NeMO Week4 - Revision history

Hivanson: added template to week 4

2024-03-04T02:34:33Z

added template to week 4

2024-02-11T20:32:05Z

invoked template

2024-02-08T07:45:01Z

presntation uploaded

2024-02-08T06:56:10Z

‎General utility of the database to the scientific community: added bullet to pro vs hobby

2024-02-08T06:55:31Z

‎References: changed a citation to fix typo hopefully

2024-02-08T06:54:52Z

‎References: added other references

2024-02-08T06:49:41Z

‎References: category added

2024-02-08T06:48:36Z

‎References: lmu biodb week 4 reference

2024-02-08T06:45:43Z

‎General utility of the database to the scientific community: tweaked one question

2024-02-08T06:42:42Z

‎Acknowledgments: added academic honesty statement at the end of acknowledgments

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 [[User:Hivanson|Hivanson]] ([[User talk:Hivanson|talk]]) 22:42, 7 February 2024 (PST)
 ===Dean===
 I utilized my homework partner, Hailey Ivanson for this assignment. We texted over the weekend to determine who would do which questions and when we would start our slides. We also worked on our slides in class on Tuesday and utilized our professor, Dr. Dahlquist during class. Hailey and I also FaceTimed on Wednesday night to discuss our slides.

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 *Neuroscience Multi-Omic (NeMO) Data Portal. (2024). Retrieved February 7, 2024, from https://portal.nemoarchive.org/
 *NeMO Archive—Home. (2024). Retrieved February 7, 2024, from https://nemoarchive.org/
 [[Category:Journal Entry]]

← Older revision		Revision as of 07:45, 8 February 2024
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		+	[[Media:Nemo_presentation.pdf \| Week 4 NeMO presentation]]
	===General information about the database===		===General information about the database===
	* '''What is the name of the database?'''		* '''What is the name of the database?'''

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 *#* I would probably not direct a colleague unfamiliar with this material to use this database, for I have a hard time searching for things on the database as a relatively experienced user. There is much jargon on the database that I am unfamiliar with and therefore do not understand about it. For this reason, I believe that someone unfamiliar with the field would have an even harder time navigating it. NeMO is of little use to someone not focused on brain mapping or brain cell transcriptomics or epigenomics.
 *# Is this a professional or "hobby" database?
-The NeMO archive database is a professional database. It is associated with and supported by the NIH, a US government organization.
+*#* The NeMO archive database is a professional database. It is associated with and supported by the NIH, a US government organization.
 ==Acknowledgments==

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 ==References==
 *Ament, S. A., Adkins, R. S., Carter, R., Chrysostomou, E., Colantuoni, C., Crabtree, J., Creasy, H. H., Degatano, K., Felix, V., Gandt, P., Garden, G. A., Giglio, M., Herb, B. R., Khajouei, F., Kiernan, E., McCracken, C., McDaniel, K., Nadendla, S., Nickel, L., … White, O. R. (2023). The Neuroscience Multi-Omic Archive: A BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain. Nucleic Acids Research, 51(D1), D1075–D1085. https://doi.org/10.1093/nar/gkac962
-*LMU BioDB 2024. (2024). Week 4. Retrieved February 7, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/Spring2024/index.php/Week_4
+*LMU BioDB 2024. (2024). Week 4. Retrieved February 7, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_4
 *Neuroscience Multi-Omic (NeMO) Data Portal. (2024). Retrieved February 7, 2024, from https://portal.nemoarchive.org/
 *NeMO Archive—Home. (2024). Retrieved February 7, 2024, from https://nemoarchive.org/

← Older revision		Revision as of 06:49, 8 February 2024
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	*LMU BioDB 2024. (2024). Week 4. Retrieved February 7, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/Spring2024/index.php/Week_4		*LMU BioDB 2024. (2024). Week 4. Retrieved February 7, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/Spring2024/index.php/Week_4
	*		*
		+
		+
		+	[[Category:Journal Entry]]

← Older revision		Revision as of 06:48, 8 February 2024
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	==References==		==References==
		+	*LMU BioDB 2024. (2024). Week 4. Retrieved February 7, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/Spring2024/index.php/Week_4
		+	*

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 *#*** The three most common file formats are TSV, FASTQ, and BAM. [https://portal.nemoarchive.org/search/s?facetTab=files data portal]
 *#** Are they standard or non-standard formats?
-*#*** Yes they are, FASTQ is the standard format for sequences, TSV is also a standard form for text based data, as well as BAM data, another standard form for representing data sequences [https://portal.nemoarchive.org/search/s?facetTab=files data portal]
+*#*** Yes they are, FASTQ is the standard format for sequences, TSV is also a standard form for text based data, BAM is another standard form for representing data sequences, it is in binary, however [https://portal.nemoarchive.org/search/s?facetTab=files data portal]
 *# Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information?
 *#** Yes, a naive user likely navigate the site as easily as an experienced user. Meaning that the search options are easily identifiable, but the problems with the site would be as much of a problem for an experienced user, for it will take just as long to load the results for anybody using the site. More experience cannot fix the fact that the database has a design flaw in the way that it runs queries every time anything is added to the filters. [https://portal.nemoarchive.org/search/s?facetTab=files data portal]