Personal Projects - Revision history

Erika at 03:41, 6 November 2009

2009-11-06T03:41:47Z

← Older revision		Revision as of 03:41, 6 November 2009
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	<nowiki>NOTE</nowiki>		<nowiki>NOTE</nowiki>
	from "Developing Bioinfo. Comp. Skills" :		from "Developing Bioinfo. Comp. Skills" :
	<i>With a little clever programming, you can develop scripts that allow you to hit a web server with multiple requests without entering them manually into a form, but if you're capable of doing that, you're probably able to download a local copy of the software and run it on your own machine. Using your own processor in such cases avoids slow data transfer to and from remote sites and is also considered more polite than running huge jobs on someone else's server.</i>		<br><i>With a little clever programming, you can develop scripts that allow you to hit a web server with multiple requests without entering them manually into a form, but if you're capable of doing that, you're probably able to download a local copy of the software and run it on your own machine. Using your own processor in such cases avoids slow data transfer to and from remote sites and is also considered more polite than running huge jobs on someone else's server.</i>

Erika at 03:41, 6 November 2009

2009-11-06T03:41:33Z

← Older revision		Revision as of 03:41, 6 November 2009
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	<nowiki>NOTE</nowiki>		<nowiki>NOTE</nowiki>
	from "Developing Bioinfo. Comp. Skills" : <i>With a little clever programming, you can develop scripts that allow you to hit a web server with multiple requests without entering them manually into a form, but if you're capable of doing that, you're probably able to download a local copy of the software and run it on your own machine. Using your own processor in such cases avoids slow data transfer to and from remote sites and is also considered more polite than running huge jobs on someone else's server.</i>		from "Developing Bioinfo. Comp. Skills" :
			<i>With a little clever programming, you can develop scripts that allow you to hit a web server with multiple requests without entering them manually into a form, but if you're capable of doing that, you're probably able to download a local copy of the software and run it on your own machine. Using your own processor in such cases avoids slow data transfer to and from remote sites and is also considered more polite than running huge jobs on someone else's server.</i>

Erika at 03:41, 6 November 2009

2009-11-06T03:41:11Z

← Older revision		Revision as of 03:41, 6 November 2009
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	Case 5: RNA = blah		Case 5: RNA = blah

	NOTE		<nowiki>NOTE</nowiki>
	from "Developing Bioinfo. Comp. Skills" : <i>With a little clever programming, you can develop scripts that allow you to hit a web server with multiple requests without entering them manually into a form, but if you're capable of doing that, you're probably able to download a local copy of the software and run it on your own machine. Using your own processor in such cases avoids slow data transfer to and from remote sites and is also considered more polite than running huge jobs on someone else's server.</i>		from "Developing Bioinfo. Comp. Skills" : <i>With a little clever programming, you can develop scripts that allow you to hit a web server with multiple requests without entering them manually into a form, but if you're capable of doing that, you're probably able to download a local copy of the software and run it on your own machine. Using your own processor in such cases avoids slow data transfer to and from remote sites and is also considered more polite than running huge jobs on someone else's server.</i>

Erika at 03:40, 6 November 2009

2009-11-06T03:40:44Z

← Older revision		Revision as of 03:40, 6 November 2009
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	Now Dr. Doolittle uses these programs to find the culprits in the other five cases. (This is to illustrate how taking the time to write a program saves time in the long run)		Now Dr. Doolittle uses these programs to find the culprits in the other five cases. (This is to illustrate how taking the time to write a program saves time in the long run)

	Case 1: RNA =		Case 1: RNA = blah
	Case 2: RNA =		<br>
	Case 3: RNA =		Case 2: RNA = blah
	Case 4: RNA =		<br>
	Case 5: RNA =		Case 3: RNA = blah
			<br>
			Case 4: RNA = blah
			<br>
			Case 5: RNA = blah

			NOTE
			from "Developing Bioinfo. Comp. Skills" : <i>With a little clever programming, you can develop scripts that allow you to hit a web server with multiple requests without entering them manually into a form, but if you're capable of doing that, you're probably able to download a local copy of the software and run it on your own machine. Using your own processor in such cases avoids slow data transfer to and from remote sites and is also considered more polite than running huge jobs on someone else's server.</i>

Erika at 00:23, 27 October 2009

2009-10-27T00:23:50Z

← Older revision		Revision as of 00:23, 27 October 2009
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	1. Using your hand out, translate this RNA sequence into a corresponding amino acid sequence		1. Using your hand out, translate this RNA sequence into a corresponding amino acid sequence
	2. Find out to which protein this amino acid sequence corresponds to by performing a BLAST search at		2. Find out to which protein this amino acid sequence corresponds by performing a BLAST search at
	http://services.uniprot.org/blast/		http://services.uniprot.org/blast/
	3. Find the 3D structure for this protein using protein data base at http://www.rcsb.org/pdb/home/home.do		3. Find the 3D structure for this protein using protein data base at http://www.rcsb.org/pdb/home/home.do

Erika at 00:22, 27 October 2009

2009-10-27T00:22:41Z

← Older revision		Revision as of 00:22, 27 October 2009
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	<b>Making life easier for a research scientist: A case study</b>		<b>Making life easier for a research scientist: A case study</b>

	A crime scene investigator, Dr. Doolittle, is called to the scene of a gruesome murder. As he pulls into the Chicago zoo, Dr. Doolittle finds the mane attraction, a large African male lion, lying in a pool of blood. The zookeeper has isolated several suspects who were found near the scene and also covered with blood: a chimpanzee, river buffalo, opposum, platypus, and rat. The lion has unfortunately been so maimed during the attack that it is difficult to tell whether the cause of death was strangulation, crushing, or biting. Fortunately Dr. Doolittle knows that that all of the suspects' genomes have been sequenced and so he collects a sample of the blood at the scene to take back to the lab.		A crime scene investigator, Dr. Doolittle, is called to the scene of a gruesome murder. As he pulls into the Chicago zoo, Dr. Doolittle finds the mane attraction, a large African male lion, lying in a pool of blood. The zookeeper has isolated several suspects who were found near the scene and are also covered with blood: a chimpanzee, river buffalo, opposum, platypus, and rat. The lion has unfortunately been so maimed during the attack that it is difficult to tell whether the cause of death was strangulation, crushing, or biting. Fortunately Dr. Doolittle knows that that all of the suspects' genomes have been sequenced and so he collects a sample of the blood at the scene to take back to the lab.

	Dr. Doolittle centrifuges this blood sample separating it into red blood cells, buffy coat and plasma. After discarding the buffy coat and plasma, he lyses the red blood cells in the plasma and extracts the total RNA. Using advance sequencing techniques, he obtains the following strand of RNA:		Dr. Doolittle centrifuges this blood sample separating it into red blood cells, buffy coat and plasma. After discarding the buffy coat and plasma, he lyses the red blood cells in the plasma and extracts the total RNA. Using advance sequencing techniques, he obtains the following strand of RNA:

Erika at 00:22, 27 October 2009

2009-10-27T00:22:08Z

← Older revision		Revision as of 00:22, 27 October 2009
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	<b>Making life easier for a ~~researcher~~: A case study</b>		<b>Making life easier for a research scientist: A case study</b>

	A crime scene investigator, Dr. Doolittle, is called to the scene of a gruesome murder. As he pulls into the Chicago zoo, Dr. Doolittle finds the mane attraction, a large African male lion, lying in a pool of blood. The zookeeper has isolated several suspects who were found near the scene and also covered with blood: a chimpanzee, river buffalo, opposum, platypus, and rat. The lion has unfortunately been so maimed during the attack that it is difficult to tell whether the cause of death was strangulation, crushing, or biting. Fortunately Dr. Doolittle knows that that all of the suspects' genomes have been sequenced and so he collects a sample of the blood at the scene to take back to the lab.		A crime scene investigator, Dr. Doolittle, is called to the scene of a gruesome murder. As he pulls into the Chicago zoo, Dr. Doolittle finds the mane attraction, a large African male lion, lying in a pool of blood. The zookeeper has isolated several suspects who were found near the scene and also covered with blood: a chimpanzee, river buffalo, opposum, platypus, and rat. The lion has unfortunately been so maimed during the attack that it is difficult to tell whether the cause of death was strangulation, crushing, or biting. Fortunately Dr. Doolittle knows that that all of the suspects' genomes have been sequenced and so he collects a sample of the blood at the scene to take back to the lab.

	Dr. Doolittle centrifuges this blood sample separating it into ~~white~~ blood cells, buffy coat and plasma. ~~Subsequently~~, he lyses the red blood cells in the plasma and extracts the total RNA. Using advance sequencing techniques, he obtains the following strand of RNA:		Dr. Doolittle centrifuges this blood sample separating it into red blood cells, buffy coat and plasma. After discarding the buffy coat and plasma, he lyses the red blood cells in the plasma and extracts the total RNA. Using advance sequencing techniques, he obtains the following strand of RNA:

	<i>For this step, we will need to design a program for ourselves to reverse translate this protein sequence into a strand of mRNA to provide the students with in the case study.</i>		<i>For this step, we will need to design a program for ourselves to reverse translate this protein sequence into a strand of mRNA to provide the students with in the case study.</i>
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	----		----

	Phew, that was a lot of work! Dr. Doolittle knows that <i>you</i> are a computer scientist (programmer?) and thinks you may be able to simplify the process he went through. He really hopes you are able to help because he's gotten calls for 5 more zoo crimes already!! As he walks you through the process you realize that, indeed, you could write a few short programs to simplify the process.		Phew, that was a lot of work! Dr. Doolittle knows that <i><u>you</u></i> are a computer scientist (programmer?) and thinks you may be able to simplify the process he went through. He really hopes you are able to help because he's gotten calls for 5 more zoo crimes already!! As he walks you through the process you realize that, indeed, you could write a few short programs to simplify the process.

	First, you write a program to translate the RNA strand to the protein sequence. <i>We'll write this program.</i>		First, you write a program to translate the RNA strand to the protein sequence. <i>We'll write this program.</i>
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	4. Run the program.		4. Run the program.
	5. Marvel at how much faster the process becomes.		5. Marvel at how much faster the process becomes.

			Now Dr. Doolittle uses these programs to find the culprits in the other five cases. (This is to illustrate how taking the time to write a program saves time in the long run)

			Case 1: RNA =
			Case 2: RNA =
			Case 3: RNA =
			Case 4: RNA =
			Case 5: RNA =

Damian at 00:17, 27 October 2009

2009-10-27T00:17:50Z

← Older revision		Revision as of 00:17, 27 October 2009
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	DFSPEVQAAWQKLVSGVAHALGHKYH		DFSPEVQAAWQKLVSGVAHALGHKYH

	~~Translate~~ this RNA sequence into an amino acid sequence ~~and find~~ out to which protein it corresponds by performing a BLAST search at http://services.uniprot.org/blast/		1. Using your hand out, translate this RNA sequence into a corresponding amino acid sequence
			2. Find out to which protein this amino acid sequence corresponds to by performing a BLAST search at
			http://services.uniprot.org/blast/
			3. Find the 3D structure for this protein using protein data base at http://www.rcsb.org/pdb/home/home.do

	----		----

Erika at 00:09, 27 October 2009

2009-10-27T00:09:29Z

← Older revision		Revision as of 00:09, 27 October 2009
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	----		----

	Phew, that was a lot of work! Dr. Doolittle knows that <i>you</i> are a computer scientist (programmer?) and thinks you may be able to simplify the process he went through. As he walks you through the process you realize that, indeed, you could write a few short programs to simplify the process.		Phew, that was a lot of work! Dr. Doolittle knows that <i>you</i> are a computer scientist (programmer?) and thinks you may be able to simplify the process he went through. He really hopes you are able to help because he's gotten calls for 5 more zoo crimes already!! As he walks you through the process you realize that, indeed, you could write a few short programs to simplify the process.

	First, you write a program to translate the RNA strand to the protein sequence. <i>We'll write this program.</i>		First, you write a program to translate the RNA strand to the protein sequence. <i>We'll write this program.</i>

Erika at 00:08, 27 October 2009

2009-10-27T00:08:18Z

← Older revision		Revision as of 00:08, 27 October 2009
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	----		----

	Phew, that was a lot of work! Dr. Doolittle knows that <i>you</i> are a computer scientist (programmer?) and thinks you may be able to ~~simply~~ the process he went through. As he walks you through the process you realize that, indeed, you could write a few short programs to simplify the process.		Phew, that was a lot of work! Dr. Doolittle knows that <i>you</i> are a computer scientist (programmer?) and thinks you may be able to simplify the process he went through. As he walks you through the process you realize that, indeed, you could write a few short programs to simplify the process.

	First, you write a program to translate the RNA strand to the protein sequence. <i>We'll write this program.</i>		First, you write a program to translate the RNA strand to the protein sequence. <i>We'll write this program.</i>