Ancient mtDNA Week 5 - Revision history

Eyoung20: added presentation

2019-10-01T06:59:09Z

added presentation

Msamdars: /* References */ change dats

2019-10-01T06:40:48Z

‎References: change dats

Msamdars: /* References */ add more references

2019-10-01T06:40:24Z

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Msamdars: /* Summary judgment */ add bullets

2019-10-01T06:39:12Z

‎Summary judgment: add bullets

Msamdars: /* General utility of the database to the scientific community */ add changes

2019-10-01T06:38:37Z

‎General utility of the database to the scientific community: add changes

Msamdars: /* Acknowledgements */ add my sig

2019-10-01T06:35:28Z

‎Acknowledgements: add my sig

Eyoung20: added section for the presentation

2019-10-01T06:34:12Z

added section for the presentation

Eyoung20: /* Acknowledgements */ added acknowledgment

2019-10-01T05:53:02Z

‎Acknowledgements: added acknowledgment

Eyoung20: /* Acknowledgements */ added signature

2019-10-01T03:54:13Z

‎Acknowledgements: added signature

Eyoung20: /* References */ added reference to week 5 assignment page

2019-10-01T03:08:51Z

‎References: added reference to week 5 assignment page

← Older revision		Revision as of 06:59, 1 October 2019
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	==Presentation==		==Presentation==
		+	[[File:Ancient_mtDNA_Presentation_.pdf]]

	==Acknowledgements==		==Acknowledgements==

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 # Ehler, E., Novotný, J., Juras, A., Chyleński, M., Moravčík, O., & Pačes, J. (2018). AmtDB: a database of ancient human mitochondrial genomes. Nucleic acids research, 47(D1), D29-D32.
 # Ramakrishnan, U., & Hadly, E. A. (2009). Using phylochronology to reveal cryptic population histories: review and synthesis of 29 ancient DNA studies. Molecular Ecology, 18(7), 1310-1330.
-# LMU BioDB 2019. (2019). Week 2. Retrieved September 11, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_5
+# LMU BioDB 2019. (2019). Week 5. Retrieved September 30, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_5
-# MediaWiki (2019). Category: Help. Retrieved September 11, 2019, from https://www.mediawiki.org/wiki/Category:Help
+# MediaWiki (2019). Category: Help. Retrieved September 30, 2019, from https://www.mediawiki.org/wiki/Category:Help

@@ Line 69: / Line 69: @@
 # Ehler, E., Novotný, J., Juras, A., Chyleński, M., Moravčík, O., & Pačes, J. (2018). AmtDB: a database of ancient human mitochondrial genomes. Nucleic acids research, 47(D1), D29-D32.
 # Ramakrishnan, U., & Hadly, E. A. (2009). Using phylochronology to reveal cryptic population histories: review and synthesis of 29 ancient DNA studies. Molecular Ecology, 18(7), 1310-1330.
-#[[week 5]]
+# LMU BioDB 2019. (2019). Week 2. Retrieved September 11, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_5

@@ Line 50: / Line 50: @@
 ===Summary judgment===
 # Would you direct a colleague unfamiliar with the field to use it?
-I would not direct a colleague unfamiliar with the biology field to use the database. However, the database is very usable to anyone lightly familiar with humans and databases with DNA sequences. The database provides the ability to do meta-analysis via the implementation of an option to download all data. Furthermore, it is extremely informative and provides information that is intriguing, including the ability to sort data by estimated dates of living. The oldest data entry appears to be from nearly 48,000 years ago.
+#* I would not direct a colleague unfamiliar with the biology field to use the database. However, the database is very usable to anyone lightly familiar with humans and databases with DNA sequences. The database provides the ability to do meta-analysis via the implementation of an option to download all data. Furthermore, it is extremely informative and provides information that is intriguing, including the ability to sort data by estimated dates of living. The oldest data entry appears to be from nearly 48,000 years ago.
 #Is this a professional or "hobby" database? The "hobby" analogy means that it was that person's hobby to make the database. It could mean that it is limited in scope, done by one or a few persons, and seems amateur.
-This seems to be a fully-funded, professional database that is fully capable of scaling up and adapting to its users' needs. It seems to have been updated fairly recently, and thus it seems that its creators and distributors are truly invested in its maintenance.
+#* This seems to be a fully-funded, professional database that is fully capable of scaling up and adapting to its users' needs. It seems to have been updated fairly recently, and thus it seems that its creators and distributors are truly invested in its maintenance.
 ==Presentation==

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 ===General utility of the database to the scientific community===
-#Are there Other links to Databases?
+#Are there links to other databases? Which ones?
 #*The site is linked to [https://www.elixir-czech.cz/ ELIXER Czech Republic]
 #*It is also linked to the [https://www.img.cas.cz/en/ Institute of Molecular Genetics of the Czech Academy of Sciences] website
 #Is it convenient to browse the data?
-#*It is very easy to browse data on this site. The data is able to be searched, advanced searched, and view by location on a map.
+#*It is very easy to browse data on this site. The data is able to be searched, advanced searched, and view by location on a map. [[File:AmtDB_Databasepage.png|thumb|200px|Search Options]] [[File:AmtDB_Advancedsearch.png|thumb|200px|Advanced Search Options ]]
 #Is it convenient to download data?
 #* Downloading data is fairly easy and there is a clear way under the actions option to do just that. You can even select which sequences you would like and then only download those.
 #*The Data can be downloaded under standard formats. DNA sequences may be downloaded as FASTA sequences (.fasta) for DNA sequences or for other data in a tabular format as a comma-separated values (.csv) file.
-#Evaluate the Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information?
+#Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information?
 #* The web site is well organized and very easy to navigate. This is probably do to the fact that the web design is clean and simple.
 #*There is FAQ & Help tab on the page that has FAQs, Metadata information, references, a log of edits to the site, and the terms of service. However there is no help with how the information can be used once downloaded or what systems it is compatible with.

← Older revision		Revision as of 06:35, 1 October 2019
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	[[User:Eyoung20\|Eyoung20]] ([[User talk:Eyoung20\|talk]]) 20:54, 30 September 2019 (PDT)		[[User:Eyoung20\|Eyoung20]] ([[User talk:Eyoung20\|talk]]) 20:54, 30 September 2019 (PDT)
		+	[[User:Msamdars\|Msamdars]] ([[User talk:Msamdars\|talk]]) 23:35, 30 September 2019 (PDT)

	==References==		==References==

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 ==Acknowledgements==
 This week, the two partners for this project are [[User:msamdars|Mihir Samdarshi]] and [[User:eyoung20|Emma Young]]. Both partners worked with each other outside of class to assist each other in finding and synthesizing the necessary information required to complete this assignment.
 Except for what is noted above, this individual journal entry was completed by us and not copied from another source.

← Older revision		Revision as of 03:54, 1 October 2019
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	Except for what is noted above, this individual journal entry was completed by us and not copied from another source.		Except for what is noted above, this individual journal entry was completed by us and not copied from another source.
		+
		+	[[User:Eyoung20\|Eyoung20]] ([[User talk:Eyoung20\|talk]]) 20:54, 30 September 2019 (PDT)

	==References==		==References==

← Older revision		Revision as of 03:08, 1 October 2019
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	# Ehler, E., Novotný, J., Juras, A., Chyleński, M., Moravčík, O., & Pačes, J. (2018). AmtDB: a database of ancient human mitochondrial genomes. Nucleic acids research, 47(D1), D29-D32.		# Ehler, E., Novotný, J., Juras, A., Chyleński, M., Moravčík, O., & Pačes, J. (2018). AmtDB: a database of ancient human mitochondrial genomes. Nucleic acids research, 47(D1), D29-D32.
	# Ramakrishnan, U., & Hadly, E. A. (2009). Using phylochronology to reveal cryptic population histories: review and synthesis of 29 ancient DNA studies. Molecular Ecology, 18(7), 1310-1330.		# Ramakrishnan, U., & Hadly, E. A. (2009). Using phylochronology to reveal cryptic population histories: review and synthesis of 29 ancient DNA studies. Molecular Ecology, 18(7), 1310-1330.
		+	#[[week 5]]