Week 9 - Revision history

Dondi: /* One Lifeline Question per Homework Pair */ Fix long-broken link.

2017-11-22T08:01:32Z

‎One Lifeline Question per Homework Pair: Fix long-broken link.

Dondi: /* Hands-On with GRNsight */ Add right-click option for downloading Raw files from GitHub.

2017-10-25T05:03:42Z

‎Hands-On with GRNsight: Add right-click option for downloading Raw files from GitHub.

Dondi: Remove Under Construction message.

2017-10-24T07:18:41Z

Remove Under Construction message.

Dondi: /* Web Service API Exploration */ Rearrange sections.

2017-10-24T07:17:48Z

‎Web Service API Exploration: Rearrange sections.

Dondi: /* Per-Service Hints */ Add remaining hints.

2017-10-24T07:15:54Z

‎Per-Service Hints: Add remaining hints.

Dondi: /* Per-Service Hints */ NCBI hints.

2017-10-24T07:04:47Z

‎Per-Service Hints: NCBI hints.

Dondi: /* UniProt */ Clean up curl-with-apostrophes example.

2017-10-24T06:58:51Z

‎UniProt: Clean up curl-with-apostrophes example.

Dondi: /* Per-Service Hints */ UniProt hints.

2017-10-24T06:57:33Z

‎Per-Service Hints: UniProt hints.

Dondi: /* Web Service API Exploration */ Lifeline details plus a few more tweaks.

2017-10-24T06:48:44Z

‎Web Service API Exploration: Lifeline details plus a few more tweaks.

Dondi: /* Homework Partners */ Assign web service APIs.

2017-10-24T06:29:33Z

‎Homework Partners: Assign web service APIs.

@@ Line 137: / Line 137: @@
 To ask a lifeline question:
-# Post the question to [[Talk:Dondi Dr. Dionisio’s talk page]] (remember that?)
+# Post the question to [[User_talk:Dondi|Dr. Dionisio’s talk page]] (remember that?)
 # Send Dr. Dionisio and Dr. Dahlquist an email notifying us of the question (our wiki does not send notifications for new talk page postings)

@@ Line 43: / Line 43: @@
 # Each feature is to be tested in combination will all three formats that GRNsight can read (Excel workbook, SIF, GraphML). This is already specified in the testing document. Choose one file for each of these formats [https://github.com/dondi/GRNsight/tree/beta/test-files/demo-files from this web page] for use in your tests and specify them in your electronic notebook. In order to have a basis for comparison, homework partners should use the same test files for their individual test sequences.
 #* For the Excel workbooks (''.xlsx'') in the linked collection above, click on the file then click ''Download'' to save the file to your computer.
-#* For the SIF (''.sif'') and GraphML (''.graphml'') files, click on the file, click on the ''Raw'' button, then either copy-paste or save the resulting file to your computer.
+#* For the SIF (''.sif'') and GraphML (''.graphml'') files, click on the file, click on the ''Raw'' button, then either copy-paste or save the resulting file to your computer. The ''.sif'' and ''.graphml'' file extensions are not very well known so the files may end up with ''.txt'' added to them; go ahead and remove that from the files after they are downloaded, confirming to the computer that you know what you’re doing.
 # Each test specifies a sequence of actions to perform, followed by their expected results. Use the latter to determine whether GRNsight passed a particular test. Report the result of each test in your electronic notebook.
 #* The version of GRNsight that you are testing is a ''beta'' version, so results that diverge from the expected ones are certainly possible.

← Older revision		Revision as of 07:18, 24 October 2017
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	'''This journal entry is due on Tuesday, October 31, at 12:01 AM PDT.''' 🎃		'''This journal entry is due on Tuesday, October 31, at 12:01 AM PDT.''' 🎃
−
−	~~{{Under Construction}}~~

	== Objectives ==		== Objectives ==

@@ Line 73: / Line 73: @@
 That said, it is again imperative that you take good notes about the things you try, and their results, so that you don’t go around in circles and eventually narrow down your exploration the the desired set of steps.
 ==== Per-Service Hints ====
@@ Line 142: / Line 132: @@
 ** Ensembl requires a ''content-type'' parameter in its URLs; use ''content-type=application/json'' to receive JSON-formatted results
 ** Ensembl lists our species as ''saccharomyces_cerevisiae'' (all lowercase, with an underscore)
 == Shared Journal Assignment ==

@@ Line 124: / Line 124: @@
 ===== SGD/YeastMine =====
 ===== Ensembl =====
 == Shared Journal Assignment ==

← Older revision		Revision as of 07:04, 24 October 2017
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	===== NCBI =====		===== NCBI =====
		+	* Relevant documentation:
		+	** https://www.ncbi.nlm.nih.gov/gene
		+	** https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch
		+	** https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Searching_a_Database
		+	** https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Downloading_Document_Summaries
		+	** https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Downloading_Full_Records
		+	* Technical information:
		+	** Your URLs will include ampersands ('''&'''), which will need special handling with '''curl''': in these cases, enclose the URL in apostrophes (e.g., '''curl -L '<nowiki>http://www.uniport.org?query=this&type=that</nowiki>'''')
		+	** Your URLs will also include brackets ('''<nowiki>[ ]</nowiki>'''), which will need special handling with '''curl''': in these cases, make sure to add the '''-g''' switch (i.e., '''curl -g '''…)
		+	** Your URLs may include spaces; typically, we replace those with ''+'' (plus) symbols
		+	* Miscellaneous information:
		+	** NCBI consists of multiple databases; we care about the ''gene'' database
		+	** NCBI abbreviates the gene name/symbol field as ''sym''
		+	** NCBI stores ''organism''s by their full name, in our case ''Saccharomyces cerevisiae'' (note the space)

	===== SGD/YeastMine =====		===== SGD/YeastMine =====

@@ Line 102: / Line 102: @@
 * Technical information:
 ** You will encounter ''redirects'' in these web services; web browsers handle this automatically, but if using '''curl''' make sure to add the '''-L''' switch (i.e., '''curl -L '''…)
-** Your URLs will include ampersands ('''&'''), which will need special handling with '''curl''': in these cases, enclose the URL in apostrophes (e.g., '''curl -L 'http://www.uniport.org?query=this&type=that')
+** Your URLs will include ampersands ('''&'''), which will need special handling with '''curl''': in these cases, enclose the URL in apostrophes (e.g., '''curl -L '<nowiki>http://www.uniport.org?query=this&type=that</nowiki>'''')
 ** UniProt primarily provides results in XML format; in one relevant step, the data can be provided in tab-delimited format, which might be easier to work with
 * Miscellaneous information:

← Older revision		Revision as of 06:57, 24 October 2017
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	===== UniProt =====		===== UniProt =====
		+	* Relevant documentation:
		+	** http://www.uniprot.org/help/api
		+	** http://www.uniprot.org/help/api_idmapping
		+	** http://www.uniprot.org/help/api_retrieve_entries
		+	* Supplementary websites:
		+	** [http://www.uniprot.org/uploadlists/ Retrieve/ID mapping] web page
		+	* Technical information:
		+	** You will encounter ''redirects'' in these web services; web browsers handle this automatically, but if using '''curl''' make sure to add the '''-L''' switch (i.e., '''curl -L '''…)
		+	** Your URLs will include ampersands ('''&'''), which will need special handling with '''curl''': in these cases, enclose the URL in apostrophes (e.g., '''curl -L 'http://www.uniport.org?query=this&type=that')
		+	** UniProt primarily provides results in XML format; in one relevant step, the data can be provided in tab-delimited format, which might be easier to work with
		+	* Miscellaneous information:
		+	** You will encounter the need for a ''taxon ID'', which identifies a specific organism; the taxon ID for our strain of ''S. cerevisiae'' is '''559292'''

	===== NCBI =====		===== NCBI =====

@@ Line 57: / Line 57: @@
 Each homework pair has been assigned one of the four gene-related web services that we have used for the “favorite gene page” assignments (Ensembl, NCBI, UniProt, SGD/YeastMine). Because there are only four such services, two homework pairs will be working on the same service, so if you wish, you may join “fources” (sorry) to explore the same web service together. Still, you must write up your findings ''individually'' in your own respective words.
-For the web service that has been assigned to you, use the information given on this page to discover how to take a gene name/symbol (e.g., ACT1, BRO1, SPT15, etc.) and access its full “data profile” within that service. This process may require multiple web service calls and will involve “reading” web service data formats such as JSON or XML.
+==== Your Mission ====
-Your foundational knowledge for this exercise begins with what you have learned from working with “your favorite gene” and from using the services’ corresponding websites. You will want to use a combination of a web browser and '''curl''', with a code-savvy editor to help make any received data more readable to you.
+For the web service that has been assigned to you, use the information given on this page to discover how to take a gene name/symbol (e.g., ACT1, BRO1, SPT15, etc.) and find your way to its full “data profile” within that service. This process may require multiple web service calls and will involve “reading” web service data formats such as JSON or XML.
-Upon determining how to go from a gene name/symbol to that gene’s individual data record, write up this process as a reproducible “recipe” in your electronic journal. In general, this recipe will consist of:
+Your foundational knowledge for this exercise begins with what you have learned from working with “your favorite gene” and from using the services’ corresponding websites. Furthermore, the final URLs that lead to the full gene data are already known to you: they are in the [[Media:Ajax-starter.zip|''ajax-starter'']] files from the [[Week 7]] assignment. You will want to use a combination of a web browser and '''curl''', with a code-savvy editor like Atom or Visual Studio Code to help make any received data more readable to you.
 * The URLs to access in order to retrieve the desired data
 * Any portions in these URLs that need to be substituted for specific queries, such as the gene name or ID within that web service
@@ Line 70: / Line 74: @@
 That said, it is again imperative that you take good notes about the things you try, and their results, so that you don’t go around in circles and eventually narrow down your exploration the the desired set of steps.
-<!-- Lifeline -->
+==== One Lifeline Question per Homework Pair ====
-<!-- Hints about each service -->
+===== Ensembl =====
 == Shared Journal Assignment ==

@@ Line 28: / Line 28: @@
 === Homework Partners ===
-Homework partners for this week are listed below. The particular web service API and GRNsight functional area that you and your partner will work on are also indicated below. You are expected to consult with your partner, sharing your domain expertise, in order to complete the assignment. However, each partner must submit his or her own work as the individual journal entry (direct copying of each other's work is not allowed). You must give the details of the interaction with your partner in the [[Week_1#Acknowledgments | Acknowledgments section]] of your journal assignment.
+Homework partners for this week are listed below. The particular GRNsight functional area and web service API that you and your partner will work on are also indicated below. You are expected to consult with your partner, sharing your domain expertise, in order to complete the assignment. However, each partner must submit his or her own work as the individual journal entry (direct copying of each other's work is not allowed). You must give the details of the interaction with your partner in the [[Week_1#Acknowledgments | Acknowledgments section]] of your journal assignment.
-{{Under Construction}}
+* Eddie Azinge, Corinne Wong ([[Media:GRNsight_Testing-D-Pad_Control.pdf|D-Pad Control]]; UniProt)
+* Eddie Bachoura, Katie Wright ([[Media:GRNsight_Testing-Viewport_Size.pdf|Viewport Size]]; UniProt)
-* Eddie Azinge, Corinne Wong (tbd; [[Media:GRNsight_Testing-D-Pad_Control.pdf|D-Pad Control]])
+* Mary Balducci, Quinn Lanners ([[Media:GRNsight_Testing-Edge_Weights_and_Gray_Threshold.pdf|Edge Weights + Gray Threshold]]; NCBI)
-* Eddie Bachoura, Katie Wright (tbd; [[Media:GRNsight_Testing-Viewport_Size.pdf|Viewport Size]])
+* Blair Hamilton, Emma Tyrnauer ([[Media:GRNsight_Testing-Gray_Threshold_and_Zoom.pdf|Gray Threshold + Zoom]]; NCBI)
-* Mary Balducci, Quinn Lanners (tbd; [[Media:GRNsight_Testing-Edge_Weights_and_Gray_Threshold.pdf|Edge Weights + Gray Threshold]])
+* Dina Bashoura, Simon Wroblewski ([[Media:GRNsight_Testing-Edge_Weights_and_Normalization.pdf|Edge Weights + Normalization]]; SGD/YeastMine)
-* Dina Bashoura, Simon Wroblewski (tbd; [[Media:GRNsight_Testing-Edge_Weights_and_Normalization.pdf|Edge Weights + Normalization]])
+* Hayden Hinsch, John Lopez ([[Media:GRNsight_Testing-Normalization_and_Zoom.pdf|Normalization + Zoom]]; SGD/YeastMine)
-* Blair Hamilton, Emma Tyrnauer (tbd; [[Media:GRNsight_Testing-Gray_Threshold_and_Zoom.pdf|Gray Threshold + Zoom]])
+* Nicole Kalcic, Arash Lari ([[Media:GRNsight_Testing-Restrict_Viewport_and_Edge_Weights.pdf|Restrict Viewport + Edge Weights]]; Ensembl)
-* Hayden Hinsch, John Lopez (tbd; [[Media:GRNsight_Testing-Normalization_and_Zoom.pdf|Normalization + Zoom]])
+* Antonio Porras, Zach Van Ysseldyk ([[Media:GRNsight_Testing-Restrict_Viewport_and_Zoom.pdf|Restrict Viewport + Zoom]]; Ensembl)
 === Hands-On with GRNsight ===