaura. Students will also be able to visualize specific gene expression patterns with in situ hybridization and immunohistochemistry on frozen sections. This work will entail collaboration with and cooperation of labs working with these organisms and with extra slides to share.
	The yeast microarray data set generated by Biloogy 356 students will be used in a dry lab in Biology 112, Cells, Genes and Inheritance. In this exercise, students will use the data set in GenMAPP to explore strategies for working with huge data sets as well as for studying the central dogma.		The yeast microarray data set generated by Biloogy 356 students will be used in a dry lab in Biology 112, Cells, Genes and Inheritance. In this exercise, students will use the data set in GenMAPP to explore strategies for working with huge data sets as well as for studying the central dogma.

Matlada at 14:43, 22 June 2007

2007-06-22T14:43:54Z

← Older revision		Revision as of 14:43, 22 June 2007
Line 2:		Line 2:
	The yeast microarray data set generated by Biloogy 356 students will be used in a dry lab in Biology 112, Cells, Genes and Inheritance. In this exercise, students will use the data set in GenMAPP to explore strategies for working with huge data sets as well as for studying the central dogma.		The yeast microarray data set generated by Biloogy 356 students will be used in a dry lab in Biology 112, Cells, Genes and Inheritance. In this exercise, students will use the data set in GenMAPP to explore strategies for working with huge data sets as well as for studying the central dogma.
	(More on mass spec and proteomics as I learn more from Chemistry on capabilities, but I could see a similar dry lab/problem space for Cell Phys with emphasis on proteomics but also using the yeast microarray data set.)		(More on mass spec and proteomics as I learn more from Chemistry on capabilities, but I could see a similar dry lab/problem space for Cell Phys with emphasis on proteomics but also using the yeast microarray data set.)
			Biology 356 is an upper-level course with a typical enrollment of 12 to 18 students. Biology 121 is an introductory level course with a typical enrollment of eighty.
	Peter's plan:		Peter's plan:
	* In the near future we should generate a written synopsis of each particular program component. This mock 'executive summary' should include: 1) Brief summary, 2) Statement of (educational) outcomes, 3) Mode of assessment, 4) Timeframes, and 4) Preliminary budget.		* In the near future we should generate a written synopsis of each particular program component. This mock 'executive summary' should include: 1) Brief summary, 2) Statement of (educational) outcomes, 3) Mode of assessment, 4) Timeframes, and 4) Preliminary budget.

Matlada at 14:41, 22 June 2007

2007-06-22T14:41:12Z

← Older revision		Revision as of 14:41, 22 June 2007
Line 1:		Line 1:
			Microarray and mass spectroscopy will be used to assess the transcriptomes and proteomes of developing organisms in Biology 356, Developmental Biology lecture and lab. In the early phase (change wording here...training phase is what I mean but doesn't sound right,) yeast will serve as a model for studying the regulation of cell cycle control genes. In the later phase of the grant, evolution of the neural crest will be explored through comparative gene expression patterns in various models such as the zebrafish and sequenced protochordates such as Ciona intestinalis and Oikopleaura. Students will also be able to visualize specific gene expression patterns with in situ hybridization and immunohistochemistry on frozen sections. This work will entail collaboration with and cooperation of labs working with these organisms and with extra slides to share.
			The yeast microarray data set generated by Biloogy 356 students will be used in a dry lab in Biology 112, Cells, Genes and Inheritance. In this exercise, students will use the data set in GenMAPP to explore strategies for working with huge data sets as well as for studying the central dogma.
			(More on mass spec and proteomics as I learn more from Chemistry on capabilities, but I could see a similar dry lab/problem space for Cell Phys with emphasis on proteomics but also using the yeast microarray data set.)
	Peter's plan:		Peter's plan:
	* In the near future we should generate a written synopsis of each particular program component. This mock 'executive summary' should include: 1) Brief summary, 2) Statement of (educational) outcomes, 3) Mode of assessment, 4) Timeframes, and 4) Preliminary budget.		* In the near future we should generate a written synopsis of each particular program component. This mock 'executive summary' should include: 1) Brief summary, 2) Statement of (educational) outcomes, 3) Mode of assessment, 4) Timeframes, and 4) Preliminary budget.

Charliep at 12:01, 14 June 2007

2007-06-14T12:01:02Z

New page

Peter's plan:
* In the near future we should generate a written synopsis of each particular program component. This mock 'executive summary' should include: 1) Brief summary, 2) Statement of (educational) outcomes, 3) Mode of assessment, 4) Timeframes, and 4) Preliminary budget.