BIOL398-01/S11:Week 2 - Revision history

Kam D. Dahlquist: /* Preparation for Journal Club 1 */ added names

Kam D. Dahlquist — Thu, 20 Jan 2011 17:34:00 GMT

Preparation for Journal Club 1: added names

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	#* What is the overall conclusion of the study and what are some future directions for research?		#* What is the overall conclusion of the study and what are some future directions for research?
	# Each group of students will be assigned one section of the paper. The group will be responsible for explaining the section, including any tables/figures in detail to the class. Groups will be assigned on 1/20/11 in class. Dr. Dahlquist will prepare the PowerPoint slides this time; for future journal club assignments, you will prepare the PowerPoint.		# Each group of students will be assigned one section of the paper. The group will be responsible for explaining the section, including any tables/figures in detail to the class. Groups will be assigned on 1/20/11 in class. Dr. Dahlquist will prepare the PowerPoint slides this time; for future journal club assignments, you will prepare the PowerPoint.
-	#* Physiological parameters section, Figure 1:	+	#* Physiological parameters section, Figure 1: James, Nick
-	#* Northern analysis section, Figure 2:	+	#* Northern analysis section, Figure 2: Carmen, Alondra
-	#* Enzyme activities section, Figure 3:	+	#* Enzyme activities section, Figure 3: Sarah

	==== Online Biological Dictionaries ====		==== Online Biological Dictionaries ====

Kam D. Dahlquist: removed under construction notice

Kam D. Dahlquist — Thu, 20 Jan 2011 16:57:11 GMT

removed under construction notice

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-	~~'''''NOTE: This page is under construction. The assignment will be finalized in class on 1/20/11.'''''~~
-
	{{BIOL398-01/S11}}		{{BIOL398-01/S11}}

Kam D. Dahlquist: /* Preparation for Journal Club 1 */ modified outline instructions

Kam D. Dahlquist — Thu, 20 Jan 2011 16:56:38 GMT

Preparation for Journal Club 1: modified outline instructions

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	#*What were the limitations in previous studies that led them to perform this work?		#*What were the limitations in previous studies that led them to perform this work?
	#*What were the methods used in the study?		#*What were the methods used in the study?
-	#*Briefly state the result shown in each of the figures ~~and tables~~.	+	#*Briefly state the result shown in each of the figures.
-	#*~~How~~ do the ~~results of this study compare to~~ the ~~results~~ of ~~previous studies.~~	+	#** What do the X and Y axes represent?
		+	#** How were the measurements made?
		+	#** What trends are shown by the plots and what conclusions can you draw from the data?
		+	#* What is the overall conclusion of the study and what are some future directions for research?
	# Each group of students will be assigned one section of the paper. The group will be responsible for explaining the section, including any tables/figures in detail to the class. Groups will be assigned on 1/20/11 in class. Dr. Dahlquist will prepare the PowerPoint slides this time; for future journal club assignments, you will prepare the PowerPoint.		# Each group of students will be assigned one section of the paper. The group will be responsible for explaining the section, including any tables/figures in detail to the class. Groups will be assigned on 1/20/11 in class. Dr. Dahlquist will prepare the PowerPoint slides this time; for future journal club assignments, you will prepare the PowerPoint.
		+	#* Physiological parameters section, Figure 1:
		+	#* Northern analysis section, Figure 2:
		+	#* Enzyme activities section, Figure 3:

	==== Online Biological Dictionaries ====		==== Online Biological Dictionaries ====

Kam D. Dahlquist: /* Shared Journal Assignment */ posted questions to answer

Kam D. Dahlquist — Thu, 20 Jan 2011 16:52:45 GMT

Shared Journal Assignment: posted questions to answer

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	* Add the "BIOL398-01/S11" category to the end of the wiki page (if someone has not already done so).		* Add the "BIOL398-01/S11" category to the end of the wiki page (if someone has not already done so).

		+	=== Reflection ===
		+
		+	Answer the following questions on the [[BIOL398-01/S11:Class Journal Week 2 \| Class Journal Week 2]] page after you have completed the individual assignment.
		+
		+	# What was the purpose of this assignment?
		+	# What aspect of this assignment came most easily to you?
		+	# What aspect of this assignment was the most challenging for you?
		+	# What (yet) do you not understand?

	</div>		</div>

Kam D. Dahlquist: /* Preparation for Journal Club 1 */ referred to sections of paper instead of table/figures

Kam D. Dahlquist — Tue, 18 Jan 2011 22:27:15 GMT

Preparation for Journal Club 1: referred to sections of paper instead of table/figures

←Older revision		Revision as of 22:27, 18 January 2011
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	#*Briefly state the result shown in each of the figures and tables.		#*Briefly state the result shown in each of the figures and tables.
	#*How do the results of this study compare to the results of previous studies.		#*How do the results of this study compare to the results of previous studies.
-	# Each group of students will be assigned one section of the paper. The group will be responsible for explaining the ~~table~~/~~figure~~ in detail to the class. Groups will be assigned on 1/20/11 in class. Dr. Dahlquist will prepare the PowerPoint slides this time; for future journal club assignments, you will prepare the PowerPoint.	+	# Each group of students will be assigned one section of the paper. The group will be responsible for explaining the section, including any tables/figures in detail to the class. Groups will be assigned on 1/20/11 in class. Dr. Dahlquist will prepare the PowerPoint slides this time; for future journal club assignments, you will prepare the PowerPoint.

	==== Online Biological Dictionaries ====		==== Online Biological Dictionaries ====

Kam D. Dahlquist: /* How to Read a Primary Research Article */ note about journal club 1 article

Kam D. Dahlquist — Tue, 18 Jan 2011 22:26:13 GMT

How to Read a Primary Research Article: note about journal club 1 article

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	=== How to Read a Primary Research Article ===		=== How to Read a Primary Research Article ===

-	A primary research article is divided into sections that each have a different purpose. Articles in ''Science'' and ''Nature'' are written in a single narrative format and do not explicitly have these headers. However, the information for each of these sections is still there.	+	A primary research article is divided into sections that each have a different purpose. Articles in ''Science'' and ''Nature'' are written in a single narrative format and do not explicitly have these headers. However, the information for each of these sections is still there. The article for the Journal Club 1 Assignment is very short and also written as a single narrative, although the information below can still be found.
	<!-- In the future, I should modify this for different types of articles; hypothesis-driven original research, discovery-based original research, methods/tool article, review. --KD -->		<!-- In the future, I should modify this for different types of articles; hypothesis-driven original research, discovery-based original research, methods/tool article, review. --KD -->

Kam D. Dahlquist: pasted in how to read a primary article

Kam D. Dahlquist — Tue, 18 Jan 2011 22:25:05 GMT

pasted in how to read a primary article

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	* [http://www.geneontology.org Gene Ontology]		* [http://www.geneontology.org Gene Ontology]
	* [http://www.cancer.gov/dictionary/ NCI Dictionary of Cancer Terms]		* [http://www.cancer.gov/dictionary/ NCI Dictionary of Cancer Terms]
		+
		+	=== How to Read a Primary Research Article ===
		+
		+	A primary research article is divided into sections that each have a different purpose. Articles in ''Science'' and ''Nature'' are written in a single narrative format and do not explicitly have these headers. However, the information for each of these sections is still there.
		+	<!-- In the future, I should modify this for different types of articles; hypothesis-driven original research, discovery-based original research, methods/tool article, review. --KD -->
		+
		+	==== Abstract ====
		+
		+	The abstract provides a brief summary of the paper. It states the significance and background, methods, major results, and conclusions from the paper. Different journals have different word limits for the abstract. The abstract is indexed on [http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed PubMed] and may be the only part of the text publicly available.
		+
		+	==== Introduction ====
		+
		+	The introduction gives the background information necessary to understand the paper.
		+	The introduction should be in the form of a logical argument that “funnels” from broad to narrow:
		+	[[Image:Funnel.jpg\|right]]
		+	* States importance of the problem
		+	* States what is known about the problem
		+	* States what is unknown about the problem
		+	* States clues that suggest how to approach the unknown
		+	* States the question the paper is trying to address
		+	* States the experimental approach
		+	* Sometimes briefly states the answer they found
		+
		+	==== Materials and Methods====
		+
		+	Describes the experiments used in the paper with enough detail so that another investigator could reproduce the experiments. However, it is usually written in a "shorthand" style that relies heavily on references to previous literature. Articles in ''Science'' and ''Nature'' severely restrict the amount of methods that can be included in the paper. In those articles, the information is embedded in the figure legends or references or is available as supplemental online material.
		+
		+	==== Results ====
		+
		+	Describes the experiments performed and the results of the experiments. The text can take the form of question, experiment, results from that experiment, repeated several times. Each main experiment should be represented by a figure or table of results. Some people read papers by looking at the figures and reading the legends, then going back to the text for details.
		+
		+	==== Discussion ====
		+
		+	States the answer to the question the paper is trying to address. It explains and defends the answer, if necessary. It puts the results in a broader perspective by comparing with previous results or models. The implications of the results are discussed and the next steps for future research are suggested.
		+
		+	==== References ====
		+
		+	List of references cited in the main text of the paper. Different journals have different styles of references, but all the essential information should be there, authors, year of publication, journal name, volume, and page numbers. The title of the article is sometimes omitted. This list is a useful resource to look for further reading on the subject of the paper.
		+
		+	==== Caveat Emptor ====
		+
		+	Just because a paper was published does not mean that it was written well or that the experiments were sound (in a worst case scenario, data may even be fraudulent). The peer review system is designed so that only good research is published, but in practice, that may not be the case. Each paper must be approached with a critical eye. You must judge whether you believe their results and conclusions based on the evidence they give.

	== Shared Journal Assignment ==		== Shared Journal Assignment ==

Kam D. Dahlquist: /* Preparation for Journal Club 1 */ clarified groups

Kam D. Dahlquist — Tue, 18 Jan 2011 22:23:13 GMT

Preparation for Journal Club 1: clarified groups

←Older revision		Revision as of 22:23, 18 January 2011
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	#*Briefly state the result shown in each of the figures and tables.		#*Briefly state the result shown in each of the figures and tables.
	#*How do the results of this study compare to the results of previous studies.		#*How do the results of this study compare to the results of previous studies.
-	# Each group of students will be assigned one ~~table or figure~~. The ~~pair~~ will be responsible for explaining the table/figure in detail to the class.	+	# Each group of students will be assigned one section of the paper. The group will be responsible for explaining the table/figure in detail to the class. Groups will be assigned on 1/20/11 in class. Dr. Dahlquist will prepare the PowerPoint slides this time; for future journal club assignments, you will prepare the PowerPoint.

	==== Online Biological Dictionaries ====		==== Online Biological Dictionaries ====

Kam D. Dahlquist: /* Individual Assignment */ link to journal club article

Kam D. Dahlquist — Tue, 18 Jan 2011 16:09:18 GMT

Individual Assignment: link to journal club article

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	== Individual Assignment ==		== Individual Assignment ==
		+
		+	The paper we will read for Journal Club 1 is:
		+
		+	[http://jb.asm.org/cgi/reprint/177/22/6672 ter Schure, E.G., Sillje, H.H.W., Verkleij, A.J., Boonstra, J., and Verrips, C.T. (1995) The Concentration of Ammonia Regulates Nitrogen Metabolism in ''Saccharomyces cerevisiae''. ''Journal of Bacteriology'' 177: 6672-6675.]

	=== Preparation for Journal Club 1 ===		=== Preparation for Journal Club 1 ===

Kam D. Dahlquist: /* Preparation for Journal Club 1 */ removed hints

Kam D. Dahlquist — Tue, 18 Jan 2011 16:03:18 GMT

Preparation for Journal Club 1: removed hints

←Older revision		Revision as of 16:03, 18 January 2011
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	# Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). List the citation(s) for the dictionary(s) you use, providing a URL to the page is fine.		# Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). List the citation(s) for the dictionary(s) you use, providing a URL to the page is fine.
	# Write an outline of the article. The length should be the equivalent of 2 pages of standard 8 1/2 by 11 inch paper. Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article.		# Write an outline of the article. The length should be the equivalent of 2 pages of standard 8 1/2 by 11 inch paper. Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article.
-	#*What is the main result presented in this paper? ~~(Hint: look at the last sentence of the introduction and restate it in plain English.)~~	+	#*What is the main result presented in this paper?
	#*What is the importance or significance of this work?		#*What is the importance or significance of this work?
	#*What were the limitations in previous studies that led them to perform this work?		#*What were the limitations in previous studies that led them to perform this work?
	#*What were the methods used in the study?		#*What were the methods used in the study?
	#*Briefly state the result shown in each of the figures and tables.		#*Briefly state the result shown in each of the figures and tables.
-	#*How do the results of this study compare to the results of previous studies ~~(See Discussion)~~.	+	#*How do the results of this study compare to the results of previous studies.
	# Each group of students will be assigned one table or figure. The pair will be responsible for explaining the table/figure in detail to the class.		# Each group of students will be assigned one table or figure. The pair will be responsible for explaining the table/figure in detail to the class.